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Najjar FN, Williamson YM, Cooper HC, Barr JR, Williams TL. Optimization of Extraction Methods for the Quantification of Proteins in Mammalian Tissues. Anal Chem 2025; 97:10173-10179. [PMID: 40338194 DOI: 10.1021/acs.analchem.4c05751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2025]
Abstract
With the development of new vaccine technologies, such as mRNA vaccines, tissue studies are becoming increasingly important. Knowledge of the antigen expression amounts and where the antigen accumulates in the body is essential for designing safe and effective vaccines. Mammalian tissues present challenges in the detection and accurate quantification of target proteins because of their complexity and the lack of protocols that efficiently extract proteins with minimal sample loss. Here, we describe a protocol for the detection and accurate quantification of protein targets in commercially available snap-frozen lung, liver, kidney, and spleen of European domestic ferrets (Mustela putorius furo) by isotope dilution mass spectrometry (IDMS). Housekeeping proteins were chosen that range in abundance to account for different masses of tissue slices of the same organ. Target peptides used for IDMS quantification were conserved across several of the common animal model systems, including baby hamster kidney, mouse, and ferret. Hemagglutinin, the primary antigen of an influenza vaccine, was added at various concentrations to demonstrate the recovery of low-abundance proteins from the complex tissue homogenate. By using housekeeping proteins and a preparation protocol that minimizes sample loss, this study shows that IDMS can accurately quantify proteins in mammalian tissues with unmatched sensitivity and specificity.
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Affiliation(s)
- Fabio N Najjar
- Oak Ridge Institute for Science and Education, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Yulanda M Williamson
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Hans C Cooper
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - John R Barr
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
| | - Tracie L Williams
- National Center for Environmental Health, Centers for Disease Control and Prevention, Atlanta, Georgia 30341, United States
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Ryu T, Kim S, Thuraisamy T, Shin J, Jang Y, Kam T, Na CH. In-Depth Cell-Type-Specific Proteome Landscape of the Brain from Human Amyloid-β Overexpression Mouse Model. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2025; 12:e2409318. [PMID: 40345165 PMCID: PMC12120748 DOI: 10.1002/advs.202409318] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Revised: 04/18/2025] [Indexed: 05/11/2025]
Abstract
Amyloid-β (Aβ) plays a crucial role in Alzheimer's disease pathogenesis. Understanding how Aβ overexpression alters the proteome of individual brain cell types is essential but challenging due to the nature of brain tissue, which contains intermingled various cell types. The current methods for cell-type-specific proteomics either require genetic modifications or complex cell isolation, limiting their use. This study introduces a novel method, in situ cell-type-specific proteome analysis using antibody-mediated biotinylation (iCAB), which applies immunohistochemistry with biotin-tyramide to target cell-specific proteins directly in tissue. Applied to 5xFAD mice, iCAB enables us to identify ≈8000 cell-type-specific proteomes with significantly more differentially expressed proteins than traditional bulk proteome methods, pinpointing unique pathways such as mRNA processing, calcium regulation, and phagocytosis for neurons, astrocytes, and microglia, respectively. This study reports in-depth the cell-type-specific brain proteome landscape of the human Aβ overexpression mouse model for the first time using an innovative tool that is powerful, straightforward, and applicable to both animal models and human tissues, without the need for prior genetic alterations.
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Affiliation(s)
- Taekyung Ryu
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Seok‐Young Kim
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Thujitha Thuraisamy
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Jisu Shin
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Yura Jang
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
| | - Tae‐In Kam
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Department of Brain and Cognitive SciencesKorea Advanced Institute of Science and TechnologyDaejeon34141South Korea
| | - Chan Hyun Na
- Department of NeurologyJohns Hopkins University School of MedicineBaltimoreMD21205USA
- Neuroregeneration and Stem Cell ProgramsInstitute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMD21205USA
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3
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Lin KT, Muneer G, Huang PR, Chen CS, Chen YJ. Mass Spectrometry-Based Proteomics for Next-Generation Precision Oncology. MASS SPECTROMETRY REVIEWS 2025. [PMID: 40269546 DOI: 10.1002/mas.21932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2024] [Revised: 03/29/2025] [Accepted: 04/01/2025] [Indexed: 04/25/2025]
Abstract
Cancer is the leading cause of death worldwide characterized by patient heterogeneity and complex tumor microenvironment. While the genomics-based testing has transformed modern medicine, the challenge of diverse clinical outcomes highlights unmet needs for precision oncology. As functional molecules regulating cellular processes, proteins hold great promise as biomarkers and drug targets. Mass spectrometry (MS)-based clinical proteomics has illuminated the molecular features of cancers and facilitated discovery of biomarkers or therapeutic targets, paving the way for innovative strategies that enhance the precision of personalized treatment. In this article, we introduced the tools and current achievements of MS-based proteomics, choice of discovery and targeted MS from discovery to validation phases, profiling sensitivity from bulk samples to single-cell level and tissue to liquid biopsy specimens, current regulatory landscape of MS-based protein laboratory-developed tests (LDTs). The challenges, success and future perspectives in translating research MS assay into clinical applications are also discussed. With well-designed validation studies to demonstrate clinical benefits and meet the regulatory requirements for both analytical and clinical performance, the future of MS-based assays is promising with numerous opportunities to improve cancer diagnosis, treatment, and monitoring.
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Affiliation(s)
- Kuen-Tyng Lin
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | - Gul Muneer
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
| | | | - Ciao-Syuan Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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4
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Rosenberger FA, Mädler SC, Thorhauge KH, Steigerwald S, Fromme M, Lebedev M, Weiss CAM, Oeller M, Wahle M, Metousis A, Zwiebel M, Schmacke NA, Detlefsen S, Boor P, Fabián O, Fraňková S, Krag A, Strnad P, Mann M. Deep Visual Proteomics maps proteotoxicity in a genetic liver disease. Nature 2025:10.1038/s41586-025-08885-4. [PMID: 40240610 DOI: 10.1038/s41586-025-08885-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Accepted: 03/11/2025] [Indexed: 04/18/2025]
Abstract
Protein misfolding diseases, including α1-antitrypsin deficiency (AATD), pose substantial health challenges, with their cellular progression still poorly understood1-3. We use spatial proteomics by mass spectrometry and machine learning to map AATD in human liver tissue. Combining Deep Visual Proteomics (DVP) with single-cell analysis4,5, we probe intact patient biopsies to resolve molecular events during hepatocyte stress in pseudotime across fibrosis stages. We achieve proteome depth of up to 4,300 proteins from one-third of a single cell in formalin-fixed, paraffin-embedded tissue. This dataset reveals a potentially clinically actionable peroxisomal upregulation that precedes the canonical unfolded protein response. Our single-cell proteomics data show α1-antitrypsin accumulation is largely cell-intrinsic, with minimal stress propagation between hepatocytes. We integrated proteomic data with artificial intelligence-guided image-based phenotyping across several disease stages, revealing a late-stage hepatocyte phenotype characterized by globular protein aggregates and distinct proteomic signatures, notably including elevated TNFSF10 (also known as TRAIL) amounts. This phenotype may represent a critical disease progression stage. Our study offers new insights into AATD pathogenesis and introduces a powerful methodology for high-resolution, in situ proteomic analysis of complex tissues. This approach holds potential to unravel molecular mechanisms in various protein misfolding disorders, setting a new standard for understanding disease progression at the single-cell level in human tissue.
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Affiliation(s)
- Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Sophia C Mädler
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Katrine Holtz Thorhauge
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Sophia Steigerwald
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Malin Fromme
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH, AachenHealth Care Provider of the European Reference Network on Rare Liver Disorders (ERN RARE LIVER), Aachen, Germany
| | - Mikhail Lebedev
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Caroline A M Weiss
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Marc Oeller
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maria Wahle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andreas Metousis
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Maximilian Zwiebel
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Niklas A Schmacke
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sönke Detlefsen
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Peter Boor
- Institute of Pathology, University Hospital Aachen RWTH, Aachen University, Aachen, Germany
| | - Ondřej Fabián
- Clinical and Transplant Pathology Centre, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
- Department of Pathology and Molecular Medicine, Third Faculty of Medicine, Charles University and Thomayer Hospital, Prague, Czech Republic
| | - Soňa Fraňková
- Department of Hepatogastroenterology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Aleksander Krag
- Department of Gastroenterology and Hepatology, Centre for Liver Research, Odense, Denmark
- Department of Clinical Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
- Danish Institute of Advanced Study (DIAS), University of Southern Denmark, Odense, Denmark
| | - Pavel Strnad
- Medical Clinic III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH, AachenHealth Care Provider of the European Reference Network on Rare Liver Disorders (ERN RARE LIVER), Aachen, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- NNF Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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Ji S, Cao L, Gao J, Du Y, Ye Z, Lou X, Liu F, Zhang Y, Xu J, Shi X, Wang H, Li P, Li Y, Chen H, Yang Z, Gao S, Zhang W, Huang D, Ni S, Wei M, Wang F, Wang Y, Ding T, Jing D, Fan G, Gong Z, Lu R, Qin Y, Chen J, Xu X, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Chang DK, Hruban RH, Gao D, Gao D, Jin G, Zhou H, Wu J, Yu X. Proteogenomic characterization of non-functional pancreatic neuroendocrine tumors unravels clinically relevant subgroups. Cancer Cell 2025; 43:776-796.e14. [PMID: 40185092 DOI: 10.1016/j.ccell.2025.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Revised: 01/27/2025] [Accepted: 03/12/2025] [Indexed: 04/07/2025]
Abstract
The majority of neuroendocrine neoplasms in pancreas are non-functional pancreatic neuroendocrine tumors (NF-PanNETs), which exhibit a high occurrence of distant metastases with limited therapeutic options. Here, we perform a comprehensive molecular characterization of 108 NF-PanNETs through integrative analysis of genomic, transcriptomic, proteomic, and phosphoproteomic profiles. Proteogenomic analysis provides functional insights into the genomic driver alterations of NF-PanNETs, revealing a potential mediator of MEN1 alterations using Men1-conditional knockout mice. Machine-learning-based modeling uncovers a three-protein signature as an independent prognostic factor, which is validated by an independent external cohort. Proteomic and phosphoproteomic-based stratification identifies four subtypes with distinct molecular characteristics, immune microenvironments, and clinicopathological features. Drug screening using patient-derived tumor organoids identifies cyclin-dependent kinase (CDK) 5 and Calcium Voltage-Gated Channel Subunit Alpha1 D (CACNA1D) as ubiquitous and subtype-specific targets, respectively, with in vivo validation using xenograft models. Together, our proteogenomic analyses illustrate a comprehensive molecular landscape of NF-PanNETs, revealing biological insights and therapeutic vulnerabilities.
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Affiliation(s)
- Shunrong Ji
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Lihua Cao
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Jing Gao
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yang Du
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Zeng Ye
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xin Lou
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Fen Liu
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yehan Zhang
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Junfeng Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Xiaohan Shi
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Penghao Li
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Yikai Li
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Hongxu Chen
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhicheng Yang
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China
| | - Suizhi Gao
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China
| | - Wuhu Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Dan Huang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Shujuan Ni
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Miaoyan Wei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Fei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Yan Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Tian Ding
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Desheng Jing
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Guixiong Fan
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Zhiyun Gong
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Renquan Lu
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Clinical Laboratory, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Yi Qin
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Jie Chen
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Center for Neuroendocrine Tumors, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Xiaowu Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, NewYork, NY 10029, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Li Ding
- Department of Medicine, McDonnell Genome Institute, Washington University, St. Louis, MO 63108, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - David K Chang
- Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1BD, UK
| | - Ralph H Hruban
- The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Dong Gao
- Key Laboratory of Multi-Cell Systems, Shanghai Key Laboratory of Molecular Andrology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Daming Gao
- Key Laboratory of Multi-Cell Systems, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Second Military Medical University (Naval Medical University), Shanghai 200433, China.
| | - Hu Zhou
- Department of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China; University of Chinese Academy of Sciences, Number 19A Yuquan Road, Beijing 100049, China; School of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China; Shanghai Institute of Materia Medica-University of Ottawa Joint Research Center in Systems and Personalized Pharmacology, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Jianmin Wu
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, Beijing 100142, China; Peking University International Cancer Institute, Peking University, Beijing 100191, China.
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai 200032, China.
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6
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Johansen A, Sandve GKF, Maxwell JR, Smithson G, Sollid LM, Stamnaes J. Biopsy Proteome Score Performs Well as an Effect Measure in a Gluten Challenge Trial of Celiac Disease. Clin Gastroenterol Hepatol 2025; 23:758-765.e8. [PMID: 39209203 DOI: 10.1016/j.cgh.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/22/2024] [Accepted: 08/13/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND AND AIMS Development of novel treatments for celiac disease is dependent on precise tools to monitor changes in gluten-induced mucosal damage. Current histology measures are subjective and difficult to standardize. Biopsy proteome scoring is an objective alternative to histology which is based on robust changes in biological pathways that directly reflect gluten-induced mucosal damage. In this study, we aimed to evaluate biopsy proteome scoring as an effect measure in a clinical trial setting by measuring intestinal remodeling in response to oral gluten challenge. METHODS We analyzed biopsies from a 14-day gluten challenge trial of treated celiac disease patients that consumed 3 g (n = 6) or 10 g (n = 7) gluten per day. Sections from individually embedded biopsies collected before and after challenge were processed for proteome scoring (n = 109) and measurement of villus height-to-crypt depth ratio (n = 58). Proteome scores were compared with histology, intraepithelial lymphocyte frequency and plasma interleukin-2. RESULTS Change in proteome scores were significant for the group of patients who consumed 10 g gluten, but not for the group who consumed 3 g gluten. Altogether, 8 of 13 patients had changes in delta proteome scores above the cutoff. Proteome scores correlated with villus height-to-crypt depth ratios both at run-in and at day 15. Proteome scores at day 15 correlated with intraepithelial lymphocyte frequency and with plasma interleukin-2 levels measured 4 hours post-gluten intake. CONCLUSION Biopsy proteome scoring is a simple and reliable measure of gluten-induced mucosal remodeling in response to 14-day oral gluten challenge. CLINICALTRIALS gov, Number: NCT03409796.
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Affiliation(s)
- Anette Johansen
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Geir Kjetil F Sandve
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Informatics, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Joseph R Maxwell
- Research and Development, Takeda Pharmaceuticals Inc. Co, Cambridge, MA, United States
| | - Glennda Smithson
- Research and Development, Takeda Pharmaceuticals Inc. Co, Cambridge, MA, United States
| | - Ludvig M Sollid
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jorunn Stamnaes
- Norwegian Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
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7
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Ha A, Woolman M, Waas M, Govindarajan M, Kislinger T. Recent implementations of data-independent acquisition for cancer biomarker discovery in biological fluids. Expert Rev Proteomics 2025; 22:163-176. [PMID: 40227112 DOI: 10.1080/14789450.2025.2491355] [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: 01/29/2025] [Revised: 03/26/2025] [Accepted: 04/06/2025] [Indexed: 04/15/2025]
Abstract
INTRODUCTION Cancer is the second-leading cause of death worldwide and accurate biomarkers for early detection and disease monitoring are needed to improve outcomes. Biological fluids, such as blood and urine, are ideal samples for biomarker measurements as they can be routinely collected with relatively minimally invasive methods. However, proteomics analysis of fluids has been a challenge due to the high dynamic range of its protein content. Advances in data-independent acquisition (DIA) mass spectrometry-based proteomics can address some of the technical challenges in the analysis of biofluids, thus enabling the ability for mass spectrometry to propel large-scale biomarker discovery. AREAS COVERED We reviewed principles of DIA and its recent applications in cancer biomarker discovery using biofluids. We summarized DIA proteomics studies using biological fluids in the context of cancer research over the past decade, and provided a comprehensive overview of the benefits and challenges of DIA-MS. EXPERT OPINION Various studies showed the potential of DIA-MS in identifying putative cancer biomarkers in a high-throughput manner. However, the lack of proper study design and standardization of methods across platforms still needs to be addressed to fully utilize the benefits of DIA-MS to accelerate the biomarker discovery and verification processes.
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Affiliation(s)
- Annie Ha
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Michael Woolman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Matthew Waas
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Meinusha Govindarajan
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas Kislinger
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
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8
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Zhang J, Wang Y, Liu Y, Chen H, Chai N, Zhao Y, Li Y, Li X, He J, Zhang H. Proteomic profiling reveals biological processes and biomarkers involved in the pathogenesis of occult breast cancer. BMC Cancer 2025; 25:231. [PMID: 39930421 PMCID: PMC11812265 DOI: 10.1186/s12885-025-13657-4] [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: 10/13/2024] [Accepted: 02/05/2025] [Indexed: 02/13/2025] Open
Abstract
BACKGROUND Occult breast cancer (OBC) is defined as axillary lymph node metastasis without any evidence of a primary tumor in the breast. Because of the limited number of clinical cases, the clinicopathological features and treatment recommendations of OBC are still controversial. In addition, its natural history is poorly understood and its proteomic signature remains unknown. MATERIALS AND METHODS We compared the clinicopathological features and prognosis of OBC patients and Non-OBC patients from the Surveillance, Epidemiology, and End Results (SEER) database and analyzed the effects of local treatment on the survival outcomes of OBC patients. Additionally, we performed a quantitative proteomic analysis for tissue samples of metastatic lymph nodes from OBC patients (OBC-LN), and paired tissue samples of metastatic lymph nodes (Non-OBC-LN) and primary tumors (Non-OBC-PT) from Non-OBC patients. We identified differentially expressed proteins in different comparable groups using Student's t test. Functional enrichment and protein-protein interaction network analyses were used to interpret the functions and interactions of the differentially expressed proteins in the comparison of OBC-LN vs Non-OBC-LN. Immunohistochemistry was used for the validation of the hub proteins. RESULTS Analysis of data from the SEER database demonstrated that OBC patients had a better prognosis than Non-OBC patients did and that either mastectomy or radiation therapy improved the outcomes of OBC patients. A total of 7208 comparable proteins were successfully quantified. Compared with those of the Non-OBC-LN samples, the OBC-LN protein profiles exhibited an active extracellular matrix and a thoroughly upregulated epithelial-mesenchymal transition phenotype. COL1A1, COL1A2, COL3A1, MMP2 and LUM were overexpressed in the OBC-LN samples and were identified as hub proteins. Immunohistochemical staining demonstrated that the five hub proteins were overexpressed in OBC-LN samples. CONCLUSION Our results provide insights for the clinical management of OBC and the proteomic signature of OBC offers molecular basis for further biological research.
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Affiliation(s)
- Jingyi Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Yidi Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Yu Liu
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - He Chen
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, China
| | - Na Chai
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Yuting Zhao
- Department of Gynecologic Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Yijun Li
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Xiaoqian Li
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China.
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, People's Republic of China.
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9
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Koh JMS, Sykes EK, Rukhaya J, Anees A, Zhong Q, Jackson C, Panizza BJ, Reddel RR, Balleine RL, Hains PG, Robinson PJ. The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections. Clin Proteomics 2025; 22:5. [PMID: 39910438 DOI: 10.1186/s12014-025-09529-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2024] [Accepted: 01/22/2025] [Indexed: 02/07/2025] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues present an important resource for cancer proteomics. They are more readily available than fresh frozen (FF) tissues and can be stored at ambient temperature for decades. FFPE blocks are largely stable for long-term preservation of tumour histology, but the antigenicity of some proteins in FFPE sections degrades over time resulting in deteriorating performance of immunohistochemistry (IHC). It is not known whether FFPE sections that have previously been cut from blocks and used for liquid chromatography-mass spectrometry (LC-MS) analysis at a later time are affected by storage time or temperature. We determined the stability of FFPE sections stored at room temperature (RT) versus - 80 °C over 48 weeks. The stored sections were processed at different timepoints (n = 11) and compared to sections that were freshly cut from FFPE blocks at each timepoint (controls). A total of 297 sections (rat brain, kidney and liver stored at RT, - 80 °C or freshly cut) were tryptically digested and analysed on TripleTOF 6600 mass spectrometers in data-dependent acquisition (DDA) mode. Kidney and liver digests were also analysed in data-independent acquisition (DIA) mode. The number of proteins and peptides identified by DDA with ProteinPilot and some common post-translational modifications (PTMs) were unaffected by the storage time or temperature. Nine of the most common FFPE-associated modifications were quantified using DIA data and all were unaffected by storage time or temperature. Therefore, FFPE tissue sections are suitable for proteomic studies for at least 48 weeks from the time of sectioning.
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Affiliation(s)
- Jennifer M S Koh
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Erin K Sykes
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Jyoti Rukhaya
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Asim Anees
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Qing Zhong
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Christopher Jackson
- Department of Otolaryngology, Head and Neck Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Queensland Head and Neck Cancer Centre, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Benedict J Panizza
- Department of Otolaryngology, Head and Neck Surgery, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Queensland Head and Neck Cancer Centre, Princess Alexandra Hospital, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Roger R Reddel
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Rosemary L Balleine
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
- Faculty of Medicine and Health, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Peter G Hains
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
| | - Phillip J Robinson
- Faculty of Medicine and Health, ProCan®, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia.
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10
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Chatterjee S, Zaia J, Sethi MK. Mass Spectrometry-Based Glycomics and Proteomics Profiling of On-Slide Digested Tissue from Complex Biological Samples. Methods Mol Biol 2025; 2884:279-303. [PMID: 39716010 DOI: 10.1007/978-1-0716-4298-6_18] [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: 12/25/2024]
Abstract
Mass spectrometry-based investigation of the heterogeneous glycoproteome from complex biological specimens is a robust approach to mapping the structure, function, and dynamics of the glycome and proteome. Sampling whole wet tissues often provides a large amount of starting material; however, there is a reasonable variability in tissue handling prior to downstream processing steps, and it is difficult to capture all the different biomolecules from a specific region. The on-slide tissue digestion approach, outlined in this protocol chapter, is a simple and cost-effective method that allows comprehensive mapping of the glycoproteome from a single spot of tissue of 1 mm or greater diameter. It provides a selection of target areas on tissue slides appropriate for tissue volumes of 10 nL or greater, corresponding to a 1 μL droplet of enzyme solution applied to a 1-mm diameter target on a 10-μm-thick tissue slice. Sequential enzymatic digestions and desalting of the biomolecules without any prior derivatization from the surface of fresh frozen or formalin-fixed paraffin-embedded tissue slides enable the simultaneous identification of glycosaminoglycan disaccharides such as hyaluronan, chondroitin sulfate and heparan sulfate, asparagine or N-linked glycans, and intact (glyco)peptides using liquid chromatography-tandem mass spectrometry. The in-depth information obtained from this method including the disaccharide compositions, glycan structures, peptide abundances, and site-specific glycan occupancies provides a detailed profiling of a single spot of tissue which has the potential to be disseminated to biomedical laboratories.
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Affiliation(s)
- Sayantani Chatterjee
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
| | - Joseph Zaia
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA
- Boston University Bioinformatics Program, Boston University, Boston, MA, USA
| | - Manveen K Sethi
- Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston University School of Medicine, Boston, MA, USA.
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11
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Tüshaus J, Eckert S, Schliemann M, Zhou Y, Pfeiffer P, Halves C, Fusco F, Weigel J, Hönikl L, Butenschön V, Todorova R, Rauert-Wunderlich H, The M, Rosenwald A, Heinemann V, Holch J, Steiger K, Delbridge C, Meyer B, Weichert W, Mogler C, Kuhn PH, Kuster B. Towards routine proteome profiling of FFPE tissue: insights from a 1,220-case pan-cancer study. EMBO J 2025; 44:304-329. [PMID: 39558110 PMCID: PMC11697351 DOI: 10.1038/s44318-024-00289-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: 06/19/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 11/20/2024] Open
Abstract
Proteome profiling of formalin-fixed paraffin-embedded (FFPE) specimens has gained traction for the analysis of cancer tissue for the discovery of molecular biomarkers. However, reports so far focused on single cancer entities, comprised relatively few cases and did not assess the long-term performance of experimental workflows. In this study, we analyze 1220 tumors from six cancer entities processed over the course of three years. Key findings include the need for a new normalization method ensuring equal and reproducible sample loading for LC-MS/MS analysis across cohorts, showing that tumors can, on average, be profiled to a depth of >4000 proteins and discovering that current software fails to process such large ion mobility-based online fractionated datasets. We report the first comprehensive pan-cancer proteome expression resource for FFPE material comprising 11,000 proteins which is of immediate utility to the scientific community, and can be explored via a web resource. It enables a range of analyses including quantitative comparisons of proteins between patients and cohorts, the discovery of protein fingerprints representing the tissue of origin or proteins enriched in certain cancer entities.
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Affiliation(s)
- Johanna Tüshaus
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Stephan Eckert
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marius Schliemann
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
- Bavarian Cancer Research Center (BZKF), Munich, Germany
| | - Yuxiang Zhou
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Pauline Pfeiffer
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Christiane Halves
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Federico Fusco
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Johannes Weigel
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Lisa Hönikl
- Department of Neurosurgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Vicki Butenschön
- Department of Neurosurgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Rumyana Todorova
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | | | - Matthew The
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany
| | | | - Volker Heinemann
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Julian Holch
- Department of Medicine III and Comprehensive Cancer Center Munich, University Hospital, Ludwig-Maximilians University Munich, Munich, Germany
| | - Katja Steiger
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Claire Delbridge
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Bernhard Meyer
- Department of Neurosurgery, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Wilko Weichert
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Carolin Mogler
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Peer-Hendrik Kuhn
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute of Pathology, School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, Freising, Germany.
- German Cancer Consortium (DKTK), Partner Site Munich, a Partnership between DKFZ and University Center Technical University of Munich, Munich, Germany.
- German Cancer Research Center (DKFZ), Heidelberg, Germany.
- Bavarian Cancer Research Center (BZKF), Munich, Germany.
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12
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Isaiah AR, Luies L, Loots DT, Williams AA, Vlok M, Chegou NN, Tutu van Furth M, van der Kuip M, Mason S. Protocol for unified metabolomics and proteomics analysis of formalin-fixed paraffin-embedded tissue. STAR Protoc 2024; 5:103442. [PMID: 39522166 PMCID: PMC11585672 DOI: 10.1016/j.xpro.2024.103442] [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: 07/04/2024] [Revised: 08/23/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
The use of archival formalin-fixed paraffin-embedded (FFPE) tissue samples for biochemical analyses is problematic because of the formation of a Schiff base, leading to low protein and metabolite yields during analytical extractions. Here, we overcome this issue using a unified protocol on FFPE tissue for metabolomics and proteomics analyses. Using 20 mg of wet mass tissue, this protocol consistently extracted more than 50 metabolites (across 11 classes of metabolites) and over 900 proteins.
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Affiliation(s)
- Abisola R Isaiah
- Focus Area Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, North West 2531, South Africa
| | - Laneke Luies
- Focus Area Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, North West 2531, South Africa
| | - Du Toit Loots
- Focus Area Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, North West 2531, South Africa
| | - Aurelia A Williams
- Focus Area Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, North West 2531, South Africa
| | - Maré Vlok
- Proteomics Unit, Central Analytical Facilities, University of Stellenbosch, Western Cape, Cape Town 7550, South Africa
| | - Novel N Chegou
- South African Medical Research Council Centre for Tuberculosis Research, Division of Immunology, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa
| | - Marceline Tutu van Furth
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Emma Children's Hospital, Amsterdam, the Netherlands
| | - Martijn van der Kuip
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam University Medical Center, Emma Children's Hospital, Amsterdam, the Netherlands
| | - Shayne Mason
- Focus Area Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, North West 2531, South Africa.
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13
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Haines M, Thorup JR, Gohsman S, Ctortecka C, Newton C, Rohrer DC, Hostetter G, Mani DR, Gillette MA, Satpathy S, Carr SA. High-throughput proteomic and phosphoproteomic analysis of formalin-fixed paraffin-embedded tissue. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.17.624038. [PMID: 39605438 PMCID: PMC11601474 DOI: 10.1101/2024.11.17.624038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2024]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) patient tissues are a valuable resource for proteomic studies with the potential to associate the derived molecular insights with clinical annotations and outcomes. Here we present an optimized, partially automated workflow for FFPE proteomics combining pathology-guided macro-dissection, Adaptive Focused Acoustics (AFA) sonication for lysis and decrosslinking, S-Trap digestion to peptides, and liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis using Orbitrap, Astral or timsTOF HT instrumentation. The workflow enables analysis of up to 96 dissected FFPE tissue samples or 10 μm scrolls, identifying 8,000-10,000 unique proteins per sample with median CVs <20%. Key optimizations include improved tissue lysis strategies, protein quantification for normalization, and peptide cleanup prior to LC-MS/MS analysis. Application to lung adenocarcinoma (LUAD) FFPE blocks confirms the platform's effectiveness in processing complex, clinically relevant samples, achieving deep proteome coverage and quantitative robustness comparable to TMT-based methods. Using the newly released Orbitrap Astral with short, 24-minute gradients, the workflow identifies up to ~10,000 unique proteins and ~11,000 localized phosphosites in LUAD FFPE tissue. This high-throughput, scalable workflow advances biomarker discovery and proteomic research in archival tissue samples.
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Affiliation(s)
- Moe Haines
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - D. R. Mani
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Shankha Satpathy
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Current address: AstraZeneca, Waltham, MA, USA
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14
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Nordmann TM, Mund A, Mann M. A new understanding of tissue biology from MS-based proteomics at single-cell resolution. Nat Methods 2024; 21:2220-2222. [PMID: 39643675 DOI: 10.1038/s41592-024-02541-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2024]
Affiliation(s)
- Thierry M Nordmann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
| | - Andreas Mund
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- OmicVision Biosciences, BioInnovation Institute, Copenhagen, Denmark.
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
- Proteomics Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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15
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Xu Y, Wang X, Li Y, Mao Y, Su Y, Mao Y, Yang Y, Gao W, Fu C, Chen W, Ye X, Liang F, Bai P, Sun Y, Li S, Xu R, Tian R. Multimodal single cell-resolved spatial proteomics reveal pancreatic tumor heterogeneity. Nat Commun 2024; 15:10100. [PMID: 39572534 PMCID: PMC11582669 DOI: 10.1038/s41467-024-54438-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/12/2024] [Indexed: 11/24/2024] Open
Abstract
Despite the advances in antibody-guided cell typing and mass spectrometry-based proteomics, their integration is hindered by challenges for processing rare cells in the heterogeneous tissue context. Here, we introduce Spatial and Cell-type Proteomics (SCPro), which combines multiplexed imaging and flow cytometry with ion exchange-based protein aggregation capture technology to characterize spatial proteome heterogeneity with single-cell resolution. The SCPro is employed to explore the pancreatic tumor microenvironment and reveals the spatial alternations of over 5000 proteins by automatically dissecting up to 100 single cells guided by multi-color imaging of centimeter-scale formalin-fixed, paraffin-embedded tissue slide. To enhance cell-type resolution, we characterize the proteome of 14 different cell types by sorting up to 1000 cells from the same tumor, which allows us to deconvolute the spatial distribution of immune cell subtypes and leads to the discovery of subtypes of regulatory T cells. Together, the SCPro provides a multimodal spatial proteomics approach for profiling tissue proteome heterogeneity.
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Affiliation(s)
- Yanfen Xu
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Xi Wang
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yuan Li
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Yiheng Mao
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Yiran Su
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Yize Mao
- Department of Pancreatobiliary Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Yun Yang
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Weina Gao
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Changying Fu
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Wendong Chen
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Xueting Ye
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Fuchao Liang
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China
| | - Panzhu Bai
- Department of System Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Ying Sun
- Department of System Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Shengping Li
- Department of Pancreatobiliary Surgery, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ruilian Xu
- Department of Oncology, The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen 518020, China, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Ruijun Tian
- State Key Laboratory of Medical Proteomics and Shenzhen Key Laboratory of Functional Proteomics, Department of Chemistry and Research Center for Chemical Biology and Omics Analysis, School of Science and Guangming Advanced Research Institute, Southern University of Science and Technology, Shenzhen, China.
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16
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Gronauer TF, Eck LK, Ludwig C, Sieber SA. A Photocrosslinking Probe to Capture the Substrates of Caseinolytic Protease P. Angew Chem Int Ed Engl 2024; 63:e202409220. [PMID: 39073273 DOI: 10.1002/anie.202409220] [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: 05/15/2024] [Revised: 07/17/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Protein homeostasis in bacteria is regulated by proteases such as the tetradecameric caseinolytic protease P (ClpP). Although substrates of ClpP have been successfully deciphered in genetically engineered cells, methods which directly trap processed proteins within native cells remain elusive. Here, we introduce an in situ trapping strategy which utilizes trifunctional probes that bind to the active site serine of ClpP and capture adjacent substrates with an attached photocrosslinking moiety. After enrichment using an alkyne handle, substrate deconvolution by mass spectrometry (MS) is performed. We show that our two traps bind substoichiometrically to ClpP, retain protease activity, exhibit unprecedented selectivity for Staphylococcus aureus ClpP in living cells and capture numerous known and novel substrates. The exemplary validation of trapped hits using a targeted proteomics approach confirmed the fidelity of this technology. In conclusion, we provide a novel chemical platform suited for the discovery of serine protease substrates beyond genetic engineering.
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Affiliation(s)
- Thomas F Gronauer
- TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
- Current affiliation: Metabolomics and Proteomics Core (MPC), Helmholtz Zentrum München German Research Center for Environmental Health, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Laura K Eck
- TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), TUM School of Life Sciences, Technical University of Munich (TUM), Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Stephan A Sieber
- TUM School of Natural Sciences, Department of Biosciences, Chair of Organic Chemistry II, Center for Functional Protein Assemblies (CPA), Technical University of Munich (TUM), Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
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17
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Egbejiogu BC, Donnarumma F, Murray KK. Infrared Laser Ablation and Capture of Formalin-Fixed Paraffin-Embedded Tissue. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024. [PMID: 39494617 DOI: 10.1021/jasms.4c00299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is a ubiquitous and invaluable resource for biomedical research and clinical applications. However, FFPE tissue proteomics is challenging due to protein cross-linking and chemical modification. Laser ablation sampling allows precise removal of material from tissue sections with high spatial control and reproducibility for offline proteomics by liquid chromatography coupled with tandem mass spectrometry. In this work, we used a pulsed mid-infrared laser for microsampling of rat liver tissue for subsequent identification and quantification of proteins. It was found that more proteins were identified by FFPE tissue laser ablation sampling compared to fresh frozen (FF) tissue laser ablation sampling and that more proteins were identified by laser ablation than by manual dissection of FFPE tissue. In contrast to previous studies, no loss of hydrophilic proteins due to residual cross-linking was observed. The efficient capture of proteins by laser ablation microsampling is attributed to efficient laser breakup of the tissue which facilitates downstream processing of the proteins.
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Affiliation(s)
- Blessing C Egbejiogu
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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18
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Schwab SK, Harris PS, Michel C, McGinnis CD, Nahomi RB, Assiri MA, Reisdorph R, Henriksen K, Orlicky DJ, Levi M, Rosenberg A, Nagaraj RH, Fritz KS. Quantifying Protein Acetylation in Diabetic Nephropathy from Formalin-Fixed Paraffin-Embedded Tissue. Proteomics Clin Appl 2024; 18:e202400018. [PMID: 38923810 DOI: 10.1002/prca.202400018] [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: 05/16/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
PURPOSE Diabetic kidney disease (DKD) is a serious complication of diabetes mellitus and a leading cause of chronic kidney disease and end-stage renal disease. One potential mechanism underlying cellular dysfunction contributing to kidney disease is aberrant protein post-translational modifications. Lysine acetylation is associated with cellular metabolic flux and is thought to be altered in patients with diabetes and dysfunctional renal metabolism. EXPERIMENTAL DESIGN A novel extraction and LC-MS/MS approach was adapted to quantify sites of lysine acetylation from formalin-fixed paraffin-embedded (FFPE) kidney tissue and from patients with DKD and non-diabetic donors (n = 5 and n = 7, respectively). RESULTS Analysis of FFPE tissues identified 840 total proteins, with 225 of those significantly changing in patients with DKD. Acetylomic analysis quantified 289 acetylated peptides, with 69 of those significantly changing. Pathways impacted in DKD patients revealed numerous metabolic pathways, specifically mitochondrial function, oxidative phosphorylation, and sirtuin signaling. Differential protein acetylation in DKD patients impacted sirtuin signaling, valine, leucine, and isoleucine degradation, lactate metabolism, oxidative phosphorylation, and ketogenesis. CONCLUSIONS AND CLINICAL RELEVANCE A quantitative acetylomics platform was developed for protein biomarker discovery in formalin-fixed and paraffin-embedded biopsies of kidney transplant patients suffering from DKD.
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Affiliation(s)
- Stefanie K Schwab
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Peter S Harris
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Cole Michel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Courtney D McGinnis
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Rooban B Nahomi
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Mohammed A Assiri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Richard Reisdorph
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kammi Henriksen
- Department of Pathology, University of Chicago Medical Center, Chicago, Illinois, USA
| | - David J Orlicky
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Moshe Levi
- Department of Biochemistry and Molecular & Cellular Biology, Georgetown University, Washington, District of Columbia, USA
| | - Avi Rosenberg
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ram H Nagaraj
- Sue Anschutz-Rodgers Eye Center and Department of Ophthalmology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kristofer S Fritz
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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19
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Montero-Calle A, Garranzo-Asensio M, Poves C, Sanz R, Dziakova J, Peláez-García A, de Los Ríos V, Martinez-Useros J, Fernández-Aceñero MJ, Barderas R. In-Depth Proteomic Analysis of Paraffin-Embedded Tissue Samples from Colorectal Cancer Patients Revealed TXNDC17 and SLC8A1 as Key Proteins Associated with the Disease. J Proteome Res 2024; 23:4802-4820. [PMID: 39441737 DOI: 10.1021/acs.jproteome.3c00749] [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: 10/25/2024]
Abstract
A deeper understanding of colorectal cancer (CRC) biology would help to identify specific early diagnostic markers. Here, we conducted quantitative proteomics on FFPE healthy, adenoma, and adenocarcinoma tissue samples from six stage I sporadic CRC patients to identify dysregulated proteins during early CRC development. Two independent quantitative 10-plex TMT experiments were separately performed. After protein extraction, trypsin digestion, and labeling, proteins were identified and quantified by using a Q Exactive mass spectrometer. A total of 2681 proteins were identified and quantified after data analysis and bioinformatics with MaxQuant and the R program. Among them, 284 and 280 proteins showed significant upregulation and downregulation (expression ratio ≥1.5 or ≤0.67, p-value ≤0.05), respectively, in adenoma and/or adenocarcinoma compared to healthy tissue. Ten dysregulated proteins were selected to study their role in CRC by WB, IHC, TMA, and ELISA using tissue and plasma samples from CRC patients, individuals with premalignant colorectal lesions (adenomas), and healthy individuals. In vitro loss-of-function cell-based assays and in vivo experiments using three CRC cell lines with different metastatic properties assessed the important roles of SLC8A1 and TXNDC17 in CRC and liver metastasis. Additionally, SLC8A1 and TXNDC17 protein levels in plasma possessed the diagnostic ability of early CRC stages.
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Affiliation(s)
- Ana Montero-Calle
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain
- Proteomics Core UCCTs, Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain
| | - María Garranzo-Asensio
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain
| | - Carmen Poves
- Gastroenterology Unit, Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain
| | - Rodrigo Sanz
- Surgical Digestive Department, Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain
| | - Jana Dziakova
- Surgical Digestive Department, Hospital Universitario Clínico San Carlos, E-28040 Madrid, Spain
| | - Alberto Peláez-García
- Molecular Pathology and Therapeutic Targets Group, Hospital La Paz Institute for Health Research (IdiPAZ), E-28046 Madrid, Spain
| | | | - Javier Martinez-Useros
- Translational Oncology Division, OncoHealth Institute, Health Research Institute-Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital/Universidad Autónoma de Madrid (IIS-FJD/UAM), E-28040 Madrid, Spain
- Area of Physiology, Department of Basic Health Sciences, Faculty of Health Sciences, Rey Juan Carlos University, Alcorcón, E-28922 Madrid, Spain
| | | | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain
- Proteomics Core UCCTs, Instituto de Salud Carlos III, Majadahonda, E-28220 Madrid, Spain
- CIBER of Frailty and Healthy Aging (CIBERFES), E-28029 Madrid, Spain
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20
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Zhang T, Li Y, Pan L, Sha J, Bailey M, Faure-Kumar E, Williams CK, Wohlschlegel J, Magaki S, Niu C, Lee Y, Su YC, Li X, Vinters HV, Geschwind DH. Brain-wide alterations revealed by spatial transcriptomics and proteomics in COVID-19 infection. NATURE AGING 2024; 4:1598-1618. [PMID: 39543407 PMCID: PMC11867587 DOI: 10.1038/s43587-024-00730-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2024] [Indexed: 11/17/2024]
Abstract
Understanding the pathophysiology of neurological symptoms observed after severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) infection is essential to optimizing outcomes and therapeutics. To date, small sample sizes and narrow molecular profiling have limited the generalizability of findings. In this study, we profiled multiple cortical and subcortical regions in postmortem brains of patients with coronavirus disease 2019 (COVID-19) and controls with matched pulmonary pathology (total n = 42) using spatial transcriptomics, bulk gene expression and proteomics. We observed a multi-regional antiviral response without direct active SARS-CoV2 infection. We identified dysregulation of mitochondrial and synaptic pathways in deep-layer excitatory neurons and upregulation of neuroinflammation in glia, consistent across both mRNA and protein. Remarkably, these alterations overlapped substantially with changes in age-related neurodegenerative diseases, including Parkinson's disease and Alzheimer's disease. Our work, combining multiple experimental and analytical methods, demonstrates the brain-wide impact of severe acute/subacute COVID-19, involving both cortical and subcortical regions, shedding light on potential therapeutic targets within pathways typically associated with pathological aging and neurodegeneration.
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Affiliation(s)
- Ting Zhang
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yunfeng Li
- Translational Pathology Core Laboratory, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Liuliu Pan
- Technology Access Program, Bruker Spatial Technology, Seattle, WA, USA
- Duality Biologics, Shanghai, China
| | - Jihui Sha
- Proteome Research Center, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Bailey
- Proof of Principle Team, Translational Science, Bruker Spatial Technology, Seattle, WA, USA
| | - Emmanuelle Faure-Kumar
- Center for Systems Biomedicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Kazu Williams
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - James Wohlschlegel
- Proteome Research Center, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - Shino Magaki
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chao Niu
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yoojin Lee
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Yu-Chyuan Su
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Xinmin Li
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Technology Center for Genomics & Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Harry V Vinters
- Section of Neuropathology, Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Daniel H Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
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21
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Shao X, Huang Y, Xu R, He Q, Zhang M, He F, Wang D. ZASP: A Highly Compatible and Sensitive ZnCl 2 Precipitation-Assisted Sample Preparation Method for Proteomic Analysis. Mol Cell Proteomics 2024; 23:100837. [PMID: 39243857 PMCID: PMC11492125 DOI: 10.1016/j.mcpro.2024.100837] [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: 12/11/2023] [Revised: 08/30/2024] [Accepted: 09/03/2024] [Indexed: 09/09/2024] Open
Abstract
Universal sample preparation for proteomic analysis that enables unbiased protein manipulation, flexible reagent use, and low protein loss is required to ensure the highest sensitivity of downstream liquid chromatography-mass spectrometry (LC-MS) analysis. To address these needs, we developed a ZnCl2 precipitation-assisted sample preparation method (ZASP) that depletes harsh detergents and impurities in protein solutions prior to trypsin digestion via 10 min of ZnCl2 and methanol-induced protein precipitation at room temperature (RT). ZASP can remove trypsin digestion and LC-MS incompatible detergents such as SDS, Triton X-100, and urea at high concentrations in solution and unbiasedly recover proteins independent of the amount of protein input. We demonstrated the sensitivity and reproducibility of ZASP in an analysis of samples with 1 μg to 1000 μg of proteins. Compared to commonly used sample preparation methods such as SDC-based in-solution digestion, acetone precipitation, FASP, and SP3, ZASP has proven to be an efficient approach. Here, we present ZASP, a practical, robust, and cost-effective proteomic sample preparation method that can be applied to profile different types of samples.
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Affiliation(s)
- Xianfeng Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; Beijing Proteome Research Center, Beijing, China; International Academy of Phronesis Medicine, Guangzhou, Guangdong, China; The π-Hub Infrastructure, Guangzhou, Guangdong, China
| | - Yuanxuan Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; Beijing Proteome Research Center, Beijing, China; International Academy of Phronesis Medicine, Guangzhou, Guangdong, China; The π-Hub Infrastructure, Guangzhou, Guangdong, China
| | - Rong Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; Guangzhou Laboratory, Guangzhou, Guangdong, China
| | - Qiqing He
- International Academy of Phronesis Medicine, Guangzhou, Guangdong, China; The π-Hub Infrastructure, Guangzhou, Guangdong, China
| | - Min Zhang
- Department of Dermatology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; Beijing Proteome Research Center, Beijing, China; International Academy of Phronesis Medicine, Guangzhou, Guangdong, China; The π-Hub Infrastructure, Guangzhou, Guangdong, China; Guangzhou Laboratory, Guangzhou, Guangdong, China.
| | - Dongxue Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China; Beijing Proteome Research Center, Beijing, China; International Academy of Phronesis Medicine, Guangzhou, Guangdong, China; The π-Hub Infrastructure, Guangzhou, Guangdong, China.
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22
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Ludwig ML, Moline D, Horrmann A, Boytim E, Larson G, Arafa AT, Sayeda M, Lozada JR, Bergom HE, Day A, Dasaraju S, Dehm SM, Murugan P, Hwang J, Drake JM, Antonarakis ES. Integrated multi-omics assessment of lineage plasticity in a prostate cancer patient with brain and dural metastases. NPJ Precis Oncol 2024; 8:215. [PMID: 39349591 PMCID: PMC11443004 DOI: 10.1038/s41698-024-00713-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 09/16/2024] [Indexed: 10/04/2024] Open
Abstract
Metastases to the brain are rare in prostate cancer. Here, we describe a patient with two treatment-emergent metastatic lesions, one to the brain with neuroendocrine prostate cancer (NEPC) histology and one to the dural membrane of adenocarcinoma histology. We performed genomic, transcriptomic, and proteomic characterization of these lesions and the primary tumor to investigate molecular features promoting these metastases. The two metastatic lesions had high genomic similarity, including TP53 mutation and PTEN deletion, with the most striking difference being the additional loss of RB1 in the NEPC lesion. Interestingly, the dural lesion expressed both androgen receptor and neuroendocrine markers, suggesting amphicrine carcinoma (AMPC). When analyzing pioneer transcription factors, the AMPC lesion exhibited elevated FOXA1 activity while the brain NEPC lesion showed elevated HOXC10, NFYB, and OTX2 expression suggesting novel roles in NEPC formation or brain tropism. Our results highlight the utility of performing multi-omic characterization, especially in rare cancer subtypes.
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Affiliation(s)
- Megan L Ludwig
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - David Moline
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Alec Horrmann
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Ella Boytim
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Gabrianne Larson
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Ali T Arafa
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA
| | - Masooma Sayeda
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - John R Lozada
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Hannah E Bergom
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Abderrahman Day
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Sandhyarani Dasaraju
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Scott M Dehm
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
| | - Paari Murugan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Justin Hwang
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Justin M Drake
- Department of Pharmacology, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
- Department of Urology, University of Minnesota, Minneapolis, MN, USA.
| | - Emmanuel S Antonarakis
- Department of Medicine, Division of Hematology, Oncology, and Transplantation, University of Minnesota, Minneapolis, MN, USA.
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.
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23
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Kabatnik S, Post F, Drici L, Bartels AS, Strauss MT, Zheng X, Madsen GI, Mund A, Rosenberger FA, Moreira J, Mann M. Spatial characterization and stratification of colorectal adenomas by deep visual proteomics. iScience 2024; 27:110620. [PMID: 39252972 PMCID: PMC11381895 DOI: 10.1016/j.isci.2024.110620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 05/13/2024] [Accepted: 07/26/2024] [Indexed: 09/11/2024] Open
Abstract
Colorectal adenomas (CRAs) are potential precursor lesions to adenocarcinomas, currently classified by morphological features. We aimed to establish a molecular feature-based risk allocation framework toward improved patient stratification. Deep visual proteomics (DVP) is an approach that combines image-based artificial intelligence with automated microdissection and ultra-high sensitive mass spectrometry. Here, we used DVP on formalin-fixed, paraffin-embedded (FFPE) CRA tissues from nine male patients, immunohistologically stained for caudal-type homeobox 2 (CDX2), a protein implicated in colorectal cancer, enabling the characterization of cellular heterogeneity within distinct tissue regions and across patients. DVP identified DMBT1, MARCKS, and CD99 as protein markers linked to recurrence, suggesting their potential for risk assessment. It also detected a metabolic shift to anaerobic glycolysis in cells with high CDX2 expression. Our findings underscore the potential of spatial proteomics to refine early stage detection and contribute to personalized patient management strategies and provided novel insights into metabolic reprogramming.
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Affiliation(s)
- Sonja Kabatnik
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Frederik Post
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Lylia Drici
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Annette Snejbjerg Bartels
- Precision Cancer Medicine Laboratory, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maximilian T Strauss
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Xiang Zheng
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Gunvor I Madsen
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Florian A Rosenberger
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - José Moreira
- Precision Cancer Medicine Laboratory, Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
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24
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Harder BJ, Lekkerkerker AN, Casavant EP, Hackney JA, Nguyen A, McBride JM, Mathews WR, Anania VG. Comprehensive profiling of the human fecal proteome from IBD patients with DIA-MS enables evaluation of disease-relevant proteins. Proteomics Clin Appl 2024; 18:e2300075. [PMID: 38552248 DOI: 10.1002/prca.202300075] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 02/26/2024] [Accepted: 03/08/2024] [Indexed: 11/18/2024]
Abstract
PURPOSE Inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), is characterized by chronic gastrointestinal inflammation. A high unmet need exists for noninvasive biomarkers in IBD to monitor changes in disease activity and guide treatment decisions. Stool is an easily accessed, disease proximal matrix in IBD, however the composition of the IBD fecal proteome remains poorly characterized. EXPERIMENTAL DESIGN A data-independent acquisition LC-MS/MS approach was used to profile the human fecal proteome in two independent cohorts (Cohort 1: healthy n = 5, UC n = 5, CD n = 5, Cohort 2: healthy n = 20, UC n = 10, and CD n = 10) to identify noninvasive biomarkers reflective of disease activity. RESULTS 688 human proteins were quantified, with 523 measured in both cohorts. In UC stool 96 proteins were differentially abundant and in CD stool 126 proteins were differentially abundant compared to healthy stool (absolute log2 fold change > 1, p-value < 0.05). Many of these fecal proteins are associated with infiltrating immune cells and ulceration/rectal bleeding, which are hallmarks of IBD pathobiology. Mapping the identified fecal proteins to a whole blood single-cell RNA sequencing data set revealed the involvement of various immune cell subsets to the IBD fecal proteome. CONCLUSIONS AND CLINICAL RELEVANCE Findings from this study not only confirmed the presence of established fecal biomarkers for IBD, such as calprotectin and lactoferrin, but also revealed new fecal proteins from multiple pathways known to be dysregulated in IBD. These novel proteins could serve as potential noninvasive biomarkers to monitor specific aspects of IBD disease activity which could expedite clinical development of novel therapeutic targets.
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Affiliation(s)
- Brandon J Harder
- Department of Translational Medicine, South San Francisco, California, USA
| | | | - Ellen P Casavant
- Department of Translational Medicine, South San Francisco, California, USA
| | - Jason A Hackney
- Department of Translational Medicine, South San Francisco, California, USA
| | - Allen Nguyen
- Department of Translational Medicine, South San Francisco, California, USA
| | | | | | - Veronica G Anania
- Department of Translational Medicine, South San Francisco, California, USA
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25
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Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024; 96:13358-13370. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.
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Affiliation(s)
- Erin M Humphries
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Clare Loudon
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - George E Craft
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
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Rosin NL, Winstone TML, Kelley M, Biernaskie J, Dufour A, Orton DJ. Targeted proteomic approach for quantification of collagen type I and type III in formalin-fixed paraffin-embedded tissue. Sci Rep 2024; 14:17769. [PMID: 39090134 PMCID: PMC11294326 DOI: 10.1038/s41598-024-68377-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 07/23/2024] [Indexed: 08/04/2024] Open
Abstract
Collagen is the most abundant protein in mammals and a major structural component of the extracellular matrix (ECM). Changes to ECM composition occur as a result of numerous physiological and pathophysiological causes, and a common means to evaluate these changes is the collagen 3 (Col3) to collagen 1 (Col1) ratio. Current methods to measure the Col3/1 ratio suffer from a lack of specificity and often under- or over-estimate collagen composition and quantity. This manuscript presents a targeted liquid chromatography tandem mass spectrometry (LC-MS/MS) method for quantification of Col3 and Col1 in FFPE tissues. Using surrogate peptides to generate calibration curves, Col3 and Col1 are readily quantified in FFPE tissue sections with high accuracy and precision. The method is applied to several tissue types from both human and reindeer sources, demonstrating its generalizability. In addition, the targeted LC-MS/MS method permits quantitation of the hydroxyprolinated form of Col3, which has significant implications for understanding not only the quantity of Col3 in tissue, but also understanding of the pathophysiology underlying many causes of ECM changes. This manuscript presents a straightforward, accurate, precise, and generalizable method for quantifying the Col3/1 ratio in a variety of tissue types and organisms.
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Affiliation(s)
- Nicole L Rosin
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Tara M L Winstone
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada
| | - Margaret Kelley
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada
| | - Jeff Biernaskie
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
- Department of Surgery, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Antoine Dufour
- Department of Physiology and Pharmacology, University of Calgary, Calgary, AB, Canada
- McCaig Institute for Bone and Joint Health, University of Calgary, Calgary, AB, Canada
| | - Dennis J Orton
- Department of Pathology and Laboratory Medicine, University of Calgary, 3535 Research Rd NW, Room 1E-415, Calgary, AB, T2I 2K8, Canada.
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27
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Johansen A, Sandve GKF, Ibsen JH, Lundin KEA, Sollid LM, Stamnaes J. Biopsy Proteome Scoring to Determine Mucosal Remodeling in Celiac Disease. Gastroenterology 2024; 167:493-504.e10. [PMID: 38467384 DOI: 10.1053/j.gastro.2024.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/14/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND & AIMS Histologic evaluation of gut biopsies is a cornerstone for diagnosis and management of celiac disease (CeD). Despite its wide use, the method depends on proper biopsy orientation, and it suffers from interobserver variability. Biopsy proteome measurement reporting on the tissue state can be obtained by mass spectrometry analysis of formalin-fixed paraffin-embedded tissue. Here we aimed to transform biopsy proteome data into numerical scores that give observer-independent measures of mucosal remodeling in CeD. METHODS A pipeline using glass-mounted formalin-fixed paraffin-embedded sections for mass spectrometry-based proteome analysis was established. Proteome data were converted to numerical scores using 2 complementary approaches: a rank-based enrichment score and a score based on machine learning using logistic regression. The 2 scoring approaches were compared with each other and with histology analyzing 18 patients with CeD with biopsies collected before and after treatment with a gluten-free diet as well as biopsies from patients with CeD with varying degree of remission (n = 22). Biopsies from individuals without CeD (n = 32) were also analyzed. RESULTS The method yielded reliable proteome scoring of both unstained and H&E-stained glass-mounted sections. The scores of the 2 approaches were highly correlated, reflecting that both approaches pick up proteome changes in the same biological pathways. The proteome scores correlated with villus height-to-crypt depth ratio. Thus, the method is able to score biopsies with poor orientation. CONCLUSIONS Biopsy proteome scores give reliable observer and orientation-independent measures of mucosal remodeling in CeD. The proteomic method can readily be implemented by nonexpert laboratories in parallel to histology assessment and easily scaled for clinical trial settings.
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Affiliation(s)
- Anette Johansen
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
| | - Geir Kjetil F Sandve
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Informatics, The Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Jostein Holen Ibsen
- Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Knut E A Lundin
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Gastroenterology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Ludvig M Sollid
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway
| | - Jorunn Stamnaes
- K.G. Jebsen Coeliac Disease Research Centre, Institute of Clinical Medicine, University of Oslo, Oslo, Norway; Department of Immunology, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
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Doll S, Schweizer L, Bollwein C, Steiger K, Pfarr N, Walker M, Wörtler K, Knebel C, von Eisenhart-Rothe R, Hartmann W, Weichert W, Mann M, Kuhn PH, Specht K. Proteomic Characterization of Undifferentiated Small Round Cell Sarcomas With EWSR1 and CIC::DUX4 Translocations Reveals Diverging Tumor Biology and Distinct Diagnostic Markers. Mod Pathol 2024; 37:100511. [PMID: 38705279 DOI: 10.1016/j.modpat.2024.100511] [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: 10/16/2023] [Revised: 04/11/2024] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Undifferentiated small round cell sarcomas (USRS) of bone and soft tissue are a group of tumors with heterogenic genomic alterations sharing similar morphology. In the present study, we performed a comparative large-scale proteomic analysis of USRS (n = 42) with diverse genomic translocations including classic Ewing sarcomas with EWSR1::FLI1 fusions (n = 24) or EWSR1::ERG fusions (n = 4), sarcomas with an EWSR1 rearrangement (n = 2), CIC::DUX4 fusion (n = 8), as well as tumors classified as USRS with no genetic data available (n = 4). Proteins extracted from formalin-fixed, paraffin-embedded pretherapeutic biopsies were analyzed qualitatively and quantitatively using shotgun mass spectrometry (MS). More than 8000 protein groups could be quantified using data-independent acquisition. Unsupervised hierarchical cluster analysis based on proteomic data allowed stratification of the 42 cases into distinct groups reflecting the different molecular genotypes. Protein signatures that significantly correlated with the respective genomic translocations were identified and used to generate a heatmap of all 42 sarcomas with assignment of cases with unknown molecular genetic data to either the EWSR1- or CIC-rearranged groups. MS-based prediction of sarcoma subtypes was molecularly confirmed in 2 cases where next-generation sequencing was technically feasible. MS also detected proteins routinely used in the immunohistochemical approach for the differential diagnosis of USRS. BCL11B highly expressed in Ewing sarcomas, and BACH2 as well as ETS-1 highly expressed in CIC::DUX4-associated sarcomas, were among proteins identified by the present proteomic study, and were chosen for immunohistochemical confirmation of MS data in our study cohort. Differential expressions of these 3 markers in the 2 genetic groups were further validated in an independent cohort of n = 34 USRS. Finally, our proteomic results point toward diverging signaling pathways in the different USRS subgroups.
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Affiliation(s)
- Sophia Doll
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany; OmicEra Diagnostics GmbH, Planegg, Bavaria, Germany
| | - Lisa Schweizer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | | | - Katja Steiger
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Nicole Pfarr
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Maria Walker
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Klaus Wörtler
- Musculoskeletal Radiology Section, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Carolin Knebel
- Department of Orthopaedic Surgery, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | | | - Wilko Weichert
- Institute of Pathology, Technical University of Munich, Munich, Germany; German Cancer Consortium (DKTK), Partner-site Munich and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Bavaria, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich, Munich, Germany
| | - Katja Specht
- Institute of Pathology, Technical University of Munich, Munich, Germany.
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Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024; 23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [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: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, Cambridge, Massachusetts, USA.
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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Naimy S, Sølberg JBK, Kuczek DE, Løvendorf MB, Bzorek M, Litman T, Mund A, Rahbek Gjerdrum LM, Clark RA, Mann M, Dyring-Andersen B. Comparative Quantitative Proteomic Analysis of Melanoma Subtypes, Nevus-Associated Melanoma, and Corresponding Nevi. J Invest Dermatol 2024; 144:1608-1621.e4. [PMID: 38185415 DOI: 10.1016/j.jid.2023.12.011] [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: 07/04/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 01/09/2024]
Abstract
A substantial part of cutaneous malignant melanomas develops from benign nevi. However, the precise molecular events driving the transformation from benign to malignant melanoma are not well-understood. We used laser microdissection and mass spectrometry to analyze the proteomes of melanoma subtypes, including superficial spreading melanomas (n = 17), nodular melanomas (n = 17), and acral melanomas (n = 15). Furthermore, we compared the proteomes of nevi cells with those of melanoma cells within the same specimens (nevus-associated melanoma (n = 14)). In total, we quantified 7935 proteins. Despite the genomic and clinical differences of the melanoma subtypes, our analysis revealed relatively similar proteomes, except for the upregulation of proteins involved in immune activation in nodular melanomas versus acral melanomas. Examining nevus-associated melanoma versus nevi, we found 1725 differentially expressed proteins (false discovery rate < 0.05). Among these proteins were 140 that overlapped with cancer hallmarks, tumor suppressors, and regulators of metabolism and cell cycle. Pathway analysis indicated aberrant activation of the phosphoinositide 3-kinase-protein kinase B-mTOR pathways and the Hippo-YAP pathway. Using a classifier, we identified six proteins capable of distinguishing melanoma from nevi samples. Our study represents a comprehensive comparative analysis of the proteome in melanoma subtypes and associated nevi, offering insights into the biological behavior of these distinct entities.
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Affiliation(s)
- Soraya Naimy
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Julie B K Sølberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark
| | - Dorota E Kuczek
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Bengtson Løvendorf
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael Bzorek
- Department of Pathology, Zealand University Hospital, Roskilde, Denmark
| | - Thomas Litman
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andreas Mund
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rachael A Clark
- Department of Dermatology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Matthias Mann
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Beatrice Dyring-Andersen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Department of Dermatology and Allergy, Herlev and Gentofte Hospital, Copenhagen University Hospitals, Copenhagen, Denmark; Leo Foundation Skin Immunology Research Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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31
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Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024; 7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [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: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Robotically assisted proteomics provides insights into the regulation of multiple proteins achieving excellent spatial resolution. However, developing an effective method for spatially resolved quantitative proteomics of formalin fixed paraffin embedded tissue (FFPE) in an accessible and economical manner remains challenging. We introduce non-robotic In-insert FFPE proteomics approach, combining glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert approach identifies 450 proteins from a 5 µm thick breast FFPE tissue voxel with 50 µm lateral dimensions covering several tens of cells. Furthermore, In-insert approach associated a keratin series and moesin (MOES) with prolactin-induced protein (PIP) indicating their prolactin and/or estrogen regulation. Our data suggest that PIP is a spatial biomarker for hormonally triggered cytoskeletal remodeling, potentially useful for screening hormonally affected hotspots in breast tissue. In-insert proteomics represents an alternative FFPE processing method, requiring minimal laboratory equipment and skills to generate spatial proteotype repositories from FFPE tissue.
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Affiliation(s)
- Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Michal Bienkowski
- Medical University of Gdansk, University of Gdansk, Mariana Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
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Pruszkowska-Przybylska P, Dupont ME, Jacobsen SB, Smerup M, Tfelt-Hansen J, Morling N, Andersen JD. Evaluation of DNAmAge in paired fresh, frozen, and formalin-fixed paraffin-embedded heart tissues. PLoS One 2024; 19:e0299557. [PMID: 38718072 PMCID: PMC11078437 DOI: 10.1371/journal.pone.0299557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/12/2024] [Indexed: 05/12/2024] Open
Abstract
The continued development in methylome analysis has enabled a more precise assessment of DNA methylation, but treatment of target tissue prior to analysis may affect DNA analysis. Prediction of age based on methylation levels in the genome (DNAmAge) has gained much interest in disease predisposition (biological age estimation), but also in chronological donor age estimation in crime case samples. Various epigenetic clocks were designed to predict the age. However, it remains unknown how the storage of the tissues affects the DNAmAge estimation. In this study, we investigated the storage method impact of DNAmAge by the comparing the DNAmAge of the two commonly used storage methods, freezing and formalin-fixation and paraffin-embedding (FFPE) to DNAmAge of fresh tissue. This was carried out by comparing paired heart tissue samples of fresh tissue, samples stored by freezing and FFPE to chronological age and whole blood samples from the same individuals. Illumina EPIC beadchip array was used for methylation analysis and the DNAmAge was evaluated with the following epigenetic clocks: Horvath, Hannum, Levine, Horvath skin+blood clock (Horvath2), PedBE, Wu, BLUP, EN, and TL. We observed differences in DNAmAge among the storage conditions. FFPE samples showed a lower DNAmAge compared to that of frozen and fresh samples. Additionally, the DNAmAge of the heart tissue was lower than that of the whole blood and the chronological age. This highlights caution when evaluating DNAmAge for FFPE samples as the results were underestimated compared with fresh and frozen tissue samples. Furthermore, the study also emphasizes the need for a DNAmAge model based on heart tissue samples for an accurate age estimation.
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Affiliation(s)
| | - Mikkel Eriksen Dupont
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Smerup
- Department of Cardiothoracic Surgery, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jacob Tfelt-Hansen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Cardiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Topitsch A, Halstenbach T, Rothweiler R, Fretwurst T, Nelson K, Schilling O. Mass Spectrometry-Based Proteomics of Poly(methylmethacrylate)-Embedded Bone. J Proteome Res 2024; 23:1810-1820. [PMID: 38634750 DOI: 10.1021/acs.jproteome.4c00046] [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: 04/19/2024]
Abstract
Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is a widely employed technique in proteomics research for studying the proteome biology of various clinical samples. Hard tissues, such as bone and teeth, are routinely preserved using synthetic poly(methyl methacrylate) (PMMA) embedding resins that enable histological, immunohistochemical, and morphological examination. However, the suitability of PMMA-embedded hard tissues for large-scale proteomic analysis remained unexplored. This study is the first to report on the feasibility of PMMA-embedded bone samples for LC-MS/MS analysis. Conventional workflows yielded merely limited coverage of the bone proteome. Using advanced strategies of prefractionation by high-pH reversed-phase liquid chromatography in combination with isobaric tandem mass tag labeling resulted in proteome coverage exceeding 1000 protein identifications. The quantitative comparison with cryopreserved samples revealed that each sample preparation workflow had a distinct impact on the proteomic profile. However, workflow replicates exhibited a high reproducibility for PMMA-embedded samples. Our findings further demonstrate that decalcification prior to protein extraction, along with the analysis of solubilization fractions, is not preferred for PMMA-embedded bone. The biological applicability of the proposed workflow was demonstrated using samples of human PMMA-embedded alveolar bone and the iliac crest, which revealed anatomical site-specific proteomic profiles. Overall, these results establish a crucial foundation for large-scale proteomics studies contributing to our knowledge of bone biology.
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Affiliation(s)
- Annika Topitsch
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Albertstraße 19a, 79104 Freiburg, Germany
- Faculty of Biology, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tim Halstenbach
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - René Rothweiler
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Tobias Fretwurst
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Katja Nelson
- Department of Oral and Maxillofacial Surgery/Translational Implantology, Faculty of Medicine, Medical Center - University of Freiburg, Hugstetter Straße 55, 79106 Freiburg, Germany
| | - Oliver Schilling
- Institute for Surgical Pathology, Faculty of Medicine, Medical Center - University of Freiburg, Breisacher Straße 115a, 79106 Freiburg, Germany
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Makhmut A, Qin D, Hartlmayr D, Seth A, Coscia F. An Automated and Fast Sample Preparation Workflow for Laser Microdissection Guided Ultrasensitive Proteomics. Mol Cell Proteomics 2024; 23:100750. [PMID: 38513891 PMCID: PMC11067455 DOI: 10.1016/j.mcpro.2024.100750] [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: 12/08/2023] [Revised: 03/13/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024] Open
Abstract
Spatial tissue proteomics integrating whole-slide imaging, laser microdissection, and ultrasensitive mass spectrometry is a powerful approach to link cellular phenotypes to functional proteome states in (patho)physiology. To be applicable to large patient cohorts and low sample input amounts, including single-cell applications, loss-minimized and streamlined end-to-end workflows are key. We here introduce an automated sample preparation protocol for laser microdissected samples utilizing the cellenONE robotic system, which has the capacity to process 192 samples in 3 h. Following laser microdissection collection directly into the proteoCHIP LF 48 or EVO 96 chip, our optimized protocol facilitates lysis, formalin de-crosslinking, and tryptic digest of low-input archival tissue samples. The seamless integration with the Evosep ONE LC system by centrifugation allows 'on-the-fly' sample clean-up, particularly pertinent for laser microdissection workflows. We validate our method in human tonsil archival tissue, where we profile proteomes of spatially-defined B-cell, T-cell, and epithelial microregions of 4000 μm2 to a depth of ∼2000 proteins and with high cell type specificity. We finally provide detailed equipment templates and experimental guidelines for broad accessibility.
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Affiliation(s)
- Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Di Qin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | | | | | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
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Xavier D, Lucas N, Williams SG, Koh JMS, Ashman K, Loudon C, Reddel R, Hains PG, Robinson PJ. Heat 'n Beat: A Universal High-Throughput End-to-End Proteomics Sample Processing Platform in under an Hour. Anal Chem 2024; 96:4093-4102. [PMID: 38427620 DOI: 10.1021/acs.analchem.3c04708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Proteomic analysis by mass spectrometry of small (≤2 mg) solid tissue samples from diverse formats requires high throughput and comprehensive proteome coverage. We developed a nearly universal, rapid, and robust protocol for sample preparation, suitable for high-throughput projects that encompass most cell or tissue types. This end-to-end workflow extends from original sample to loading the mass spectrometer and is centered on a one-tube homogenization and digestion method called Heat 'n Beat (HnB). It is applicable to most tissues, regardless of how they were fixed or embedded. Sample preparation was divided into separate challenges. The initial sample washing and final peptide cleanup steps were adapted to three tissue sources: fresh frozen (FF), optimal cutting temperature (OCT) compound embedded (FF-OCT), and formalin-fixed paraffin embedded (FFPE). Third, for core processing, tissue disruption and lysis were decreased to a 7 min heat and homogenization treatment, and reduction, alkylation, and proteolysis were optimized into a single step. The refinements produced near doubled peptide yield when compared to our earlier method ABLE delivered a consistently high digestion efficiency of 85-90%, reported by ProteinPilot, and required only 38 min for core processing in a single tube, with the total processing time being 53-63 min. The robustness of HnB was demonstrated on six organ types, a cell line, and a cancer biopsy. Its suitability for high-throughput applications was demonstrated on a set of 1171 FF-OCT human cancer biopsies, which were processed for end-to-end completion in 92 h, producing highly consistent peptide yield and quality for over 3513 MS runs.
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Affiliation(s)
- Dylan Xavier
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Natasha Lucas
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Steven G Williams
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Jennifer M S Koh
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Keith Ashman
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Clare Loudon
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Roger Reddel
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Peter G Hains
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
| | - Phillip J Robinson
- ProCan, Faculty of Medicine and Health, The University of Sydney, Children's Medical Research Institute, Westmead, NSW 2145, Australia
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36
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Dokanei S, Minai‐Tehrani D, Moghoofei M, Rostamian M. Investigating the relationship between Epstein-Barr virus infection and gastric cancer: A systematic review and meta-analysis. Health Sci Rep 2024; 7:e1976. [PMID: 38505684 PMCID: PMC10948593 DOI: 10.1002/hsr2.1976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 02/06/2024] [Accepted: 02/28/2024] [Indexed: 03/21/2024] Open
Abstract
Background and Aims Gastric cancer (GC) is a common cancer type worldwide, and various factors can be involved in its occurrence. One of these factors is Epstein-Barr virus (EBV) infection. In this regard, a systematic review and meta-analysis was conducted to achieve a better understanding of the EBV prevalence in GC samples. Methods English databases were searched and studies that reported the prevalence and etiological factors of EBV related to GC from July 2007 to November 2022 were retrieved. The reported data were selected based on the inclusion and exclusion criteria. The pooled prevalence of EBV infection with 95% confidence intervals was calculated. Quality assessment, heterogeneity testing, and publication bias assessment were also performed. The literature search showed 953 studies, of which 87 studies met our inclusion criteria and were used for meta-analysis. Results The pooled prevalence of EBV infection related to GC was estimated to be 9.5% (95% confidence interval [CI]: 8.2%-11%) in the general population. The prevalence of EBV infection related to GC by gender was 13.5% (95% CI: 11.1%-16.3%) in males and 7.6% (95% CI: 5.4%-10.6%) in females. No significant differences were observed in terms of geographical region. Out of the 87 studies included in the meta-analysis, the most common diagnostic test was in situ hybridization (58 cases). Conclusions Altogether, the results indicated that EBV infection is one of the important factors in the development of GC. However, this does not necessarily mean that EBV infection directly causes GC since other factors may also be involved in the development of GC. Therefore, it is recommended to conduct extensive epidemiological studies on various aspects of the relationship between this virus and GC, which can provide valuable information for understanding the relationship between EBV and GC.
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Affiliation(s)
- Saman Dokanei
- Faculty of Life Sciences and BiotechnologyShahid Beheshti University (GC)TehranIran
| | | | - Mohsen Moghoofei
- Department of Microbiology, Faculty of MedicineKermanshah University of Medical SciencesKermanshahIran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health InstituteKermanshah University of Medical SciencesKermanshahIran
- Student Research CommitteeKermanshah University of Medical SciencesKermanshahIran
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Patton A, Dermawan JK. Current updates in sarcoma biomarker discovery: emphasis on next-generation sequencing-based methods. Pathology 2024; 56:274-282. [PMID: 38185613 DOI: 10.1016/j.pathol.2023.10.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 10/25/2023] [Accepted: 10/29/2023] [Indexed: 01/09/2024]
Abstract
Soft tissue sarcomas comprise a heterogeneous group of neoplasms. Although soft tissue malignancies make up only 2% of adult cancers, classification based on histomorphology presents a diagnostic challenge. Characterisation of soft tissue sarcomas by molecular analysis is rapidly evolving to improve diagnostic accuracy and develop targeted therapies. This review highlights the advances in molecular techniques, including current next-generation sequencing-based assays (fusion detection by RNA sequencing, targeted/whole exome sequencing, microRNA profiling), as well as emerging methods (liquid biopsies, DNA methylation profiling, single-cell molecular profiling and next-generation immunohistochemistry) for future clinical applications.
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Affiliation(s)
- Ashley Patton
- Department of Pathology & Laboratory Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Josephine K Dermawan
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA.
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38
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Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024; 23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [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: 01/17/2024]
Abstract
Cell surface proteins represent an important class of molecules for therapeutic targeting and cellular phenotyping. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, post-translational modifications, hydrophobic regions, and processing requirements. To improve their identification, we optimized a Cell-Surface Capture (CSC) workflow that incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), nonenzymatic deamidation (digestion and deglycosylation buffers), and data acquisition methods (DDA, DIA, and TMT). Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid, SDS/urea-based lysis buffers, single-pot solid-phased-enhanced sample-preparation (SP3), and streptavidin magnetic beads for maximal surfaceome coverage. Notably, with semiautomated processing, sample handling was simplified and between ∼600 and 900 cell surface N-glycoproteins were identified from only 25-200 μg of HeLa protein. CSC also revealed significant differences between in vitro monolayer cultures and in vivo tumor xenografts of murine CT26 colon adenocarcinoma samples that may aid in target identification for drug development. Overall, the improved efficiency of the magnetic-based CSC workflow identified both previously reported and novel N-glycosites with less material and high reproducibility that should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.
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Affiliation(s)
| | - Paolo Manzanillo
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Han-Yin Yang
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [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: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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40
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Yan HJ, Lin SC, Xu SH, Gao YB, Zhou BJ, Zhou R, Chen FM, Li FR. Proteomic analysis reveals LRPAP1 as a key player in the micropapillary pattern metastasis of lung adenocarcinoma. Heliyon 2024; 10:e23913. [PMID: 38226250 PMCID: PMC10788494 DOI: 10.1016/j.heliyon.2023.e23913] [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: 08/04/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/17/2024] Open
Abstract
Objectives Lung adenocarcinomas have different prognoses depending on their histological growth patterns. Micropapillary growth within lung adenocarcinoma, particularly metastasis, is related to dismal prognostic outcome. Metastasis accounts for a major factor leading to mortality among lung cancer patients. Understanding the mechanisms underlying early stage metastasis can help develop novel treatments for improving patient survival. Methods Here, quantitative mass spectrometry was conducted for comparing protein expression profiles among various histological subtypes, including adenocarcinoma in situ, minimally invasive adenocarcinoma, and invasive adenocarcinoma (including acinar and micropapillary [MIP] types). To determine the mechanism of MIP-associated metastasis, we identified a protein that was highly expressed in MIP. The expression of the selected highly expressed MIP protein was verified via immunohistochemical (IHC) analysis and its function was validated by an in vitro migration assay. Results Proteomic data revealed that low-density lipoprotein receptor-related protein-associated protein 1 (LRPAP1) was highly expressed in MIP group, which was confirmed by IHC. The co-expressed proteins in this study, PSMD1 and HSP90AB1, have been reported to be highly expressed in different cancers and play an essential role in metastasis. We observed that LRPAP1 promoted lung cancer progression, including metastasis, invasion and proliferation in vitro and in vivo. Conclusion LRPAP1 is necessary for MIP-associated metastasis and is the candidate novel anti-metastasis therapeutic target.
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Affiliation(s)
- Hao-jie Yan
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Post-doctoral Scientific Research Station of Basic Medicine, Jinan University, 510632, Guangzhou, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Sheng-cheng Lin
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 518172, Shenzhen, China
| | | | - Yu-biao Gao
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Bao-jin Zhou
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, 201203, Shanghai, China
| | - Ruo Zhou
- Deepxomics Co., Ltd, 518112, Shenzhen, China
| | - Fu-ming Chen
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
| | - Fu-rong Li
- Translational Medicine Collaborative Innovation Center, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), 518020, Shenzhen, China
- Guangdong Engineering Technology Research Center of Stem Cell and Cell Therapy, Shenzhen Key Laboratory of Stem Cell Research and Clinical Transformation, Shenzhen Immune Cell Therapy Public Service Platform, 518020, Shenzhen, China
- Institute of Health Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
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41
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Thielert M, Weiss CAM, Mann M, Rosenberger FA. Spatial Proteomics of Single Hepatocytes with Multiplexed Data-Independent Acquisition (mDIA). Methods Mol Biol 2024; 2817:97-113. [PMID: 38907150 DOI: 10.1007/978-1-0716-3934-4_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/23/2024]
Abstract
Spatially resolved mass spectrometry-based proteomics at single-cell resolution promises to provide insights into biological heterogeneity. We describe a protocol based on multiplexed data-independent acquisition (mDIA) with dimethyl labeling to enhance proteome depth, accuracy, and throughput while minimizing costs. It enables high-quality proteome analysis of single isolated hepatocytes and utilizes liver zonation for single-cell proteomics benchmarking. This adaptable, modular protocol will promote the use of single-cell proteomics in spatial biology.
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Affiliation(s)
- Marvin Thielert
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Caroline A M Weiss
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Proteomics Program, Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Florian A Rosenberger
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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42
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Wang YE, Zeng WL, Cao ST, Zou JP, Liu CT, Shi JM, Li J, Qiu F, Wang Y. Development of a sample preparation method for micro-proteomics analysis of the formaldehyde-fixed paraffin-embedded liver tissue samples. Talanta 2024; 266:125106. [PMID: 37639870 DOI: 10.1016/j.talanta.2023.125106] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023]
Abstract
Liver micro-proteomics based on the routinely used formaldehyde-fixed paraffin-embedded (FFPE) samples is valuable for innovative research, but the technical approach for sample preparation is often challenging. In this study, we aimed to develop a method for sample preparation for micro-proteomics on using the FFPE liver samples. We collected 2000 individual cells per batch from FFPE liver slices with laser capture microdissection and used them as test samples. We used the microscale fresh-frozen liver samples or HepG2 cells as control samples. For the FFPE samples, we first established a procedure for protein extraction. 2 h incubation at 95 °C in alkaline amine buffer supplemented with 4% sodium dodecyl sulfate allows improved production, efficiency, and quality of protein extraction. Then, we developed a dedicated protocol HDMSP for the micro-concentrated (<0.05 μg/μL) protein preparation for mass spectrometry (MS) based analysis, in which 2 μg/μL carboxyl magnetic beads and 70% acetonitrile are used to induce protein precipitation. For the 0.01 μg/μL protein control samples, protein recovery rate (PRR) by HDMSP is 72.1%, while the PRR is 5.9% if using a standard method solid phase-enhanced sample preparation. For the FFPE samples, the HDMSP PRR is 88.8%, and the subsequent MS analysis demonstrates increased depth, robustness, and quantitation accuracy for HDMSP relative to the control of in-gel digestion. Moreover, the physicochemical properties and subcellular location of the FFPE liver micro-proteome are comparable to those of the fresh-frozen control samples processed with filter-aided sample preparation (FASP). HDMSP is also comparable to FASP in terms of reproducibility and physicochemical properties in liver subcellular proteomes, and meanwhile reduces the sample preparation time by 15.9% and the experimental cost by 30.8%. Overall, the new method is simple and highly effective for preparing the microscale FFPE liver protein samples for MS analysis. This study provides a useful solution for FFPE liver micro-proteomics.
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Affiliation(s)
- Yong-Er Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Wei-Lan Zeng
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Sheng-Tian Cao
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Jun-Peng Zou
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Cui-Ting Liu
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jun-Min Shi
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jing Li
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Feng Qiu
- The Seventh Affiliated Hospital of Southern Medical University, Foshan, China.
| | - Yan Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China; The Seventh Affiliated Hospital of Southern Medical University, Foshan, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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43
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024; 2823:193-223. [PMID: 39052222 PMCID: PMC11648944 DOI: 10.1007/978-1-0716-3922-1_13] [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] [Indexed: 07/27/2024]
Abstract
Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).
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Affiliation(s)
| | | | | | - Bin Fang
- H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - John M Koomen
- H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Molecular Oncology/Pathology, Moffitt Cancer Center, Tampa, FL, USA.
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Mar D, Babenko IM, Zhang R, Noble WS, Denisenko O, Vaisar T, Bomsztyk K. A High-Throughput PIXUL-Matrix-Based Toolbox to Profile Frozen and Formalin-Fixed Paraffin-Embedded Tissues Multiomes. J Transl Med 2024; 104:100282. [PMID: 37924947 PMCID: PMC10872585 DOI: 10.1016/j.labinv.2023.100282] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/23/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023] Open
Abstract
Large-scale high-dimensional multiomics studies are essential to unravel molecular complexity in health and disease. We developed an integrated system for tissue sampling (CryoGrid), analytes preparation (PIXUL), and downstream multiomic analysis in a 96-well plate format (Matrix), MultiomicsTracks96, which we used to interrogate matched frozen and formalin-fixed paraffin-embedded (FFPE) mouse organs. Using this system, we generated 8-dimensional omics data sets encompassing 4 molecular layers of intracellular organization: epigenome (H3K27Ac, H3K4m3, RNA polymerase II, and 5mC levels), transcriptome (messenger RNA levels), epitranscriptome (m6A levels), and proteome (protein levels) in brain, heart, kidney, and liver. There was a high correlation between data from matched frozen and FFPE organs. The Segway genome segmentation algorithm applied to epigenomic profiles confirmed known organ-specific superenhancers in both FFPE and frozen samples. Linear regression analysis showed that proteomic profiles, known to be poorly correlated with transcriptomic data, can be more accurately predicted by the full suite of multiomics data, compared with using epigenomic, transcriptomic, or epitranscriptomic measurements individually.
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Affiliation(s)
- Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Ilona M Babenko
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Ran Zhang
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, Washington; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, Washington
| | - Tomas Vaisar
- Diabetes Institute, University of Washington, Seattle, Washington
| | - Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington; Matchstick Technologies, Inc, Kirkland, Washington.
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Tüshaus J, Sakhteman A, Lechner S, The M, Mucha E, Krisp C, Schlegel J, Delbridge C, Kuster B. A region-resolved proteomic map of the human brain enabled by high-throughput proteomics. EMBO J 2023; 42:e114665. [PMID: 37916885 PMCID: PMC10690467 DOI: 10.15252/embj.2023114665] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 11/03/2023] Open
Abstract
Substantial efforts are underway to deepen our understanding of human brain morphology, structure, and function using high-resolution imaging as well as high-content molecular profiling technologies. The current work adds to these approaches by providing a comprehensive and quantitative protein expression map of 13 anatomically distinct brain regions covering more than 11,000 proteins. This was enabled by the optimization, characterization, and implementation of a high-sensitivity and high-throughput microflow liquid chromatography timsTOF tandem mass spectrometry system (LC-MS/MS) capable of analyzing more than 2,000 consecutive samples prepared from formalin-fixed paraffin embedded (FFPE) material. Analysis of this proteomic resource highlighted brain region-enriched protein expression patterns and functional protein classes, protein localization differences between brain regions and individual markers for specific areas. To facilitate access to and ease further mining of the data by the scientific community, all data can be explored online in a purpose-built R Shiny app (https://brain-region-atlas.proteomics.ls.tum.de).
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Affiliation(s)
- Johanna Tüshaus
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Amirhossein Sakhteman
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Severin Lechner
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Matthew The
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
| | - Eike Mucha
- Bruker Daltonics GmbH & Co. KGBremenGermany
| | | | - Jürgen Schlegel
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Claire Delbridge
- Department of Neuropathology, Klinikum Rechts der ISAR, School of MedicineTechnical University MunichMunichGermany
| | - Bernhard Kuster
- Proteomics and Bioanalytics, Department of Molecular Life Sciences, School of Life SciencesTechnical University of MunichMunichGermany
- German Cancer Consortium (DKTK), Munich SiteHeidelbergGermany
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Brouwer NP, Webbink L, Haddad TS, Rutgers N, van Vliet S, Wood CS, Jansen PW, Lafarge MW, de Wilt JH, Hugen N, Simmer F, Jamieson NB, Tauriello DV, Kölzer VH, Vermeulen M, Nagtegaal ID. Transcriptomics and proteomics reveal distinct biology for lymph node metastases and tumour deposits in colorectal cancer. J Pathol 2023; 261:401-412. [PMID: 37792663 DOI: 10.1002/path.6196] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/12/2023] [Accepted: 08/02/2023] [Indexed: 10/06/2023]
Abstract
Both lymph node metastases (LNMs) and tumour deposits (TDs) are included in colorectal cancer (CRC) staging, although knowledge regarding their biological background is lacking. This study aimed to compare the biology of these prognostic features, which is essential for a better understanding of their role in CRC spread. Spatially resolved transcriptomic analysis using digital spatial profiling was performed on TDs and LNMs from 10 CRC patients using 1,388 RNA targets, for the tumour cells and tumour microenvironment. Shotgun proteomics identified 5,578 proteins in 12 different patients. Differences in RNA and protein expression were analysed, and spatial deconvolution was performed. Image-based consensus molecular subtype (imCMS) analysis was performed on all TDs and LNMs included in the study. Transcriptome and proteome profiles identified distinct clusters for TDs and LNMs in both the tumour and tumour microenvironment segment, with upregulation of matrix remodelling, cell adhesion/motility, and epithelial-mesenchymal transition (EMT) in TDs (all p < 0.05). Spatial deconvolution showed a significantly increased abundance of fibroblasts, macrophages, and regulatory T-cells (p < 0.05) in TDs. Consistent with a higher fibroblast and EMT component, imCMS classified 62% of TDs as poor prognosis subtype CMS4 compared to 36% of LNMs (p < 0.05). Compared to LNMs, TDs have a more invasive state involving a distinct tumour microenvironment and upregulation of EMT, which are reflected in a more frequent histological classification of TDs as CMS4. These results emphasise the heterogeneity of locoregional spread and the fact that TDs should merit more attention both in future research and during staging. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Nelleke Pm Brouwer
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Loth Webbink
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Tariq S Haddad
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Natasja Rutgers
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Shannon van Vliet
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Colin S Wood
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, UK
- Academic Unit of Surgery, Glasgow Royal Infirmary, University of Glasgow, UK
| | - Pascal Wtc Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, The Netherlands
| | - Maxime W Lafarge
- Department of Pathology and Molecular Pathology, University and University Hospital of Zürich, Zürich, Switzerland
| | - Johannes Hw de Wilt
- Department of Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Niek Hugen
- Department of Surgery, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Femke Simmer
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Nigel B Jamieson
- Wolfson Wohl Cancer Research Centre, School of Cancer Sciences, University of Glasgow, UK
- Academic Unit of Surgery, Glasgow Royal Infirmary, University of Glasgow, UK
| | - Daniele Vf Tauriello
- Department of Medical Biosciences, Research Institute for Medical Innovation, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Viktor H Kölzer
- Department of Pathology and Molecular Pathology, University and University Hospital of Zürich, Zürich, Switzerland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, The Netherlands
- The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology, Radboud University Medical Centre, Nijmegen, The Netherlands
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47
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Cho A, Ahn J, Kim A, Lee JH, Ryu HS, Kim KM, Yi EC. Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9616. [PMID: 37817342 DOI: 10.1002/rcm.9616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE The comprehensive analysis of formalin-fixed paraffin-embedded (FFPE) tissues is essential for retrospective clinical studies. However, detecting low-abundance proteins and obtaining proteome-scale data from FFPE samples pose analytical challenges in mass spectrometry-based proteomics. To overcome this challenge, our study focuses on implementing an isobaric labeling approach to improve the detection of low-abundance target proteins in FFPE tissues, thereby enhancing the qualitative and quantitative analysis. METHODS We employed an isobaric labeling approach utilizing synthetic peptides or proteins to enable the qualitative and quantitative measurement of target proteins in FFPE tissue samples. To achieve this, we incorporated tandem mass tag (TMT)-labeled recombinant proteins or synthetic peptides into TMT-labeled metastatic breast cancer FFPE tissues. Through this strategy, we successfully detect coexisting CD276 (B7-H3) and CD147 proteins while identifying over 6000 proteins using targeted analysis of individual FFPE tissue sections. RESULTS Our findings provide compelling evidence that the incorporation of isobaric labeling, along with the inclusion of TMT-labeled peptides or proteins, greatly enhances the detection of target proteins in FFPE tissue samples. By employing this approach, we were able to obtain robust qualitative measurements of CD276 and CD147 proteins, showcasing its effectiveness in identifying more than 6000 proteins in FFPE samples. CONCLUSIONS The integration of an isobaric labeling approach, in conjunction with synthetic peptides or proteins, presents a valuable strategy for enhancing the detection and validation of target proteins in FFPE tissue analysis. This technique holds immense potential in retrospective clinical studies, as it enables comprehensive analysis of low-abundance proteins and facilitating proteome-scale investigations in FFPE samples. By leveraging this methodology, researchers can unlock new insights into disease mechanisms and advance our understanding of complex biological processes.
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Affiliation(s)
- Ara Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Ahn
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Andrew Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeong Hyun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kristine M Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
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48
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Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023; 14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour at three spatial resolutions, the highest being 40 µm, to reveal distinct abundance patterns of thousands of proteins. We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns and correlate proteins in the context of tissue heterogeneity and cellular features such as extracellular matrix or proximity to blood vessels. We identify PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, we demonstrate spatially-aware deep proteo-phenotyping of tissue heterogeneity, to re-define understanding tissue biology and pathology at the molecular level.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Janina Oetjen
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Philip D Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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49
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Makhmut A, Qin D, Fritzsche S, Nimo J, König J, Coscia F. A framework for ultra-low-input spatial tissue proteomics. Cell Syst 2023; 14:1002-1014.e5. [PMID: 37909047 DOI: 10.1016/j.cels.2023.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 08/03/2023] [Accepted: 10/06/2023] [Indexed: 11/02/2023]
Abstract
Spatial proteomics combining microscopy-based cell phenotyping with ultrasensitive mass-spectrometry-based proteomics is an emerging and powerful concept to study cell function and heterogeneity in (patho)physiology. However, optimized workflows that preserve morphological information for phenotype discovery and maximize proteome coverage of few or even single cells from laser microdissected tissue are currently lacking. Here, we report a robust and scalable workflow for the proteomic analysis of ultra-low-input archival material. Benchmarking in murine liver resulted in up to 2,000 quantified proteins from single hepatocyte contours and nearly 5,000 proteins from 50-cell regions. Applied to human tonsil, we profiled 146 microregions including T and B lymphocyte niches and quantified cell-type-specific markers, cytokines, and transcription factors. These data also highlighted proteome dynamics within activated germinal centers, illuminating sites undergoing B cell proliferation and somatic hypermutation. This approach has broad implications in biomedicine, including early disease profiling and drug target and biomarker discovery. A record of this paper's transparent peer review process is included in the supplemental information.
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Affiliation(s)
- Anuar Makhmut
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Di Qin
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Sonja Fritzsche
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Jose Nimo
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Janett König
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany
| | - Fabian Coscia
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Spatial Proteomics Group, Berlin, Germany.
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50
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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