1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Xia YQ, Yang Y, Liu Y, Li CH, Liu PF. Investigation of copper-induced intestinal damage and proteome alterations in Takifugu rubripes: Potential health risks and environmental toxicology detection. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 282:116718. [PMID: 39024957 DOI: 10.1016/j.ecoenv.2024.116718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/20/2024]
Abstract
Copper is one of the predominant water pollutants. Excessive exposure to copper can cause harm to animal health, affecting the central nervous system and causing blood abnormalities. Cuproptosis is a novel form of cell death that differs from previous programmed cell death methods. However, the impact of copper on the intestines remains unclear. Therefore, we investigated the effects of different concentrations of copper exposure on the intestinal proteome of Takifugu rubripes (T. rubripes). Relevant biomarkers were used to detect cuproptosis. We revealed the crosstalk relationship between cuproptosis and self-rescue at different concentrations, and discussed the feasibility of using potential cuproptosis indicators as anti-infection factors. We observed intestinal damage in the three copper exposure groups, especially in T. rubripes treated with 100 and 500 μg/L copper, with shedding and breakage of intestinal villus and fuzzy and loose structure of intestinal mucosa. The presence of copper stress not only causes cuproptosis but also oxidative damage caused by reactive oxygen species (ROS). The results of quantitative proteomics by TMT showed that compared to the 50 and 100 μg/L copper exposure groups, the expression of glutaminase, pyruvate kinase, and skin mucus lectin in the 500 μg/L group was significantly increased. The positive mediators COX5A and CTNNB1, as well as the negative mediators CD4 and FDXR, were found to be differentially expressed. Using the protein expression trends of cuproptosis indicator factors FDX1 and DLAT to indicate the concentration of copper ions in the environment. In addition, we found a new effect of promoting ferroptosis: providing additional copper ions can activate the phenomenon of ferroptosis. Our results expand our understanding of the potential health risks of copper in T. rubripes. At the same time, it is of great significance for the process of copper poisoning and the development of new environmental toxicology detection reagents.
Collapse
Affiliation(s)
- Yu-Qing Xia
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China
| | - Yi Yang
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, PR China
| | - Ying Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China
| | - Cheng-Hua Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University), Ministry of Education, 52 Heishijiao Street, Dalian 116023, PR China; College of Marine Technology and Environment, Dalian Ocean University, 52 Heishijiao Street, Dalian 116023, PR China.
| |
Collapse
|
3
|
Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. Nat Commun 2024; 15:5888. [PMID: 39003254 PMCID: PMC11246512 DOI: 10.1038/s41467-024-50046-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 06/27/2024] [Indexed: 07/15/2024] Open
Abstract
Archived patient-derived tissue specimens play a central role in understanding disease and developing therapies. To address specificity and sensitivity shortcomings of existing single-cell resolution proteoform analysis tools, we introduce a hybrid microfluidic platform (DropBlot) designed for proteoform analyses in chemically fixed single cells. DropBlot serially integrates droplet-based encapsulation and lysis of single fixed cells, with on-chip microwell-based antigen retrieval, with single-cell western blotting of target antigens. A water-in-oil droplet formulation withstands the harsh chemical (SDS, 6 M urea) and thermal conditions (98 °C, 1-2 hr) required for effective antigen retrieval, and supports analysis of retrieved protein targets by single-cell electrophoresis. We demonstrate protein-target retrieval from unfixed, paraformaldehyde-fixed (PFA), and methanol-fixed cells. Key protein targets (HER2, GAPDH, EpCAM, Vimentin) retrieved from PFA-fixed cells were resolved and immunoreactive. Relevant to biorepositories, DropBlot profiled targets retrieved from human-derived breast tumor specimens archived for six years, offering a workflow for single-cell protein-biomarker analysis of sparing biospecimens.
Collapse
Affiliation(s)
- Yang Liu
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- School of Chemical, Materials and Biomedical Engineering, University of Georgia, Athens, GA, 30602, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
| |
Collapse
|
4
|
Di Fraia D, Marino A, Lee JH, Kelmer Sacramento E, Baumgart M, Bagnoli S, Tomaz da Silva P, Kumar Sahu A, Siano G, Tiessen M, Terzibasi-Tozzini E, Gagneur J, Frydman J, Cellerino A, Ori A. Impaired biogenesis of basic proteins impacts multiple hallmarks of the aging brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.20.549210. [PMID: 38260253 PMCID: PMC10802395 DOI: 10.1101/2023.07.20.549210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Aging and neurodegeneration entail diverse cellular and molecular hallmarks. Here, we studied the effects of aging on the transcriptome, translatome, and multiple layers of the proteome in the brain of a short-lived killifish. We reveal that aging causes widespread reduction of proteins enriched in basic amino acids that is independent of mRNA regulation, and it is not due to impaired proteasome activity. Instead, we identify a cascade of events where aberrant translation pausing leads to reduced ribosome availability resulting in proteome remodeling independently of transcriptional regulation. Our research uncovers a vulnerable point in the aging brain's biology - the biogenesis of basic DNA/RNA binding proteins. This vulnerability may represent a unifying principle that connects various aging hallmarks, encompassing genome integrity and the biosynthesis of macromolecules.
Collapse
Affiliation(s)
- Domenico Di Fraia
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Antonio Marino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | - Jae Ho Lee
- Department of Biology, Stanford University, Stanford, CA, USA
| | | | - Mario Baumgart
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Pedro Tomaz da Silva
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Munich Center for Machine Learning, Munich, Germany
| | - Amit Kumar Sahu
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Max Tiessen
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| | | | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, Garching, Germany
- Computational Health Center, Helmholtz Center Munich, Neuherberg, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Alessandro Cellerino
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
- BIO@SNS, Scuola Normale Superiore, Pisa, Italy
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, Germany
| |
Collapse
|
5
|
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: 0] [Impact Index Per Article: 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.
Collapse
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.
| |
Collapse
|
6
|
Santinha D, Vilaça A, Estronca L, Schüler SC, Bartoli C, De Sandre-Giovannoli A, Figueiredo A, Quaas M, Pompe T, Ori A, Ferreira L. Remodeling of the Cardiac Extracellular Matrix Proteome During Chronological and Pathological Aging. Mol Cell Proteomics 2024; 23:100706. [PMID: 38141925 PMCID: PMC10828820 DOI: 10.1016/j.mcpro.2023.100706] [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: 07/07/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 12/25/2023] Open
Abstract
Impaired extracellular matrix (ECM) remodeling is a hallmark of many chronic inflammatory disorders that can lead to cellular dysfunction, aging, and disease progression. The ECM of the aged heart and its effects on cardiac cells during chronological and pathological aging are poorly understood across species. For this purpose, we first used mass spectrometry-based proteomics to quantitatively characterize age-related remodeling of the left ventricle (LV) of mice and humans during chronological and pathological (Hutchinson-Gilford progeria syndrome (HGPS)) aging. Of the approximately 300 ECM and ECM-associated proteins quantified (named as Matrisome), we identified 13 proteins that were increased during aging, including lactadherin (MFGE8), collagen VI α6 (COL6A6), vitronectin (VTN) and immunoglobulin heavy constant mu (IGHM), whereas fibulin-5 (FBLN5) was decreased in most of the data sets analyzed. We show that lactadherin accumulates with age in large cardiac blood vessels and when immobilized, triggers phosphorylation of several phosphosites of GSK3B, MAPK isoforms 1, 3, and 14, and MTOR kinases in aortic endothelial cells (ECs). In addition, immobilized lactadherin increased the expression of pro-inflammatory markers associated with an aging phenotype. These results extend our knowledge of the LV proteome remodeling induced by chronological and pathological aging in different species (mouse and human). The lactadherin-triggered changes in the proteome and phosphoproteome of ECs suggest a straight link between ECM component remodeling and the aging process of ECs, which may provide an additional layer to prevent cardiac aging.
Collapse
Affiliation(s)
- Deolinda Santinha
- Faculty of Medicine, University of Coimbra, Celas, Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga, Coimbra, Portugal
| | - Andreia Vilaça
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga, Coimbra, Portugal; CARIM School for Cardiovascular Diseases, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Luís Estronca
- Faculty of Medicine, University of Coimbra, Celas, Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga, Coimbra, Portugal
| | - Svenja C Schüler
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | | | - Annachiara De Sandre-Giovannoli
- Aix Marseille Univ, INSERM, MMG, U1251, Marseille, France; Molecular genetics laboratory, La Timone children's hospital, Marseille, France
| | - Arnaldo Figueiredo
- Serviço de Urologia e Transplantação Renal, Centro Hospitalar Universitário Coimbra EPE, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maximillian Quaas
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Tilo Pompe
- Institute of Biochemistry, Faculty of Life Sciences, Leipzig University, Leipzig, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.
| | - Lino Ferreira
- Faculty of Medicine, University of Coimbra, Celas, Coimbra, Portugal; CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga, Coimbra, Portugal.
| |
Collapse
|
7
|
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 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] [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).
Collapse
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.
| |
Collapse
|
8
|
Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
Collapse
Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
| |
Collapse
|
9
|
Ceanga M, Rahmati V, Haselmann H, Schmidl L, Hunter D, Brauer AK, Liebscher S, Kreye J, Prüss H, Groc L, Hallermann S, Dalmau J, Ori A, Heckmann M, Geis C. Human NMDAR autoantibodies disrupt excitatory-inhibitory balance, leading to hippocampal network hypersynchrony. Cell Rep 2023; 42:113166. [PMID: 37768823 DOI: 10.1016/j.celrep.2023.113166] [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: 05/31/2022] [Revised: 06/30/2023] [Accepted: 09/07/2023] [Indexed: 09/30/2023] Open
Abstract
Anti-NMDA receptor autoantibodies (NMDAR-Abs) in patients with NMDAR encephalitis cause severe disease symptoms resembling psychosis and cause cognitive dysfunction. After passive transfer of patients' cerebrospinal fluid or human monoclonal anti-GluN1-autoantibodies in mice, we find a disrupted excitatory-inhibitory balance resulting from CA1 neuronal hypoexcitability, reduced AMPA receptor (AMPAR) signaling, and faster synaptic inhibition in acute hippocampal slices. Functional alterations are also reflected in widespread remodeling of the hippocampal proteome, including changes in glutamatergic and GABAergic neurotransmission. NMDAR-Abs amplify network γ oscillations and disrupt θ-γ coupling. A data-informed network model reveals that lower AMPAR strength and faster GABAA receptor current kinetics chiefly account for these abnormal oscillations. As predicted in silico and evidenced ex vivo, positive allosteric modulation of AMPARs alleviates aberrant γ activity, reinforcing the causative effects of the excitatory-inhibitory imbalance. Collectively, NMDAR-Ab-induced aberrant synaptic, cellular, and network dynamics provide conceptual insights into NMDAR-Ab-mediated pathomechanisms and reveal promising therapeutic targets that merit future in vivo validation.
Collapse
Affiliation(s)
- Mihai Ceanga
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747 Jena, Germany
| | - Vahid Rahmati
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747 Jena, Germany
| | - Holger Haselmann
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747 Jena, Germany
| | - Lars Schmidl
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747 Jena, Germany
| | - Daniel Hunter
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Anna-Katherina Brauer
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Martinsried, Germany; Biomedical Center, Ludwig Maximilians University Munich, Martinsried, Germany
| | - Sabine Liebscher
- Institute of Clinical Neuroimmunology, Klinikum der Universität München, Ludwig Maximilians University Munich, Martinsried, Germany; Biomedical Center, Ludwig Maximilians University Munich, Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jakob Kreye
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany; Department of Pediatric Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Harald Prüss
- Department of Neurology and Experimental Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany; German Center for Neurodegenerative Diseases (DZNE) Berlin, Berlin, Germany
| | - Laurent Groc
- Université de Bordeaux, CNRS, Interdisciplinary Institute for Neuroscience, UMR 5297, 33000 Bordeaux, France
| | - Stefan Hallermann
- Carl Ludwig Institute for Physiology, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Josep Dalmau
- Catalan Institution for Research and Advanced Studies (ICREA) and IDIBAPS-Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Manfred Heckmann
- Department of Neurophysiology, Institute of Physiology, University of Würzburg, 97070 Würzburg, Germany
| | - Christian Geis
- Section of Translational Neuroimmunology, Department of Neurology, Jena University Hospital, 07747 Jena, Germany.
| |
Collapse
|
10
|
Gerovska D, Noer JB, Qin Y, Ain Q, Januzi D, Schwab M, Witte OW, Araúzo-Bravo MJ, Kretz A. A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1 G93A model of ALS. Cell Biosci 2023; 13:170. [PMID: 37705092 PMCID: PMC10498603 DOI: 10.1186/s13578-023-01116-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 08/27/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Numerous genes, including SOD1, mutated in familial and sporadic amyotrophic lateral sclerosis (f/sALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. One possible outcome of chromosomal instability and repair processes is extrachromosomal circular DNA (eccDNA) formation. Therefore, eccDNA might accumulate in f/sALS with yet unknown function. METHODS We combined rolling circle amplification with linear DNA digestion to purify eccDNA from the cervical spinal cord of 9 co-isogenic symptomatic hSOD1G93A mutants and 10 controls, followed by deep short-read sequencing. We mapped the eccDNAs and performed differential analysis based on the split read signal of the eccDNAs, referred as DifCir, between the ALS and control specimens, to find differentially produced per gene circles (DPpGC) in the two groups. Compared were eccDNA abundances, length distributions and genic profiles. We further assessed proteome alterations in ALS by mass spectrometry, and matched the DPpGCs with differentially expressed proteins (DEPs) in ALS. Additionally, we aligned the ALS-specific DPpGCs to ALS risk gene databases. RESULTS We found a six-fold enrichment in the number of unique eccDNAs in the genotoxic ALS-model relative to controls. We uncovered a distinct genic circulome profile characterized by 225 up-DPpGCs, i.e., genes that produced more eccDNAs from distinct gene sequences in ALS than under control conditions. The inter-sample recurrence rate was at least 89% for the top 6 up-DPpGCs. ALS proteome analyses revealed 42 corresponding DEPs, of which 19 underlying genes were itemized for an ALS risk in GWAS databases. The up-DPpGCs and their DEP tandems mainly impart neuron-specific functions, and gene set enrichment analyses indicated an overrepresentation of the adenylate cyclase modulating G protein pathway. CONCLUSIONS We prove, for the first time, a significant enrichment of eccDNA in the ALS-affected spinal cord. Our triple circulome, proteome and genome approach provide indication for a potential importance of certain eccDNAs in ALS neurodegeneration and a yet unconsidered role as ALS biomarkers. The related functional pathways might open up new targets for therapeutic intervention.
Collapse
Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastian, Spain
| | - Julie B Noer
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Yating Qin
- Department of Biology, Section for Ecology and Evolution, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Quratul Ain
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
- Department of Internal Medicine IV, Hepatology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Donjetë Januzi
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Matthias Schwab
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
| | - Otto W Witte
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany
- Jena Center for Healthy Ageing, Jena University Hospital, Jena, Thuringia, Germany
| | - Marcos J Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, 20014, San Sebastian, Spain.
- Basque Foundation for Science, IKERBASQUE, 48013, Bilbao, Spain.
- Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics Group, 48149, Münster, North Rhine-Westphalia, Germany.
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940, Leioa, Spain.
| | - Alexandra Kretz
- Department of Neurology, Jena University Hospital, 07747, Jena, Thuringia, Germany.
- Jena Center for Healthy Ageing, Jena University Hospital, Jena, Thuringia, Germany.
| |
Collapse
|
11
|
Liu Y, Herr AE. DropBlot: single-cell western blotting of chemically fixed cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.04.556277. [PMID: 37732260 PMCID: PMC10508777 DOI: 10.1101/2023.09.04.556277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
To further realize proteomics of archived tissues for translational research, we introduce a hybrid microfluidic platform for high-specificity, high-sensitivity protein detection from individual chemically fixed cells. To streamline processing-to-analysis workflows and minimize signal loss, DropBlot serially integrates sample preparation using droplet-based antigen retrieval from single fixed cells with unified analysis-on-a-chip comprising microwell-based antigen extraction followed by chip-based single-cell western blotting. A water-in-oil droplet formulation proves robust to the harsh chemical (SDS, 6M urea) and thermal conditions (98°C, 1-2 hr.) required for sufficient antigen retrieval, and the electromechanical conditions required for electrotransfer of retrieved antigen from microwell-encapsulated droplets to single-cell electrophoresis. Protein-target retrieval was demonstrated for unfixed, paraformaldehyde-(PFA), and methanol-fixed cells. We observed higher protein electrophoresis separation resolution from PFA-fixed cells with sufficient immunoreactivity confirmed for key targets (HER2, GAPDH, EpCAM, Vimentin) from both fixation chemistries. Multiple forms of EpCAM and Vimentin were detected, a hallmark strength of western-blot analysis. DropBlot of PFA-fixed human-derived breast tumor specimens (n = 5) showed antigen retrieval from cells archived frozen for 6 yrs. DropBlot could provide a precision integrated workflow for single-cell resolution protein-biomarker mining of precious biospecimen repositories.
Collapse
|
12
|
Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
Collapse
|
13
|
Kitata RB, Velickovic M, Xu Z, Zhao R, Scholten D, Chu RK, Orton DJ, Chrisler WB, Mathews JV, Piehowski PD, Liu T, Smith RD, Liu H, Wasserfall CH, Tsai CF, Shi T. Robust collection and processing for label-free single voxel proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553333. [PMID: 37645907 PMCID: PMC10462033 DOI: 10.1101/2023.08.14.553333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
With advanced mass spectrometry (MS)-based proteomics, genome-scale proteome coverage can be achieved from bulk tissues. However, such bulk measurement lacks spatial resolution and obscures important tissue heterogeneity, which make it impossible for proteome mapping of tissue microenvironment. Here we report an integrated wet collection of single tissue voxel and Surfactant-assisted One-Pot voxel processing method termed wcSOP for robust label-free single voxel proteomics. wcSOP capitalizes on buffer droplet-assisted wet collection of single tissue voxel dissected by LCM into the PCR tube cap and MS-compatible surfactant-assisted one-pot voxel processing in the collection cap. This convenient method allows reproducible label-free quantification of ∼900 and ∼4,600 proteins for single voxel from fresh frozen human spleen tissue at 20 μm × 20 μm × 10 μm (close to single cells) and 200 μm × 200 μm × 10 μm (∼100 cells), respectively. 100s-1000s of protein signatures with differential expression levels were identified to be spatially resolved between spleen red and white pulp regions depending on the voxel size. Region-specific signaling pathways were enriched from single voxel proteomics data. Antibody-based CODEX imaging was used to validate label-free MS quantitation for single voxel analysis. The wcSOP-MS method paves the way for routine robust single voxel proteomics and spatial proteomics.
Collapse
|
14
|
Gurkar AU, Gerencser AA, Mora AL, Nelson AC, Zhang AR, Lagnado AB, Enninful A, Benz C, Furman D, Beaulieu D, Jurk D, Thompson EL, Wu F, Rodriguez F, Barthel G, Chen H, Phatnani H, Heckenbach I, Chuang JH, Horrell J, Petrescu J, Alder JK, Lee JH, Niedernhofer LJ, Kumar M, Königshoff M, Bueno M, Sokka M, Scheibye-Knudsen M, Neretti N, Eickelberg O, Adams PD, Hu Q, Zhu Q, Porritt RA, Dong R, Peters S, Victorelli S, Pengo T, Khaliullin T, Suryadevara V, Fu X, Bar-Joseph Z, Ji Z, Passos JF. Spatial mapping of cellular senescence: emerging challenges and opportunities. NATURE AGING 2023; 3:776-790. [PMID: 37400722 PMCID: PMC10505496 DOI: 10.1038/s43587-023-00446-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/30/2023] [Indexed: 07/05/2023]
Abstract
Cellular senescence is a well-established driver of aging and age-related diseases. There are many challenges to mapping senescent cells in tissues such as the absence of specific markers and their relatively low abundance and vast heterogeneity. Single-cell technologies have allowed unprecedented characterization of senescence; however, many methodologies fail to provide spatial insights. The spatial component is essential, as senescent cells communicate with neighboring cells, impacting their function and the composition of extracellular space. The Cellular Senescence Network (SenNet), a National Institutes of Health (NIH) Common Fund initiative, aims to map senescent cells across the lifespan of humans and mice. Here, we provide a comprehensive review of the existing and emerging methodologies for spatial imaging and their application toward mapping senescent cells. Moreover, we discuss the limitations and challenges inherent to each technology. We argue that the development of spatially resolved methods is essential toward the goal of attaining an atlas of senescent cells.
Collapse
Affiliation(s)
- Aditi U Gurkar
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Ana L Mora
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA
| | - Andrew C Nelson
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Anru R Zhang
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine and Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - Anthony B Lagnado
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Archibald Enninful
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | | | - David Furman
- Buck Institute for Research on Aging, Novato, CA, USA
- Stanford 1000 Immunomes Project, Stanford School of Medicine, Stanford University, Stanford, CA, USA
- Instituto de Investigaciones en Medicina Traslacional (IIMT), Universidad Austral, Pilar, Argentina
| | - Delphine Beaulieu
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Diana Jurk
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Elizabeth L Thompson
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Fei Wu
- Buck Institute for Research on Aging, Novato, CA, USA
| | - Fernanda Rodriguez
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Grant Barthel
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Hao Chen
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Hemali Phatnani
- Columbia University Irving Medical Center and New York Genome Center, Columbia University, New York, NY, USA
| | | | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jeremy Horrell
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Joana Petrescu
- Columbia University Irving Medical Center and New York Genome Center, Columbia University, New York, NY, USA
| | - Jonathan K Alder
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Jun Hee Lee
- Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Laura J Niedernhofer
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Manoj Kumar
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, USA
| | - Melanie Königshoff
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marta Bueno
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Miiko Sokka
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | | | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI, USA
| | - Oliver Eickelberg
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Qianjiang Hu
- Aging Institute, University of Pittsburgh School of Medicine/UPMC and Division of Pulmonary, Allergy and Critical Care Medicine, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Quan Zhu
- University of California, San Diego, CA, USA
| | - Rebecca A Porritt
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Runze Dong
- Department of Biochemistry, Institute for Protein Design and Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Samuel Peters
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Stella Victorelli
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA
| | - Thomas Pengo
- Department of Laboratory Medicine and Pathology, Department of Biochemistry, Molecular Biology and Biophysics, Department of Neuroscience and Institute on the Biology of Aging and Metabolism, Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Timur Khaliullin
- Dorothy M. Davis Heart and Lung Research Institute, Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, the Ohio State University, Columbus, OH, USA
| | - Vidyani Suryadevara
- Department of Radiology, Molecular Imaging Program at Stanford, Stanford University, Stanford, CA, USA
| | - Xiaonan Fu
- Department of Biochemistry, Institute for Protein Design and Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
| | - Ziv Bar-Joseph
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Zhicheng Ji
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine and Department of Biostatistics and Bioinformatics, Duke University School of Medicine, Durham, NC, USA
| | - João F Passos
- Department of Physiology and Biomedical Engineering, Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
15
|
Schwab K, Coronel L, Riege K, Sacramento EK, Rahnis N, Häckes D, Cirri E, Groth M, Hoffmann S, Fischer M. Multi-omics analysis identifies RFX7 targets involved in tumor suppression and neuronal processes. Cell Death Discov 2023; 9:80. [PMID: 36864036 PMCID: PMC9981735 DOI: 10.1038/s41420-023-01378-1] [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: 01/23/2023] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 03/04/2023] Open
Abstract
Recurrently mutated in lymphoid neoplasms, the transcription factor RFX7 is emerging as a tumor suppressor. Previous reports suggested that RFX7 may also have a role in neurological and metabolic disorders. We recently reported that RFX7 responds to p53 signaling and cellular stress. Furthermore, we found RFX7 target genes to be dysregulated in numerous cancer types also beyond the hematological system. However, our understanding of RFX7's target gene network and its role in health and disease remains limited. Here, we generated RFX7 knock-out cells and employed a multi-omics approach integrating transcriptome, cistrome, and proteome data to obtain a more comprehensive picture of RFX7 targets. We identify novel target genes linked to RFX7's tumor suppressor function and underscoring its potential role in neurological disorders. Importantly, our data reveal RFX7 as a mechanistic link that enables the activation of these genes in response to p53 signaling.
Collapse
Affiliation(s)
- Katjana Schwab
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Luis Coronel
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Konstantin Riege
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Erika K. Sacramento
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Norman Rahnis
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - David Häckes
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Emilio Cirri
- grid.418245.e0000 0000 9999 5706Core Facility for Proteomics, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Marco Groth
- grid.418245.e0000 0000 9999 5706Core Facility for Next-Generation Sequencing, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Steve Hoffmann
- grid.418245.e0000 0000 9999 5706Computational Biology Group, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Martin Fischer
- Computational Biology Group, Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745, Jena, Germany.
| |
Collapse
|
16
|
Carrillo-Rodriguez P, Selheim F, Hernandez-Valladares M. Mass Spectrometry-Based Proteomics Workflows in Cancer Research: The Relevance of Choosing the Right Steps. Cancers (Basel) 2023; 15:cancers15020555. [PMID: 36672506 PMCID: PMC9856946 DOI: 10.3390/cancers15020555] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
The qualitative and quantitative evaluation of proteome changes that condition cancer development can be achieved with liquid chromatography-mass spectrometry (LC-MS). LC-MS-based proteomics strategies are carried out according to predesigned workflows that comprise several steps such as sample selection, sample processing including labeling, MS acquisition methods, statistical treatment, and bioinformatics to understand the biological meaning of the findings and set predictive classifiers. As the choice of best options might not be straightforward, we herein review and assess past and current proteomics approaches for the discovery of new cancer biomarkers. Moreover, we review major bioinformatics tools for interpreting and visualizing proteomics results and suggest the most popular machine learning techniques for the selection of predictive biomarkers. Finally, we consider the approximation of proteomics strategies for clinical diagnosis and prognosis by discussing current barriers and proposals to circumvent them.
Collapse
Affiliation(s)
- Paula Carrillo-Rodriguez
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Vall d'Hebron Institute of Oncology (VHIO), 08035 Barcelona, Spain
| | - Frode Selheim
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
| | - Maria Hernandez-Valladares
- Proteomics Unit of University of Bergen (PROBE), University of Bergen, Jonas Lies vei 91, 5009 Bergen, Norway
- Department of Physical Chemistry, University of Granada, Avenida de la Fuente Nueva S/N, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, 18012 Granada, Spain
| |
Collapse
|
17
|
Franciosa G, Kverneland AH, Jensen AWP, Donia M, Olsen JV. Proteomics to study cancer immunity and improve treatment. Semin Immunopathol 2023; 45:241-251. [PMID: 36598558 PMCID: PMC10121539 DOI: 10.1007/s00281-022-00980-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]
Abstract
Cancer survival and progression depend on the ability of tumor cells to avoid immune recognition. Advances in the understanding of cancer immunity and tumor immune escape mechanisms enabled the development of immunotherapeutic approaches. In patients with otherwise incurable metastatic cancers, immunotherapy resulted in unprecedented response rates with the potential for durable complete responses. However, primary and acquired resistance mechanisms limit the efficacy of immunotherapy. Further therapeutic advances require a deeper understanding of the interplay between immune cells and tumors. Most high-throughput studies within the past decade focused on an omics characterization at DNA and RNA level. However, proteins are the molecular effectors of genomic information; therefore, the study of proteins provides deeper understanding of cellular functions. Recent advances in mass spectrometry (MS)-based proteomics at a system-wide scale may allow translational and clinical discoveries by enabling the analysis of understudied post-translational modifications, subcellular protein localization, cell signaling, and protein-protein interactions. In this review, we discuss the potential contribution of MS-based proteomics to preclinical and clinical research findings in the context of tumor immunity and cancer immunotherapies.
Collapse
Affiliation(s)
- Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Anders H Kverneland
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Agnete W P Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marco Donia
- National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
18
|
Mukherjee A, Ghosh S, Biswas D, Rao A, Shetty P, Epari S, Moiyadi A, Srivastava S. Clinical Proteomics for Meningioma: An Integrated Workflow for Quantitative Proteomics and Biomarker Validation in Formalin-Fixed Paraffin-Embedded Tissue Samples. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:512-520. [PMID: 36036964 DOI: 10.1089/omi.2022.0082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Clinical proteomics is a rapidly emerging frontier in laboratory medicine. High-throughput proteomic investigations of biopsy tissues provide mechanistic insights into complex human diseases. For large-scale proteomics, formalin-fixed and paraffin-embedded (FFPE) tissue samples offer a viable alternative to fresh-frozen (FF) tissues that have restricted availability. In this context, meningioma is one of the most common primary brain tumors where innovation in diagnostics and therapeutic targets can benefit from clinical proteomics. We present here an integrated workflow for quantitative proteomics and biomarker validation of meningioma FFPE tissues. Applying label-free quantitative (LFQ) proteomics, we reproducibly (Pearson's correlation: 0.84-0.91) obtained an in-depth proteome coverage (nearly 4000 proteins per sample) from 120 min gradient of single unfractionated mass spectrometry run. Furthermore, building upon LFQ data and literature curated set of meningioma-associated proteins, we validated VIM, AHNAK, and CLU from FFPE tissues using selected reaction monitoring (SRM) assay and compared its performance with FF tissues. This study illustrates how knowledge from label-free proteomics can be integrated for selecting peptides for targeted validation and suggests that FFPE tissues are comparable to FF tissues for SRM assays. This quantitative clinical proteomics workflow is scalable for large-scale clinical diagnostics studies in the future, for example, utilizing the global repository of FFPE tissues in meningioma and possibly in other cancers.
Collapse
Affiliation(s)
- Arijit Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Susmita Ghosh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aishwarya Rao
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | | | | | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| |
Collapse
|
19
|
Mani DR, Krug K, Zhang B, Satpathy S, Clauser KR, Ding L, Ellis M, Gillette MA, Carr SA. Cancer proteogenomics: current impact and future prospects. Nat Rev Cancer 2022; 22:298-313. [PMID: 35236940 DOI: 10.1038/s41568-022-00446-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/21/2022] [Indexed: 02/07/2023]
Abstract
Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.
Collapse
Affiliation(s)
- D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Li Ding
- Department of Medicine and Genetics, Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO, USA
| | - Matthew Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
| |
Collapse
|
20
|
Fan T, Wang X, Zhang S, Deng P, Jiang Y, Liang Y, Jie S, Wang Q, Li C, Tian G, Zhang Z, Ren Z, Li B, Chen Y, He Z, Luo Y, Chen M, Wu H, Yu Z, Pi H, Zhou Z, Zhang Z. NUPR1 promotes the proliferation and metastasis of oral squamous cell carcinoma cells by activating TFE3-dependent autophagy. Signal Transduct Target Ther 2022; 7:130. [PMID: 35462576 PMCID: PMC9035452 DOI: 10.1038/s41392-022-00939-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/11/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most common type of oral malignancy, and metastasis accounts for the poor prognosis of OSCC. Autophagy is considered to facilitate OSCC development by mitigating various cellular stresses; nevertheless, the mechanisms of autophagy in OSCC cell proliferation and metastasis remain unknown. In our study, high-sensitivity label-free quantitative proteomics analysis revealed nuclear protein 1 (NUPR1) as the most significantly upregulated protein in formalin-fixed paraffin-embedded tumour samples derived from OSCC patients with or without lymphatic metastasis. Moreover, NUPR1 is aberrantly expressed in the OSCC tissues and predicts low overall survival rates for OSCC patients. Notably, based on tandem mass tag-based quantitative proteomic analysis between stable NUPR1 knockdown OSCC cells and scrambled control OSCC cells, we confirmed that NUPR1 maintained autophagic flux and lysosomal functions by directly increasing transcription factor E3 (TFE3) activity, which promoted OSCC cell proliferation and metastasis in vitro and in vivo. Collectively, our data revealed that the NUPR1–TFE3 axis is a critical regulator of the autophagic machinery in OSCC progression, and this study may provide a potential therapeutic target for the treatment of OSCC.
Collapse
|
21
|
Di Fraia D, Anitei M, Mackmull MT, Parca L, Behrendt L, Andres-Pons A, Gilmour D, Helmer Citterich M, Kaether C, Beck M, Ori A. Conserved exchange of paralog proteins during neuronal differentiation. Life Sci Alliance 2022; 5:5/6/e202201397. [PMID: 35273078 PMCID: PMC8917807 DOI: 10.26508/lsa.202201397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/17/2022] [Indexed: 11/24/2022] Open
Abstract
Paralog proteins promote fine tuning of protein complexes. The author identified a specific paralog signature conserved across vertebrate neuronal differentiation. Altering the ratio of SEC23 paralogs in the COPII complex influences neuronal differentiation in a opposite way. Gene duplication enables the emergence of new functions by lowering the evolutionary pressure that is posed on the ancestral genes. Previous studies have highlighted the role of specific paralog genes during cell differentiation, for example, in chromatin remodeling complexes. It remains unexplored whether similar mechanisms extend to other biological functions and whether the regulation of paralog genes is conserved across species. Here, we analyze the expression of paralogs across human tissues, during development and neuronal differentiation in fish, rodents and humans. Whereas ∼80% of paralog genes are co-regulated, a subset of paralogs shows divergent expression profiles, contributing to variability of protein complexes. We identify 78 substitutions of paralog pairs that occur during neuronal differentiation and are conserved across species. Among these, we highlight a substitution between the paralogs SEC23A and SEC23B members of the COPII complex. Altering the ratio between these two genes via RNAi-mediated knockdown is sufficient to influence neuron differentiation. We propose that remodeling of the vesicular transport system via paralog substitutions is an evolutionary conserved mechanism enabling neuronal differentiation.
Collapse
Affiliation(s)
| | - Mihaela Anitei
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | - Marie-Therese Mackmull
- Eidgenössische Technische Hochschule (ETH) Zürich Inst. f. Molekulare Systembiologie, Zürich, Switzerland
| | - Luca Parca
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Laura Behrendt
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| | | | - Darren Gilmour
- Department of Molecular Life Sciences, University of Zurich, Zürich, Switzerland
| | | | | | - Martin Beck
- Department of Molecular Sociology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute, Jena, Germany
| |
Collapse
|
22
|
Different syngeneic tumors show distinctive intrinsic tumor-immunity and mechanisms of actions (MOA) of anti-PD-1 treatment. Sci Rep 2022; 12:3278. [PMID: 35228603 PMCID: PMC8885837 DOI: 10.1038/s41598-022-07153-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 02/02/2022] [Indexed: 01/04/2023] Open
Abstract
Cancers are immunologically heterogeneous. A range of immunotherapies target abnormal tumor immunity via different mechanisms of actions (MOAs), particularly various tumor-infiltrate leukocytes (TILs). We modeled loss of function (LOF) in four common anti-PD-1 antibody-responsive syngeneic tumors, MC38, Hepa1-6, CT-26 and EMT-6, by systematical depleting a series of TIL lineages to explore the mechanisms of tumor immunity and treatment. CD8+-T-cells, CD4+-T-cells, Treg, NK cells and macrophages were individually depleted through either direct administration of anti-marker antibodies/reagents or using DTR (diphtheria toxin receptor) knock-in mice, for some syngeneic tumors, where specific subsets were depleted following diphtheria toxin (DT) administration. These LOF experiments revealed distinctive intrinsic tumor immunity and thus different MOAs in their responses to anti-PD-1 antibody among different syngeneic tumors. Specifically, the intrinsic tumor immunity and the associated anti-PD-1 MOA were predominately driven by CD8+ cytotoxic TILs (CTL) in all syngeneic tumors, excluding Hepa1-6 where CD4+ Teff TILs played a key role. TIL-Treg also played a critical role in supporting tumor growth in all four syngeneic models as well as M2-macrophages. Pathway analysis using pharmacodynamic readouts of immuno-genomics and proteomics on MC38 and Hepa1-6 also revealed defined, but distinctive, immune pathways of activation and suppression between the two, closely associated with the efficacy and consistent with TIL-pharmacodynamic readouts. Understanding tumor immune-pathogenesis and treatment MOAs in the different syngeneic animal models, not only assists the selection of the right model for evaluating new immunotherapy of a given MOA, but also can potentially help to understand the potential disease mechanisms and strategize optimal immune-therapies in patients.
Collapse
|
23
|
Nunna S, Huang YP, Rasa M, Krepelova A, Annunziata F, Adam L, Käppel S, Hsu MH, Neri F. Characterization of Novel α-Mangostin and Paeonol Derivatives With Cancer-Selective Cytotoxicity. Mol Cancer Ther 2022; 21:257-270. [PMID: 34789561 PMCID: PMC9398122 DOI: 10.1158/1535-7163.mct-20-0787] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 04/22/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023]
Abstract
α-Mangostin (aMan) and Paeonol (Pae) have shown anticancer and anti-inflammatory properties. However, these two natural compounds have no clinical value because of their low solubility and low membrane permeability. In this study, we screened chemically synthesized derivatives from these two natural compounds as potential novel chemicals that increase cancer cell cytotoxicity over nontransformed human cells. We found that two derivative compounds, named α-Mangostin-1 (aMan1) and Paeonol-1 (Pae1) more efficiently and more specifically induced cytotoxicity in HCT116, HT29, and SW48 colorectal cancer cell lines than the parental compounds. Both aMan1 and Pae1 arrested HCT116 cells in the G1 phase and HT29 and SW48 cells in the G2-M phase of the cell cycle. Both aMan1 and Pae1 induced apoptosis in human colorectal cancer cells, through a caspase-dependent mechanism. aMan1 and Pae1 induced selective transcriptional responses in colorectal cancer cells involving genes related to metabolic stress and DNA damage response signaling pathways. Finally, experiments on primary colon organoids showed that both derivatives were able to kill cancer-derived organoids without affecting the viability of organoids derived from healthy tissue, where the parental compounds and the currently used chemotherapeutic drug irinotecan failed. In conclusion, our findings expand the knowledge of natural compound derivatives as anticancer agents and open new avenues of research in the derivation of lead compounds aimed at developing novel chemotherapeutic drugs for colorectal cancer treatment that selectively target cancer, but not healthy cells.
Collapse
Affiliation(s)
- Suneetha Nunna
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Ying-Pei Huang
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany.,Nuclear Science & Technology Development Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Mahdi Rasa
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Anna Krepelova
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany
| | | | - Lisa Adam
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Sandra Käppel
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany
| | - Ming-Hua Hsu
- Department of Chemistry, National Changhua University of Education, Changhua, Taiwan, ROC.,Department of Medical and Applied Sciences, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Francesco Neri
- Leibniz-Institute on Ageing - Fritz-Lipmann-Institute (FLI), Jena, Germany.,Corresponding Author: Francesco Neri, Epigenetics group, Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), Jena, 07745, Germany. E-mail:
| |
Collapse
|
24
|
Di Sanzo S, Spengler K, Leheis A, Kirkpatrick JM, Rändler TL, Baldensperger T, Dau T, Henning C, Parca L, Marx C, Wang ZQ, Glomb MA, Ori A, Heller R. Mapping protein carboxymethylation sites provides insights into their role in proteostasis and cell proliferation. Nat Commun 2021; 12:6743. [PMID: 34795246 PMCID: PMC8602705 DOI: 10.1038/s41467-021-26982-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 10/29/2021] [Indexed: 12/19/2022] Open
Abstract
Posttranslational mechanisms play a key role in modifying the abundance and function of cellular proteins. Among these, modification by advanced glycation end products has been shown to accumulate during aging and age-associated diseases but specific protein targets and functional consequences remain largely unexplored. Here, we devise a proteomic strategy to identify sites of carboxymethyllysine modification, one of the most abundant advanced glycation end products. We identify over 1000 sites of protein carboxymethylation in mouse and primary human cells treated with the glycating agent glyoxal. By using quantitative proteomics, we find that protein glycation triggers a proteotoxic response and indirectly affects the protein degradation machinery. In primary endothelial cells, we show that glyoxal induces cell cycle perturbation and that carboxymethyllysine modification reduces acetylation of tubulins and impairs microtubule dynamics. Our data demonstrate the relevance of carboxymethyllysine modification for cellular function and pinpoint specific protein networks that might become compromised during aging.
Collapse
Affiliation(s)
- Simone Di Sanzo
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Katrin Spengler
- grid.275559.90000 0000 8517 6224Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 07743 Jena, Germany
| | - Anja Leheis
- grid.275559.90000 0000 8517 6224Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 07743 Jena, Germany
| | - Joanna M. Kirkpatrick
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), 07745 Jena, Germany ,grid.451388.30000 0004 1795 1830Present Address: Proteomics Science Technology Platform, The Francis Crick Institute, MW1 1AT London, UK
| | - Theresa L. Rändler
- grid.275559.90000 0000 8517 6224Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 07743 Jena, Germany
| | - Tim Baldensperger
- grid.9018.00000 0001 0679 2801Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Therese Dau
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Christian Henning
- grid.9018.00000 0001 0679 2801Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Luca Parca
- grid.413503.00000 0004 1757 9135Bioinformatics Unit, IRCCS Casa Sollievo della Sofferenza, S. Giovanni Rotondo, Italy
| | - Christian Marx
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Zhao-Qi Wang
- grid.418245.e0000 0000 9999 5706Leibniz Institute on Aging – Fritz Lipmann Institute (FLI), 07745 Jena, Germany ,grid.9613.d0000 0001 1939 2794Faculty of Biological Sciences, Friedrich-Schiller-University of Jena, Jena, Germany
| | - Marcus A. Glomb
- grid.9018.00000 0001 0679 2801Institute of Chemistry, Food Chemistry, Martin-Luther-University Halle-Wittenberg, 06120 Halle/Saale, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI), 07745, Jena, Germany.
| | - Regine Heller
- Institute of Molecular Cell Biology, Center for Molecular Biomedicine, Jena University Hospital, 07743, Jena, Germany.
| |
Collapse
|
25
|
Eckert S, Chang YC, Bayer FP, The M, Kuhn PH, Weichert W, Kuster B. Evaluation of Disposable Trap Column nanoLC-FAIMS-MS/MS for the Proteomic Analysis of FFPE Tissue. J Proteome Res 2021; 20:5402-5411. [PMID: 34735149 DOI: 10.1021/acs.jproteome.1c00695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomic biomarker discovery using formalin-fixed paraffin-embedded (FFPE) tissue requires robust workflows to support the analysis of large cohorts of patient samples. It also requires finding a reasonable balance between achieving a high proteomic depth and limiting the overall analysis time. To this end, we evaluated the merits of online coupling of single-use disposable trap column nanoflow liquid chromatography, high-field asymmetric-waveform ion-mobility spectrometry (FAIMS), and tandem mass spectrometry (nLC-FAIMS-MS/MS). The data show that ≤600 ng of peptide digest should be loaded onto the chromatographic part of the system. Careful characterization of the FAIMS settings enabled the choice of optimal combinations of compensation voltages (CVs) as a function of the employed LC gradient time. We found nLC-FAIMS-MS/MS to be on par with StageTip-based off-line basic pH reversed-phase fractionation in terms of proteomic depth and reproducibility of protein quantification (coefficient of variation ≤15% for 90% of all proteins) but requiring 50% less sample and substantially reducing sample handling. Using FFPE materials from the lymph node, lung, and prostate tissue as examples, we show that nLC-FAIMS-MS/MS can identify 5000-6000 proteins from the respective tissue within a total of 3 h of analysis time.
Collapse
Affiliation(s)
- Stephan Eckert
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Yun-Chien Chang
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Florian P Bayer
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Matthew The
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany
| | - Peer-Hendrik Kuhn
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Wilko Weichert
- Institute of Pathology, Technical University of Munich (TUM), Munich 81675, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising 85354, Germany.,German Cancer Consortium (DKTK), Partner-Site Munich and German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising 85354, Germany
| |
Collapse
|
26
|
Dabaghi M, Rasa SMM, Cirri E, Ori A, Neri F, Quaas R, Hilger I. Iron Oxide Nanoparticles Carrying 5-Fluorouracil in Combination with Magnetic Hyperthermia Induce Thrombogenic Collagen Fibers, Cellular Stress, and Immune Responses in Heterotopic Human Colon Cancer in Mice. Pharmaceutics 2021; 13:pharmaceutics13101625. [PMID: 34683917 PMCID: PMC8541380 DOI: 10.3390/pharmaceutics13101625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 01/01/2023] Open
Abstract
In this study we looked for the main protein pathway regulators which were responsible for the therapeutic impact on colon cancers when combining magnetic hyperthermia with the chemotherapeutic agent 5-fluorouracil (5FU). To this end, chitosan-coated magnetic nanoparticles (MNP) functionalized with 5FU were intratumorally injected into subcutaneous human colon cancer xenografts (HT-29) in mice and exposed to an alternating magnetic field. A decreased tumor growth was found particularly for the combined thermo-chemotherapy vs. the corresponding monotherapies. By using computational analysis of the tumor proteome, we found upregulated functional pathway categories termed "cellular stress and injury", "intracellular second messenger and nuclear receptor signaling", "immune responses", and "growth proliferation and development". We predict TGF-beta, and other mediators, as important upstream regulators. In conclusion, our findings show that the combined thermo-chemotherapy induces thrombogenic collagen fibers which are able to impair tumor nutrient supply. Further on, we associate several responses to the recognition of damage associated molecular patterns (DAMPs) by phagocytic cells, which immigrate into the tumor area. The activation of some pathways associated with cell survival implies the necessity to conduct multiple therapy sessions in connection with a corresponding monitoring, which could possibly be performed on the base of the identified protein regulators.
Collapse
Affiliation(s)
- Mohammad Dabaghi
- Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Friedrich Schiller University Jena, Am Klinikum 1, D-07740 Jena, Germany;
| | - Seyed Mohammad Mahdi Rasa
- Leibniz Institute on Aging Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (S.M.M.R.); (E.C.); (A.O.); (F.N.)
| | - Emilio Cirri
- Leibniz Institute on Aging Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (S.M.M.R.); (E.C.); (A.O.); (F.N.)
| | - Alessandro Ori
- Leibniz Institute on Aging Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (S.M.M.R.); (E.C.); (A.O.); (F.N.)
| | - Francesco Neri
- Leibniz Institute on Aging Fritz Lipmann Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany; (S.M.M.R.); (E.C.); (A.O.); (F.N.)
| | - Rainer Quaas
- Chemicell GmbH, Erseburgstrasse 22–23, 12103 Berlin, Germany;
| | - Ingrid Hilger
- Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Friedrich Schiller University Jena, Am Klinikum 1, D-07740 Jena, Germany;
- Correspondence: ; Tel.: +0049-3641-9325921
| |
Collapse
|
27
|
Pino L, Schilling B. Proximity labeling and other novel mass spectrometric approaches for spatiotemporal protein dynamics. Expert Rev Proteomics 2021; 18:757-765. [PMID: 34496693 PMCID: PMC8650568 DOI: 10.1080/14789450.2021.1976149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/31/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Proteins are highly dynamic and their biological function is controlled by not only temporal abundance changes but also via regulated protein-protein interaction networks, which respond to internal and external perturbations. A wealth of novel analytical reagents and workflows allow studying spatiotemporal protein environments with great granularity while maintaining high throughput and ease of analysis. AREAS COVERED We review technology advances for measuring protein-protein proximity interactions with an emphasis on proximity labeling, and briefly summarize other spatiotemporal approaches including protein localization, and their dynamic changes over time, specifically in human cells and mammalian tissues. We focus especially on novel technologies and workflows emerging within the past 5 years. This includes enrichment-based techniques (proximity labeling and crosslinking), separation-based techniques (organelle fractionation and size exclusion chromatography), and finally sorting-based techniques (laser capture microdissection and mass spectrometry imaging). EXPERT OPINION Spatiotemporal proteomics is a key step in assessing biological complexity, understanding refined regulatory mechanisms, and forming protein complexes and networks. Studying protein dynamics across space and time holds promise for gaining deep insights into how protein networks may be perturbed during disease and aging processes, and offer potential avenues for therapeutic interventions, drug discovery, and biomarker development.
Collapse
Affiliation(s)
- Lindsay Pino
- University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Birgit Schilling
- Buck Institute for Research on Aging, Novato, California, CA 94945, USA
| |
Collapse
|
28
|
Schädel P, Troisi F, Czapka A, Gebert N, Pace S, Ori A, Werz O. Aging drives organ-specific alterations of the inflammatory microenvironment guided by immunomodulatory mediators in mice. FASEB J 2021; 35:e21558. [PMID: 33855766 DOI: 10.1096/fj.202002684r] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/03/2021] [Accepted: 03/11/2021] [Indexed: 12/31/2022]
Abstract
Aging is accompanied by chronic, low-grade systemic inflammation, termed inflammaging, a main driver of age-associated diseases. Such sterile inflammation is typically characterized by elevated levels of pro-inflammatory mediators, such as cytokines, chemokines and reactive oxygen species causing organ damage. Lipid mediators play important roles in the fine-tuning of both the promotion and the resolution of inflammation. Yet, it remains unclear how lipid mediators fit within the concept of inflammaging and how their biosynthesis and function is affected by aging. Here, we provide comprehensive signature profiles of inflammatory markers in organs afflicted with inflammation of young and old C57BL/6 mice. We reveal an organ-specific footprint of inflammation-related cytokines, chemokines and lipid mediators, which are distinctively affected by aging. While some organs are characterized by a pronounced pro-inflammatory microenvironment and impaired resolution during aging, others display elevated levels of pro-resolving mediators or an overall decrease in inflammatory signaling. Our results demonstrate that it proves difficult to establish a unifying concept for alterations of immunomodulatory mediators as consequence of aging and that organ specificity needs to be considered. Moreover, our data imply that inclusion of lipid mediators into the concept of inflammaging provides a comprehensive tool to characterize the inflammatory microenvironment during aging on a broader and yet, more detailed scope.
Collapse
Affiliation(s)
- Patrick Schädel
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Fabiana Troisi
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany.,Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Munich, Germany
| | - Anna Czapka
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Nadja Gebert
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Simona Pace
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
29
|
Mao Y, Wang X, Huang P, Tian R. Spatial proteomics for understanding the tissue microenvironment. Analyst 2021; 146:3777-3798. [PMID: 34042124 DOI: 10.1039/d1an00472g] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The human body comprises rich populations of cells, which are arranged into tissues and organs with diverse functionalities. These cells exhibit a broad spectrum of phenotypes and are often organized as a heterogeneous but sophisticatedly regulated ecosystem - tissue microenvironment, inside which every cell interacts with and is reciprocally influenced by its surroundings through its life span. Therefore, it is critical to comprehensively explore the cellular machinery and biological processes in the tissue microenvironment, which is best exemplified by the tumor microenvironment (TME). The past decade has seen increasing advances in the field of spatial proteomics, the main purpose of which is to characterize the abundance and spatial distribution of proteins and their post-translational modifications in the microenvironment of diseased tissues. Herein, we outline the achievements and remaining challenges of mass spectrometry-based tissue spatial proteomics. Exciting technology developments along with important biomedical applications of spatial proteomics are highlighted. In detail, we focus on high-quality resources built by scalpel macrodissection-based region-resolved proteomics, method development of sensitive sample preparation for laser microdissection-based spatial proteomics, and antibody recognition-based multiplexed tissue imaging. In the end, critical issues and potential future directions for spatial proteomics are also discussed.
Collapse
Affiliation(s)
- Yiheng Mao
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, 150001, China. and Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xi Wang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China and Shenzhen People's Hospital, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen 518020, China
| | - Peiwu Huang
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|