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Faktor J, Kote S, Bienkowski M, Hupp TR, Marek-Trzonkowska N. Novel FFPE proteomics method suggests prolactin induced protein as hormone induced cytoskeleton remodeling spatial biomarker. Commun Biol 2024; 7:708. [PMID: 38851810 PMCID: PMC11162451 DOI: 10.1038/s42003-024-06354-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/20/2024] [Indexed: 06/10/2024] Open
Abstract
Robotically assisted proteomics provides insights into the regulation of multiple proteins achieving excellent spatial resolution. However, developing an effective method for spatially resolved quantitative proteomics of formalin fixed paraffin embedded tissue (FFPE) in an accessible and economical manner remains challenging. We introduce non-robotic In-insert FFPE proteomics approach, combining glass insert FFPE tissue processing with spatial quantitative data-independent mass spectrometry (DIA). In-insert approach identifies 450 proteins from a 5 µm thick breast FFPE tissue voxel with 50 µm lateral dimensions covering several tens of cells. Furthermore, In-insert approach associated a keratin series and moesin (MOES) with prolactin-induced protein (PIP) indicating their prolactin and/or estrogen regulation. Our data suggest that PIP is a spatial biomarker for hormonally triggered cytoskeletal remodeling, potentially useful for screening hormonally affected hotspots in breast tissue. In-insert proteomics represents an alternative FFPE processing method, requiring minimal laboratory equipment and skills to generate spatial proteotype repositories from FFPE tissue.
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Affiliation(s)
- Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland.
| | - Michal Bienkowski
- Medical University of Gdansk, University of Gdansk, Mariana Smoluchowskiego 17, 80-214, Gdansk, Poland
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kladki 24, 80-822, Gdansk, Poland
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2
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Yue L, Gong T, Jiang W, Qian L, Gong W, Sun Y, Cai X, Xu H, Liu F, Wang H, Li S, Zhu Y, Zheng Z, Wu Q, Guo T. Proteomic profiling of ovarian clear cell carcinomas identifies prognostic biomarkers for chemotherapy. Proteomics 2024; 24:e2300242. [PMID: 38171885 DOI: 10.1002/pmic.202300242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 01/05/2024]
Abstract
Clear cell ovarian carcinoma (CCOC) is a relatively rare subtype of ovarian cancer (OC) with high degree of resistance to standard chemotherapy. Little is known about the underlying molecular mechanisms, and it remains a challenge to predict its prognosis after chemotherapy. Here, we first analyzed the proteome of 35 formalin-fixed paraffin-embedded (FFPE) CCOC tissue specimens from a cohort of 32 patients with CCOC (H1 cohort) and characterized 8697 proteins using data-independent acquisition mass spectrometry (DIA-MS). We then performed proteomic analysis of 28 fresh frozen (FF) CCOC tissue specimens from an independent cohort of 24 patients with CCOC (H2 cohort), leading to the identification of 9409 proteins with DIA-MS. After bioinformatics analysis, we narrowed our focus to 15 proteins significantly correlated with the recurrence free survival (RFS) in both cohorts. These proteins are mainly involved in DNA damage response, extracellular matrix (ECM), and mitochondrial metabolism. Parallel reaction monitoring (PRM)-MS was adopted to validate the prognostic potential of the 15 proteins in the H1 cohort and an independent confirmation cohort (H3 cohort). Interferon-inducible transmembrane protein 1 (IFITM1) was observed as a robust prognostic marker for CCOC in both PRM data and immunohistochemistry (IHC) data. Taken together, this study presents a CCOC proteomic data resource and a single promising protein, IFITM1, which could potentially predict the recurrence and survival of CCOC.
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Affiliation(s)
- Liang Yue
- School of Life Sciences, Fudan University, Shanghai, China
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Tingting Gong
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University
| | - Wenhao Jiang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Liujia Qian
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Wangang Gong
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Yaoting Sun
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Xue Cai
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Heli Xu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Fanghua Liu
- Department of Clinical Epidemiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - He Wang
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Sainan Li
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
- National Health Commission Key Laboratory of Reproductive Health, Institute of Reproductive and Child Health, Peking University, Beijing, China
| | - Yi Zhu
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Zhiguo Zheng
- Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Qijun Wu
- Department of Clinical Epidemiology, Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Tiannan Guo
- Westlake Center for Intelligent Proteomics, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang Province, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
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3
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Kong L, Li Y, Deng Z, Chen X, Xia Y, Shen B, Ning R, Zhang L, Yin Z. Tibial cortex transverse transport regulates Orai1/STIM1-mediated NO release and improve the migration and proliferation of vessels via increasing osteopontin expression. J Orthop Translat 2024; 45:107-119. [PMID: 38524870 PMCID: PMC10960091 DOI: 10.1016/j.jot.2024.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/31/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Background Diabetic foot is a major complication of diabetes. The bone transverse transport method could be applied in clinics for treatment, which could improve the metabolism of the tissues via lasting distraction forces. However, the process' specific regulating mechanism is still unknown. Methods Based on the notion that the healing of bones involves the recruitment of calcium ions, in this study, we established the model of tibial cortex transverse transport (TTT) on rats and then used tissue immunologic detection, such as the double fluorescent staining to explore the expression of the calcium channels' calcium release-activated calcium modulator 1 (Orai1)/stromal interaction molecule 1 (STIM1), which belong to the store-operated calcium entry (SOCE) signaling pathways on the tissues around the bone transport area. By using the laser capture microdissection (LCM) tool, we acquired samples of tissues around the bone and endeavored to identify pivotal protein molecules. Subsequently, we validated the functions of key protein molecules through in vitro and in vivo experiments. Results After protein profile analysis, we found the differentially expressed key protein osteopontin (OPN). The in vitro experiments verified that, being stimulated by OPN, the migration, proliferation, and angiogenesis of human umbilical vein endothelial cells (HUVEC) were observed to be enhanced. The activation of Orai1/STIM1 might increase the activity of endothelial nitric oxide synthase (eNOS) and its effect on releasing nitric oxide (NO). Subsequently, the migration and proliferation of the HUVECs are improved, which ultimately accelerates wound healing. These signaling pathway was also observed in the OPN-stimulated healing process of the skin wound surface of diabetic mice. Conclusion This study identifies the molecular biological mechanism of OPN-benefited the migration and proliferation of the HUVECs and provides ideas for searching for new therapeutic targets for drugs that repair diabetes-induced wounds to replace invasive treatment methods. The translational potential of this article The OPN is highly expressed in the tissues surrounding the TTT bone transfer area, which may possibly stimulate the activation of eNOS to increase NO release through the SOCE pathway mediated by Orai1/STIM1. This mechanism may play a significant role in the angiogenesis of diabetic foot's wounds promoted by TTT, providing new therapeutic strategies for the non-surgical treatment for this disease.
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Affiliation(s)
- Lingchao Kong
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
- Department of Orthopedics, The Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yangyang Li
- School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, PR China
| | - Zhongfang Deng
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, PR China
| | - Xiaoyu Chen
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, PR China
| | - Yin Xia
- Department of Anesthesiology, Anhui Provincial Children's Hospital, Hefei, Anhui, PR China
| | - Bing Shen
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, PR China
| | - Rende Ning
- Department of Orthopedics, The Third Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Lesha Zhang
- Department of Physiology, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, PR China
| | - Zongsheng Yin
- Department of Orthopedics, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
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4
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Lee YJ, Rio DC. A mutation in the low-complexity domain of splicing factor hnRNPA1 linked to amyotrophic lateral sclerosis disrupts distinct neuronal RNA splicing networks. Genes Dev 2024; 38:11-30. [PMID: 38182429 PMCID: PMC10903937 DOI: 10.1101/gad.351104.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/14/2023] [Indexed: 01/07/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a debilitating neurodegenerative disease characterized by loss of motor neurons. Human genetic studies have linked mutations in RNA-binding proteins as causative for this disease. The hnRNPA1 protein, a known pre-mRNA splicing factor, is mutated in some ALS patients. Here, two human cell models were generated to investigate how a mutation in the C-terminal low-complexity domain (LCD) of hnRNPA1 can cause splicing changes of thousands of transcripts that collectively are linked to the DNA damage response, cilium organization, and translation. We show that the hnRNPA1 D262V mutant protein binds to new binding sites on differentially spliced transcripts from genes that are linked to ALS. We demonstrate that this ALS-linked hnRNPA1 mutation alters normal RNA-dependent protein-protein interactions. Furthermore, cells expressing this hnRNPA1 mutant exhibit a cell aggregation phenotype, markedly reduced growth rates, changes in stress granule kinetics, and aberrant growth of neuronal processes. This study provides insight into how a single amino acid mutation in a splicing factor can alter RNA splicing networks of genes linked to ALS.
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Affiliation(s)
- Yeon J Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, California 94720, USA
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5
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Dieters-Castator DZ, Manzanillo P, Yang HY, Modak RV, Rardin MJ, Gibson BW. Magnetic Bead-Based Workflow for Sensitive and Streamlined Cell Surface Proteomics. J Proteome Res 2024; 23:618-632. [PMID: 38226771 DOI: 10.1021/acs.jproteome.3c00432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Cell surface proteins represent an important class of molecules for therapeutic targeting and cellular phenotyping. However, their enrichment and detection via mass spectrometry-based proteomics remains challenging due to low abundance, post-translational modifications, hydrophobic regions, and processing requirements. To improve their identification, we optimized a Cell-Surface Capture (CSC) workflow that incorporates magnetic bead-based processing. Using this approach, we evaluated labeling conditions (biotin tags and catalysts), enrichment specificity (streptavidin beads), missed cleavages (lysis buffers), nonenzymatic deamidation (digestion and deglycosylation buffers), and data acquisition methods (DDA, DIA, and TMT). Our findings support the use of alkoxyamine-PEG4-biotin plus 5-methoxy-anthranilic acid, SDS/urea-based lysis buffers, single-pot solid-phased-enhanced sample-preparation (SP3), and streptavidin magnetic beads for maximal surfaceome coverage. Notably, with semiautomated processing, sample handling was simplified and between ∼600 and 900 cell surface N-glycoproteins were identified from only 25-200 μg of HeLa protein. CSC also revealed significant differences between in vitro monolayer cultures and in vivo tumor xenografts of murine CT26 colon adenocarcinoma samples that may aid in target identification for drug development. Overall, the improved efficiency of the magnetic-based CSC workflow identified both previously reported and novel N-glycosites with less material and high reproducibility that should help advance the field of surfaceomics by providing insight in cellular phenotypes not previously documented.
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Affiliation(s)
| | - Paolo Manzanillo
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Han-Yin Yang
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Rucha V Modak
- Inflammation, Amgen Research, South San Francisco, California 94080, United States
| | - Matthew J Rardin
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
| | - Bradford W Gibson
- Discovery Proteomics, Amgen Research, South San Francisco, California 94080, United States
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6
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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7
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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8
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Wang YE, Zeng WL, Cao ST, Zou JP, Liu CT, Shi JM, Li J, Qiu F, Wang Y. Development of a sample preparation method for micro-proteomics analysis of the formaldehyde-fixed paraffin-embedded liver tissue samples. Talanta 2024; 266:125106. [PMID: 37639870 DOI: 10.1016/j.talanta.2023.125106] [Citation(s) in RCA: 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.
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Affiliation(s)
- Yong-Er Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Wei-Lan Zeng
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Sheng-Tian Cao
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Jun-Peng Zou
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China
| | - Cui-Ting Liu
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jun-Min Shi
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Jing Li
- Biomedical Research Center, Southern Medical University, Guangzhou, China
| | - Feng Qiu
- The Seventh Affiliated Hospital of Southern Medical University, Foshan, China.
| | - Yan Wang
- Biomedical Research Center, Southern Medical University, Guangzhou, China; School of Pharmaceutical Science, Southern Medical University, Guangzhou, China; The Seventh Affiliated Hospital of Southern Medical University, Foshan, China; School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, China; Guangdong Provincial Key Laboratory of Viral Hepatitis Research, Nanfang Hospital, Southern Medical University, Guangzhou, China.
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9
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Shin IJ, Tangrea M, Emmert-Buck M, Johann DJ. A Microdissection Protocol for Proteogenomic Analysis of Histological Sections to Advance Drug Development. Methods Mol Biol 2024; 2823:55-75. [PMID: 39052214 DOI: 10.1007/978-1-0716-3922-1_5] [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
Combining proteogenomics with laser capture microdissection (LCM) in cancer research offers a targeted way to explore the intricate interactions between tumor cells and the different microenvironment components. This is especially important for immuno-oncology (IO) research where improvements in the predictability of IO-based drugs are sorely needed, and depends on a better understanding of the spatial relationships involving the tumor, blood supply, and immune cell interactions, in the context of their associated microenvironments. LCM is used to isolate and obtain distinct histological cell types, which may be routinely performed on complex and heterogeneous solid tumor specimens. Once cells have been captured, nucleic acids and proteins may be extracted for in-depth multimodality molecular profiling assays. Optimizing the minute tissue quantities from LCM captured cells is challenging. Following the isolation of nucleic acids, RNA-seq may be performed for gene expression and DNA sequencing performed for the discovery and analysis of actionable mutations, copy number variation, methylation profiles, etc. However, there remains a need for highly sensitive proteomic methods targeting small-sized samples. A significant part of this protocol is an enhanced liquid chromatography mass spectrometry (LC-MS) analysis of micro-scale and/or nano-scale tissue sections. This is achieved with a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) approach developed for LC-MS analysis of fresh-frozen tissue specimens obtained via LCM. Included is a detailed in-gel digestion method adjusted and specifically designed to maximize the proteome coverage from amount-limited LCM samples to better facilitate in-depth molecular profiling. Described is a proteogenomic approach leveraged from microdissected fresh frozen tissue. The protocols may also be applicable to other types of specimens having limited nucleic acids, protein quantity, and/or sample volume.
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Affiliation(s)
- Ik Jae Shin
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael Tangrea
- Department of Biology, Loyola University Maryland, Baltimore, MD, USA
| | | | - Donald J Johann
- Winthrop P Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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10
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Cho A, Ahn J, Kim A, Lee JH, Ryu HS, Kim KM, Yi EC. Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9616. [PMID: 37817342 DOI: 10.1002/rcm.9616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE The comprehensive analysis of formalin-fixed paraffin-embedded (FFPE) tissues is essential for retrospective clinical studies. However, detecting low-abundance proteins and obtaining proteome-scale data from FFPE samples pose analytical challenges in mass spectrometry-based proteomics. To overcome this challenge, our study focuses on implementing an isobaric labeling approach to improve the detection of low-abundance target proteins in FFPE tissues, thereby enhancing the qualitative and quantitative analysis. METHODS We employed an isobaric labeling approach utilizing synthetic peptides or proteins to enable the qualitative and quantitative measurement of target proteins in FFPE tissue samples. To achieve this, we incorporated tandem mass tag (TMT)-labeled recombinant proteins or synthetic peptides into TMT-labeled metastatic breast cancer FFPE tissues. Through this strategy, we successfully detect coexisting CD276 (B7-H3) and CD147 proteins while identifying over 6000 proteins using targeted analysis of individual FFPE tissue sections. RESULTS Our findings provide compelling evidence that the incorporation of isobaric labeling, along with the inclusion of TMT-labeled peptides or proteins, greatly enhances the detection of target proteins in FFPE tissue samples. By employing this approach, we were able to obtain robust qualitative measurements of CD276 and CD147 proteins, showcasing its effectiveness in identifying more than 6000 proteins in FFPE samples. CONCLUSIONS The integration of an isobaric labeling approach, in conjunction with synthetic peptides or proteins, presents a valuable strategy for enhancing the detection and validation of target proteins in FFPE tissue analysis. This technique holds immense potential in retrospective clinical studies, as it enables comprehensive analysis of low-abundance proteins and facilitating proteome-scale investigations in FFPE samples. By leveraging this methodology, researchers can unlock new insights into disease mechanisms and advance our understanding of complex biological processes.
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Affiliation(s)
- Ara Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Ahn
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Andrew Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeong Hyun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kristine M Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
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11
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Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023; 14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour at three spatial resolutions, the highest being 40 µm, to reveal distinct abundance patterns of thousands of proteins. We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns and correlate proteins in the context of tissue heterogeneity and cellular features such as extracellular matrix or proximity to blood vessels. We identify PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, we demonstrate spatially-aware deep proteo-phenotyping of tissue heterogeneity, to re-define understanding tissue biology and pathology at the molecular level.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Janina Oetjen
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Philip D Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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12
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Chen H, Zhang Y, Zhou H, Chen W, Peng J, Feng Y, Fan L, Li J, Zi J, Ren Y, Li Q, Liu S. Routine Workflow of Spatial Proteomics on Micro-formalin-Fixed Paraffin-Embedded Tissues. Anal Chem 2023; 95:16733-16743. [PMID: 37922386 DOI: 10.1021/acs.analchem.3c03848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
In the era of single-cell biology, spatial proteomics has emerged as an important frontier. However, it still faces several challenges in technology. Formalin-fixed paraffin-embedded (FFPE) tissues are an important material in spatial proteomics, in which fixed tissues are excised using laser capture microdissection (LCM), followed by protein identification with mass spectrometry. For a satisfied spatial proteomics upon FFPE tissues, the excision area is expected to be as small as possible, and the identified proteins are countered upon as much as possible. For a general laboratory for spatial proteomics, a routine workflow is required, not relying on any special device, and is easily operating. In view of these challenges in technology, we initiated a technology evaluation throughout the entire procedure of proteomic analysis with micro-FFPE tissues. In contrast to the protocols reported previously, several innovations in technology were proposed and conducted, such as removal of destaining, decross-linking with "hang-down", solution simplification for peptide generation and balancing to excision area, and capture rate of micro-FFPE tissues. After optimization of all the necessary steps, a routine workflow was established, in which the minimized area for protein identification was 0.002 mm2, while the excision area for a consistent proteomic analysis was 0.05 mm2. Using the developed workflow and collecting the micro-FFPE tissues continuously, for the first time, a spatial proteomic atlas of mouse brain was preliminarily constructed, which exhibited the typical characteristics of spatial-dependent protein abundance and functional enrichment.
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Affiliation(s)
- Hao Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yuefei Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Haichao Zhou
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weiran Chen
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Gongda Road 1, Huzhou 313200, China
| | - Jiayi Peng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Feng
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Linyuan Fan
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jun Li
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- College of Pharmaceutical Science, Zhejiang University of Technology, Gongda Road 1, Huzhou 313200, China
| | - Jin Zi
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Shanghai University of Traditional Chinese Medicine, Shanghai 200120, China
| | - Qidan Li
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- BGI-Shenzhen, Shenzhen, Guangdong 518083, China
- Zhejiang Cancer Hospital, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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13
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Gosline SJC, Veličković M, Pino JC, Day LZ, Attah IK, Swensen AC, Danna V, Posso C, Rodland KD, Chen J, Matthews CE, Campbell-Thompson M, Laskin J, Burnum-Johnson K, Zhu Y, Piehowski PD. Proteome Mapping of the Human Pancreatic Islet Microenvironment Reveals Endocrine-Exocrine Signaling Sphere of Influence. Mol Cell Proteomics 2023; 22:100592. [PMID: 37328065 PMCID: PMC10460696 DOI: 10.1016/j.mcpro.2023.100592] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 04/24/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023] Open
Abstract
The need for a clinically accessible method with the ability to match protein activity within heterogeneous tissues is currently unmet by existing technologies. Our proteomics sample preparation platform, named microPOTS (Microdroplet Processing in One pot for Trace Samples), can be used to measure relative protein abundance in micron-scale samples alongside the spatial location of each measurement, thereby tying biologically interesting proteins and pathways to distinct regions. However, given the smaller pixel/voxel number and amount of tissue measured, standard mass spectrometric analysis pipelines have proven inadequate. Here we describe how existing computational approaches can be adapted to focus on the specific biological questions asked in spatial proteomics experiments. We apply this approach to present an unbiased characterization of the human islet microenvironment comprising the entire complex array of cell types involved while maintaining spatial information and the degree of the islet's sphere of influence. We identify specific functional activity unique to the pancreatic islet cells and demonstrate how far their signature can be detected in the adjacent tissue. Our results show that we can distinguish pancreatic islet cells from the neighboring exocrine tissue environment, recapitulate known biological functions of islet cells, and identify a spatial gradient in the expression of RNA processing proteins within the islet microenvironment.
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Affiliation(s)
- Sara J C Gosline
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | | | - James C Pino
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Le Z Day
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Isaac K Attah
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Adam C Swensen
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Vincent Danna
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Camilo Posso
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Karin D Rodland
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Clayton E Matthews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida, USA
| | - Julia Laskin
- Department of Chemistry, Purdue University, West Lafayette, Indiana, USA
| | | | - Ying Zhu
- Pacific Northwest National Laboratories, Richland, Washington, USA
| | - Paul D Piehowski
- Pacific Northwest National Laboratories, Richland, Washington, USA.
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14
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Abstract
The biology of a cell, whether it is a unicellular organism or part of a multicellular network, is influenced by cell type, temporal changes in cell state, and the cell's environment. Spatial cues play a critical role in the regulation of microbial pathogenesis strategies. Information about where the pathogen is-in a tissue or in proximity to a host cell-regulates gene expression and the compartmentalization of gene products in the microbe and the host. Our understanding of host and pathogen identity has bloomed with the accessibility of transcriptomics and proteomics techniques. A missing piece of the puzzle has been our ability to evaluate global transcript and protein expression in the context of the subcellular niche, primary cell, or native tissue environment during infection. This barrier is now lower with the advent of new spatial omics techniques to understand how location regulates cellular functions. This review will discuss how recent advances in spatial proteomics and transcriptomics approaches can address outstanding questions in microbial pathogenesis.
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Affiliation(s)
- Samantha Lempke
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Dana May
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Sarah E. Ewald
- Department of Microbiology, Immunology, and Cancer Biology at the Carter Immunology Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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15
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Venz S, von Bohlen Und Halbach V, Hentschker C, Junker H, Kuss AW, Sura T, Krüger E, Völker U, von Bohlen Und Halbach O, Jensen LR, Hammer E. Global Protein Profiling in Processed Immunohistochemistry Tissue Sections. Int J Mol Sci 2023; 24:11308. [PMID: 37511068 PMCID: PMC10379013 DOI: 10.3390/ijms241411308] [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: 06/16/2023] [Revised: 07/07/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Tissue sections, which are widely used in research and diagnostic laboratories and have already been examined by immunohistochemistry (IHC), may subsequently provide a resource for proteomic studies, even though only small amount of protein is available. Therefore, we established a workflow for tandem mass spectrometry-based protein profiling of IHC specimens and characterized defined brain area sections. We investigated the CA1 region of the hippocampus dissected from brain slices of adult C57BL/6J mice. The workflow contains detailed information on sample preparation from brain slices, including removal of antibodies and cover matrices, dissection of region(s) of interest, protein extraction and digestion, mass spectrometry measurement, and data analysis. The Gene Ontology (GO) knowledge base was used for further annotation. Literature searches and Gene Ontology annotation of the detected proteins verify the applicability of this method for global protein profiling using formalin-fixed and embedded material and previously used IHC slides.
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Affiliation(s)
- Simone Venz
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | | | - Christian Hentschker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Heike Junker
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Andreas Walter Kuss
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Thomas Sura
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Elke Krüger
- Institute of Medical Biochemistry and Molecular Biology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | | | - Lars Riff Jensen
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Elke Hammer
- Interfaculty Institute of Genetics and Functional Genomics, University Medicine Greifswald, 17475 Greifswald, Germany
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16
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Yim YY, Nestler EJ. Cell-Type-Specific Neuroproteomics of Synapses. Biomolecules 2023; 13:998. [PMID: 37371578 PMCID: PMC10296650 DOI: 10.3390/biom13060998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/08/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
In the last two decades, our knowledge of synaptic proteomes and their relationship to normal brain function and neuropsychiatric disorders has been expanding rapidly through the use of more powerful neuroproteomic approaches. However, mass spectrometry (MS)-based neuroproteomic studies of synapses still require cell-type, spatial, and temporal proteome information. With the advancement of sample preparation and MS techniques, we have just begun to identify and understand proteomes within a given cell type, subcellular compartment, and cell-type-specific synapse. Here, we review the progress and limitations of MS-based neuroproteomics of synapses in the mammalian CNS and highlight the recent applications of these approaches in studying neuropsychiatric disorders such as major depressive disorder and substance use disorders. Combining neuroproteomic findings with other omics studies can generate an in-depth, comprehensive map of synaptic proteomes and possibly identify new therapeutic targets and biomarkers for several central nervous system disorders.
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Affiliation(s)
- Yun Young Yim
- Nash Family Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
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17
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Villalobos-Cantor S, Barrett RM, Condon AF, Arreola-Bustos A, Rodriguez KM, Cohen MS, Martin I. Rapid cell type-specific nascent proteome labeling in Drosophila. eLife 2023; 12:83545. [PMID: 37092974 PMCID: PMC10125018 DOI: 10.7554/elife.83545] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 04/09/2023] [Indexed: 04/25/2023] Open
Abstract
Controlled protein synthesis is required to regulate gene expression and is often carried out in a cell type-specific manner. Protein synthesis is commonly measured by labeling the nascent proteome with amino acid analogs or isotope-containing amino acids. These methods have been difficult to implement in vivo as they require lengthy amino acid replacement procedures. O-propargyl-puromycin (OPP) is a puromycin analog that incorporates into nascent polypeptide chains. Through its terminal alkyne, OPP can be conjugated to a fluorophore-azide for directly visualizing nascent protein synthesis, or to a biotin-azide for capture and identification of newly-synthesized proteins. To achieve cell type-specific OPP incorporation, we developed phenylacetyl-OPP (PhAc-OPP), a puromycin analog harboring an enzyme-labile blocking group that can be removed by penicillin G acylase (PGA). Here, we show that cell type-specific PGA expression in Drosophila can be used to achieve OPP labeling of newly-synthesized proteins in targeted cell populations within the brain. Following a brief 2 hr incubation of intact brains with PhAc-OPP, we observe robust imaging and affinity purification of OPP-labeled nascent proteins in PGA-targeted cell populations. We apply this method to show a pronounced age-related decline in neuronal protein synthesis in the fly brain, demonstrating the capability of PhAc-OPP to quantitatively capture in vivo protein synthesis states. This method, which we call POPPi (PGA-dependent OPP incorporation), should be applicable for rapidly visualizing protein synthesis and identifying nascent proteins synthesized under diverse physiological and pathological conditions with cellular specificity in vivo.
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Affiliation(s)
- Stefanny Villalobos-Cantor
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Ruth M Barrett
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alec F Condon
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Alicia Arreola-Bustos
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
| | - Kelsie M Rodriguez
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Michael S Cohen
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
| | - Ian Martin
- Jungers Center for Neurosciences, Department of Neurology, Oregon Health and Science University, Portland, United States
- Department of Chemical Physiology and Biochemistry, Oregon Health and Science University, Portland, United States
- Parkinson Center of Oregon, Oregon Health and Science University, Portland, United States
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18
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Hou Z, Liu H. Mapping the Protein Kinome: Current Strategy and Future Direction. Cells 2023; 12:cells12060925. [PMID: 36980266 PMCID: PMC10047437 DOI: 10.3390/cells12060925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/23/2023] [Accepted: 03/13/2023] [Indexed: 03/30/2023] Open
Abstract
The kinome includes over 500 different protein kinases, which form an integrated kinase network that regulates cellular phosphorylation signals. The kinome plays a central role in almost every cellular process and has strong linkages with many diseases. Thus, the evaluation of the cellular kinome in the physiological environment is essential to understand biological processes, disease development, and to target therapy. Currently, a number of strategies for kinome analysis have been developed, which are based on monitoring the phosphorylation of kinases or substrates. They have enabled researchers to tackle increasingly complex biological problems and pathological processes, and have promoted the development of kinase inhibitors. Additionally, with the increasing interest in how kinases participate in biological processes at spatial scales, it has become urgent to develop tools to estimate spatial kinome activity. With multidisciplinary efforts, a growing number of novel approaches have the potential to be applied to spatial kinome analysis. In this paper, we review the widely used methods used for kinome analysis and the challenges encountered in their applications. Meanwhile, potential approaches that may be of benefit to spatial kinome study are explored.
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Affiliation(s)
- Zhanwu Hou
- Center for Mitochondrial Biology and Medicine, Douglas C. Wallace Institute for Mitochondrial and Epigenetic Information Sciences, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China
| | - Huadong Liu
- School of Health and Life Science, University of Health and Rehabilitation Sciences, Qingdao 266071, China
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19
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Schloesser D, Lindenthal L, Sauer J, Chung KJ, Chavakis T, Griesser E, Baskaran P, Maier-Habelsberger U, Fundel-Clemens K, Schlotthauer I, Watson CK, Swee LK, Igney F, Park JE, Huber-Lang MS, Thomas MJ, El Kasmi KC, Murray PJ. Senescent cells suppress macrophage-mediated corpse removal via upregulation of the CD47-QPCT/L axis. J Cell Biol 2023; 222:213731. [PMID: 36459066 PMCID: PMC9723804 DOI: 10.1083/jcb.202207097] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 12/03/2022] Open
Abstract
Progressive accrual of senescent cells in aging and chronic diseases is associated with detrimental effects in tissue homeostasis. We found that senescent fibroblasts and epithelia were not only refractory to macrophage-mediated engulfment and removal, but they also paralyzed the ability of macrophages to remove bystander apoptotic corpses. Senescent cell-mediated efferocytosis suppression (SCES) was independent of the senescence-associated secretory phenotype (SASP) but instead required direct contact between macrophages and senescent cells. SCES involved augmented senescent cell expression of CD47 coinciding with increased CD47-modifying enzymes QPCT/L. SCES was reversible by interfering with the SIRPα-CD47-SHP-1 axis or QPCT/L activity. While CD47 expression increased in human and mouse senescent cells in vitro and in vivo, another ITIM-containing protein, CD24, contributed to SCES specifically in human epithelial senescent cells where it compensated for genetic deficiency in CD47. Thus, CD47 and CD24 link the pathogenic effects of senescent cells to homeostatic macrophage functions, such as efferocytosis, which we hypothesize must occur efficiently to maintain tissue homeostasis.
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Affiliation(s)
| | | | - Julia Sauer
- Boehringer Ingelheim, Biberach an der Riß, Germany
| | - Kyoung-Jin Chung
- Institute for Clinical Chemistry and Laboratory of Medicine, Faculty of Medicine at University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Triantafyllos Chavakis
- Institute for Clinical Chemistry and Laboratory of Medicine, Faculty of Medicine at University Hospital, Technische Universität Dresden, Dresden, Germany
| | - Eva Griesser
- Boehringer Ingelheim, Biberach an der Riß, Germany
| | | | | | | | | | | | - Lee Kim Swee
- Boehringer Ingelheim, Biberach an der Riß, Germany
| | | | | | - Markus S Huber-Lang
- Institute of Clinical and Experimental Trauma-Immunology, University Hospital Ulm, Ulm, Germany
| | | | | | - Peter J Murray
- Max Planck Institute of Biochemistry, Martinsried, Germany
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20
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Hepker M, Clabaugh G, Jin H, Kanthasamy AG. New protocol for kinetic assay seeding ability recovery "KASAR" from formalin-fixed paraffin-embedded tissues. Front Mol Biosci 2023; 10:1087982. [PMID: 36793788 PMCID: PMC9922999 DOI: 10.3389/fmolb.2023.1087982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/19/2023] [Indexed: 01/31/2023] Open
Abstract
The real-time quaking-induced conversion (RT-QuIC) alpha-synuclein (aSyn) protein kinetic seeding assay has been very useful for detecting pathological aggregates in various synucleinopathies including Parkinson's disease (PD). This biomarker assay relies on fresh frozen tissue to effectively seed and amplify aSyn aggregating protein. With vast repositories of formalin-fixed paraffin-embedded (FFPE) tissues, it is paramount to harness the power of kinetic assays to unlock the diagnostic potential of archived FFPE biospecimens. However, the major challenge posed by significantly reduced amplification of formalin-fixed tissues in the assay suggests that formalin fixation deterred monomer interaction with the sample seed and depressed subsequent protein aggregation. To overcome this challenge, we developed a kinetic assay seeding ability recovery (KASAR) protocol to maintain the integrity of the tissue and seeding protein. For this, we implemented a series of heating steps with the brain tissue suspended in a buffer composed of 500 mM tris-HCl (pH 7.5) and 0.02% SDS after the standard deparaffinization of the tissue sections. Initially, samples from seven human brain samples, including four samples from patients diagnosed with dementia with Lewy bodies (DLB) and three samples from healthy controls without DLB, were compared to fresh frozen samples under three different, but clinically common sample storage conditions: formalin-fixed, FFPE, and FFPE slices cut 5 µm thick. The KASAR protocol was able to recover seeding activity for all positive samples in all storage conditions. Next, 28 FFPE samples from the submandibular gland (SMG) of patients diagnosed with PD, incidental Lewy body disease (ILBD), or healthy controls were tested with 93% of results replicating when blinded. With samples of only a few milligrams, this protocol recovered the same quality of seeding in formalin-fixed tissue as fresh frozen tissue. Moving forward, protein aggregate kinetic assays, in conjunction with the KASAR protocol, can be used to understand and diagnose neurodegenerative diseases more comprehensively. Overall, our KASAR protocol unlocks and restores the seeding ability of formalin-fixed paraffin-embedded tissues for the amplification of biomarker protein aggregates in kinetic assays.
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Affiliation(s)
- Monica Hepker
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, United States
| | - Griffin Clabaugh
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of GA, Athens, GA, United States
| | - Huajun Jin
- Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of GA, Athens, GA, United States
| | - Anumantha G. Kanthasamy
- Parkinson Disorders Research Laboratory, Iowa Center for Advanced Neurotoxicology, Department of Biomedical Sciences, Iowa State University, Ames, IA, United States,Center for Neurological Disease Research, Department of Physiology and Pharmacology, University of GA, Athens, GA, United States,*Correspondence: Anumantha G. Kanthasamy,
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Pu J, Xue C, Huo S, Shen Q, Qu Y, Yang X, An B, Angel TE, Chen Z, Mehl JT, Tang H, Yang E, Sikorski TW, Qu J. Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS. Anal Chem 2023; 95:924-934. [PMID: 36534410 PMCID: PMC10581745 DOI: 10.1021/acs.analchem.2c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate, absolute liquid chromatography-mass spectrometry (LC-MS)-based quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues would greatly expand sample availability for pharmaceutical/clinical investigations but remains challenging owing to the following issues: (i) efficient/quantitative recovery of target signature peptides from FFPE tissues is essential but an optimal procedure for targeted, absolute quantification is lacking; (ii) most FFPE samples are long-term-stored; severe immunohistochemistry (IHC) signal losses of target proteins during storage were widely reported, while the effect of storage on LC-MS-based methods was unknown; and (iii) the proper strategy to prepare calibration/quality-control samples to ensure accurate targeted protein analysis in FFPE tissues remained elusive. Using targeted quantification of monoclonal antibody (mAb), antigen, and 40 tissue markers in FFPE tissues as a model system, we extensively investigate those issues and develope an LC-MS-based strategy enabling accurate and precise targeted protein quantification in FFPE samples. First, we demonstrated a surfactant cocktail-based procedure (f-SEPOD), providing high/reproducible recovery of target signature peptides from FFPE tissues. Second, a heat-accelerated degradation study within a roughly estimated 5 year storage period recapitulated the loss of protein IHC signals while LC-MS signals of all targets remained constant. This indicates that the storage of FFPE tissues mainly causes decreased immunoreactivity but unlikely chemical degradation of proteins, which strongly suggests that the storage of FFPE tissues does not cause significant quantitative bias for LC-MS-based methods. Third, while a conventional spike-and-extract approach for calibration caused substantial negative biases, a novel approach, using FFPE-treated calibration standards, enabled accurate and precise quantification. With the pipeline, we conducted the first-ever pharmacokinetics measurement of mAb and its target in FFPE tissues, where time courses by FFPE vs fresh tissues showed excellent correlation.
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Affiliation(s)
- Jie Pu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Chao Xue
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Shihan Huo
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Qingqing Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xinxin Yang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Bo An
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas E. Angel
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - John T. Mehl
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Huaping Tang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Eric Yang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Timothy W. Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States; Phone: (610) 270-4978
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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22
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Obi EN, Tellock DA, Thomas GJ, Veenstra TD. Biomarker Analysis of Formalin-Fixed Paraffin-Embedded Clinical Tissues Using Proteomics. Biomolecules 2023; 13:biom13010096. [PMID: 36671481 PMCID: PMC9855471 DOI: 10.3390/biom13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
The relatively recent developments in mass spectrometry (MS) have provided novel opportunities for this technology to impact modern medicine. One of those opportunities is in biomarker discovery and diagnostics. Key developments in sample preparation have enabled a greater range of clinical samples to be characterized at a deeper level using MS. While most of these developments have focused on blood, tissues have also been an important resource. Fresh tissues, however, are difficult to obtain for research purposes and require significant resources for long-term storage. There are millions of archived formalin-fixed paraffin-embedded (FFPE) tissues within pathology departments worldwide representing every possible tissue type including tumors that are rare or very small. Owing to the chemical technique used to preserve FFPE tissues, they were considered intractable to many newer proteomics techniques and primarily only useful for immunohistochemistry. In the past couple of decades, however, researchers have been able to develop methods to extract proteins from FFPE tissues in a form making them analyzable using state-of-the-art technologies such as MS and protein arrays. This review will discuss the history of these developments and provide examples of how they are currently being used to identify biomarkers and diagnose diseases such as cancer.
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23
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Ya D, Zhang Y, Cui Q, Jiang Y, Yang J, Tian N, Xiang W, Lin X, Li Q, Liao R. Application of spatial transcriptome technologies to neurological diseases. Front Cell Dev Biol 2023; 11:1142923. [PMID: 36936681 PMCID: PMC10020196 DOI: 10.3389/fcell.2023.1142923] [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: 01/12/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.
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Affiliation(s)
- Dongshan Ya
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yingmei Zhang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qi Cui
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Yanlin Jiang
- Department of Pharmacology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Jiaxin Yang
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Ning Tian
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Wenjing Xiang
- Department of Neurology ward 2, Guilin People’s Hospital, Guilin, China
| | - Xiaohui Lin
- Department of Geriatrics, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Qinghua Li
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
| | - Rujia Liao
- Laboratory of Neuroscience, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Department of Neurology, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- Guangxi Clinical Research Center for Neurological Diseases, Affiliated Hospital of Guilin Medical University, Guilin Medical University, Guilin, China
- *Correspondence: Rujia Liao,
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24
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Nwosu AJ, Misal SA, Truong T, Carson RH, Webber KGI, Axtell NB, Liang Y, Johnston SM, Virgin KL, Smith EG, Thomas GV, Morgan T, Price JC, Kelly RT. In-Depth Mass Spectrometry-Based Proteomics of Formalin-Fixed, Paraffin-Embedded Tissues with a Spatial Resolution of 50-200 μm. J Proteome Res 2022; 21:2237-2245. [PMID: 35916235 PMCID: PMC9767749 DOI: 10.1021/acs.jproteome.2c00409] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Formalin-fixed, paraffin-embedded (FFPE) tissues are banked in large repositories to cost-effectively preserve valuable specimens for later study. With the rapid growth of spatial proteomics, FFPE tissues can serve as a more accessible alternative to more commonly used frozen tissues. However, extracting proteins from FFPE tissues is challenging due to cross-links formed between proteins and formaldehyde. Here, we have adapted the nanoPOTS sample processing workflow, which was previously applied to single cells and fresh-frozen tissues, to profile protein expression from FFPE tissues. Following the optimization of extraction solvents, times, and temperatures, we identified an average of 1312 and 3184 high-confidence master proteins from 10 μm thick FFPE-preserved mouse liver tissue squares having lateral dimensions of 50 and 200 μm, respectively. The observed proteome coverage for FFPE tissues was on average 88% of that achieved for similar fresh-frozen tissues. We also characterized the performance of our fully automated sample preparation and analysis workflow, termed autoPOTS, for FFPE spatial proteomics. This modified nanodroplet processing in one pot for trace samples (nanoPOTS) and fully automated processing in one pot for trace sample (autoPOTS) workflows provides the greatest coverage reported to date for high-resolution spatial proteomics applied to FFPE tissues. Data are available via ProteomeXchange with identifier PXD029729.
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Affiliation(s)
- Andikan J Nwosu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Santosh A Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Richard H Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Nathaniel B Axtell
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Kenneth L Virgin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ethan G Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - George V Thomas
- Knight Cancer Center, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - Terry Morgan
- Department of Pathology, Oregon Health & Science University, Portland, Oregon 97239, United States
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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25
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Griesser E, Schönberger T, Stierstorfer B, Wyatt H, Rist W, Lamla T, Thomas MJ, Lamb D, Geillinger-Kästle KE. Characterization of a flexible AAV-DTR/DT mouse model of acute epithelial lung injury. Am J Physiol Lung Cell Mol Physiol 2022; 323:L206-L218. [PMID: 35762632 DOI: 10.1152/ajplung.00364.2021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Animal models are important to mimic certain pathways or biological aspects of human pathologies including acute and chronic pulmonary diseases. We developed a novel and flexible mouse model of acute epithelial lung injury based on adeno-associated virus (AAV) variant 6.2 mediated expression of the human diphtheria toxin receptor (DTR). Following intratracheal administration of diphtheria toxin (DT), a cell-specific death of bronchial and alveolar epithelial cells can be observed. In contrast to other lung injury models, the here described mouse model provides the possibility of targeted injury using specific tropisms of AAV vectors or cell type specific promotors to drive the human DTR expression. Also, generation of cell specific mouse lines is not required. Detailed characterization of the AAV-DTR/DT mouse model including titration of viral genome (vg) load and administered DT amount revealed increasing cell numbers in bronchoalveolar lavage (BAL; macrophages, neutrophils, and unspecified cells) and elevation of degenerated cells and infiltrated leukocytes in lung tissue, dependent of vg load and DT dose. Cytokine levels in BAL fluid showed different patterns with higher vg load, e.g. IFNγ, TNFα, and IP10 increasing and IL-5 and IL-6 decreasing, while lung function was not affected. Additionally, laser-capture microdissection (LCM)-based proteomics of bronchial epithelium and alveolar tissue revealed upregulated immune and inflammatory response in all regions and extracellular matrix deposition in infiltrated alveoli. Overall, our novel AAV-DTR/DT model allows investigation of repair mechanisms following epithelial injury and resembles specific mechanistic aspects of acute and chronic pulmonary diseases.
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Affiliation(s)
- Eva Griesser
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany, Germany
| | - Tanja Schönberger
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany, Germany
| | - Birgit Stierstorfer
- Non-clinical Drug Safety, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Hannah Wyatt
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany, Germany
| | - Wolfgang Rist
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany, Germany
| | - Thorsten Lamla
- Drug Discovery Sciences, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany, Germany
| | - Matthew James Thomas
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany.,University of Bath, Bath, United Kingdom
| | - David Lamb
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany
| | - Kerstin E Geillinger-Kästle
- Immunology and Respiratory Diseases Research, Boehringer Ingelheim Pharma GmbH and Co. KG, Biberach an der Riss, Germany
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26
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Mund A, Brunner AD, Mann M. Unbiased spatial proteomics with single-cell resolution in tissues. Mol Cell 2022; 82:2335-2349. [PMID: 35714588 DOI: 10.1016/j.molcel.2022.05.022] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 05/05/2022] [Accepted: 05/18/2022] [Indexed: 12/19/2022]
Abstract
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify the entire complement of proteins in cells or tissues. Here, we review challenges and recent advances in the LC-MS-based analysis of minute protein amounts, down to the level of single cells. Application of this technology revealed that single-cell transcriptomes are dominated by stochastic noise due to the very low number of transcripts per cell, whereas the single-cell proteome appears to be complete. The spatial organization of cells in tissues can be studied by emerging technologies, including multiplexed imaging and spatial transcriptomics, which can now be combined with ultra-sensitive proteomics. Combined with high-content imaging, artificial intelligence and single-cell laser microdissection, MS-based proteomics provides an unbiased molecular readout close to the functional level. Potential applications range from basic biological questions to precision medicine.
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Affiliation(s)
- Andreas Mund
- Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Andreas-David Brunner
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Drug Discovery Sciences, Birkendorfer Str. 65, D-88397, Biberach Riss, Germany
| | - Matthias Mann
- Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.
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27
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Leitner DF, William C, Faustin A, Askenazi M, Kanshin E, Snuderl M, McGuone D, Wisniewski T, Ueberheide B, Gould L, Devinsky O. Proteomic differences in hippocampus and cortex of sudden unexplained death in childhood. Acta Neuropathol 2022; 143:585-599. [PMID: 35333953 PMCID: PMC8953962 DOI: 10.1007/s00401-022-02414-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/18/2022] [Accepted: 03/19/2022] [Indexed: 11/01/2022]
Abstract
Sudden unexplained death in childhood (SUDC) is death of a child over 1 year of age that is unexplained after review of clinical history, circumstances of death, and complete autopsy with ancillary testing. Multiple etiologies may cause SUDC. SUDC and sudden unexpected death in epilepsy (SUDEP) share clinical and pathological features, suggesting some similarities in mechanism of death and possible abnormalities in hippocampus and cortex. To identify molecular signaling pathways, we performed label-free quantitative mass spectrometry on microdissected frontal cortex, hippocampal dentate gyrus (DG), and cornu ammonis (CA1-3) in SUDC (n = 19) and pediatric control cases (n = 19) with an explained cause of death. At a 5% false discovery rate (FDR), we found differential expression of 660 proteins in frontal cortex, 170 in DG, and 57 in CA1-3. Pathway analysis of altered proteins identified top signaling pathways associated with activated oxidative phosphorylation (p = 6.3 × 10-15, z = 4.08) and inhibited EIF2 signaling (p = 2.0 × 10-21, z = - 2.56) in frontal cortex, and activated acute phase response in DG (p = 8.5 × 10-6, z = 2.65) and CA1-3 (p = 4.7 × 10-6, z = 2.00). Weighted gene correlation network analysis (WGCNA) of clinical history indicated that SUDC-positive post-mortem virology (n = 4/17) had the most significant module in each brain region, with the top most significant associated with decreased mRNA metabolic processes (p = 2.8 × 10-5) in frontal cortex. Additional modules were associated with clinical history, including fever within 24 h of death (top: increased mitochondrial fission in DG, p = 1.8 × 10-3) and febrile seizure history (top: decreased small molecule metabolic processes in frontal cortex, p = 8.8 × 10-5) in all brain regions, neuropathological hippocampal findings in the DG (top: decreased focal adhesion, p = 1.9 × 10-3). Overall, cortical and hippocampal protein changes were present in SUDC cases and some correlated with clinical features. Our studies support that proteomic studies of SUDC cohorts can advance our understanding of the pathogenesis of these tragedies and may inform the development of preventive strategies.
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28
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Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues. Molecules 2022; 27:molecules27031137. [PMID: 35164409 PMCID: PMC8838561 DOI: 10.3390/molecules27031137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 μm thick FF tissues, and 4 μm thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm2 and 15 μm thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 μm thick FFPE tissue with the average of 270 protein identifications (1 mm2), similar to the results on 4 μm thick FF. Moreover, we found that temperature increases during incubation with urea on 4 μm thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides.
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29
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Capturing the third dimension in drug discovery: Spatially-resolved tools for interrogation of complex 3D cell models. Biotechnol Adv 2021; 55:107883. [PMID: 34875362 DOI: 10.1016/j.biotechadv.2021.107883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 02/07/2023]
Abstract
Advanced three-dimensional (3D) cell models have proven to be capable of depicting architectural and microenvironmental features of several tissues. By providing data of higher physiological and pathophysiological relevance, 3D cell models have been contributing to a better understanding of human development, pathology onset and progression mechanisms, as well as for 3D cell-based assays for drug discovery. Nonetheless, the characterization and interrogation of these tissue-like structures pose major challenges on the conventional analytical methods, pushing the development of spatially-resolved technologies. Herein, we review recent advances and pioneering technologies suitable for the interrogation of multicellular 3D models, while capable of retaining biological spatial information. We focused on imaging technologies and omics tools, namely transcriptomics, proteomics and metabolomics. The advantages and shortcomings of these novel methodologies are discussed, alongside the opportunities to intertwine data from the different tools.
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30
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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.
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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
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31
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Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P. Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun 2021; 12:3576. [PMID: 34117251 PMCID: PMC8196151 DOI: 10.1038/s41467-021-23855-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
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Affiliation(s)
- Corinna Friedrich
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), MDC graduate school, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Simon Schallenberg
- grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marieluise Kirchner
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ziehm
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Christin Beier
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Jens Neudecker
- grid.6363.00000 0001 2218 4662Department of Surgery - Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.5252.00000 0004 1936 973XInstitute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Mertins
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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32
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Yang Z, Sun L. Recent technical progress in sample preparation and liquid-phase separation-mass spectrometry for proteomic analysis of mass-limited samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1214-1225. [PMID: 33629703 DOI: 10.1039/d1ay00171j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Mass spectrometry (MS)-based proteomics has enabled the identification and quantification of thousands of proteins from complex proteomes in a single experiment. However, its performance for mass-limited proteome samples (e.g., single cells and tissue samples from laser capture microdissection) is still not satisfying. The development of novel proteomic methodologies with better overall sensitivity is vital. During the last several years, substantial technical progress has been achieved for the preparation and liquid-phase separation-MS characterization of mass-limited proteome samples. In this review, we summarize recent technological progress of sample preparation, liquid chromatography (LC)-MS, capillary zone electrophoresis (CZE)-MS and MS instrumentation for bottom-up proteomics of trace biological samples, highlight some exciting applications of the novel techniques for single-cell proteomics, and provide a very brief perspective about the field at the end.
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Affiliation(s)
- Zhichang Yang
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
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33
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Zheng N, Taylor K, Gu H, Santockyte R, Wang XT, McCarty J, Adelakun O, Zhang YJ, Pillutla R, Zeng J. Antipeptide Immunocapture with In-Sample Calibration Curve Strategy for Sensitive and Robust LC-MS/MS Bioanalysis of Clinical Protein Biomarkers in Formalin-Fixed Paraffin-Embedded Tumor Tissues. Anal Chem 2020; 92:14713-14722. [PMID: 33047598 DOI: 10.1021/acs.analchem.0c03271] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite huge promises, bioanalysis of protein biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for clinical applications is still very challenging. Here, we describe a sensitive and robust LC-MS/MS assay to quantify clinical protein biomarkers in FFPE tumor sections using automated antipeptide antibody immunocapture followed by in-sample calibration curve (ISCC) strategy with multiple isotopologue reaction monitoring (MIRM) technique. ISCC approach with MIRM of stable isotopically labeled (SIL) peptides eliminated the need for authentic matrices for external calibration curves, overcame the matrix effects, and validated the quantification range in each individual sample. Specifically, after deparaffinization, rehydration, antigen retrieval, and homogenization, the protein analytes in FFPE tumor tissues were spiked with a known concentration of one SIL peptide for each analyte, followed by trypsin digestion and antipeptide immunocapture enrichment prior to MIRM-ISCC-based LC-MS/MS analysis. This approach has been successfully used for sensitive quantification of programmed cell death-1 (PD-1) and programmed cell death-ligand 1 (PD-L1) in 15 representative FFPE tumor samples from lung, colorectal, and head and neck cancer patients. Except for one sample, PD-L1 and PD-1 in all samples were quantifiable using this assay with concentrations of 27.85-798.43 (amol/μg protein) for PD-L1 and 16.96-129.89 (amol/μg protein) for PD-1. These results were generally in agreement with the immunohistochemistry (IHC) data but with some exceptions. This approach demonstrated the feasibility to quantify low abundant protein biomarkers in FFPE tissues with improved sensitivity, specificity, and robustness and showed great potential as an orthogonal analytical approach to IHC for clinical applications.
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Affiliation(s)
- Naiyu Zheng
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Kristin Taylor
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Huidong Gu
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Rasa Santockyte
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Xi-Tao Wang
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jean McCarty
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Olufemi Adelakun
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Yan J Zhang
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Renuka Pillutla
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
| | - Jianing Zeng
- Department of Translational Medicine, Bristol Myers Squibb, Route 206 and Province Line Road, Princeton, New Jersey 08543, United States
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Abstract
Parkinson's disease (PD) is a leading cause of neurodegeneration that is defined by the selective loss of dopaminergic neurons and the accumulation of protein aggregates called Lewy bodies (LBs). The unequivocal identification of Mendelian inherited mutations in 13 genes in PD has provided transforming insights into the pathogenesis of this disease. The mechanistic analysis of several PD genes, including α-synuclein (α-syn), leucine-rich repeat kinase 2 (LRRK2), PTEN-induced kinase 1 (PINK1), and Parkin, has revealed central roles for protein aggregation, mitochondrial damage, and defects in endolysosomal trafficking in PD neurodegeneration. In this review, we outline recent advances in our understanding of these gene pathways with a focus on the emergent role of Rab (Ras analog in brain) GTPases and vesicular trafficking as a common mechanism that underpins how mutations in PD genes lead to neuronal loss. These advances have led to previously distinct genes such as vacuolar protein-sorting-associated protein 35 (VPS35) and LRRK2 being implicated in a common signaling pathway. A greater understanding of these common nodes of vesicular trafficking will be crucial for linking other PD genes and improving patient stratification in clinical trials underway against α-syn and LRRK2 targets.
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Affiliation(s)
- Pawan Kishor Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom;
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom;
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35
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Eggeling F, Hoffmann F. Microdissection—An Essential Prerequisite for Spatial Cancer Omics. Proteomics 2020; 20:e2000077. [DOI: 10.1002/pmic.202000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022]
Affiliation(s)
- Ferdinand Eggeling
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
| | - Franziska Hoffmann
- Department of OtorhinolaryngologyMALDI Imaging and Core Unit Proteome AnalysisDFG Core Unit Jena Biophotonic and Imaging Laboratory (JBIL)Jena University Hospital Am Klinikum 1 Jena 07747 Germany
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