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Miles HN, Tomlin D, Ricke WA, Li L. Integrating intracellular and extracellular proteomic profiling for in-depth investigations of cellular communication in a model of prostate cancer. Proteomics 2023; 23:e2200287. [PMID: 37226375 PMCID: PMC10667563 DOI: 10.1002/pmic.202200287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/26/2023]
Abstract
Cellular communication is essential for cell-cell interactions, maintaining homeostasis and progression of certain disease states. While many studies examine extracellular proteins, the holistic extracellular proteome is often left uncaptured, leaving gaps in our understanding of how all extracellular proteins may impact communication and interaction. We used a cellular-based proteomics approach to more holistically profile both the intracellular and extracellular proteome of prostate cancer. Our workflow was generated in such a manner that multiple experimental conditions can be observed with the opportunity for high throughput integration. Additionally, this workflow is not limited to a proteomic aspect, as metabolomic and lipidomic studies can be integrated for a multi-omics workflow. Our analysis showed coverage of over 8000 proteins while also garnering insights into cellular communication in the context of prostate cancer development and progression. Identified proteins covered a variety of cellular processes and pathways, allowing for the investigation of multiple aspects into cellular biology. This workflow demonstrates advantages for integrating intra- and extracellular proteomic analyses as well as potential for multi-omics researchers. This approach possesses great value for future investigations into the systems biology aspects of disease development and progression.
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Affiliation(s)
- Hannah N. Miles
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Devin Tomlin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - William A. Ricke
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- George M. O’Brien Urology Research Center of Excellence, University of Wisconsin-Madison School of Medicine and Public Health, Madison, WI 53705, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
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Luo Z, Li X, Wang L, Shu C. Impact of the transforming growth factor-β pathway on vascular restenosis and its mechanism. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:1252-1259. [PMID: 37875366 PMCID: PMC10930841 DOI: 10.11817/j.issn.1672-7347.2023.230064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Indexed: 10/26/2023]
Abstract
As a crucial regulatory molecule in the context of vascular stenosis, transforming growth factor-β (TGF-β), plays a pivotal role in its initiation and progression. TGF-β, a member of the TGF-β superfamily, can bind to the TGF-β receptor and transduce extracellular to intracellular signals through canonical Smad dependent or noncanonical signaling pathways to regulate cell growth, proliferation, differentiation, and apoptosis. Restenosis remains one of the most challenging problems in cardiac, cerebral, and peripheral vascular disease worldwide. The mechanisms for occurrence and development of restenosis are diverse and complex. The TGF-β pathway exhibits diversity across various cell types. Hence, clarifying the specific roles of TGF-β within different cell types and its precise impact on vascular stenosis provides strategies for future research in the field of stenosis.
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Affiliation(s)
- Zhongchen Luo
- Institute of Vascular Diseases, Central South University, Changsha 410011.
- Department of Vascular Surgery, Vascular Center, Second Xiangya Hospital, Central South University, Changsha 410011.
| | - Xin Li
- Institute of Vascular Diseases, Central South University, Changsha 410011
- Department of Vascular Surgery, Vascular Center, Second Xiangya Hospital, Central South University, Changsha 410011
| | - Lunchang Wang
- Institute of Vascular Diseases, Central South University, Changsha 410011
- Department of Vascular Surgery, Vascular Center, Second Xiangya Hospital, Central South University, Changsha 410011
| | - Chang Shu
- Institute of Vascular Diseases, Central South University, Changsha 410011.
- Department of Vascular Surgery, Vascular Center, Second Xiangya Hospital, Central South University, Changsha 410011.
- Center of Vascular Surgery, Fuwai Hospital, Chinese Academy of Medical Science, Beijing 100037, China.
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Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P, Nalpas N. Recent progress in quantitative phosphoproteomics. Expert Rev Proteomics 2023; 20:469-482. [PMID: 38116637 DOI: 10.1080/14789450.2023.2295872] [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: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. AREAS COVERED State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. EXPERT OPINION Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.
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Affiliation(s)
- Katharina Zittlau
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Payal Nashier
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Boris Macek
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
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Liu R, Wei P, Keller C, Orefice NS, Shi Y, Li Z, Huang J, Cui Y, Frost DC, Han S, Cross TWL, Rey FE, Li L. Integrated Label-Free and 10-Plex DiLeu Isobaric Tag Quantitative Methods for Profiling Changes in the Mouse Hypothalamic Neuropeptidome and Proteome: Assessment of the Impact of the Gut Microbiome. Anal Chem 2020; 92:14021-14030. [PMID: 32926775 DOI: 10.1021/acs.analchem.0c02939] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Gut microbiota can regulate host physiological and pathological status through gut-brain communications or pathways. However, the impact of the gut microbiome on neuropeptides and proteins involved in regulating brain functions and behaviors is still not clearly understood. To address the problem, integrated label-free and 10-plex DiLeu isobaric tag-based quantitative methods were implemented to compare the profiling of neuropeptides and proteins in the hypothalamus of germ-free (GF)- vs conventionally raised (ConvR)-mice. A total of 2943 endogenous peptides from 63 neuropeptide precursors and 3971 proteins in the mouse hypothalamus were identified. Among these 368 significantly changed peptides (fold changes over 1.5 and a p-value of <0.05), 73.6% of the peptides showed higher levels in GF-mice than in ConvR-mice, and 26.4% of the peptides had higher levels in ConvR-mice than in GF-mice. These peptides were mainly from secretogranin-2, phosphatidylethanolamine-binding protein-1, ProSAAS, and proenkephalin-A. A quantitative proteomic analysis employing DiLeu isobaric tags revealed that 282 proteins were significantly up- or down-regulated (fold changes over 1.2 and a p-value of <0.05) among the 3277 quantified proteins. These neuropeptides and proteins were mainly involved in regulating behaviors, transmitter release, signaling pathways, and synapses. Interestingly, pathways including long-term potentiation, long-term depression, and circadian entrainment were involved. In the present study, a combined label-free and 10-plex DiLeu-based quantitative method enabled a comprehensive profiling of gut microbiome-induced dynamic changes of neuropeptides and proteins in the hypothalamus, suggesting that the gut microbiome might mediate a range of behavioral changes, brain development, and learning and memory through these neuropeptides and proteins.
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Affiliation(s)
- Rui Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing 210023, P. R. China.,Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China
| | - Pingli Wei
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Caitlin Keller
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Nicola Salvatore Orefice
- Department of Medicine, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Waisman Center, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yatao Shi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Zihui Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yusi Cui
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Dustin C Frost
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Shuying Han
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210023, P. R. China.,Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, and National and Local Collaborative Engineering Center of Chinese Medicinal Resources Industrialization and Formulae Innovative Medicine, Nanjing 210023, P. R. China
| | - Tzu-Wen L Cross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Cardiovascular Research Center, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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