1
|
Beutgen VM, Shinkevich V, Pörschke J, Meena C, Steitz AM, Pogge von Strandmann E, Graumann J, Gómez-Serrano M. Secretome analysis using Affinity Proteomics and Immunoassays: a focus on Tumor Biology. Mol Cell Proteomics 2024:100830. [PMID: 39147028 DOI: 10.1016/j.mcpro.2024.100830] [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: 02/29/2024] [Revised: 07/20/2024] [Accepted: 08/12/2024] [Indexed: 08/17/2024] Open
Abstract
The study of the cellular secretome using proteomic techniques continues to capture the attention of the research community across a broad range of topics in biomedical research. Due to their untargeted nature, independence from the model system employed, historically superior depth of analysis, as well as comparative affordability, mass spectrometry-based approaches traditionally dominate such analyses. More recently, however, affinity-based proteomic assays have massively gained in analytical depth, which together with their high sensitivity, dynamic range coverage as well as high throughput capabilities render them exquisitely suited to secretome analysis. In this review, we revisit the analytical challenges implied by secretomics and provide an overview of affinity-based proteomic platforms currently available for such analyses, using the study of the tumor secretome as an example for basic and translational research.
Collapse
Affiliation(s)
- Vanessa M Beutgen
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Veronika Shinkevich
- Institute of Pharmacology, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany
| | - Johanna Pörschke
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Celina Meena
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Anna M Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Elke Pogge von Strandmann
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany
| | - Johannes Graumann
- Institute of Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany; Core Facility Translational Proteomics, Biochemical/Pharmacological Centre, Philipps University, Marburg, Germany.
| | - María Gómez-Serrano
- Institute for Tumor Immunology, Center for Tumor Biology and Immunology, Philipps University, Marburg, Germany.
| |
Collapse
|
2
|
Das P, Saha S, Kumar Guha P, Kumar Bhunia A. Quantum dot-protein interface: Interaction of the CdS quantum dot with human hemoglobin for the study of the energy transfer process and binding mechanism along with detection of the unfolding of hemoglobin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 324:124937. [PMID: 39137709 DOI: 10.1016/j.saa.2024.124937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/12/2024] [Accepted: 08/04/2024] [Indexed: 08/15/2024]
Abstract
In this study, the interaction of the human hemoglobin with cost effective and chemically fabricated CdS quantum dots (QDs) (average sizes ≈3nm) has been investigated. The semiconductor QDs showed maximum visible absorption at 445 nm with excitonic formation and band gap of ≈ 2.88 eV along with hexagonal crystalline phase. The binding of QDs-Hb occurs through corona formation to the ground sate complex formation. The life time of the heme pocket binding and reorganization were found to be t1 = 43 min and t2 = 642 min, respectively. The emission quenching of the Hb has been indicated large energy transfer between CdS QDs and Hb with tertiary deformation of Hb. The binding thermodynamics showed highly exothermic nature. The ultrafast decay during corona formation was studied from TCSPC. The results showed that the energy transfer efficiency increases with the increase of the QDs concentration and maximum ≈71.5 % energy transfer occurs and average ultrafast lifetime varies from 5.45 ns to1.51 ns. The deformation and unfolding of the secondary structure of Hb with changes of the α-helix (≈74 % to ≈51.07 %) and β-sheets (≈8.63 % to ≈10.25 %) have been observed from circular dichroism spectrum. The SAXS spectrum showed that the radius of gyration of CdS QDs-Hb bioconjugate increased (up to 23 ± 0.45 nm) with the increase of the concentration of QDs compare with pure Hb (11 ± 0.23 nm) and Hb becoming more unfolded.
Collapse
Affiliation(s)
- Priyanka Das
- Department of Physics, Vidyasagar University, Paschim Medinipur 721102, West Bengal, India
| | - Satyajit Saha
- Department of Physics, Vidyasagar University, Paschim Medinipur 721102, West Bengal, India
| | - Prasanta Kumar Guha
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology Kharagpur, Paschim Medinipur, 721302, India; School of Nano Science and Technology, Indian Institute of Technology Kharagpur, Paschim Medinipur 721302, India
| | - Amit Kumar Bhunia
- Department of Physics, Government General Degree College Gopiballavpur-II, Jhargram 721517, India.
| |
Collapse
|
3
|
Jiang Y, Meyer JG. Rapid Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry. J Proteome Res 2024; 23:3649-3658. [PMID: 39007500 DOI: 10.1021/acs.jproteome.4c00302] [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: 07/16/2024]
Abstract
Noninvasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography-mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method that integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein corona enrichment for high-throughput and efficient plasma proteomic profiling. We realized over 280 protein identifications in 1.4 min collection time, which enables a potential throughput of approximately 1000 samples daily. The identified proteins are involved in valuable pathways, and 44 of the proteins are FDA-approved biomarkers. The robustness and quantitative accuracy of this method were evaluated across multiple NPs and concentrations with a mean coefficient of variation of 17%. Moreover, different protein corona profiles were observed among various NPs based on their distinct surface modifications, and all NP protein profiles exhibited deeper coverage and better quantification than neat plasma. Our streamlined workflow merges coverage and throughput with precise quantification, leveraging both DISPA and NP protein corona enrichment. This underscores the significant potential of DISPA when paired with NP sample preparation techniques for plasma proteome studies.
Collapse
Affiliation(s)
- Yuming Jiang
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jesse G Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
| |
Collapse
|
4
|
Zhang J, Weng Y, Liu Y, Wang N, Feng S, Qiu S, Lin D. Molecular separation-assisted label-free SERS combined with machine learning for nasopharyngeal cancer screening and radiotherapy resistance prediction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2024; 257:112968. [PMID: 38955080 DOI: 10.1016/j.jphotobiol.2024.112968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 04/30/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024]
Abstract
Nasopharyngeal cancer (NPC) is a malignant tumor with high prevalence in Southeast Asia and highly invasive and metastatic characteristics. Radiotherapy is the primary strategy for NPC treatment, however there is still lack of effect method for predicting the radioresistance that is the main reason for treatment failure. Herein, the molecular profiles of patient plasma from NPC with radiotherapy sensitivity and resistance groups as well as healthy group, respectively, were explored by label-free surface enhanced Raman spectroscopy (SERS) based on surface plasmon resonance for the first time. Especially, the components with different molecular weight sizes were analyzed via the separation process, helping to avoid the possible missing of diagnostic information due to the competitive adsorption. Following that, robust machine learning algorithm based on principal component analysis and linear discriminant analysis (PCA-LDA) was employed to extract the feature of blood-SERS data and establish an effective predictive model with the accuracy of 96.7% for identifying the radiotherapy resistance subjects from sensitivity ones, and 100% for identifying the NPC subjects from healthy ones. This work demonstrates the potential of molecular separation-assisted label-free SERS combined with machine learning for NPC screening and treatment strategy guidance in clinical scenario.
Collapse
Affiliation(s)
- Jun Zhang
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Youliang Weng
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fujian Branch of Fudan University Shanghai Cancer Center, Fuzhou 350014, PR China
| | - Yi Liu
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Nan Wang
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Shangyuan Feng
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China
| | - Sufang Qiu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fujian Branch of Fudan University Shanghai Cancer Center, Fuzhou 350014, PR China.
| | - Duo Lin
- Key Laboratory of OptoElectronic Science and Technology for Medicine, Ministry of Education, Fujian Provincial Key Laboratory for Photonics Technology, Fujian Normal University, Fuzhou 350117, PR China.
| |
Collapse
|
5
|
Zhang S, Ghalandari B, Chen Y, Wang Q, Liu K, Sun X, Ding X, Song S, Jiang L, Ding X. Boronic Acid-Rich Lanthanide Metal-Organic Frameworks Enable Deep Proteomics with Ultratrace Biological Samples. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2401559. [PMID: 38958107 DOI: 10.1002/adma.202401559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/21/2024] [Indexed: 07/04/2024]
Abstract
Label-free proteomics is widely used to identify disease mechanism and potential therapeutic targets. However, deep proteomics with ultratrace clinical specimen remains a major technical challenge due to extensive contact loss during complex sample pretreatment. Here, a hybrid of four boronic acid-rich lanthanide metal-organic frameworks (MOFs) with high protein affinity is introduced to capture proteins in ultratrace samples jointly by nitrogen-boronate complexation, cation-π and ionic interactions. A MOFs Aided Sample Preparation (MASP) workflow that shrinks sample volume and integrates lysis, protein capture, protein digestion and peptide collection steps into a single PCR tube to minimize sample loss caused by non-specific absorption, is proposed further. MASP is validated to quantify ≈1800 proteins in 10 HEK-293T cells. MASP is applied to profile cerebrospinal fluid (CSF) proteome from cerebral stroke and brain damaged patients, and identified ≈3700 proteins in 1 µL CSF. MASP is further demonstrated to detect ≈9600 proteins in as few as 50 µg mouse brain tissues. MASP thus enables deep, scalable, and reproducible proteome on precious clinical samples with low abundant proteins.
Collapse
Affiliation(s)
- Shuang Zhang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Behafarid Ghalandari
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Youming Chen
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Qingwen Wang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Kun Liu
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinyi Sun
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xinwen Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Sunfengda Song
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Lai Jiang
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Xianting Ding
- Department of Anesthesiology and Surgical Intensive Care Unit, Xinhua Hospital, School of Medicine and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| |
Collapse
|
6
|
van Straten D, Sork H, van de Schepop L, Frunt R, Ezzat K, Schiffelers RM. Biofluid specific protein coronas affect lipid nanoparticle behavior in vitro. J Control Release 2024; 373:481-492. [PMID: 39032575 DOI: 10.1016/j.jconrel.2024.07.044] [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: 11/01/2023] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Lipid nanoparticles (LNPs) have successfully entered the clinic for the delivery of mRNA- and siRNA-based therapeutics, most recently as vaccines for COVID-19. Nevertheless, there is a lack of understanding regarding their in vivo behavior, in particular cell targeting. Part of this LNP tropism is based on the adherence of endogenous protein to the particle surface. This protein forms a so-called corona that can change, amongst other things, the circulation time, biodistribution and cellular uptake of these particles. The formation of this protein corona, in turn, is dependent on the nanoparticle properties (e.g., size, charge, surface chemistry and hydrophobicity) as well as the biological environment from which it is derived. With the potential of gene therapy to target virtually any disease, administration sites other than intravenous route are considered, resulting in tissue specific protein coronas. For neurological diseases, intracranial administration of LNPs results in a cerebral spinal fluid derived protein corona, possibly changing the properties of the lipid nanoparticle compared to intravenous administration. Here, the differences between plasma and CSF derived protein coronas on a clinically relevant LNP formulation were studied in vitro. Protein analysis showed that LNPs incubated in human CSF (C-LNPs) developed a protein corona composition that differed from that of LNPs incubated in plasma (P-LNPs). Lipoproteins as a whole, but in particular apolipoprotein E, represented a higher percentage of the total protein corona on C-LNPs than on P-LNPs. This resulted in improved cellular uptake of C-LNPs compared to P-LNPs, regardless of cell origin. Importantly, the higher LNP uptake did not directly translate into more efficient cargo delivery, underlining that further assessment of such mechanisms is necessary. These findings show that biofluid specific protein coronas alter LNP functionality, suggesting that the site of administration could affect LNP efficacy in vivo and needs to be considered during the development of the formulation.
Collapse
Affiliation(s)
- Demian van Straten
- CDL Research, University Medical Center Utrecht, Utrecht, the Netherlands.
| | - Helena Sork
- Institute of Technology, University of Tartu, 50411 Tartu, Estonia
| | | | - Rowan Frunt
- CDL Research, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | | |
Collapse
|
7
|
Li S, Jin B, Ma Y, Yang X, Fan J, Xie Y, Xu C, Dai X, Wang M, Liu Q, Fu T, Liu Y, Tan W. Proteome Fishing for CRISPR/Cas12a-Based Orthogonal Multiplex Aptamer Sensing. J Am Chem Soc 2024; 146:19874-19885. [PMID: 39007743 DOI: 10.1021/jacs.4c03061] [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: 07/16/2024]
Abstract
Detection of serum protein biomarkers is extremely challenging owing to the superior complexity of serum. Here, we report a method of proteome fishing from the serum. It uses a magnetic nanoparticle-protein corona and a multiplexed aptamer panel, which we incubated with the nanoparticle-protein corona for biomarker recognition. To transfer protein biomarker detection to aptamer detection, we established a CRISPR/Cas12a-based orthogonal multiplex aptamer sensing (COMPASS) platform by profiling the aptamers of protein corona with clinical nonsmall cell lung cancer (NSCLC) serum samples. Furthermore, we determined the four out of nine (FOON) panel (including HE4, NSE, AFP, and VEGF165) to be the most cost-effective and accurate panel for COMPASS in NSCLC diagnosis. The diagnostic accuracy of NSCLC by the FOON panel with internal and external cohorts was 95.56% (ROC-AUC = 99.40%) and 89.58% (ROC-AUC = 95.41%), respectively. Our developed COMPASS technology circumvents the otherwise challenging multiplexed serum protein amplification problem and avoids aptamer degradation in serum. Therefore, this novel COMPASS could lead to the development of a facile, cost-effective, intelligent, and high-throughput diagnostic platform for large-cohort cancer screening.
Collapse
Affiliation(s)
- Shuangqin Li
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Baichuan Jin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yintao Ma
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- College of Computer Science and Technology, Zhejiang University of Technology, Hangzhou, Zhejiang 310023, China
| | - Xu Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Jinlong Fan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yueli Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Chenlu Xu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
| | - Xin Dai
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Mengjie Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Qiqi Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, Zhejiang 310024, China
| | - Ting Fu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yuan Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| |
Collapse
|
8
|
Chang MEK, Lange J, Cartier JM, Moore TW, Soriano SM, Albracht B, Krawitzky M, Guturu H, Alavi A, Stukalov A, Zhou X, Elgierari EM, Chu J, Benz R, Cuevas JC, Ferdosi S, Hornburg D, Farokhzad O, Siddiqui A, Batzoglou S, Leach RJ, Liss MA, Kopp RP, Flory MR. A Scaled Proteomic Discovery Study for Prostate Cancer Diagnostic Markers Using Proteograph TM and Trapped Ion Mobility Mass Spectrometry. Int J Mol Sci 2024; 25:8010. [PMID: 39125581 PMCID: PMC11311733 DOI: 10.3390/ijms25158010] [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: 06/12/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 08/12/2024] Open
Abstract
There is a significant unmet need for clinical reflex tests that increase the specificity of prostate-specific antigen blood testing, the longstanding but imperfect tool for prostate cancer diagnosis. Towards this endpoint, we present the results from a discovery study that identifies new prostate-specific antigen reflex markers in a large-scale patient serum cohort using differentiating technologies for deep proteomic interrogation. We detect known prostate cancer blood markers as well as novel candidates. Through bioinformatic pathway enrichment and network analysis, we reveal associations of differentially abundant proteins with cytoskeletal, metabolic, and ribosomal activities, all of which have been previously associated with prostate cancer progression. Additionally, optimized machine learning classifier analysis reveals proteomic signatures capable of detecting the disease prior to biopsy, performing on par with an accepted clinical risk calculator benchmark.
Collapse
Affiliation(s)
- Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jane Lange
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Jessie May Cartier
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Travis W. Moore
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Sophia M. Soriano
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Brenna Albracht
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | | | | | | | | | | | | | | | - Ryan Benz
- Seer Inc., Redwood City, CA 94065, USA
| | | | | | | | | | | | | | - Robin J. Leach
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Michael A. Liss
- Roger L. & Laura D. Zeller Charitable Foundation in Urologic Oncology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Ryan P. Kopp
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97201, USA; (M.E.K.C.); (S.M.S.)
| |
Collapse
|
9
|
Huang CF, Hollas MA, Sanchez A, Bhattacharya M, Ho G, Sundaresan A, Caldwell MA, Zhao X, Benz R, Siddiqui A, Kelleher NL. Deep Profiling of Plasma Proteoforms with Engineered Nanoparticles for Top-down Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.20.604425. [PMID: 39071411 PMCID: PMC11275834 DOI: 10.1101/2024.07.20.604425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The dynamic range challenge for detection of proteins and their proteoforms in human plasma has been well documented. Here, we use the nanoparticle protein corona approach to enrich low-abundant proteins selectively and reproducibly from human plasma and use top-down proteomics to quantify differential enrichment for the 2841 detected proteoforms from 114 proteins. Furthermore, nanoparticle enrichment allowed top-down detection of proteoforms between ∼1 µg/mL and ∼10 pg/mL in absolute abundance, providing up to 10 5 -fold increase in proteome depth over neat plasma in which only proteoforms from abundant proteins (>1 µg/mL) were detected. The ability to monitor medium and some low abundant proteoforms through reproducible enrichment significantly extends the applicability of proteoform research by adding depth beyond albumin, immunoglobins and apolipoproteins to uncover many involved in immunity and cell signaling. As proteoforms carry unique information content relative to peptides, this report opens the door to deeper proteoform sequencing in clinical proteomics of disease or aging cohorts.
Collapse
|
10
|
Lin M, Xu F, Sun J, Song J, Shen Y, Lu S, Ding H, Lan L, Chen C, Ma W, Wu X, Song Z, Wang W. Integrative multi-omics analysis unravels the host response landscape and reveals a serum protein panel for early prognosis prediction for ARDS. Crit Care 2024; 28:213. [PMID: 38956604 PMCID: PMC11218270 DOI: 10.1186/s13054-024-05000-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024] Open
Abstract
BACKGROUND The multidimensional biological mechanisms underpinning acute respiratory distress syndrome (ARDS) continue to be elucidated, and early biomarkers for predicting ARDS prognosis are yet to be identified. METHODS We conducted a multicenter observational study, profiling the 4D-DIA proteomics and global metabolomics of serum samples collected from patients at the initial stage of ARDS, alongside samples from both disease control and healthy control groups. We identified 28-day prognosis biomarkers of ARDS in the discovery cohort using the LASSO method, fold change analysis, and the Boruta algorithm. The candidate biomarkers were validated through parallel reaction monitoring (PRM) targeted mass spectrometry in an external validation cohort. Machine learning models were applied to explore the biomarkers of ARDS prognosis. RESULTS In the discovery cohort, comprising 130 adult ARDS patients (mean age 72.5, 74.6% male), 33 disease controls, and 33 healthy controls, distinct proteomic and metabolic signatures were identified to differentiate ARDS from both control groups. Pathway analysis highlighted the upregulated sphingolipid signaling pathway as a key contributor to the pathological mechanisms underlying ARDS. MAP2K1 emerged as the hub protein, facilitating interactions with various biological functions within this pathway. Additionally, the metabolite sphingosine 1-phosphate (S1P) was closely associated with ARDS and its prognosis. Our research further highlights essential pathways contributing to the deceased ARDS, such as the downregulation of hematopoietic cell lineage and calcium signaling pathways, contrasted with the upregulation of the unfolded protein response and glycolysis. In particular, GAPDH and ENO1, critical enzymes in glycolysis, showed the highest interaction degree in the protein-protein interaction network of ARDS. In the discovery cohort, a panel of 36 proteins was identified as candidate biomarkers, with 8 proteins (VCAM1, LDHB, MSN, FLG2, TAGLN2, LMNA, MBL2, and LBP) demonstrating significant consistency in an independent validation cohort of 183 patients (mean age 72.6 years, 73.2% male), confirmed by PRM assay. The protein-based model exhibited superior predictive accuracy compared to the clinical model in both the discovery cohort (AUC: 0.893 vs. 0.784; Delong test, P < 0.001) and the validation cohort (AUC: 0.802 vs. 0.738; Delong test, P = 0.008). INTERPRETATION Our multi-omics study demonstrated the potential biological mechanism and therapy targets in ARDS. This study unveiled several novel predictive biomarkers and established a validated prediction model for the poor prognosis of ARDS, offering valuable insights into the prognosis of individuals with ARDS.
Collapse
Affiliation(s)
- Mengna Lin
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Feixiang Xu
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jianfeng Song
- Department of Emergency Medicine, Minhang Hospital, Fudan University, Shanghai, China
| | - Yao Shen
- Department of Respiratory Medicine, Pudong Hospital, Fudan University, Shanghai, China
| | - Su Lu
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Hailin Ding
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lulu Lan
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chen Chen
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen Ma
- School of Public Health, Fudan University, Shanghai, China
| | - Xueling Wu
- Department of Respiratory Medicine, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China.
| | - Zhenju Song
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
- Department of Emergency Medicine, Zhongshan Hospital, Fudan University, Shanghai, China.
- Institute of Emergency Rescue and Critical Care, Fudan University, Shanghai, China.
| | - Weibing Wang
- Shanghai Institute of Infectious Disease and Biosecurity, School of Public Health, Fudan University, Shanghai, China.
- School of Public Health, Fudan University, Shanghai, China.
| |
Collapse
|
11
|
Beenken A, Kiryluk K. Blood Proteomics for Biomarkers of Kidney Pathology. J Am Soc Nephrol 2024; 35:835-837. [PMID: 38819933 PMCID: PMC11230708 DOI: 10.1681/asn.0000000000000395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2024] Open
Affiliation(s)
- Andrew Beenken
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York
| | | |
Collapse
|
12
|
Houerbi N, Kim J, Overbey EG, Batra R, Schweickart A, Patras L, Lucotti S, Ryon KA, Najjar D, Meydan C, Damle N, Chin C, Narayanan SA, Guarnieri JW, Widjaja G, Beheshti A, Tobias G, Vatter F, Hirschberg JW, Kleinman A, Afshin EE, MacKay M, Chen Q, Miller D, Gajadhar AS, Williamson L, Tandel P, Yang Q, Chu J, Benz R, Siddiqui A, Hornburg D, Gross S, Shirah B, Krumsiek J, Mateus J, Mao X, Matei I, Mason CE. Secretome profiling reveals acute changes in oxidative stress, brain homeostasis, and coagulation following short-duration spaceflight. Nat Commun 2024; 15:4862. [PMID: 38862464 PMCID: PMC11166969 DOI: 10.1038/s41467-024-48841-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/15/2024] [Indexed: 06/13/2024] Open
Abstract
As spaceflight becomes more common with commercial crews, blood-based measures of crew health can guide both astronaut biomedicine and countermeasures. By profiling plasma proteins, metabolites, and extracellular vesicles/particles (EVPs) from the SpaceX Inspiration4 crew, we generated "spaceflight secretome profiles," which showed significant differences in coagulation, oxidative stress, and brain-enriched proteins. While >93% of differentially abundant proteins (DAPs) in vesicles and metabolites recovered within six months, the majority (73%) of plasma DAPs were still perturbed post-flight. Moreover, these proteomic alterations correlated better with peripheral blood mononuclear cells than whole blood, suggesting that immune cells contribute more DAPs than erythrocytes. Finally, to discern possible mechanisms leading to brain-enriched protein detection and blood-brain barrier (BBB) disruption, we examined protein changes in dissected brains of spaceflight mice, which showed increases in PECAM-1, a marker of BBB integrity. These data highlight how even short-duration spaceflight can disrupt human and murine physiology and identify spaceflight biomarkers that can guide countermeasure development.
Collapse
Affiliation(s)
- Nadia Houerbi
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - JangKeun Kim
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Eliah G Overbey
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Richa Batra
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Annalise Schweickart
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Laura Patras
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
- Department of Molecular Biology and Biotechnology, Center of Systems Biology, Biodiversity and Bioresources, Faculty of Biology and Geology, Babes-Bolyai University, Cluj-Napoca, Romania
| | - Serena Lucotti
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Krista A Ryon
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Deena Najjar
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Namita Damle
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Chin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - S Anand Narayanan
- Department of Nutrition & Integrative Physiology, Florida State University, Tallahassee, FL, USA
| | - Joseph W Guarnieri
- Center of Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Gabrielle Widjaja
- Center of Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Afshin Beheshti
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- KBR, Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Gabriel Tobias
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
- Seer, Inc., Redwood City, CA, 94065, USA
| | - Fanny Vatter
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA
- Seer, Inc., Redwood City, CA, 94065, USA
| | | | - Ashley Kleinman
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Evan E Afshin
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Matthew MacKay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Qiuying Chen
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Dawson Miller
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | | | | | | | - Qiu Yang
- Seer, Inc., Redwood City, CA, 94065, USA
| | | | - Ryan Benz
- Seer, Inc., Redwood City, CA, 94065, USA
| | | | | | - Steven Gross
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Bader Shirah
- Department of Neuroscience, King Faisal Specialist Hospital & Research Centre, Jeddah, Saudi Arabia
| | - Jan Krumsiek
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Jaime Mateus
- Space Exploration Technologies Corporation (SpaceX), Hawthorne, CA, USA
| | - Xiao Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University Health, Loma Linda, CA, 92350, USA
| | - Irina Matei
- Children's Cancer and Blood Foundation Laboratories, Departments of Pediatrics and Cell and Developmental Biology, Drukier Institute for Children's Health, Weill Cornell Medicine, New York, NY, USA.
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, 10065, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
- Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, 10021, USA.
- The Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, 10021, USA.
- WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, 10021, USA.
| |
Collapse
|
13
|
Liu K, Zhang S, Xu S, Yang W, Li Y, Chen Y, Shen F, Wang Y, Chen Z, Li H, Ding X. Ultrasensitive Proteomics of Trace Cardiac Tissues with Anchor-Nanoparticles. Anal Chem 2024; 96:9460-9467. [PMID: 38820243 DOI: 10.1021/acs.analchem.4c00739] [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: 06/02/2024]
Abstract
Pathological cardiac hypertrophy is a complex process that often leads to heart failure. Label-free proteomics has emerged as an important platform to reveal protein variations and to elucidate the mechanisms of cardiac hypertrophy. Endomyocardial biopsy is a minimally invasive technique for sampling cardiac tissue, but it yields only limited amounts of an ethically permissible specimen. After regular pathological examination, the remaining trace samples pose significant challenges for effective protein extraction and mass spectrometry analysis. Herein, we developed trace cardiac tissue proteomics based on the anchor-nanoparticles (TCPA) method. We identified an average of 6666 protein groups using ∼50 μg of myocardial interventricular septum samples by TCPA. We then applied TCPA to acquire proteomics from patients' cardiac samples both diagnosed as hypertrophic hearts and myocarditis controls and identified significant alterations in pathways such as regulation of actin cytoskeleton, oxidative phosphorylation, and cGMP-PKG signaling pathway. Moreover, we found multiple lipid metabolic pathways to be dysregulated in transthyretin cardiac amyloidosis compared to other types of cardiac hypertrophy. TCPA offers a new technique for studying pathological cardiac hypertrophy and can serve as a platform toolbox for proteomic research in other cardiac diseases.
Collapse
Affiliation(s)
- Kun Liu
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Shuang Zhang
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Sudan Xu
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Wenyi Yang
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Ya Li
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Youming Chen
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Feng Shen
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Yuchen Wang
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Zixuan Chen
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Hongli Li
- Department of Cardiology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related Genes, Institute for Personalized Medicine, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China
| |
Collapse
|
14
|
Soo PC, Lee CC, Shie MF, Patil AA, Descanzo MJN, Chin YC, Chen HA, Horng YT, Lin CB, Lee JJ, Chiang CK, Peng WP. Enhancing the sequence coverage of nanodiamond-extracted early secretory proteins from the Mycobacterium tuberculosis complex. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:3464-3474. [PMID: 38804556 DOI: 10.1039/d4ay00314d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
The unambiguous identification of protein species requires high sequence coverage. In this study, we successfully improved the sequence coverage of early secretory 10 kDa cell filtrate protein (CFP-10) and 6 kDa early secretory antigenic target (ESAT-6) proteins from the Mycobacterium tuberculosis complex (MTC) in broth culture media with the use of the 4-chloro-α-cyanocinnamic acid (Cl-CCA) matrix. Conventional matrices, α-cyano-hydroxy-cinnamic acid (CHCA) and 2,5-dihydroxybenzoic acid (DHB), were also used for comparison. After nanodiamond (ND) extraction, the sequence coverage of the CFP-10 protein was 87% when CHCA and DHB matrices were used, and the ESAT-6 protein was not detected. On the other hand, the sequence coverage for ND-extracted CFP-10 and ESAT-6 could reach 94% and 100%, respectively, when the Cl-CCA matrix was used and with the removal of interference from bovine serum albumin (BSA) protein and α-crystallin (ACR) protein. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was also adopted to analyze the protein mass spectra. A total of 6 prominent ion signals were observed, including ESAT-6 protein peaks at mass-to-charge ratios (m/z) of ∼7931, ∼7974, ∼9768, and ∼9813 and CFP-10 protein peaks at m/z of ∼10 100 and ∼10 660. The ESAT-6 ion signals were always detected concurrently with CFP-10 ion signals, but CFP-10 ion signals could be detected alone without the ESAT-6 ion signals. Furthermore, the newly found ESAT-6 peaks were also confirmed using a Mag-Beads-Protein G kit with an ESAT-6 antibody to capture the ESAT-6 protein, which was also consistent with the sequence coverage analysis.
Collapse
Affiliation(s)
- Po-Chi Soo
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Ching-Chieh Lee
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Meng-Fu Shie
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Avinash A Patil
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | | | - Ya-Ching Chin
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Hsi-An Chen
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| | - Yu-Tze Horng
- Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan
| | - Chih-Bin Lin
- Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Jen-Jyh Lee
- Department of Internal Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Cheng-Kang Chiang
- Department of Chemistry, National Dong Hwa University, Shoufeng, Hualien, Taiwan
| | - Wen-Ping Peng
- Department of Physics, National Dong Hwa University, Shoufeng, Hualien, Taiwan.
| |
Collapse
|
15
|
Salvati A. The biomolecular corona of nanomedicines: effects on nanomedicine outcomes and emerging opportunities. Curr Opin Biotechnol 2024; 87:103101. [PMID: 38461749 DOI: 10.1016/j.copbio.2024.103101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/05/2023] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Upon administration, nanomedicines adsorb a corona of endogenous biomolecules on their surface, which can affect nanomedicine interactions with cells, targeting, and efficacy. While strategies to reduce protein binding are available, the high selectivity of the adsorbed corona is enabling novel applications, such as for biomarker discovery and rare protein identification. Additionally, the adsorbed molecules can promote interactions with specific cell receptors, thus conferring the nanomedicine new endogenous targeting capabilities. This has been reported for Onpattro, a lipid nanoparticle targeting the hepatocytes via apolipoproteins in its corona. Recently, selective organ-targeting (SORT) nanoparticles have been proposed, which exploit corona-mediated interactions to deliver nanoparticles outside the liver. Strategies for corona seeding and corona engineering are emerging to increase the selectivity of similar endogenous targeting mechanisms.
Collapse
Affiliation(s)
- Anna Salvati
- Department of Nanomedicine & Drug Targeting, Groningen Research Institute of Pharmacy, University of Groningen, A. Deusinglaan 1, 9713AV Groningen, the Netherlands.
| |
Collapse
|
16
|
Honoré B, Hajari JN, Pedersen TT, Ilginis T, Al-Abaiji HA, Lønkvist CS, Saunte JP, Olsen DA, Brandslund I, Vorum H, Slidsborg C. Proteomic analysis of diabetic retinopathy identifies potential plasma-protein biomarkers for diagnosis and prognosis. Clin Chem Lab Med 2024; 62:1177-1197. [PMID: 38332693 DOI: 10.1515/cclm-2023-1128] [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: 04/26/2023] [Accepted: 01/16/2024] [Indexed: 02/10/2024]
Abstract
OBJECTIVES To identify molecular pathways and prognostic- and diagnostic plasma-protein biomarkers for diabetic retinopathy at various stages. METHODS This exploratory, cross-sectional proteomics study involved plasma from 68 adults, including 15 healthy controls and 53 diabetes patients for various stages of diabetic retinopathy: non-diabetic retinopathy, non-proliferative diabetic retinopathy, proliferative diabetic retinopathy and diabetic macular edema. Plasma was incubated with peptide library beads and eluted proteins were tryptic digested, analyzed by liquid chromatography-tandem mass-spectrometry followed by bioinformatics. RESULTS In the 68 samples, 248 of the 731 identified plasma-proteins were present in all samples. Analysis of variance showed differential expression of 58 proteins across the five disease subgroups. Protein-Protein Interaction network (STRING) showed enrichment of various pathways during the diabetic stages. In addition, stage-specific driver proteins were detected for early and advanced diabetic retinopathy. Hierarchical clustering showed distinct protein profiles according to disease severity and disease type. CONCLUSIONS Molecular pathways in the cholesterol metabolism, complement system, and coagulation cascade were enriched in patients at various stages of diabetic retinopathy. The peroxisome proliferator-activated receptor signaling pathway and systemic lupus erythematosus pathways were enriched in early diabetic retinopathy. Stage-specific proteins for early - and advanced diabetic retinopathy as determined herein could be 'key' players in driving disease development and potential 'target' proteins for future therapies. For type 1 and 2 diabetes mellitus, the proteomic profiles were especially distinct during the early disease stage. Validation studies should aim to clarify the role of the detected molecular pathways, potential biomarkers, and potential 'target' proteins for future therapies in diabetic retinopathy.
Collapse
Affiliation(s)
- Bent Honoré
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Javad Nouri Hajari
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Tobias Torp Pedersen
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Tomas Ilginis
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Hajer Ahmad Al-Abaiji
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Claes Sepstrup Lønkvist
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Jon Peiter Saunte
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Dorte Aalund Olsen
- Department of Biochemistry and Immunology, University of Southern Denmark, Vejle Hospital, Southern Denmark, Denmark
| | - Ivan Brandslund
- Department of Biochemistry and Immunology, University of Southern Denmark, Vejle Hospital, Southern Denmark, Denmark
| | - Henrik Vorum
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Ophthalmology, Aalborg University Hospital, Aalborg, Denmark
| | - Carina Slidsborg
- Department of Ophthalmology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
17
|
Dorsch A, Förschner F, Ravandeh M, da Silva Brito WA, Saadati F, Delcea M, Wende K, Bekeschus S. Nanoplastic Size and Surface Chemistry Dictate Decoration by Human Saliva Proteins. ACS APPLIED MATERIALS & INTERFACES 2024; 16:25977-25993. [PMID: 38741563 DOI: 10.1021/acsami.4c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Environmental pollution with plastic polymers has become a global problem, leaving no continent and habitat unaffected. Plastic waste is broken down into smaller parts by environmental factors, which generate micro- and nanoplastic particles (MNPPs), ultimately ending up in the human food chain. Before entering the human body, MNPPs make their first contact with saliva in the human mouth. However, it is unknown what proteins attach to plastic particles and whether such protein corona formation is affected by the particle's biophysical properties. To this end, we employed polystyrene MNPPs of two different sizes and three different charges and incubated them individually with saliva donated by healthy human volunteers. Particle zeta potential and size analyses were performed using dynamic light scattering complemented by nanoliquid chromatography high-resolution mass spectrometry (nLC/HRMS) to qualitatively and quantitatively reveal the protein soft and hard corona for each particle type. Notably, protein profiles and relative quantities were dictated by plastic particle size and charge, which in turn affected their hydrodynamic size, polydispersity, and zeta potential. Strikingly, we provide evidence of the latter to be dynamic processes depending on exposure times. Smaller particles seemed to be more reactive with the surrounding proteins, and cultures of the particles with five different cell lines (HeLa, HEK293, A549, HepG2, and HaCaT) indicated protein corona effects on cellular metabolic activity and genotoxicity. In summary, our data suggest nanoplastic size and surface chemistry dictate the decoration by human saliva proteins, with important implications for MNPP uptake in humans.
Collapse
Affiliation(s)
- Anna Dorsch
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Fritz Förschner
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Mehdi Ravandeh
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Walison Augusto da Silva Brito
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Department of General Pathology, State University of Londrina, Rodovia Celso Garcia Cid, Londrina 86057-970, Brazil
| | - Fariba Saadati
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Mihaela Delcea
- Biophysical Chemistry Department, University of Greifswald, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Kristian Wende
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
| | - Sander Bekeschus
- ZIK plasmatis, Leibniz Institute for Plasma Science and Technology (INP), Felix-Hausdorff-Str. 2, 17489 Greifswald, Germany
- Department of Dermatology and Venereology, Rostock University Medical Center, Strempelstr. 13, 18057 Rostock, Germany
| |
Collapse
|
18
|
Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin─Madison, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53715, United States
| | - Nicholas M Riley
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
19
|
Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
Collapse
Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
20
|
Serrano LR, Peters-Clarke TM, Arrey TN, Damoc E, Robinson ML, Lancaster NM, Shishkova E, Moss C, Pashkova A, Sinitcyn P, Brademan DR, Quarmby ST, Peterson AC, Zeller M, Hermanson D, Stewart H, Hock C, Makarov A, Zabrouskov V, Coon JJ. The One Hour Human Proteome. Mol Cell Proteomics 2024; 23:100760. [PMID: 38579929 PMCID: PMC11103439 DOI: 10.1016/j.mcpro.2024.100760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/23/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024] Open
Abstract
We describe deep analysis of the human proteome in less than 1 h. We achieve this expedited proteome characterization by leveraging state-of-the-art sample preparation, chromatographic separations, and data analysis tools, and by using the new Orbitrap Astral mass spectrometer equipped with a quadrupole mass filter, a high-field Orbitrap mass analyzer, and an asymmetric track lossless (Astral) mass analyzer. The system offers high tandem mass spectrometry acquisition speed of 200 Hz and detects hundreds of peptide sequences per second within data-independent acquisition or data-dependent acquisition modes of operation. The fast-switching capabilities of the new quadrupole complement the sensitivity and fast ion scanning of the Astral analyzer to enable narrow-bin data-independent analysis methods. Over a 30-min active chromatographic method consuming a total analysis time of 56 min, the Q-Orbitrap-Astral hybrid MS collects an average of 4319 MS1 scans and 438,062 tandem mass spectrometry scans per run, producing 235,916 peptide sequences (1% false discovery rate). On average, each 30-min analysis achieved detection of 10,411 protein groups (1% false discovery rate). We conclude, with these results and alongside other recent reports, that the 1-h human proteome is within reach.
Collapse
Affiliation(s)
- Lia R Serrano
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Trenton M Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Eugen Damoc
- Thermo Fisher Scientific GmbH, Bremen, Germany
| | - Margaret Lea Robinson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Noah M Lancaster
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | - Corinne Moss
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | | | - Pavel Sinitcyn
- Morgridge Institute for Research, Madison, Wisconsin, USA
| | | | - Scott T Quarmby
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA
| | | | | | | | | | | | | | | | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.
| |
Collapse
|
21
|
Ruple BA, Mattingly ML, Godwin JS, McIntosh MC, Kontos NJ, Agyin-Birikorang A, Michel JM, Plotkin DL, Chen SY, Ziegenfuss TN, Fruge AD, Gladden LB, Robinson AT, Mobley CB, Mackey AL, Roberts MD. The effects of resistance training on denervated myofibers, senescent cells, and associated protein markers in middle-aged adults. FASEB J 2024; 38:e23621. [PMID: 38651653 PMCID: PMC11047210 DOI: 10.1096/fj.202302103rrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Denervated myofibers and senescent cells are hallmarks of skeletal muscle aging. However, sparse research has examined how resistance training affects these outcomes. We investigated the effects of unilateral leg extensor resistance training (2 days/week for 8 weeks) on denervated myofibers, senescent cells, and associated protein markers in apparently healthy middle-aged participants (MA, 55 ± 8 years old, 17 females, 9 males). We obtained dual-leg vastus lateralis (VL) muscle cross-sectional area (mCSA), VL biopsies, and strength assessments before and after training. Fiber cross-sectional area (fCSA), satellite cells (Pax7+), denervated myofibers (NCAM+), senescent cells (p16+ or p21+), proteins associated with denervation and senescence, and senescence-associated secretory phenotype (SASP) proteins were analyzed from biopsy specimens. Leg extensor peak torque increased after training (p < .001), while VL mCSA trended upward (interaction p = .082). No significant changes were observed for Type I/II fCSAs, NCAM+ myofibers, or senescent (p16+ or p21+) cells, albeit satellite cells increased after training (p = .037). While >90% satellite cells were not p16+ or p21+, most p16+ and p21+ cells were Pax7+ (>90% on average). Training altered 13 out of 46 proteins related to muscle-nerve communication (all upregulated, p < .05) and 10 out of 19 proteins related to cellular senescence (9 upregulated, p < .05). Only 1 out of 17 SASP protein increased with training (IGFBP-3, p = .031). In conclusion, resistance training upregulates proteins associated with muscle-nerve communication in MA participants but does not alter NCAM+ myofibers. Moreover, while training increased senescence-related proteins, this coincided with an increase in satellite cells but not alterations in senescent cell content or SASP proteins. These latter findings suggest shorter term resistance training is an unlikely inducer of cellular senescence in apparently healthy middle-aged participants. However, similar study designs are needed in older and diseased populations before definitive conclusions can be drawn.
Collapse
Affiliation(s)
| | | | | | | | | | | | - J. Max Michel
- School of Kinesiology, Auburn University, Auburn, AL, USA
| | | | | | | | | | | | | | | | - Abigail L. Mackey
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, DK
- Institute of Sports Medicine Copenhagen, Department of Orthopaedic Surgery, Copenhagen University Hospital – Bispebjerg and Frederiksberg, Copenhagen, Denmark
| | | |
Collapse
|
22
|
Gao Y, Kim H, Kitata RB, Lin TT, Swensen AC, Shi T, Liu T. Multiplexed quantitative proteomics in prostate cancer biomarker development. Adv Cancer Res 2024; 161:31-69. [PMID: 39032952 DOI: 10.1016/bs.acr.2024.04.003] [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: 07/23/2024]
Abstract
Prostate cancer (PCa) is the most common non-skin cancer among men in the United States. However, the widely used protein biomarker in PCa, prostate-specific antigen (PSA), while useful for initial detection, its use alone cannot detect aggressive PCa and can lead to overtreatment. This chapter provides an overview of PCa protein biomarker development. It reviews the state-of-the-art liquid chromatography-mass spectrometry-based proteomics technologies for PCa biomarker development, such as enhancing the detection sensitivity of low-abundance proteins through antibody-based or antibody-independent protein/peptide enrichment, enriching post-translational modifications such as glycosylation as well as information-rich extracellular vesicles, and increasing accuracy and throughput using advanced data acquisition methodologies. This chapter also summarizes recent PCa biomarker validation studies that applied those techniques in diverse specimen types, including cell lines, tissues, proximal fluids, urine, and blood, developing novel protein biomarkers for various clinical applications, including early detection and diagnosis, prognosis, and therapeutic intervention of PCa.
Collapse
Affiliation(s)
- Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
| |
Collapse
|
23
|
Brisnovali NF, Franco I, Abdelgawwad A, Tsou HLP, Cao TH, Riva A, Rutter GA, Akalestou E. Effects of SGLT2 Ablation or Inhibition on Corticosterone Secretion in High-Fat-Fed Mice: Exploring a Nexus with Cytokine Levels. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590099. [PMID: 38712064 PMCID: PMC11071289 DOI: 10.1101/2024.04.18.590099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Despite recent therapeutic advances, achieving optimal glycaemic control remains a challenge in managing Type 2 Diabetes (T2D). Sodium-glucose co-transporter type 2 (SGLT2) inhibitors have emerged as effective treatments by promoting urinary glucose excretion. However, the full scope of their mechanisms extends beyond glycaemic control. At present, their immunometabolic effects remain elusive. To investigate the effects of SGLT2 inhibition or deletion, we compared the metabolic and immune phenotype between high fat diet-fed control, chronically dapagliflozin-treated mice and total-body SGLT2/Slc5a2 knockout mice. SGLT2 null mice exhibited superior glucose tolerance and insulin sensitivity compared to control or dapagliflozin-treated mice, independent of glycosuria and body weight. Moreover, SGLT2 null mice demonstrated physiological regulation of corticosterone secretion, with lowered morning levels compared to control mice. Systemic cytokine profiling also unveiled significant alterations in inflammatory mediators, particularly interleukin 6 (IL-6). Furthermore, unbiased proteomic analysis demonstrated downregulation of acute-phase proteins and upregulation of glutathione-related proteins, suggesting a role in the modulation of antioxidant responses. Conversely, IL-6 increased SGLT2 expression in kidney HK2 cells suggesting a role for cytokines in the effects of hyperglycemia. Collectively, our study elucidates a potential interplay between SGLT2 activity, immune modulation, and metabolic homeostasis.
Collapse
Affiliation(s)
- Niki F. Brisnovali
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Isabelle Franco
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Amira Abdelgawwad
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Hio Lam Phoebe Tsou
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Thong Huy Cao
- Department of Cardiovascular Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom
- National Institute for Health and Care Research Leicester Biomedical Research Centre, University Hospitals of Leicester NHS Trust, Glenfield Hospital, Leicester, United Kingdom
- Leicester van Geest Multi-OMICS facility, University of Leicester, Leicester, United Kingdom
| | - Antonio Riva
- The Roger Williams Institute of Hepatology, Foundation for Liver Research, London, United Kingdom
- Faculty of Life Sciences and Medicine, King’s College London, London, United Kingdom
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM) and University of Montreal, Montreal, QC, Canada
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Elina Akalestou
- Section of Cell Biology and Functional Genomics, Division of Diabetes, Endocrinology and Metabolism, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Cardiovascular Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| |
Collapse
|
24
|
Roberts MD, Ruple BA, Godwin JS, McIntosh MC, Chen SY, Kontos NJ, Agyin-Birikorang A, Michel M, Plotkin DL, Mattingly ML, Mobley B, Ziegenfuss TN, Fruge AD, Kavazis AN. A novel deep proteomic approach in human skeletal muscle unveils distinct molecular signatures affected by aging and resistance training. Aging (Albany NY) 2024; 16:6631-6651. [PMID: 38643460 PMCID: PMC11087122 DOI: 10.18632/aging.205751] [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: 06/12/2023] [Accepted: 03/18/2024] [Indexed: 04/22/2024]
Abstract
The skeletal muscle proteome alterations to aging and resistance training have been reported in prior studies. However, conventional proteomics in skeletal muscle typically yields wide protein abundance ranges that mask the detection of lowly expressed proteins. Thus, we adopted a novel deep proteomics approach whereby myofibril (MyoF) and non-MyoF fractions were separately subjected to protein corona nanoparticle complex formation prior to digestion and Liquid Chromatography Mass Spectrometry (LC-MS). Specifically, we investigated MyoF and non-MyoF proteomic profiles of the vastus lateralis muscle of younger (Y, 22±2 years old; n=5) and middle-aged participants (MA, 56±8 years old; n=6). Additionally, MA muscle was analyzed following eight weeks of resistance training (RT, 2d/week). Across all participants, the number of non-MyoF proteins detected averaged to be 5,645±266 (range: 4,888-5,987) and the number of MyoF proteins detected averaged to be 2,611±326 (range: 1,944-3,101). Differences in the non-MyoF (8.4%) and MyoF (2.5%) proteomes were evident between age cohorts, and most differentially expressed non-MyoF proteins (447/543) were more enriched in MA versus Y. Biological processes in the non-MyoF fraction were predicted to be operative in MA versus Y including increased cellular stress, mRNA splicing, translation elongation, and ubiquitin-mediated proteolysis. RT in MA participants only altered ~0.3% of MyoF and ~1.0% of non-MyoF proteomes. In summary, aging and RT predominantly affect non-contractile proteins in skeletal muscle. Additionally, marginal proteome adaptations with RT suggest more rigorous training may stimulate more robust effects or that RT, regardless of age, subtly alters basal state skeletal muscle protein abundances.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Max Michel
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | | | - Brooks Mobley
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA
| | | | - Andrew D. Fruge
- College of Nursing, Auburn University, Auburn, AL 36849, USA
| | | |
Collapse
|
25
|
Li N, Huang J, He S, Zheng Q, Ye F, Qin Z, Wang D, Xiao T, Mao M, Zhou Z, Tang T, Zhang L, Wang X, Wang Y, Lyu Y, Liu L, Dai L, Wang J, Guan J. The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling. J Nanobiotechnology 2024; 22:164. [PMID: 38600601 PMCID: PMC11007927 DOI: 10.1186/s12951-024-02404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protein abundances in plasma make the clinical application of plasma proteomics highly challenging. We designed and synthesized zeolite-based nanoparticles to deplete high-abundance plasma proteins. The resulting novel plasma proteomic assay can measure approximately 3000 plasma proteins in a 45 min chromatographic gradient. Compared to those in neat and depleted plasma, the plasma proteins identified by our assay exhibited distinct biological profiles, as validated in several public datasets. A pilot investigation of the proteomic profile of a hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of the plasma proteome in distinguishing individuals with and without HCC. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we established a robust and efficient plasma proteomic assay with unprecedented identification depth, paving the way for the translation of plasma proteomics into clinical applications.
Collapse
Affiliation(s)
- Nan Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jingnan Huang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Shangwen He
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Qiaocong Zheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Department of Oncology, People's Hospital of YangJiang, Yangjiang, 529500, Guangdong, China
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhengxing Qin
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Dong Wang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Ting Xiao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Mengyuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhenhua Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Tingxi Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Longshan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiaoqing Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yingqiao Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ying Lyu
- Department of Traditional Chinese Medicine, Nanfang Hospital,, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Laiyu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Lingyun Dai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Jigang Wang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, 510515, Guangdong, China.
| |
Collapse
|
26
|
Saei AA, Mahmoudi M. Multi-omics exploration of biomolecular corona in nanomedicine therapeutics and diagnostics. Nanomedicine (Lond) 2024; 19:1223-1226. [PMID: 38593028 PMCID: PMC11285268 DOI: 10.2217/nnm-2024-0104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 03/25/2024] [Indexed: 04/11/2024] Open
Affiliation(s)
- Amir Ata Saei
- Center for Translational Microbiome Research, Department of Microbiology, Tumor & Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden
| | - Morteza Mahmoudi
- Department of Radiology & Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
27
|
Wu CC, Tsantilas KA, Park J, Plubell D, Sanders JA, Naicker P, Govender I, Buthelezi S, Stoychev S, Jordaan J, Merrihew G, Huang E, Parker ED, Riffle M, Hoofnagle AN, Noble WS, Poston KL, Montine TJ, MacCoss MJ. Mag-Net: Rapid enrichment of membrane-bound particles enables high coverage quantitative analysis of the plasma proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.10.544439. [PMID: 38617345 PMCID: PMC11014469 DOI: 10.1101/2023.06.10.544439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Membrane-bound particles in plasma are composed of exosomes, microvesicles, and apoptotic bodies and represent ~1-2% of the total protein composition. Proteomic interrogation of this subset of plasma proteins augments the representation of tissue-specific proteins, representing a "liquid biopsy," while enabling the detection of proteins that would otherwise be beyond the dynamic range of liquid chromatography-tandem mass spectrometry of unfractionated plasma. We have developed an enrichment strategy (Mag-Net) using hyper-porous strong-anion exchange magnetic microparticles to sieve membrane-bound particles from plasma. The Mag-Net method is robust, reproducible, inexpensive, and requires <100 μL plasma input. Coupled to a quantitative data-independent mass spectrometry analytical strategy, we demonstrate that we can collect results for >37,000 peptides from >4,000 plasma proteins with high precision. Using this analytical pipeline on a small cohort of patients with neurodegenerative disease and healthy age-matched controls, we discovered 204 proteins that differentiate (q-value < 0.05) patients with Alzheimer's disease dementia (ADD) from those without ADD. Our method also discovered 310 proteins that were different between Parkinson's disease and those with either ADD or healthy cognitively normal individuals. Using machine learning we were able to distinguish between ADD and not ADD with a mean ROC AUC = 0.98 ± 0.06.
Collapse
Affiliation(s)
- Christine C. Wu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jea Park
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Deanna Plubell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Justin A. Sanders
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | | | | | | | | | | | - Gennifer Merrihew
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Eric Huang
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Edward D. Parker
- Vision Core Lab, Department of Ophthalmology, University of Washington, Seattle, WA, USA
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Computer Science, University of Washington, Seattle, WA, USA
| | - Kathleen L. Poston
- Department of Neurology & Neurological Sciences, Stanford University, Palo Alto CA, USA
| | | | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
28
|
Geng S, Guo P, Wang J, Zhang Y, Shi Y, Li X, Cao M, Song Y, Zhang H, Zhang Z, Zhang K, Song H, Shi J, Liu J. Ultrasensitive Optical Detection and Elimination of Residual Microtumors with a Postoperative Implantable Hydrogel Sensor for Preventing Cancer Recurrence. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307923. [PMID: 38174840 DOI: 10.1002/adma.202307923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 12/16/2023] [Indexed: 01/05/2024]
Abstract
In vivo optical imaging of trace biomarkers in residual microtumors holds significant promise for cancer prognosis but poses a formidable challenge. Here, a novel hydrogel sensor is designed for ultrasensitive and specific imaging of the elusive biomarker. This hydrogel sensor seamlessly integrates a molecular beacon nanoprobe with fibroblasts, offering both high tissue retention capability and an impressive signal-to-noise ratio for imaging. Signal amplification is accomplished through exonuclease I-mediated biomarker recycling. The resulting hydrogel sensor sensitively detects the biomarker carcinoembryonic antigen with a detection limit of 1.8 pg mL-1 in test tubes. Moreover, it successfully identifies residual cancer nodules with a median diameter of less than 2 mm in mice bearing partially removed primary triple-negative breast carcinomas (4T1). Notably, this hydrogel sensor is proven effective for the sensitive diagnosis of invasive tumors in post-surgical mice with infiltrating 4T1 cells, leveraging the role of fibroblasts in locally enriching tumor cells. Furthermore, the residual microtumor is rapidly photothermal ablation by polydopamine-based nanoprobe under the guidance of visualization, achieving ≈100% suppression of tumor recurrence and lung metastasis. This work offers a promising alternative strategy for visually detecting residual microtumors, potentially enhancing the prognosis of cancer patients following surgical interventions.
Collapse
Affiliation(s)
- Shizhen Geng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Pengke Guo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Jing Wang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yunya Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yaru Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Xinling Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Mengnian Cao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Yutong Song
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Hongling Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Zhenzhong Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Haiwei Song
- Department of Biochemistry, National University of Singapore, SingaporeCity, 138673, Singapore
| | - Jinjin Shi
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| | - Junjie Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, 450001, China
- Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou, 450001, China
| |
Collapse
|
29
|
López-Estévez AM, Lapuhs P, Pineiro-Alonso L, Alonso MJ. Personalized Cancer Nanomedicine: Overcoming Biological Barriers for Intracellular Delivery of Biopharmaceuticals. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2309355. [PMID: 38104275 DOI: 10.1002/adma.202309355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/09/2023] [Indexed: 12/19/2023]
Abstract
The success of personalized medicine in oncology relies on using highly effective and precise therapeutic modalities such as small interfering RNA (siRNA) and monoclonal antibodies (mAbs). Unfortunately, the clinical exploitation of these biological drugs has encountered obstacles in overcoming intricate biological barriers. Drug delivery technologies represent a plausible strategy to overcome such barriers, ultimately facilitating the access to intracellular domains. Here, an overview of the current landscape on how nanotechnology has dealt with protein corona phenomena as a first and determinant biological barrier is presented. This continues with the analysis of strategies facilitating access to the tumor, along with conceivable methods for enhanced tumor penetration. As a final step, the cellular barriers that nanocarriers must confront in order for their biological cargo to reach their target are deeply analyzed. This review concludes with a critical analysis and future perspectives of the translational advances in personalized oncological nanomedicine.
Collapse
Affiliation(s)
- Ana María López-Estévez
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Philipp Lapuhs
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - Laura Pineiro-Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacology, Pharmaceutics and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, Santiago de Compostela, 15782, Spain
| |
Collapse
|
30
|
Gao R, Xu X, Kumar P, Liu Y, Zhang H, Guo X, Sun M, Colombari FM, de Moura AF, Hao C, Ma J, Turali Emre ES, Cha M, Xu L, Kuang H, Kotov NA, Xu C. Tapered chiral nanoparticles as broad-spectrum thermally stable antivirals for SARS-CoV-2 variants. Proc Natl Acad Sci U S A 2024; 121:e2310469121. [PMID: 38502692 PMCID: PMC10990083 DOI: 10.1073/pnas.2310469121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/19/2024] [Indexed: 03/21/2024] Open
Abstract
The incessant mutations of viruses, variable immune responses, and likely emergence of new viral threats necessitate multiple approaches to novel antiviral therapeutics. Furthermore, the new antiviral agents should have broad-spectrum activity and be environmentally stable. Here, we show that biocompatible tapered CuS nanoparticles (NPs) efficiently agglutinate coronaviruses with binding affinity dependent on the chirality of surface ligands and particle shape. L-penicillamine-stabilized NPs with left-handed curved apexes display half-maximal inhibitory concentrations (IC50) as low as 0.66 pM (1.4 ng/mL) and 0.57 pM (1.2 ng/mL) for pseudo-type SARS-CoV-2 viruses and wild-type Wuhan-1 SARS-CoV-2 viruses, respectively, which are about 1,100 times lower than those for antibodies (0.73 nM). Benefiting from strong NPs-protein interactions, the same particles are also effective against other strains of coronaviruses, such as HCoV-HKU1, HCoV-OC43, HCoV-NL63, and SARS-CoV-2 Omicron variants with IC50 values below 10 pM (21.8 ng/mL). Considering rapid response to outbreaks, exposure to elevated temperatures causes no change in the antiviral activity of NPs while antibodies are completely deactivated. Testing in mice indicates that the chirality-optimized NPs can serve as thermally stable analogs of antiviral biologics complementing the current spectrum of treatments.
Collapse
Affiliation(s)
- Rui Gao
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Xinxin Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Prashant Kumar
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
| | - Ye Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, Yunnan650000, People’s Republic of China
| | - Hongyu Zhang
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Xiao Guo
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Maozhong Sun
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Felippe Mariano Colombari
- Brazilian Biorenewables National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo13083-100, Brazil
| | - André F. de Moura
- Department of Chemistry, Federal University of São Carlos, São Carlos, São Paulo13565-905, Brazil
| | - Changlong Hao
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Jessica Ma
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Emine Sumeyra Turali Emre
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Minjeong Cha
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| | - Nicholas A. Kotov
- Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI48109
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI48109
- NSF Center for Complex Particles and Particle Systems (COMPASS), University of Michigan, Ann Arbor, MI48109
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu214122, People’s Republic of China
| |
Collapse
|
31
|
Metatla I, Roger K, Chhuon C, Ceccacci S, Chapelle M, Pierre-Olivier Schmit, Demichev V, Guerrera IC. Neat plasma proteomics: getting the best out of the worst. Clin Proteomics 2024; 21:22. [PMID: 38475715 DOI: 10.1186/s12014-024-09477-6] [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: 01/11/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Plasma proteomics holds immense potential for clinical research and biomarker discovery, serving as a non-invasive "liquid biopsy" for tissue sampling. Mass spectrometry (MS)-based proteomics, thanks to improvement in speed and robustness, emerges as an ideal technology for exploring the plasma proteome for its unbiased and highly specific protein identification and quantification. Despite its potential, plasma proteomics is still a challenge due to the vast dynamic range of protein abundance, hindering the detection of less abundant proteins. Different approaches can help overcome this challenge. Conventional depletion methods face limitations in cost, throughput, accuracy, and off-target depletion. Nanoparticle-based enrichment shows promise in compressing dynamic range, but cost remains a constraint. Enrichment strategies for extracellular vesicles (EVs) can enhance plasma proteome coverage dramatically, but current methods are still too laborious for large series. Neat plasma remains popular for its cost-effectiveness, time efficiency, and low volume requirement. We used a test set of 33 plasma samples for all evaluations. Samples were digested using S-Trap and analyzed on Evosep One and nanoElute coupled to a timsTOF Pro using different elution gradients and ion mobility ranges. Data were mainly analyzed using library-free searches using DIA-NN. This study explores ways to improve proteome coverage in neat plasma both in MS data acquisition and MS data analysis. We demonstrate the value of sampling smaller hydrophilic peptides, increasing chromatographic separation, and using library-free searches. Additionally, we introduce the EV boost approach, that leverages on the extracellular vesicle fraction to enhance protein identification in neat plasma samples. Globally, our optimized analysis workflow allows the quantification of over 1000 proteins in neat plasma with a 24SPD throughput. We believe that these considerations can be of help independently of the LC-MS platform used.
Collapse
Affiliation(s)
- Ines Metatla
- Proteomics Platform Necker, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France
| | - Kevin Roger
- Proteomics Platform Necker, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France
| | - Cerina Chhuon
- Proteomics Platform Necker, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France
| | - Sara Ceccacci
- Proteomics Platform Necker, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France
| | - Manuel Chapelle
- Bruker Daltonique SA, 34 Rue de l'Industrie, 67166, Wissembourg Cedex, France
| | | | - Vadim Demichev
- Department of Biochemistry, Charité-Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Ida Chiara Guerrera
- Proteomics Platform Necker, Université Paris Cité-Structure Fédérative de Recherche Necker, INSERM US24/CNRS UAR3633, 75015, Paris, France.
| |
Collapse
|
32
|
Ashkarran AA, Gharibi H, Modaresi SM, Sayadi M, Jafari M, Lin Z, Ritz D, Kakhniashvili D, Sun L, Landry MP, Saei AA, Mahmoudi M. Deep Plasma Proteome Profiling by Modulating Single Nanoparticle Protein Corona with Small Molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.582595. [PMID: 38496642 PMCID: PMC10942461 DOI: 10.1101/2024.03.06.582595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The protein corona, a dynamic biomolecular layer that forms on nanoparticle (NP) surfaces upon exposure to biological fluids is emerging as a valuable diagnostic tool for improving plasma proteome coverage analyzed by liquid chromatography-mass spectrometry (LC-MS/MS). Here, we show that spiking small molecules, including metabolites, lipids, vitamins, and nutrients, into plasma can induce diverse protein corona patterns on otherwise identical NPs, significantly enhancing the depth of plasma proteome profiling. The protein coronas on polystyrene NPs when exposed to plasma treated with an array of small molecules (n=10) allowed for detection of 1793 proteins marking an 8.25-fold increase in the number of quantified proteins compared to plasma alone (218 proteins) and a 2.63-fold increase relative to the untreated protein corona (681 proteins). Furthermore, we discovered that adding 1000 μg/ml phosphatidylcholine could singularly increase the number of unique proteins within the protein corona (897 proteins). This specific concentration of phosphatidylcholine selectively depleted the four most abundant plasma proteins, including albumin, thus reducing concentration dynamic range of plasma proteome and boosting LC-MS/MS sensitivity for detection of proteins with lower abundance. By employing an optimized data-independent acquisition (DIA) approach, the inclusion of phosphatidylcholine led to the detection of 1436 proteins in plasma. This significant achievement is made utilizing only a single NP type and one small molecule to analyze a single plasma sample, setting a new standard in proteomic depth of the plasma sample. Given the critical role of plasma proteomics in biomarker discovery and disease monitoring, we anticipate widespread adoption of this methodology for identification and clinical translation of proteomic biomarkers into FDA approved diagnostics.
Collapse
Affiliation(s)
- Ali Akbar Ashkarran
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| | - Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Maryam Sayadi
- Department of Biomedical Engineering, Michigan State University, East Lansing, MI 48824, USA
| | - Maryam Jafari
- Division of ENT Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Zijin Lin
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| | - Danilo Ritz
- Proteomics Core Facility, Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - David Kakhniashvili
- Proteomics and Metabolomics Core Facility, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 South Shaw Lane, East Lansing, MI 48824, United States
| | - Markita P. Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Neuroscience, University of California, Berkeley, Berkeley, CA, 94720, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94063, USA
| | - Amir Ata Saei
- Biozentrum, University of Basel, 4056 Basel, Switzerland
- Center for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm 17165, Sweden
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
33
|
Abhari RE, Snelling SJ, Augustynak E, Davis S, Fischer R, Carr AJ, Mouthuy PA. A Hybrid Electrospun-Extruded Polydioxanone Suture for Tendon Tissue Regeneration. Tissue Eng Part A 2024; 30:214-224. [PMID: 38126344 PMCID: PMC10954604 DOI: 10.1089/ten.tea.2023.0273] [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: 09/23/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Many surgical tendon repairs fail despite advances in surgical materials and techniques. Tendon repair failure can be partially attributed to the tendon's poor intrinsic healing capacity and the repurposing of sutures from other clinical applications. Electrospun materials show promise as a biological scaffold to support endogenous tendon repair, but their relatively low tensile strength has limited their clinical translation. It is hypothesized that combining electrospun fibers with a material with increased tensile strength may improve the suture's mechanical properties while retaining biophysical cues necessary to encourage cell-mediated repair. This article describes the production of a hybrid electrospun-extruded suture with a sheath of submicron electrospun fibers and a core of melt-extruded fibers. The porosity and tensile strength of this hybrid suture is compared with an electrospun-only braided suture and clinically used sutures Vicryl and polydioxanone (PDS). Bioactivity is assessed by measuring the adsorbed serum proteins on electrospun and melt-extruded filaments using mass spectrometry. Human hamstring tendon fibroblast attachment and proliferation were quantified and compared between the hybrid and control sutures. Combining an electrospun sheath with melt-extruded cores created a hybrid braid with increased tensile strength (70.1 ± 0.3N) compared with an electrospun only suture (12.9 ± 1 N, p < 0.0001). The hybrid suture had a similar force at break to clinical sutures, but lower stiffness and stress. The Young's modulus was 772.6 ± 32 MPa for the hybrid suture, 1693.0 ± 69 MPa for PDS, and 3838.0 ± 132 MPa for Vicryl, p < 0.0001. Hybrid sutures had lower overall porosity than electrospun-only sutures (40 ± 4% and 60 ± 7%, respectively, p = 0.0018) but had a significantly larger overall porosity and average pore diameter compared with surgical sutures. There were similar clusters of adsorbed proteins on electrospun and melt-extruded filaments, which were distinct from PDS. Tendon fibroblast attachment and cell proliferation on hybrid and electrospun sutures were significantly higher than on clinical sutures. This study demonstrated that a bioactive suture with increased tensile strength and lower stiffness could be produced by adding a core of 10 μm melt-extruded fibers to a sheath of electrospun fibers. In contrast to currently used sutures, the hybrid sutures promoted a bioactive response: serum proteins adsorbed, and fibroblasts attached, survived, grew along the sutures, and adopted appropriate morphologies.
Collapse
Affiliation(s)
- Roxanna E. Abhari
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Sarah J.B. Snelling
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Edyta Augustynak
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Simon Davis
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Roman Fischer
- Nuffield Department of Medicine, Target Discovery Institute, Centre for Medicines Discovery, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Medicine, Chinese Academy for Medical Sciences Oxford Institute, University of Oxford, Oxford, United Kingdom
| | - Andrew J. Carr
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| | - Pierre-Alexis Mouthuy
- Nuffield Department of Orthopaedics, Rheumatology, and Musculoskeletal Sciences, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
34
|
Samodova D, Hoel A, Hansen TH, Clausen L, Telléus GK, Marti HP, Pedersen O, Støving RK, Deshmukh AS. Plasma proteome profiling reveals metabolic and immunologic differences between Anorexia Nervosa subtypes. Metabolism 2024; 152:155760. [PMID: 38104923 DOI: 10.1016/j.metabol.2023.155760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
AIMS/HYPOTHESIS Anorexia Nervosa (AN) is a severe psychiatric disorder of an unknown etiology with a crude mortality rate of about 5 % per decade, making it one of the deadliest of all psychiatric illnesses. AN is broadly classified into two main subtypes, restricting and binge/purging disorder. Despite extensive research efforts during several decades, the underlying pathophysiology of AN remains poorly understood. In this study, we aimed to identify novel protein biomarkers for AN by performing a proteomics analysis of fasting plasma samples from 78 females with AN (57 restrictive and 21 binge/purge type) and 70 healthy controls. METHODS Using state-of-the-art mass spectrometry-based proteomics technology in conjunction with an advanced bioinformatics pipeline, we quantify >500 plasma proteins. RESULTS Differential expression analysis and correlation of proteomics data with clinical variables led to identification of a panel of novel protein biomarkers with potential pathophysiological significance for AN. Our findings demonstrate evidence of a humoral immune system response, altered lipid metabolism and potential alteration of plasma cells in AN patients. Additionally, we stratified AN patients based on the quantified proteins and suggest a potential autoimmune nature in the restrictive subtype of AN. CONCLUSIONS/INTERPRETATION In summary, on top of biomarkers of AN subtypes, this study provides a comprehensive map of plasma proteins that constitute a resource for further studies of the pathophysiology of AN.
Collapse
Affiliation(s)
- Diana Samodova
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - August Hoel
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Tue Haldor Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Loa Clausen
- Department of Child and Adolescent Psychiatry, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Faculty of Health, Aarhus University, Aarhus, Denmark
| | - Gry Kjaersdam Telléus
- Unit for Psychiatric Research, Aalborg University Hospital, Aalborg, Denmark; Department of Communication and Psychology, Aalborg University, Aalborg, Denmark
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Center for Clinical Metabolic Research, Gentofte University Hospital, Copenhagen, Denmark
| | - Rene Klinkby Støving
- Center for Eating Disorders and Research Unit for Medical Endocrinology, Odense University Hospital, Mental Health Services in the Region of Southern Denmark, Denmark; Clinical Institute, University of Southern Denmark, Department of Endocrinology and Center for Eating Disorders, Odense University Hospital, J. B. Winsløws Vej 4, 5000 Odense, Denmark.
| | - Atul Shahaji Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.
| |
Collapse
|
35
|
Zhou Y, Zheng H, Tan Z, Kang E, Xue P, Li X, Guan F. Optimizing and integrating depletion and precipitation methods for plasma proteomics through data-independent acquisition-mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2024; 1235:124046. [PMID: 38382157 DOI: 10.1016/j.jchromb.2024.124046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/23/2024]
Abstract
The application of plasma proteomics is a reliable approach for the discovery of biomarkers. However, the utilization of mass spectrometry-based proteomics in plasma encounters limitations due to the presence of high-abundant proteins (HAPs) and the vast dynamic range. To address this issue, we conducted an optimization and integration of depletion and precipitation strategies eliminating interference from HAPs. The optimized procedure involved utilizing 40 µL of beads for the removal of 1 µL of plasma, and maintaining a ratio of 1:1:1 between plasma, urea, and trichloroacetic acid for the precipitation of 50 µL of plasma. To facilitate high-throughput processing, experimental procedures were carried out utilizing 96-well plates. The depletion method identified a total of 1510 proteins, whereas the precipitated method yielded a total of 802 proteins. The integration of these methods yielded a total of 1794 proteins, including a wide concentration range spanning over 8 orders of magnitude. Furthermore, these approaches exhibited a commendable level of reproducibility, as indicated by median coefficients of variation of 14.7 % and 21.1 % for protein intensities, respectively. The integrative method was found to be effective in precisely quantifying yeast proteins that were intentionally spiked in plasma at predetermined rations of 5, 2, 0.5, and 0.2 with a high genuine positive recovery with a range of 71 % to 91 % of all yeast proteins. The use of a complementary and finely tuned approach involving depletion and precipitation demonstrates tremendous potential in the field of discovering protein biomarkers from large-scale cohort studies.
Collapse
Affiliation(s)
- Yue Zhou
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Helong Zheng
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Zengqi Tan
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Enci Kang
- Xi'an Gaoxin No.1 High School International Division, Xi'an, Shaanxi, China
| | - Peng Xue
- Guangzhou National Laboratory, Guangzhou, Guangdong, China
| | - Xiang Li
- College of Life Science, Northwest University, Xi'an, Shaanxi, China
| | - Feng Guan
- College of Life Science, Northwest University, Xi'an, Shaanxi, China.
| |
Collapse
|
36
|
Vitko D, Chou WF, Nouri Golmaei S, Lee JY, Belthangady C, Blume J, Chan JK, Flores-Campuzano G, Hu Y, Liu M, Marispini MA, Mora MG, Ramaswamy S, Ranjan P, Williams PB, Zawada RJX, Ma P, Wilcox BE. timsTOF HT Improves Protein Identification and Quantitative Reproducibility for Deep Unbiased Plasma Protein Biomarker Discovery. J Proteome Res 2024; 23:929-938. [PMID: 38225219 PMCID: PMC10913052 DOI: 10.1021/acs.jproteome.3c00646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024]
Abstract
Mass spectrometry (MS) is a valuable tool for plasma proteome profiling and disease biomarker discovery. However, wide-ranging plasma protein concentrations, along with technical and biological variabilities, present significant challenges for deep and reproducible protein quantitation. Here, we evaluated the qualitative and quantitative performance of timsTOF HT and timsTOF Pro 2 mass spectrometers for analysis of neat plasma samples (unfractionated) and plasma samples processed using the Proteograph Product Suite (Proteograph) that enables robust deep proteomics sampling prior to mass spectrometry. Samples were evaluated across a wide range of peptide loading masses and liquid chromatography (LC) gradients. We observed up to a 76% increase in total plasma peptide precursors identified and a >2-fold boost in quantifiable plasma peptide precursors (CV < 20%) with timsTOF HT compared to Pro 2. Additionally, approximately 4.5 fold more plasma peptide precursors were detected by both timsTOF HT and timsTOF Pro 2 in the Proteograph analyzed plasma vs neat plasma. In an exploratory analysis of 20 late-stage lung cancer and 20 control plasma samples with the Proteograph, which were expected to exhibit distinct proteomes, an approximate 50% increase in total and statistically significant plasma peptide precursors (q < 0.05) was observed with timsTOF HT compared to Pro 2. Our data demonstrate the superior performance of timsTOF HT for identifying and quantifying differences between biologically diverse samples, allowing for improved disease biomarker discovery in large cohort studies. Moreover, researchers can leverage data sets from this study to optimize their liquid chromatography-mass spectrometry (LC-MS) workflows for plasma protein profiling and biomarker discovery. (ProteomeXchange identifier: PXD047854 and PXD047839).
Collapse
Affiliation(s)
- Dijana Vitko
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Wan-Fang Chou
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Sara Nouri Golmaei
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Joon-Yong Lee
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Chinmay Belthangady
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - John Blume
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Jessica K. Chan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | | | - Yuntao Hu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Manway Liu
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Mark A. Marispini
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Megan G. Mora
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Saividya Ramaswamy
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Purva Ranjan
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Preston B. Williams
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Robert J. X. Zawada
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Philip Ma
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| | - Bruce E. Wilcox
- PrognomiQ Inc., 1900 Alameda de las Pulgas, San Mateo, California 94403, United States
| |
Collapse
|
37
|
Lee GY, Li AA, Moon I, Katritsis D, Pantos Y, Stingo F, Fabbrico D, Molinaro R, Taraballi F, Tao W, Corbo C. Protein Corona Sensor Array Nanosystem for Detection of Coronary Artery Disease. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2306168. [PMID: 37880910 DOI: 10.1002/smll.202306168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 09/26/2023] [Indexed: 10/27/2023]
Abstract
Coronary artery disease (CAD) is the most common type of heart disease and represents the leading cause of death in both men and women worldwide. Early detection of CAD is crucial for decreasing mortality, prolonging survival, and improving patient quality of life. Herein, a non-invasive is described, nanoparticle-based diagnostic technology which takes advantages of proteomic changes in the nano-bio interface for CAD detection. Nanoparticles (NPs) exposed to biological fluids adsorb on their surface a layer of proteins, the "protein corona" (PC). Pathological changes that alter the plasma proteome can directly result in changes in the PC. By forming disease-specific PCs on six NPs with varying physicochemical properties, a PC-based sensor array is developed for detection of CAD using specific PC pattern recognition. While the PC of a single NP may not provide the required specificity, it is reasoned that multivariate PCs across NPs with different surface chemistries, can provide the desirable information to selectively discriminate the condition under investigation. The results suggest that such an approach can detect CAD with an accuracy of 92.84%, a sensitivity of 87.5%, and a specificity of 82.5%. These new findings demonstrate the potential of PC-based sensor array detection systems for clinical use.
Collapse
Affiliation(s)
- Gha Young Lee
- Center for Nanomedicine, Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Andrew A Li
- Tepper School of Business, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Intae Moon
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, 4307, USA
| | - Demos Katritsis
- Comprehensive Cardiology Care at Hygeia Hospital, Athens, 15123, Greece
- Johns Hopkins Medicine, Baltimore, MD, 21287, USA
| | - Yoannis Pantos
- Comprehensive Cardiology Care at Hygeia Hospital, Athens, 15123, Greece
| | - Francesco Stingo
- Department of Statistics, Computer Sciences and Applications, University of Florence, Florence, 50121, Italy
| | - Davide Fabbrico
- Department of Statistics, Computer Sciences and Applications, University of Florence, Florence, 50121, Italy
| | - Roberto Molinaro
- Department of Cardiovascular, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Francesca Taraballi
- Center for Musculoskeletal Regeneration, Houston Methodist Academic Institute & Orthopedics and Sports Medicine, Houston Methodist Hospital, Houston, TX, 77030, USA
| | - Wei Tao
- Center for Nanomedicine, Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Claudia Corbo
- University of Milano-Bicocca, Department of Medicine and Surgery, NANOMIB Center, Monza, 20900, Italy
- IRCCS Istituto Ortopedico Galeazzi, Milan, 20161, Italy
| |
Collapse
|
38
|
Poussin C, Titz B, Xiang Y, Baglia L, Berg R, Bornand D, Choukrallah MA, Curran T, Dijon S, Dossin E, Dulize R, Etter D, Fatarova M, Medlin LF, Haiduc A, Kishazi E, Kolli AR, Kondylis A, Kottelat E, Laszlo C, Lavrynenko O, Eb-Levadoux Y, Nury C, Peric D, Rizza M, Schneider T, Guedj E, Calvino F, Sierro N, Guy P, Ivanov NV, Picavet P, Spinelli S, Hoeng J, Peitsch MC. Blood and urine multi-omics analysis of the impact of e-vaping, smoking, and cessation: from exposome to molecular responses. Sci Rep 2024; 14:4286. [PMID: 38383592 PMCID: PMC10881465 DOI: 10.1038/s41598-024-54474-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 02/12/2024] [Indexed: 02/23/2024] Open
Abstract
Cigarette smoking is a major preventable cause of morbidity and mortality. While quitting smoking is the best option, switching from cigarettes to non-combustible alternatives (NCAs) such as e-vapor products is a viable harm reduction approach for smokers who would otherwise continue to smoke. A key challenge for the clinical assessment of NCAs is that self-reported product use can be unreliable, compromising the proper evaluation of their risk reduction potential. In this cross-sectional study of 205 healthy volunteers, we combined comprehensive exposure characterization with in-depth multi-omics profiling to compare effects across four study groups: cigarette smokers (CS), e-vapor users (EV), former smokers (FS), and never smokers (NS). Multi-omics analyses included metabolomics, transcriptomics, DNA methylomics, proteomics, and lipidomics. Comparison of the molecular effects between CS and NS recapitulated several previous observations, such as increased inflammatory markers in CS. Generally, FS and EV demonstrated intermediate molecular effects between the NS and CS groups. Stratification of the FS and EV by combustion exposure markers suggested that this position on the spectrum between CS and NS was partially driven by non-compliance/dual use. Overall, this study highlights the importance of in-depth exposure characterization before biological effect characterization for any NCA assessment study.
Collapse
Affiliation(s)
- Carine Poussin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Bjoern Titz
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Yang Xiang
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland.
| | - Laurel Baglia
- University of Rochester Medical Center, Rochester, NY, USA
| | - Rachel Berg
- University of Rochester Medical Center, Rochester, NY, USA
| | - David Bornand
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | | | - Timothy Curran
- University of Rochester Medical Center, Rochester, NY, USA
| | - Sophie Dijon
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Eric Dossin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Remi Dulize
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Doris Etter
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Maria Fatarova
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Loyse Felber Medlin
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Adrian Haiduc
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Edina Kishazi
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Aditya R Kolli
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Athanasios Kondylis
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Emmanuel Kottelat
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Csaba Laszlo
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Oksana Lavrynenko
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Yvan Eb-Levadoux
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Catherine Nury
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Dariusz Peric
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Melissa Rizza
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Thomas Schneider
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Emmanuel Guedj
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Florian Calvino
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Nicolas Sierro
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Philippe Guy
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland.
| | - Nikolai V Ivanov
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland.
| | - Patrick Picavet
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | | | - Julia Hoeng
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| | - Manuel C Peitsch
- PMI R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland
| |
Collapse
|
39
|
Jiang Y, Meyer JG. 1.4 min Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579213. [PMID: 38370692 PMCID: PMC10871276 DOI: 10.1101/2024.02.06.579213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Non-invasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method, which integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein coronas enrichment for high throughput and efficient plasma proteomic profiling. We realized over 280 protein identifications in 1.4 minutes collection time, which enables a potential throughput of approximately 1,000 samples daily. The identified proteins are involved in valuable pathways and 44 of the proteins are FDA approved biomarkers. The robustness and quantitative accuracy of this method were evaluated across multiple NPs and concentrations with a mean coefficient of variation at 17%. Moreover, different protein corona profiles were observed among various nanoparticles based on their distinct surface modifications, and all NP protein profiles exhibited deeper coverage and better quantification than neat plasma. Our streamlined workflow merges coverage and throughput with precise quantification, leveraging both DISPA and NP protein corona enrichments. This underscores the significant potential of DISPA when paired with NP sample preparation techniques for plasma proteome studies.
Collapse
Affiliation(s)
- Yuming Jiang
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Jesse G. Meyer
- Department of Computational Biomedicine, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
- Smidt Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, USA
| |
Collapse
|
40
|
Patiño T, Llacer-Wintle J, Pujals S, Albertazzi L, Sánchez S. Unveiling protein corona formation around self-propelled enzyme nanomotors by nanoscopy. NANOSCALE 2024; 16:2904-2912. [PMID: 38054755 DOI: 10.1039/d3nr03749e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The interaction of nanoparticles with biological media is a topic of general interest for drug delivery systems and among those for active nanoparticles, also called nanomotors. Herein, we report the use of super resolution microscopy, in particular, stochastic optical reconstruction microscopy (STORM), to characterize the formation of a protein corona around active enzyme-powered nanomotors. First, we characterized the distribution and number of enzymes on nano-sized particles and characterized their motion capabilities. Then, we incubated the nanomotors with fluorescently labelled serum proteins. Interestingly, we observed a significant decrease of protein corona formation (20%) and different composition, which was studied by proteomic analysis. Moreover, motion was not hindered, as nanomotors displayed enhanced diffusion regardless of the protein corona. Elucidating how active particles interact with biological media and maintain their self-propulsion after protein corona formation will pave the way for the use of these systems in complex biological fluids in biomedicine.
Collapse
Affiliation(s)
- Tania Patiño
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
- Biomedical Engineering Department, Institute for Complex Molecular Systems. Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Joaquin Llacer-Wintle
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
| | - Sílvia Pujals
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
- Biomedical Engineering Department, Institute for Complex Molecular Systems. Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands
| | - Samuel Sánchez
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, Barcelona, 08010, Spain
| |
Collapse
|
41
|
Fu L, Guldiken N, Remih K, Karl AS, Preisinger C, Strnad P. Serum/Plasma Proteome in Non-Malignant Liver Disease. Int J Mol Sci 2024; 25:2008. [PMID: 38396688 PMCID: PMC10889128 DOI: 10.3390/ijms25042008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/31/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
The liver is the central metabolic organ and produces 85-90% of the proteins found in plasma. Accordingly, the plasma proteome is an attractive source of liver disease biomarkers that reflects the different cell types present in this organ, as well as the processes such as responses to acute and chronic injury or the formation of an extracellular matrix. In the first part, we summarize the biomarkers routinely used in clinical evaluations and their biological relevance in the different stages of non-malignant liver disease. Later, we describe the current proteomic approaches, including mass spectrometry and affinity-based techniques, that allow a more comprehensive assessment of the liver function but also require complex data processing. The many approaches of analysis and interpretation and their potential caveats are delineated. While these advances hold the promise to transform our understanding of liver diseases and support the development and validation of new liver-related drugs, an interdisciplinary collaboration is needed.
Collapse
Affiliation(s)
- Lei Fu
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Nurdan Guldiken
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Katharina Remih
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Anna Sophie Karl
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| | - Christian Preisinger
- Proteomics Facility, Interdisciplinary Centre for Clinical Research (IZKF), Medical School, RWTH Aachen University, Pauwelsstraße 30, 52074 Aachen, Germany;
| | - Pavel Strnad
- Department of Internal Medicine III, Gastroenterology, Metabolic Diseases and Intensive Care, University Hospital RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany; (L.F.); (N.G.); (K.R.); (A.S.K.)
| |
Collapse
|
42
|
Wang M, Dai X, Yang X, Jin B, Xie Y, Xu C, Liu Q, Wang L, Ying L, Lu W, Chen Q, Fu T, Su D, Liu Y, Tan W. Serum Protein Fishing for Machine Learning-Boosted Diagnostic Classification of Small Nodules of Lung. ACS NANO 2024; 18:4038-4055. [PMID: 38270088 DOI: 10.1021/acsnano.3c07217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Diagnosis of benign and malignant small nodules of the lung remains an unmet clinical problem which is leading to serious false positive diagnosis and overtreatment. Here, we developed a serum protein fishing-based spectral library (ProteoFish) for data independent acquisition analysis and a machine learning-boosted protein panel for diagnosis of early Non-Small Cell Lung Cancer (NSCLC) and classification of benign and malignant small nodules. We established an extensive NSCLC protein bank consisting of 297 clinical subjects. After testing 5 feature extraction algorithms and six machine learning models, the Lasso algorithm for a 15-key protein panel selection and Random Forest was chosen for diagnostic classification. Our random forest classifier achieved 91.38% accuracy in benign and malignant small nodule diagnosis, which is superior to the existing clinical assays. By integrating with machine learning, the 15-key protein panel may provide insights to multiplexed protein biomarker fishing from serum for facile cancer screening and tackling the current clinical challenge in prospective diagnostic classification of small nodules of the lung.
Collapse
Affiliation(s)
- Mengjie Wang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Xin Dai
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Xu Yang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Baichuan Jin
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Yueli Xie
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Chenlu Xu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Academy of Medical Engineering and Translational Medicine, Medical College, Tianjin University, Tianjin 300072, China
| | - Qiqi Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Lichao Wang
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Lisha Ying
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Weishan Lu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Qixun Chen
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Dan Su
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Yuan Liu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, Hunan, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
- Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| |
Collapse
|
43
|
Wolf J, Franco JA, Yip R, Dabaja MZ, Velez G, Liu F, Bassuk AG, Mruthyunjaya P, Dufour A, Mahajan VB. Liquid Biopsy Proteomics in Ophthalmology. J Proteome Res 2024; 23:511-522. [PMID: 38171013 PMCID: PMC10845144 DOI: 10.1021/acs.jproteome.3c00756] [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: 11/11/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024]
Abstract
Minimally invasive liquid biopsies from the eye capture locally enriched fluids that contain thousands of proteins from highly specialized ocular cell types, presenting a promising alternative to solid tissue biopsies. The advantages of liquid biopsies include sampling the eye without causing irreversible functional damage, potentially better reflecting tissue heterogeneity, collecting samples in an outpatient setting, monitoring therapeutic response with sequential sampling, and even allowing examination of disease mechanisms at the cell level in living humans, an approach that we refer to as TEMPO (Tracing Expression of Multiple Protein Origins). Liquid biopsy proteomics has the potential to transform molecular diagnostics and prognostics and to assess disease mechanisms and personalized therapeutic strategies in individual patients. This review addresses opportunities, challenges, and future directions of high-resolution liquid biopsy proteomics in ophthalmology, with particular emphasis on the large-scale collection of high-quality samples, cutting edge proteomics technology, and artificial intelligence-supported data analysis.
Collapse
Affiliation(s)
- Julian Wolf
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Joel A. Franco
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Rui Yip
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Mohamed Ziad Dabaja
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Gabriel Velez
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Fei Liu
- Department
of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Alexander G. Bassuk
- Department
of Pediatrics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Prithvi Mruthyunjaya
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
| | - Antoine Dufour
- Departments
of Physiology and Pharmacology & Biochemistry and Molecular Biology,
Cumming School of Medicine, University of
Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Vinit B. Mahajan
- Molecular
Surgery Laboratory, Stanford University, Palo Alto, California 94305, United States
- Department
of Ophthalmology, Byers Eye Institute, Stanford
University, Palo Alto, California 94303, United States
- Veterans
Affairs Palo Alto Health Care System, Palo Alto, California 94304, United States
| |
Collapse
|
44
|
Suhre K, Venkataraman GR, Guturu H, Halama A, Stephan N, Thareja G, Sarwath H, Motamedchaboki K, Donovan MKR, Siddiqui A, Batzoglou S, Schmidt F. Nanoparticle enrichment mass-spectrometry proteomics identifies protein-altering variants for precise pQTL mapping. Nat Commun 2024; 15:989. [PMID: 38307861 PMCID: PMC10837160 DOI: 10.1038/s41467-024-45233-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technologies face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, mass spectrometry-based proteomics approach. We identify 184 protein-altering variants in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.
Collapse
Affiliation(s)
- Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar.
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | | | | | - Anna Halama
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Nisha Stephan
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | - Gaurav Thareja
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | - Hina Sarwath
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| | | | | | - Asim Siddiqui
- Seer, Inc., Redwood City, Redwood City, CA, 94065, USA
| | | | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine-Qatar, Education City, 24144, Doha, Qatar
| |
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
Wenk D, Zuo C, Kislinger T, Sepiashvili L. Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers. Clin Proteomics 2024; 21:6. [PMID: 38287260 PMCID: PMC10826105 DOI: 10.1186/s12014-024-09452-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological matrices with numerous advantages that make it attractive for clinical applications in oncology. The use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodologies has allowed laboratories to overcome challenges associated with immunoassays that are more widely used for tumor marker measurements. Yet, clinical implementation of targeted proteomics methodologies has so far been limited to a few cancer markers. This is due to numerous challenges associated with paucity of robust validation studies of new biomarkers and the labor-intensive and operationally complex nature of LC-MS/MS workflows. The purpose of this review is to provide an overview of targeted proteomics applications in cancer, workflows used in targeted proteomics, and requirements for clinical validation and implementation of targeted proteomics assays. We will also discuss advantages and challenges of targeted MS-based proteomics assays for clinical cancer biomarker analysis and highlight some recent developments that will positively contribute to the implementation of this technique into clinical laboratories.
Collapse
Affiliation(s)
- Deborah Wenk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charlotte Zuo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Research Tower, Room 9-807, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Lusia Sepiashvili
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Ave, Rm 3606, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Sickkids Research Institute, Toronto, ON, Canada.
| |
Collapse
|
47
|
Nakajima D, Konno R, Miyashita Y, Ishikawa M, Ohara O, Kawashima Y. Proteome Analysis of Serum Purified Using Solanum tuberosum and Lycopersicon esculentum Lectins. Int J Mol Sci 2024; 25:1315. [PMID: 38279312 PMCID: PMC10816257 DOI: 10.3390/ijms25021315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/28/2024] Open
Abstract
Serum and plasma exhibit a broad dynamic range of protein concentrations, posing challenges for proteome analysis. Various technologies have been developed to reduce this complexity, including high-abundance depletion methods utilizing antibody columns, extracellular vesicle enrichment techniques, and trace protein enrichment using nanobead cocktails. Here, we employed lectins to address this, thereby extending the scope of biomarker discovery in serum or plasma using a novel approach. We enriched serum proteins using 37 different lectins and subjected them to LC-MS/MS analysis with data-independent acquisition. Solanum tuberosum lectin (STL) and Lycopersicon esculentum lectin (LEL) enabled the detection of more serum proteins than the other lectins. STL and LEL bind to N-acetylglucosamine oligomers, emphasizing the significance of capturing these oligomer-binding proteins when analyzing serum trace proteins. Combining STL and LEL proved more effective than using them separately, allowing us to identify over 3000 proteins from serum through single-shot proteome analysis. We applied the STL/LEL trace-protein enrichment method to the sera of systemic lupus erythematosus model mice. This revealed differences in >1300 proteins between the systemic lupus erythematosus model and control mouse sera, underscoring the utility of this method for biomarker discovery.
Collapse
Affiliation(s)
- Daisuke Nakajima
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Ryo Konno
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Yasuomi Miyashita
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
- Department of Developmental Biology, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Chiba, Japan
| | - Masaki Ishikawa
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| | - Yusuke Kawashima
- Department of Applied Genomics, Kazusa DNA Research Institute, 2-5-23 Kazusa Kamatari, Kisarazu 292-0818, Chiba, Japan; (D.N.); (R.K.); (Y.M.); (M.I.); (O.O.)
| |
Collapse
|
48
|
Tian W, Shi D, Zhang Y, Wang H, Tang H, Han Z, Wong CCL, Cui L, Zheng J, Chen Y. Deep proteomic analysis of obstetric antiphospholipid syndrome by DIA-MS of extracellular vesicle enriched fractions. Commun Biol 2024; 7:99. [PMID: 38225453 PMCID: PMC10789860 DOI: 10.1038/s42003-024-05789-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/03/2024] [Indexed: 01/17/2024] Open
Abstract
Proteins in the plasma/serum mirror an individual's physiology. Circulating extracellular vesicles (EVs) proteins constitute a large portion of the plasma/serum proteome. Thus, deep and unbiased proteomic analysis of circulating plasma/serum extracellular vesicles holds promise for discovering disease biomarkers as well as revealing disease mechanisms. We established a workflow for simple, deep, and reproducible proteome analysis of both serum large and small EVs enriched fractions by ultracentrifugation plus 4D-data-independent acquisition mass spectrometry (4D-DIA-MS). In our cohort study of obstetric antiphospholipid syndrome (OAPS), 4270 and 3328 proteins were identified from large and small EVs enriched fractions respectively. Both of them revealed known or new pathways related to OAPS. Increased levels of von Willebrand factor (VWF) and insulin receptor (INSR) were identified as candidate biomarkers, which shed light on hypercoagulability and abnormal insulin signaling in disease progression. Our workflow will significantly promote our understanding of plasma/serum-based disease mechanisms and generate new biomarkers.
Collapse
Affiliation(s)
- Wenmin Tian
- Department of Biochemistry and Biophysics, Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Dongxue Shi
- Department of Biochemistry and Biophysics, Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yinmei Zhang
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, P R China
| | - Hongli Wang
- Department of Biochemistry and Biophysics, Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Haohao Tang
- Department of Biochemistry and Biophysics, Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Zhongyu Han
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, P R China
| | - Catherine C L Wong
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, 100730, Beijing, China
- Tsinghua University-Peking University Joint Center for Life Sciences, Peking University, 100084, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, P R China.
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, P R China.
| | - Yang Chen
- Department of Biochemistry and Biophysics, Center for Precision Medicine Multi-Omics Research, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| |
Collapse
|
49
|
Lacar B, Ferdosi S, Alavi A, Stukalov A, Venkataraman GR, de Geus M, Dodge H, Wu CY, Kivisakk P, Das S, Guturu H, Hyman B, Batzoglou S, Arnold SE, Siddiqui A. Identification of Novel Biomarkers for Alzheimer's Disease and Related Dementias Using Unbiased Plasma Proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574446. [PMID: 38260620 PMCID: PMC10802486 DOI: 10.1101/2024.01.05.574446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Alzheimer's disease (AD) and related dementias (ADRD) is a complex disease with multiple pathophysiological drivers that determine clinical symptomology and disease progression. These diseases develop insidiously over time, through many pathways and disease mechanisms and continue to have a huge societal impact for affected individuals and their families. While emerging blood-based biomarkers, such as plasma p-tau181 and p-tau217, accurately detect Alzheimer neuropthology and are associated with faster cognitive decline, the full extension of plasma proteomic changes in ADRD remains unknown. Earlier detection and better classification of the different subtypes may provide opportunities for earlier, more targeted interventions, and perhaps a higher likelihood of successful therapeutic development. In this study, we aim to leverage unbiased mass spectrometry proteomics to identify novel, blood-based biomarkers associated with cognitive decline. 1,786 plasma samples from 1,005 patients were collected over 12 years from partcipants in the Massachusetts Alzheimer's Disease Research Center Longitudinal Cohort Study. Patient metadata includes demographics, final diagnoses, and clinical dementia rating (CDR) scores taken concurrently. The Proteograph™ Product Suite (Seer, Inc.) and liquid-chromatography mass-spectrometry (LC-MS) analysis were used to process the plasma samples in this cohort and generate unbiased proteomics data. Data-independent acquisition (DIA) mass spectrometry results yielded 36,259 peptides and 4,007 protein groups. Linear mixed effects models revealed 138 differentially abundant proteins between AD and healthy controls. Machine learning classification models for AD diagnosis identified potential candidate biomarkers including MBP, BGLAP, and APoD. Cox regression models were created to determine the association of proteins with disease progression and suggest CLNS1A, CRISPLD2, and GOLPH3 as targets of further investigation as potential biomarkers. The Proteograph workflow provided deep, unbiased coverage of the plasma proteome at a speed that enabled a cohort study of almost 1,800 samples, which is the largest, deep, unbiased proteomics study of ADRD conducted to date.
Collapse
Affiliation(s)
| | | | | | | | | | - Matthijs de Geus
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Hiroko Dodge
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Chao-Yi Wu
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Pia Kivisakk
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | - Sudeshna Das
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | | | - Brad Hyman
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | | | - Steven E. Arnold
- Massachusetts General Hospital (MGH), 55 Fruit Street, Boston, Massachusetts 02114
| | | |
Collapse
|
50
|
Gharibi H, Ashkarran AA, Jafari M, Voke E, Landry MP, Saei AA, Mahmoudi M. A uniform data processing pipeline enables harmonized nanoparticle protein corona analysis across proteomics core facilities. Nat Commun 2024; 15:342. [PMID: 38184668 PMCID: PMC10771434 DOI: 10.1038/s41467-023-44678-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/20/2023] [Indexed: 01/08/2024] Open
Abstract
Protein corona, a layer of biomolecules primarily comprising proteins, forms dynamically on nanoparticles in biological fluids and is crucial for predicting nanomedicine safety and efficacy. The protein composition of the corona layer is typically analyzed using liquid chromatography-mass spectrometry (LC-MS/MS). Our recent study, involving identical samples analyzed by 17 proteomics facilities, highlighted significant data variability, with only 1.8% of proteins consistently identified across these centers. Here, we implement an aggregated database search unifying parameters such as variable modifications, enzyme specificity, number of allowed missed cleavages and a stringent 1% false discovery rate at the protein and peptide levels. Such uniform search dramatically harmonizes the proteomics data, increasing the reproducibility and the percentage of consistency-identified unique proteins across distinct cores. Specifically, out of the 717 quantified proteins, 253 (35.3%) are shared among the top 5 facilities (and 16.2% among top 11 facilities). Furthermore, we note that reduction and alkylation are important steps in protein corona sample processing and as expected, omitting these steps reduces the number of total quantified peptides by around 20%. These findings underscore the need for standardized procedures in protein corona analysis, which is vital for advancing clinical applications of nanoscale biotechnologies.
Collapse
Affiliation(s)
- Hassan Gharibi
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ali Akbar Ashkarran
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI, USA
| | - Maryam Jafari
- Division of ENT Diseases, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Elizabeth Voke
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Amir Ata Saei
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17165, Sweden.
- Biozentrum, University of Basel, 4056, Basel, Switzerland.
| | - Morteza Mahmoudi
- Department of Radiology and Precision Health Program, Michigan State University, East Lansing, MI, USA.
| |
Collapse
|