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Li W, Guo L, Ding XL, Ding Y, Ji LN, Xia XH, Wang K. High-Throughput Single-Molecule Surface-Enhanced Raman Spectroscopic Profiling of Single-Amino Acid Substitutions in Peptides by a Gold Plasmonic Nanopore. ACS NANO 2024; 18:19200-19207. [PMID: 38996344 DOI: 10.1021/acsnano.4c04775] [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: 07/14/2024]
Abstract
Simultaneous detection and structural characterization of protein variants on a single platform are highly desirable but technically challenging. Herein, we present a single-molecule spectral system based on a gold plasmonic nanopore for analyzing two peptides and their single-point mutated variants. The gold plasmonic nanopore enabled the high-throughput acquisition of surface-enhanced Raman scattering (SERS) spectra at the single-molecule level by electrically driving analytes into hot spots. Furthermore, a statistical method based on Boolean operations was developed to extract prominent features from fluctuated single-molecule SERS spectra. The effects of the single-amino acid substitutions on both the intramolecular interactions and the peptide conformations were directly characterized by the nanopore system, and the results agreed with the predictions by AlphaFold2. This study highlights the mutual benefits of spectroscopy and nanopore technology, whereby the gold plasmonic nanopore offers a powerful tool for the structural analysis of single-molecule proteins.
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Affiliation(s)
- Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Linru Guo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xin-Lei Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yanru Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
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Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
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Patel KJ, Yang D, Best JR, Chambers C, Lee PE, Henri‐Bhargava A, Funnell CR, Foti DJ, Pettersen JA, Feldman HH, Nygaard HB, Hsiung GR, DeMarco ML. Clinical value of Alzheimer's disease biomarker testing. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2024; 10:e12464. [PMID: 38596484 PMCID: PMC10999950 DOI: 10.1002/trc2.12464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 04/11/2024]
Abstract
INTRODUCTION In the Investigating the Impact of Alzheimer's Disease Diagnostics in British Columbia (IMPACT-AD BC) study, we aimed to understand how Alzheimer's disease (AD) cerebrospinal fluid (CSF) biomarker testing-used in medical care-impacted medical decision-making (medical utility), personal decision-making (personal utility), and health system economics. METHODS The study was designed as an observational, longitudinal cohort study. A total of 149 patients were enrolled between February 2019 and July 2021. Patients referred to memory clinics were approached to participate if their dementia specialist ordered AD CSF biomarker testing as part of their routine medical care, and the clinical scenario met the appropriate use criteria for lumbar puncture and AD CSF biomarker testing. For the medical utility pillar, detailed clinical management plans were collected via physician questionnaires pre- and post-biomarker disclosure. RESULTS Patients with completed management questionnaires (n = 142) had a median age of 64 (interquartile range: 59-69) years, 48% were female, and 60% had CSF biomarker profiles on the AD continuum. Clinical management changed in 89.4% of cases. AD biomarker testing was associated with decreased need for other diagnostic procedures, including brain imaging (-52.0%) and detailed neuropsychological assessments (-63.2%), increased referrals and counseling (57.0%), and guided AD-related drug prescriptions (+88.4% and -50.0% in biomarker-positive and -negative cases, respectively). DISCUSSION AD biomarker testing was associated with significant and positive changes in clinical management, including decreased health care resource use, therapy optimization, and increased patient and family member counseling. While certain changes in management were linked to the AD biomarker profile (e.g., referral to clinical trials), the majority of changes were independent of baseline clinical presentation and level of cognitive impairment, demonstrating a broad value for AD biomarker testing in individuals meeting the appropriate use criteria for testing.
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Affiliation(s)
- Khushbu J. Patel
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - David Yang
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - John R. Best
- Gerontology Research CentreSimon Fraser UniversityVancouverCanada
| | - Colleen Chambers
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
| | - Philip E. Lee
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Djavad Mowafaghian Centre for Brain HealthDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- UBC Hospital Clinic for Alzheimer Disease and Related DisordersUniversity of British ColumbiaVancouverCanada
| | - Alexandre Henri‐Bhargava
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Division of Medical SciencesUniversity of VictoriaVictoriaCanada
| | - Clark R. Funnell
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Djavad Mowafaghian Centre for Brain HealthDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- UBC Hospital Clinic for Alzheimer Disease and Related DisordersUniversity of British ColumbiaVancouverCanada
| | - Dean J. Foti
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Djavad Mowafaghian Centre for Brain HealthDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- UBC Hospital Clinic for Alzheimer Disease and Related DisordersUniversity of British ColumbiaVancouverCanada
| | - Jacqueline A. Pettersen
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Division of Medical SciencesUniversity of Northern British ColumbiaPrince GeorgeCanada
| | - Howard H. Feldman
- Department of NeurosciencesUniversity of California San DiegoSan DiegoCaliforniaUSA
- Alzheimer Disease Cooperative StudyUniversity of California San DiegoSan DiegoCaliforniaUSA
- Alzheimer's and Related Neurodegenerative ResearchUniversity of California San DiegoSan DiegoCaliforniaUSA
| | - Haakon B. Nygaard
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Djavad Mowafaghian Centre for Brain HealthDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- UBC Hospital Clinic for Alzheimer Disease and Related DisordersUniversity of British ColumbiaVancouverCanada
| | - Ging‐Yuek R. Hsiung
- Division of NeurologyDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- Djavad Mowafaghian Centre for Brain HealthDepartment of MedicineUniversity of British ColumbiaVancouverCanada
- UBC Hospital Clinic for Alzheimer Disease and Related DisordersUniversity of British ColumbiaVancouverCanada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory MedicineUniversity of British ColumbiaVancouverCanada
- Department of Pathology and Laboratory MedicineSt. Paul's HospitalProvidence Health CareVancouverCanada
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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.
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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.
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Forgrave LM, van der Gugten JG, Nguyen Q, DeMarco ML. Establishing pre-analytical requirements and maximizing peptide recovery in the analytical phase for mass spectrometric quantification of amyloid-β peptides 1-42 and 1-40 in CSF. Clin Chem Lab Med 2021; 60:198-206. [PMID: 34881836 DOI: 10.1515/cclm-2021-0549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 11/16/2021] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Amyloid-β (Aβ) peptides in cerebrospinal fluid (CSF), including Aβ42 (residues 1-42) and Aβ40 (residues 1-40), are utilized as biomarkers in the diagnostic workup of Alzheimer's disease. Careful consideration has been given to the pre-analytical and analytical factors associated with measurement of these peptides via immunoassays; however, far less information is available for mass spectrometric methods. As such, we performed a comprehensive evaluation of pre-analytical and analytical factors specific to Aβ quantification using mass spectrometry. METHODS Using our quantitative mass spectrometry assay for Aβ42 and Aβ40 in CSF, we investigated the potential for interference from hemolysate, bilirubin, lipids, and anti-Aβ-antibodies. We also optimized the composition of the calibrator surrogate matrix and Aβ recovery during and after solid phase extraction (SPE). RESULTS There was no interreference observed with total protein up to 12 g/L, hemolysate up to 10% (v/v), bilirubin up to 0.5% (v/v), intralipid up to 1% (v/v), or anti-Aβ-antibodies at expected therapeutic concentrations. For hemolysate, bilirubin and lipids, visual CSF contamination thresholds were established. In the analytical phase, Aβ recovery was increased by ∼50% via SPE solvent modifications and by over 150% via modification of the SPE collection plate, which also extended analyte stability in the autosampler. CONCLUSIONS Attention to mass spectrometric-specific pre-analytical and analytical considerations improved analytical sensitivity and reproducibility, as well as, established CSF specimen acceptance and rejection criteria for use by the clinical laboratory.
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Affiliation(s)
- Lauren M Forgrave
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - J Grace van der Gugten
- Department of Pathology and Laboratory Medicine, St. Paul's Hospital, Providence Health Care, Vancouver, Canada
| | - Quyen Nguyen
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, St. Paul's Hospital, Providence Health Care, Vancouver, Canada
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Jin Y, Vadukul DM, Gialama D, Ge Y, Thrush R, White JT, Aprile FA. The Diagnostic Potential of Amyloidogenic Proteins. Int J Mol Sci 2021; 22:4128. [PMID: 33923609 PMCID: PMC8074075 DOI: 10.3390/ijms22084128] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/12/2021] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Neurodegenerative disorders are a highly prevalent class of diseases, whose pathological mechanisms start before the appearance of any clear symptoms. This fact has prompted scientists to search for biomarkers that could aid early treatment. These currently incurable pathologies share the presence of aberrant aggregates called amyloids in the nervous system, which are composed of specific proteins. In this review, we discuss how these proteins, their conformations and modifications could be exploited as biomarkers for diagnostic purposes. We focus on proteins that are associated with the most prevalent neurodegenerative disorders, including Alzheimer's and Parkinson's diseases, amyotrophic lateral sclerosis, and frontotemporal dementia. We also describe current challenges in detection, the most recent techniques with diagnostic potentials and possible future developments in diagnosis.
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Affiliation(s)
| | | | | | | | | | | | - Francesco Antonio Aprile
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, UK; (Y.J.); (D.M.V.); (D.G.); (Y.G.); (R.T.); (J.T.W.)
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