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Mirian C, Thastrup M, Mathiasen R, Schmiegelow K, Olsen JV, Østergaard O. Mass spectrometry-based proteomics of cerebrospinal fluid in pediatric central nervous system malignancies: a systematic review with meta-analysis of individual patient data. Fluids Barriers CNS 2024; 21:14. [PMID: 38350915 PMCID: PMC10863112 DOI: 10.1186/s12987-024-00515-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: 09/21/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The cerebrospinal fluid (CSF) proteome could offer important insights into central nervous system (CNS) malignancies. To advance proteomic research in pediatric CNS cancer, the current study aims to (1) evaluate past mass spectrometry-based workflows and (2) synthesize previous CSF proteomic data, focusing on both qualitative summaries and quantitative re-analysis. MAIN: In our analysis of 11 studies investigating the CSF proteome in pediatric patients with acute lymphoblastic leukemia (ALL) or primary brain tumors, we observed significant methodological variability. This variability negatively affects comparative analysis of the included studies, as per GRADE criteria for quality of evidence. The qualitative summaries covered 161 patients and 134 non-tumor controls, while the application of validation cohort varied among the studies. The quantitative re-analysis comprised 15 B-ALL vs 6 "healthy" controls and 15 medulloblastoma patients vs 22 non-tumor controls. Certain CSF proteins were identified as potential indicators of specific malignancies or stages of neurotoxicity during chemotherapy, yet definitive conclusions were impeded by inconsistent data. There were no proteins with statistically significant differences when comparing cases versus controls that were corroborated across studies where quantitative reanalysis was feasible. From a gene ontology enrichment, we observed that age disparities between unmatched case and controls may mislead to protein correlations more indicative of age-related CNS developmental stages rather than neuro-oncological disease. Despite efforts to batch correct (HarmonizR) and impute missing values, merging of dataset proved unfeasible and thereby limited meaningful data integration across different studies. CONCLUSION Infrequent publications on rare pediatric cancer entities, which often involve small sample sizes, are inherently prone to result in heterogeneous studies-particularly when conducted within a rapidly evolving field like proteomics. As a result, obtaining clear evidence, such as CSF proteome biomarkers for CNS dissemination or early-stage neurotoxicity, is currently impractical. Our general recommendations comprise the need for standardized methodologies, collaborative efforts, and improved data sharing in pediatric CNS malignancy research. We specifically emphasize the possible importance of considering natural age-related variations in CSF due to different CNS development stages when matching cases and controls in future studies.
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Affiliation(s)
- Christian Mirian
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark.
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Maria Thastrup
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - René Mathiasen
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Paediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Velgaard Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Østergaard
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Kourti M, Aivaliotis M, Hatzipantelis E. Proteomics in Childhood Acute Lymphoblastic Leukemia: Challenges and Opportunities. Diagnostics (Basel) 2023; 13:2748. [PMID: 37685286 PMCID: PMC10487225 DOI: 10.3390/diagnostics13172748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/20/2023] [Accepted: 08/21/2023] [Indexed: 09/10/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children and one of the success stories in cancer therapeutics. Risk-directed therapy based on clinical, biologic and genetic features has played a significant role in this accomplishment. Despite the observed improvement in survival rates, leukemia remains one of the leading causes of cancer-related deaths. Implementation of next-generation genomic and transcriptomic sequencing tools has illustrated the genomic landscape of ALL. However, the underlying dynamic changes at protein level still remain a challenge. Proteomics is a cutting-edge technology aimed at deciphering the mechanisms, pathways, and the degree to which the proteome impacts leukemia subtypes. Advances in mass spectrometry enable high-throughput collection of global proteomic profiles, representing an opportunity to unveil new biological markers and druggable targets. The purpose of this narrative review article is to provide a comprehensive overview of studies that have utilized applications of proteomics in an attempt to gain insight into the pathogenesis and identification of biomarkers in childhood ALL.
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Affiliation(s)
- Maria Kourti
- Third Department of Pediatrics, School of Medicine, Aristotle University and Hippokration General Hospital, 54642 Thessaloniki, Greece
| | - Michalis Aivaliotis
- Laboratory of Biological Chemistry, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
| | - Emmanouel Hatzipantelis
- Children & Adolescent Hematology-Oncology Unit, Second Department of Pediatrics, School of Medicine, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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Donnelly CG, Johnson AL, Reed S, Finno CJ. Cerebrospinal fluid and serum proteomic profiles accurately distinguish neuroaxonal dystrophy from cervical vertebral compressive myelopathy in horses. J Vet Intern Med 2023; 37:689-696. [PMID: 36929645 DOI: 10.1111/jvim.16660] [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: 10/24/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND Cervical vertebral compressive myelopathy (CVCM) and equine neuroaxonal dystrophy/degenerative myeloencephalopathy (eNAD/EDM) are leading causes of spinal ataxia in horses. The conditions can be difficult to differentiate, and there is currently no diagnostic modality that offers a definitive antemortem diagnosis. OBJECTIVE Evaluate novel proteomic techniques and machine learning algorithms to predict biomarkers that can aid in the antemortem diagnosis of noninfectious spinal ataxia in horses. ANIMALS Banked serum and cerebrospinal fluid (CSF) samples from necropsy-confirmed adult eNAD/EDM (n = 47) and CVCM (n = 25) horses and neurologically normal adult horses (n = 45). METHODS . A subset of serum and CSF samples from eNAD/EDM (n = 5) and normal (n = 5) horses was used to evaluate the proximity extension assay (PEA). All samples were assayed by PEA for 368 neurologically relevant proteins. Data were analyzed using machine learning algorithms to define potential diagnostic biomarkers. RESULTS Of the 368 proteins, 84 were detected in CSF and 146 in serum. Eighteen of 84 proteins in CSF and 30/146 in serum were differentially abundant among the 3 groups, after correction for multiple testing. Modeling indicated that a 2-protein test using CSF had the highest accuracy for discriminating among all 3 groups. Cerebrospinal fluid R-spondin 1 (RSPO1) and neurofilament-light (NEFL), in parallel, predicted normal horses with an accuracy of 87.18%, CVCM with 84.62%, and eNAD/EDM with 73.5%. MAIN LIMITATIONS Cross-species platform. Uneven sample size. CONCLUSIONS AND CLINICAL IMPORTANCE Proximity extension assay technology allows for rapid screening of equine biologic matrices for potential protein biomarkers. Machine learning analysis allows for unbiased selection of highly accurate biomarkers from high-dimensional data.
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Affiliation(s)
- Callum G Donnelly
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Amy L Johnson
- Department of Clinical Studies, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania, USA
| | - Steve Reed
- Rood and Riddle Equine Hospital, Lexington, Kentucky, USA
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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Nian Q, Li J, Han Z, Liang Q, Liu M, Yang C, Rodrigues-Lima F, Jiang T, Zhao L, Zeng J, Liu C, Shi J. SPARC in hematologic malignancies and novel technique for hematological disease with its abnormal expression. Biomed Pharmacother 2022; 153:113519. [DOI: 10.1016/j.biopha.2022.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/27/2022] Open
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Moh ESX, Nishtala K, Iqbal S, Staikopoulos V, Kapur D, Hutchinson MR, Packer NH. Long-term intrathecal administration of morphine vs. baclofen: Differences in CSF glycoconjugate profiles using multiglycomics. Glycobiology 2021; 32:50-59. [PMID: 34969075 DOI: 10.1093/glycob/cwab098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/29/2021] [Accepted: 08/29/2021] [Indexed: 11/13/2022] Open
Abstract
Opioid use for treatment of persistent pain has increased dramatically over the past two decades, but it has not resulted in improved pain management outcomes. To understand the molecular mechanisms of opioids, molecular signatures that arise from opioid exposure are often sought after, using various analytical methods. In this study, we performed proteomics, and multiglycomics via sequential analysis of polysialic acids, glycosaminoglycans, N-glycans and O-glycans, using the same cerebral spinal fluid (CSF) sample from patients that had long-term (>2 years), intrathecal morphine or baclofen administered via an indwelling pump. Proteomics and N-glycomics signatures between the two treatment groups were highly conserved, while significant differences were observed in polysialic acid, heparan sulfate glycosaminoglycan and O-glycan profiles between the two treatment groups. This represents the first study to investigate the potential relationships between diverse CSF conjugated glycans and long-term intrathecal drug exposure. The unique changes, observed by a sequential analytical workflow, reflect previously undescribed molecular effects of opioid administration and pain management.
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Affiliation(s)
- Edward S X Moh
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Krishnatej Nishtala
- Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Sameera Iqbal
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
| | - Vasiliki Staikopoulos
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Dilip Kapur
- Pain Management Unit, Flinders Medical Centre, Adelaide, South Australia, 5042, Australia
| | - Mark R Hutchinson
- ARC Centre of Excellence for Nanoscale BioPhotonics, The University of Adelaide, South Australia, 5000, Australia.,Adelaide Medical School, The University of Adelaide, Adelaide, South Australia, 5000, Australia
| | - Nicolle H Packer
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, New South Wales, 2109, Australia.,Department of Molecular Science, Macquarie University, Sydney, New South Wales, 2109, Australia
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Dunphy K, O’Mahoney K, Dowling P, O’Gorman P, Bazou D. Clinical Proteomics of Biofluids in Haematological Malignancies. Int J Mol Sci 2021; 22:ijms22158021. [PMID: 34360786 PMCID: PMC8348619 DOI: 10.3390/ijms22158021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 12/25/2022] Open
Abstract
Since the emergence of high-throughput proteomic techniques and advances in clinical technologies, there has been a steady rise in the number of cancer-associated diagnostic, prognostic, and predictive biomarkers being identified and translated into clinical use. The characterisation of biofluids has become a core objective for many proteomic researchers in order to detect disease-associated protein biomarkers in a minimally invasive manner. The proteomes of biofluids, including serum, saliva, cerebrospinal fluid, and urine, are highly dynamic with protein abundance fluctuating depending on the physiological and/or pathophysiological context. Improvements in mass-spectrometric technologies have facilitated the in-depth characterisation of biofluid proteomes which are now considered hosts of a wide array of clinically relevant biomarkers. Promising efforts are being made in the field of biomarker diagnostics for haematologic malignancies. Several serum and urine-based biomarkers such as free light chains, β-microglobulin, and lactate dehydrogenase are quantified as part of the clinical assessment of haematological malignancies. However, novel, minimally invasive proteomic markers are required to aid diagnosis and prognosis and to monitor therapeutic response and minimal residual disease. This review focuses on biofluids as a promising source of proteomic biomarkers in haematologic malignancies and a key component of future diagnostic, prognostic, and disease-monitoring applications.
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Affiliation(s)
- Katie Dunphy
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Kelly O’Mahoney
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Paul Dowling
- Department of Biology, National University of Ireland, W23 F2K8 Maynooth, Ireland; (K.D.); (P.D.)
| | - Peter O’Gorman
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
| | - Despina Bazou
- Department of Haematology, Mater Misericordiae University Hospital, D07 WKW8 Dublin, Ireland; (K.O.); (P.O.)
- Correspondence:
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Shawahna R, Mosleh S, Odeh Y, Halawa R, Al-Ghoul M. Clinical characteristics and outcomes of patients with pediatric acute lymphoblastic leukemia after induction of chemotherapy: a pilot descriptive correlational study from Palestine. BMC Res Notes 2021; 14:259. [PMID: 34225806 PMCID: PMC8256561 DOI: 10.1186/s13104-021-05678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Accepted: 06/29/2021] [Indexed: 12/03/2022] Open
Abstract
Objective Pediatric acute lymphoblastic leukemia (ALL) is the most prevalent type of cancer among children. This study was conducted to describe and correlate the clinical characteristics and outcomes of treatment of patients with pediatric ALL in the main referral hospital in Palestine. Results Complete data of 69 patients were included in this analysis. The majority (79.7%) of the patients had B-ALL phenotype. After induction chemotherapy, remission was experienced by the vast majority of the patients and 5 (7.2%) experienced relapses. Cytogenetics for patients with B-ALL phenotype indicated that 10 (18.2%) patients had t(12, 21) translocation, 5 (9.1%) had hyperdiploidy, 4 (7.3%) had t(1, 19) translocation, and 2 (3.6%) had t(9, 22) translocation. The initial white blood cells (p value < 0.001), absolute neutrophils (p value = 0.011), and hemoglobin (p value < 0.001) were significantly lower in patients with B-cell ALL. Platelet counts were significantly lower (p value = 0.012) in patients with splenomegaly and those with bleeding symptoms (p value = 0.008). Presence of palmar pollar was positively associated (p value = 0.035) with T-cell ALL. Presence of hepatomegaly was positively associated (p value < 0.001) with splenomegaly.
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Affiliation(s)
- Ramzi Shawahna
- Department of Physiology, Pharmacology and Toxicology, Faculty of Medicine and Health Sciences, An-Najah National University, New Campus, Building: 19, Office: 1340, P.O. Box 7, Nablus, Palestine. .,An-Najah BioSciences Unit, Centre for Poisons Control, Chemical and Biological Analyses, An-Najah National University, Nablus, Palestine.
| | - Sultan Mosleh
- Department of Medicine, Faculty of Medicine and Health Sciences, An-Najah National University, Nablus, Palestine
| | - Yahya Odeh
- An-Najah National University Hospital, An-Najah National University, Nablus, Palestine
| | - Rami Halawa
- An-Najah National University Hospital, An-Najah National University, Nablus, Palestine
| | - Majd Al-Ghoul
- An-Najah National University Hospital, An-Najah National University, Nablus, Palestine
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Pellegrini L, Bonfio C, Chadwick J, Begum F, Skehel M, Lancaster MA. Human CNS barrier-forming organoids with cerebrospinal fluid production. Science 2020; 369:eaaz5626. [PMID: 32527923 PMCID: PMC7116154 DOI: 10.1126/science.aaz5626] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
Cerebrospinal fluid (CSF) is a vital liquid, providing nutrients and signaling molecules and clearing out toxic by-products from the brain. The CSF is produced by the choroid plexus (ChP), a protective epithelial barrier that also prevents free entry of toxic molecules or drugs from the blood. Here, we establish human ChP organoids with a selective barrier and CSF-like fluid secretion in self-contained compartments. We show that this in vitro barrier exhibits the same selectivity to small molecules as the ChP in vivo and that ChP-CSF organoids can predict central nervous system (CNS) permeability of new compounds. The transcriptomic and proteomic signatures of ChP-CSF organoids reveal a high degree of similarity to the ChP in vivo. Finally, the intersection of single-cell transcriptomics and proteomic analysis uncovers key human CSF components produced by previously unidentified specialized epithelial subtypes.
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Affiliation(s)
- Laura Pellegrini
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Claudia Bonfio
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jessica Chadwick
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Farida Begum
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mark Skehel
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Madeline A Lancaster
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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