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Kodali MC, Antone J, Alsop E, Jayakumar R, Parikh K, Chiot A, Sanchez-Molina P, Ajami B, Arnold SE, Jensen K, Das S, Weinberg MS. Cryopreservation of cerebrospinal fluid cells preserves the transcriptional landscape for single-cell analysis. J Neuroinflammation 2024; 21:71. [PMID: 38521932 PMCID: PMC10960996 DOI: 10.1186/s12974-024-03047-1] [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: 10/04/2023] [Accepted: 02/14/2024] [Indexed: 03/25/2024] Open
Abstract
Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approach to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
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Affiliation(s)
- Mahesh Chandra Kodali
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | - Jerry Antone
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Eric Alsop
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Khushi Parikh
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Aude Chiot
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Paula Sanchez-Molina
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Bahareh Ajami
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, USA
- Department of Behavioral and Systems Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Steven E Arnold
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Kendall Jensen
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sudeshna Das
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Marc S Weinberg
- Department of Neurology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Department of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.
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Halawa T, Baeesa S, Fadul MM, Badahdah AA, Enani M, Fathaddin AA, Kawass D, Alkhotani A, Bahakeem B, Kurdi M. The Role of Liquid Biopsy in the Diagnosis and Prognosis of WHO Grade 4 Astrocytoma. Cureus 2023; 15:e41221. [PMID: 37525780 PMCID: PMC10387356 DOI: 10.7759/cureus.41221] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/02/2023] Open
Abstract
Liquid biopsy, as a non-invasive diagnostic tool, has recently gained significant attention in the field of oncology. It involves the analysis of various biomarkers present in bodily fluids, such as blood or cerebrospinal fluid, to provide information about the underlying cancer. In the case of WHO grade 4 astrocytomas, liquid biopsy has the potential to significantly impact the diagnosis and prognosis of this aggressive malignant brain tumor. By detecting specific genetic mutations, such as IDH1 or EGFR, and monitoring levels of circulating tumor DNA, liquid biopsy can aid in the early detection and monitoring of disease progression. This innovative approach is gradually being acknowledged as a less invasive and cost-effective procedure for cancer diagnosis and management to improve patient outcomes and quality of life. Various kinds of biomarkers circulating in cerebrospinal fluid (CSF), such as circulating tumor cells (CTC) and different types of nucleic acids like cell-free DNA (cfDNA), cell-free RNA (ctRNA), and microRNAs (miRNA), have been identified. These biomarkers, which require dependable detection methods, are comparatively simple to obtain and allow for repeated measurements, making them significantly superior for disease monitoring. This review aims to compare the latest liquid biopsy analysis tools for both CSF and plasma in the central nervous system.
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Affiliation(s)
- Taher Halawa
- Department of Pediatrics, Faculty of Medicine King Abdulaziz University, Rabigh, SAU
| | - Saleh Baeesa
- Department of Neuroscience, King Faisal Specialist Hospital and Research Centre, Jeddah, SAU
| | - Motaz M Fadul
- Department of Pathology, Faculty of Medicine King Abdulaziz University, Rabigh, SAU
| | - Adnan A Badahdah
- Department of Internal Medicine, University of Jeddah, Jeddah, SAU
| | - Maryam Enani
- Department of Surgery, King Abdulaziz University Hospital, Jeddah, SAU
| | - Amany A Fathaddin
- Department of Pathology, College of Medicine, King Saud University, Riyadh, SAU
- Department of Pathology, King Saud University Medical City, Riyadh, SAU
| | - Dania Kawass
- Department of Family Medicine, Faculty of Medicine King Abdulaziz University, Jeddah, SAU
| | - Alaa Alkhotani
- Department of Pathology, Umm Al-Qura University, Makkah, SAU
| | - Basem Bahakeem
- Department of Internal Medicine, Umm Al-Qura University, Makkah, SAU
| | - Maher Kurdi
- Department of Pathology, Faculty of Medicine King Abdulaziz University, Rabigh, SAU
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Yekula A, Tracz J, Rincon-Torroella J, Azad T, Bettegowda C. Single-Cell RNA Sequencing of Cerebrospinal Fluid as an Advanced Form of Liquid Biopsy for Neurological Disorders. Brain Sci 2022; 12:brainsci12070812. [PMID: 35884620 PMCID: PMC9313114 DOI: 10.3390/brainsci12070812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 11/16/2022] Open
Abstract
Diagnosis and longitudinal monitoring of neurological diseases are limited by the poor specificity and limited resolution of currently available techniques. Analysis of circulating cells in cerebrospinal fluid (CSF) has emerged as a promising strategy for the diagnosis, molecular characterization, and monitoring of neurological disease. In comparison to bulk sequencing analysis, single-cell sequencing studies can provide novel insights into rare cell populations and uncover heterogeneity in gene expression at a single-cell resolution, which has several implications for understanding disease pathology and treatment. Parallel development of standardized biofluid collection protocols, pre-processing strategies, reliable single-cell isolation strategies, downstream genomic analysis, and robust computational analysis is paramount for comprehensive single-cell sequencing analysis. Here we perform a comprehensive review of studies focusing on single-cell sequencing of cells in the CSF of patients with oncological or non-oncological diseases of the central nervous system.
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Affiliation(s)
- Anudeep Yekula
- Department of Surgery, Yale School of Medicine, New Haven, CT 06510, USA;
| | - Jovanna Tracz
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Jordina Rincon-Torroella
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Tej Azad
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
| | - Chetan Bettegowda
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; (J.T.); (J.R.-T.); (T.A.)
- Correspondence:
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Otto F, Harrer C, Pilz G, Wipfler P, Harrer A. Role and Relevance of Cerebrospinal Fluid Cells in Diagnostics and Research: State-of-the-Art and Underutilized Opportunities. Diagnostics (Basel) 2021; 12:diagnostics12010079. [PMID: 35054246 PMCID: PMC8774636 DOI: 10.3390/diagnostics12010079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 12/07/2021] [Accepted: 12/28/2021] [Indexed: 01/15/2023] Open
Abstract
Cerebrospinal fluid (CSF) has recently experienced a revival in diagnostics and research. However, little progress has been made regarding CSF cell analysis. For almost a century, CSF cell count and cytomorphological examination have been central diagnostic parameters, with CSF pleocytosis as a hallmark finding of neuroinflammation and cytology offering valuable clues regarding infectious, autoimmune, and malignant aetiologies. A great deal of information, however, remains unattended as modern immune phenotyping technologies have not yet been broadly incorporated into routine CSF analysis. This is a serious deficit considering the central role of CSF cells as effectors in central nervous system (CNS) immune defence and autoimmune CNS processes, and the diagnostic challenges posed by clinically overlapping infectious and immune-mediated CNS diseases. Here, we summarize historical, specimen-intrinsic, methodological, and technical issues determining the state-of-the-art diagnostics of CSF cells and outline future perspectives for this underutilized window into meningeal and CNS immunity.
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Affiliation(s)
- Ferdinand Otto
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Christine Harrer
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Georg Pilz
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Peter Wipfler
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
| | - Andrea Harrer
- Department of Neurology, Paracelsus Medical University, Christian-Doppler-Klinik, 5020 Salzburg, Austria; (F.O.); (C.H.); (G.P.); (P.W.)
- Department of Dermatology and Allergology, Paracelsus Medical University, Landeskrankenhaus, 5020 Salzburg, Austria
- Correspondence:
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S1 guidelines "lumbar puncture and cerebrospinal fluid analysis" (abridged and translated version). Neurol Res Pract 2020; 2:8. [PMID: 33324914 PMCID: PMC7650145 DOI: 10.1186/s42466-020-0051-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 02/03/2020] [Indexed: 12/12/2022] Open
Abstract
Introduction Cerebrospinal fluid (CSF) analysis is important for detecting inflammation of the nervous system and the meninges, bleeding in the area of the subarachnoid space that may not be visualized by imaging, and the spread of malignant diseases to the CSF space. In the diagnosis and differential diagnosis of neurodegenerative diseases, the importance of CSF analysis is increasing. Measuring the opening pressure of CSF in idiopathic intracranial hypertension and at spinal tap in normal pressure hydrocephalus constitute diagnostic examination procedures with therapeutic benefits.Recommendations (most important 3-5 recommendations on a glimpse): The indications and contraindications must be checked before lumbar puncture (LP) is performed, and sampling CSF requires the consent of the patient.Puncture with an atraumatic needle is associated with a lower incidence of postpuncture discomfort. The frequency of postpuncture syndrome correlates inversely with age and body mass index, and it is more common in women and patients with a history of headache. The sharp needle is preferably used in older or obese patients, also in punctures expected to be difficult.In order to avoid repeating LP, a sufficient quantity of CSF (at least 10 ml) should be collected. The CSF sample and the serum sample taken at the same time should be sent to a specialized laboratory immediately so that the emergency and basic CSF analysis program can be carried out within 2 h.The indication for LP in anticoagulant therapy should always be decided on an individual basis. The risk of interrupting anticoagulant therapy must be weighed against the increased bleeding risk of LP with anticoagulant therapy.As a quality assurance measure in CSF analysis, it is recommended that all cytological, clinical-chemical, and microbiological findings are combined in an integrated summary report and evaluated by an expert in CSF analysis. Conclusions In view of the importance and developments in CSF analysis, the S1 guideline "Lumbar puncture and cerebrospinal fluid analysis" was recently prepared by the German Society for CSF analysis and clinical neurochemistry (DGLN) and published in German in accordance with the guidelines of the AWMF (https://www.awmf.org). /uploads/tx_szleitlinien/030-141l_S1_Lumbalpunktion_und_Liquordiagnostik_2019-08.pdf). The present article is an abridged translation of the above cited guideline. The guideline has been jointly edited by the DGLN and DGN.
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Uhr M, Tumani H, Lange P. [Strategies for cerebrospinal fluid analysis - Integrated results report]. DER NERVENARZT 2016; 87:1271-1275. [PMID: 27785524 DOI: 10.1007/s00115-016-0232-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Cerebrospinal fluid (CSF) analysis requires a combined assessment of all individual test findings in an integrated total report in order to achieve a reliable and specific diagnostic conclusion. Such a standard assessment strategy allows the identification of disease-typical result patterns and plausibility checks to avoid analytical errors. The integrated total report consists of 1) a basic CSF program with cytological and protein chemical parameters, 2) an expanded CSF program with special parameters for detection of pathogens and markers of neurodegeneration and 3) a final contextual interpretation considering methodological and clinical aspects.
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Affiliation(s)
- M Uhr
- Max-Planck-Institut für Psychiatrie, Kraepelinstr. 2-10, 80804, München, Deutschland.
| | - H Tumani
- Fachklinik für Neurologie Dietenbronn, Schwendi, Deutschland.,Neurologische Uniklinik im RKU, Ulm, Deutschland
| | - P Lange
- Klinik für Neurologie UMG, Göttingen, Deutschland
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