1
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Higdon LE, Scheiding S, Kus AM, Lim N, Long SA, Anderson MS, Wiedeman AE. Impact on in-depth immunophenotyping of delay to peripheral blood processing. Clin Exp Immunol 2024; 217:119-132. [PMID: 38693758 PMCID: PMC11239563 DOI: 10.1093/cei/uxae041] [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: 10/20/2023] [Revised: 02/20/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
Peripheral blood mononuclear cell (PBMC) immunophenotyping is crucial in tracking activation, disease state, and response to therapy in human subjects. Many studies require the shipping of blood from clinical sites to a laboratory for processing to PBMC, which can lead to delays that impact sample quality. We used an extensive cytometry by time-of-flight (CyTOF) immunophenotyping panel to analyze the impacts of delays to processing and distinct storage conditions on cell composition and quality of PBMC from seven adults across a range of ages, including two with rheumatoid arthritis. Two or more days of delay to processing resulted in extensive red blood cell contamination and increased variability of cell counts. While total memory and naïve B- and T-cell populations were maintained, 4-day delays reduced the frequencies of monocytes. Variation across all immune subsets increased with delays of up to 7 days in processing. Unbiased clustering analysis to define more granular subsets confirmed changes in PBMC composition, including decreases of classical and non-classical monocytes, basophils, plasmacytoid dendritic cells, and follicular helper T cells, with each subset impacted at a distinct time of delay. Expression of activation markers and chemokine receptors changed by Day 2, with differential impacts across subsets and markers. Our data support existing recommendations to process PBMC within 36 h of collection but provide guidance on appropriate immunophenotyping experiments with longer delays.
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Affiliation(s)
- Lauren E Higdon
- Biomarker and Discovery Research, Immune Tolerance Network, San Francisco, CA, USA
| | - Sheila Scheiding
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Anna M Kus
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Noha Lim
- Biomarker and Discovery Research, Immune Tolerance Network, San Francisco, CA, USA
| | - S Alice Long
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
| | - Mark S Anderson
- Biomarker and Discovery Research, Immune Tolerance Network, San Francisco, CA, USA
| | - Alice E Wiedeman
- Center for Translational Immunology, Benaroya Research Institute, Seattle, WA, USA
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2
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Browne DJ, Miller CM, Doolan DL. Technical pitfalls when collecting, cryopreserving, thawing, and stimulating human T-cells. Front Immunol 2024; 15:1382192. [PMID: 38812513 PMCID: PMC11133553 DOI: 10.3389/fimmu.2024.1382192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024] Open
Abstract
The collection, cryopreservation, thawing, and culture of peripheral blood mononuclear cells (PBMCs) can profoundly influence T cell viability and immunogenicity. Gold-standard PBMC processing protocols have been developed by the Office of HIV/AIDS Network Coordination (HANC); however, these protocols are not universally observed. Herein, we have explored the current literature assessing how technical variation during PBMC processing can influence cellular viability and T cell immunogenicity, noting inconsistent findings between many of these studies. Amid the mounting concerns over scientific replicability, there is growing acknowledgement that improved methodological rigour and transparent reporting is required to facilitate independent reproducibility. This review highlights that in human T cell studies, this entails adopting stringent standardised operating procedures (SOPs) for PBMC processing. We specifically propose the use of HANC's Cross-Network PBMC Processing SOP, when collecting and cryopreserving PBMCs, and the HANC member network International Maternal Pediatric Adolescent AIDS Clinical Trials (IMPAACT) PBMC Thawing SOP when thawing PBMCs. These stringent and detailed protocols include comprehensive reporting procedures to document unavoidable technical variations, such as delayed processing times. Additionally, we make further standardisation and reporting recommendations to minimise and document variability during this critical experimental period. This review provides a detailed overview of the challenges inherent to a procedure often considered routine, highlighting the importance of carefully considering each aspect of SOPs for PBMC collection, cryopreservation, thawing, and culture to ensure accurate interpretation and comparison between studies.
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Affiliation(s)
- Daniel J. Browne
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Catherine M. Miller
- College of Medicine and Dentistry, James Cook University, Cairns, QLD, Australia
| | - Denise L. Doolan
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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3
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Xu R, Shi X, Huang H, Tan WS, Cai H. Development of a Me 2SO-free cryopreservation medium and its long-term cryoprotection on the CAR-NK cells. Cryobiology 2024; 114:104835. [PMID: 38070820 DOI: 10.1016/j.cryobiol.2023.104835] [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: 04/22/2023] [Revised: 11/22/2023] [Accepted: 12/04/2023] [Indexed: 12/17/2023]
Abstract
Cryopreservation is a crucial step in the supply process of off-the-shelf chimeric antigen receptor engineered natural killer (CAR-NK) cell products. Concerns have been raised over the clinical application of dimethyl sulfoxide (Me2SO) due to the potential for adverse reactions following infusion and limited cell-specific cytotoxic effects if misapplied. In this study, we developed a Me2SO-free cryopreservation medium specifically tailored for CAR-NK cells to address this limitation. The cryopreservation medium was formulated using human serum albumin (HSA) and glycerol as the base components. Following initial screening of seven clinically-compatible solutions, four with cryoprotective properties were identified. These were combined and optimized into a single formulation: IF-M. The viability, phenotype, and function of CAR-NK cells were evaluated after short-term and long-term cryopreservation to assess the effectiveness of IF-M, with Me2SO serving as the control group. The viability and recovery of CAR-NK cells in the IF-M group were significantly higher than those in the Me2SO group within 90 days of cryopreservation. Moreover, after 1 year of cryopreservation the cytotoxic capacity of CAR-NK cells cryopreserved with IF-M was comparable to that of fresh CAR-NK cells and significantly superior to that of CAR-NK cells cryopreserved in Me2SO. The CD107a expression intensity of CAR-NK cells in IF-M group was significantly higher than that of Me2SO group. No statistical differences were observed in other indicators under different cryopreservation times. These results underscore the robustness of IF-M as a suitable replacement for traditional Me2SO-based cryopreservation medium for the long-term cryopreservation and clinical application of off-the-shelf CAR-NK cells.
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Affiliation(s)
- Ruisheng Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Xiaodi Shi
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Huimin Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Wen-Song Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Haibo Cai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
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4
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Blümke A, Ijeoma E, Simon J, Wellington R, Purwaningrum M, Doulatov S, Leber E, Scatena M, Giachelli CM. Comparison of osteoclast differentiation protocols from human induced pluripotent stem cells of different tissue origins. Stem Cell Res Ther 2023; 14:319. [PMID: 37936199 PMCID: PMC10631132 DOI: 10.1186/s13287-023-03547-6] [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: 06/20/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Ever since their discovery, induced pluripotent stem cells (iPSCs) have been extensively differentiated into a large variety of cell types. However, a limited amount of work has been dedicated to differentiating iPSCs into osteoclasts. While several differentiation protocols have been published, it remains unclear which protocols or differentiation methods are preferable regarding the differentiation of osteoclasts. METHODS In this study, we compared the osteoclastogenesis capacity of a peripheral blood mononuclear cell (PBMC)-derived iPSC line to a fibroblast-derived iPSC line in conjunction with either embryoid body-based or monolayer-based differentiation strategies. Both cell lines and differentiation protocols were investigated regarding their ability to generate osteoclasts and their inherent robustness and ease of use. The ability of both cell lines to remain undifferentiated while propagating using a feeder-free system was assessed using alkaline phosphatase staining. This was followed by evaluating mesodermal differentiation and the characterization of hematopoietic progenitor cells using flow cytometry. Finally, osteoclast yield and functionality based on resorptive activity, Cathepsin K and tartrate-resistant acid phosphatase (TRAP) expression were assessed. The results were validated using qRT-PCR throughout the differentiation stages. RESULTS Embryoid body-based differentiation yielded CD45+, CD14+, CD11b+ subpopulations which in turn differentiated into osteoclasts which demonstrated TRAP positivity, Cathepsin K expression and mineral resorptive capabilities. This was regardless of which iPSC line was used. Monolayer-based differentiation yielded lower quantities of hematopoietic cells that were mostly CD34+ and did not subsequently differentiate into osteoclasts. CONCLUSIONS The outcome of this study demonstrates the successful differentiation of osteoclasts from iPSCs in conjunction with the embryoid-based differentiation method, while the monolayer-based method did not yield osteoclasts. No differences were observed regarding osteoclast differentiation between the PBMC and fibroblast-derived iPSC lines.
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Affiliation(s)
- Alexander Blümke
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
- Department of Orthopedics and Trauma Surgery, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Erica Ijeoma
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Jessica Simon
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Rachel Wellington
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
- Molecular and Cellular Biology Program, School of Medicine, University of Washington, Seattle, WA, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Medania Purwaningrum
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sergei Doulatov
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Elizabeth Leber
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Marta Scatena
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA
| | - Cecilia M Giachelli
- Department of Bioengineering, Department of Medicine, University of Washington, Foege Hall University of Washington, 3720 15th, Ave NE, Box 355061, Seattle, WA, 98195, USA.
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5
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Monaghan JF, Cullen D, Wynne C, Lyng FM, Meade AD. Effect of pre-analytical variables on Raman and FTIR spectral content of lymphocytes. Analyst 2023; 148:5422-5434. [PMID: 37750362 DOI: 10.1039/d3an00686g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
The use of Fourier transform infrared (FTIR) and Raman spectroscopy (RS) for the analysis of lymphocytes in clinical applications is increasing in the field of biomedicine. The pre-analytical phase, which is the most vulnerable stage of the testing process, is where most errors and sample variance occur; however, it is unclear how pre-analytical variables affect the FTIR and Raman spectra of lymphocytes. In this study, we evaluated how pre-analytical procedures undertaken before spectroscopic analysis influence the spectral integrity of lymphocytes purified from the peripheral blood of male volunteers (n = 3). Pre-analytical variables investigated were associated with (i) sample preparation, (blood collection systems, anticoagulant, needle gauges), (ii) sample storage (fresh or frozen), and (iii) sample processing (inter-operator variability, time to lymphocyte isolation). Although many of these procedural pre-analytical variables did not alter the spectral signature of the lymphocytes, evidence of spectral effects due to the freeze-thaw cycle, in vitro culture inter-operator variability and the time to lymphocyte isolation was observed. Although FTIR and RS possess clinical potential, their translation into a clinical environment is impeded by a lack of standardisation and harmonisation of protocols related to the preparation, storage, and processing of samples, which hinders uniform, accurate, and reproducible analysis. Therefore, further development of protocols is required to successfully integrate these techniques into current clinical workflows.
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Affiliation(s)
- Jade F Monaghan
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Central Quad, City Campus, Grangegorman, D07 XT95, Ireland.
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Aungier Street, D02 HW71, Ireland
| | - Daniel Cullen
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Central Quad, City Campus, Grangegorman, D07 XT95, Ireland.
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Aungier Street, D02 HW71, Ireland
| | - Claire Wynne
- School of Biological, Health and Sports Sciences, Technological University Dublin, Central Quad, City Campus, Grangegorman, D07 XT95, Ireland
| | - Fiona M Lyng
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Central Quad, City Campus, Grangegorman, D07 XT95, Ireland.
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Aungier Street, D02 HW71, Ireland
| | - Aidan D Meade
- School of Physics, Clinical and Optometric Sciences, Technological University Dublin, Central Quad, City Campus, Grangegorman, D07 XT95, Ireland.
- Radiation and Environmental Science Centre, Focas Research Institute, Technological University Dublin, Aungier Street, D02 HW71, Ireland
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Congrave-Wilson Z, Kim M, Sutherland A, Jumarang J, Lee Y, Del Valle J, Cheng WA, da Silva Antunes R, Pannaraj PS. Effect of wash media type during PBMC isolation on downstream characterization of SARS-CoV-2-specific T cells. J Immunol Methods 2023; 519:113520. [PMID: 37390890 PMCID: PMC10306416 DOI: 10.1016/j.jim.2023.113520] [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: 03/19/2023] [Revised: 06/13/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Protocols for the isolation of peripheral blood mononuclear cells (PBMCs) from whole blood vary greatly between laboratories, especially in published studies of SARS-CoV-2-specific T cell responses following infection and vaccination. Research on the effects of different wash media types or centrifugation speeds and brake usage during the PBMC isolation process on downstream T cell activation and functionality is limited. Blood samples from 26 COVID-19-vaccinated participants were processed with different PBMC isolation methods using either PBS or RPMI as the wash media with high centrifugation speed and brakes or RPMI as the wash media with low speed and brakes (RPMI+ method). SARS-CoV-2 spike-specific T cells were quantified and characterized via a flow cytometry-based activation induced markers (AIM) assay and an interferon-γ (IFNγ) FluoroSpot assay and responses were compared between processing methods. Samples washed with RPMI showed higher AIM+ CD4 T cell responses than those washed with PBS and showed a shift away from naïve and towards an effector memory phenotype. The activation marker OX40 showed higher SARS-CoV-2 spike-induced upregulation on RPMI-washed CD4 T cells, while differences in CD137 upregulation were minimal between processing methods. The magnitude of the AIM+ CD8 T cell response was similar between processing methods but showed higher stimulation indices. Background frequencies of CD69+ CD8 T cells were increased in PBS-washed samples and were associated with higher baseline numbers of IFNγ-producing cells in the FluoroSpot assay. Slower braking in the RPMI+ method did not improve detection of SARS-CoV-2-specific T cells and caused longer processing times. Thus, the use of RPMI media with full centrifugation brakes during the wash steps of PBMC isolation was found to be most effective and efficient. Further studies are needed to elucidate the pathways involved in RPMI-mediated preservation of downstream T cell activity.
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Affiliation(s)
- Zion Congrave-Wilson
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Minjun Kim
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Jaycee Jumarang
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Yesun Lee
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Jennifer Del Valle
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States
| | - Wesley A Cheng
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Pia S Pannaraj
- Division of Infectious Diseases, Children's Hospital Los Angeles, Los Angeles, CA, United States; Department of Pediatrics and Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States; Division of Infectious Diseases, Department of Pediatrics, University of California San Diego, La Jolla, CA, United States.
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7
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Blümke A, Ijeoma E, Simon J, Wellington R, Purwaningrum M, Doulatov S, Leber E, Scatena M, Giachelli CM. Comparison of osteoclast differentiation protocols from human induced pluripotent stem cells of different tissue origins. RESEARCH SQUARE 2023:rs.3.rs-3089289. [PMID: 37461708 PMCID: PMC10350192 DOI: 10.21203/rs.3.rs-3089289/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Background Ever since their discovery, induced pluripotent stem cells (iPSCs) have been extensively differentiated into a large variety of cell types. However, a limited amount of work has been dedicated to differentiating iPSCs into osteoclasts. While several differentiation protocols have been published, it remains unclear which protocols or differentiation methods are preferrable regarding the differentiation of osteoclasts. Methods In this study we compare the osteoclastogenesis capacity of a peripheral blood mononuclear cell (PBMC)-derived iPSC line to a fibroblast-derived iPSC line in conjunction with either embryoid body-based or monolayer-based differentiation strategies. Both cell lines and differentiation protocols were investigated regarding their ability to generate osteoclasts and their inherent robustness and ease of use. The ability of both cell lines to remain undifferentiated while propagating using a feeder-free system was assessed using alkaline phosphatase staining. This was followed by evaluating mesodermal differentiation and the characterization of hematopoietic progenitor cells using flow cytometry. Finally, osteoclast yield and functionality based on resorptive activity, Cathepsin K and tartrate-resistant acid phosphatase (TRAP) expression were assessed. Results were validated using qRT-PCR throughout the differentiation stages. Results Embryoid-body based differentiation yielded CD45+, CD14+, CD11b+ subpopulations which in turn differentiated into osteoclasts which demonstrated TRAP positivity, Cathepsin K expression and mineral resorptive capabilities. This was regardless of which iPSC line was used. Monolayer-based differentiation yielded lower quantities of hematopoietic cells that were mostly CD34+ and did not subsequently differentiate into osteoclasts. Conclusions The outcome of this study demonstrates the successful differentiation of osteoclasts from iPSCs in conjunction with the embryoid-based differentiation method, while the monolayer-based method did not yield osteoclasts. No differences were observed regarding osteoclast differentiation between the PBMC and fibroblast-derived iPSC lines.
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Affiliation(s)
| | - Erica Ijeoma
- University of Washington Department of Bioengineering
| | - Jessica Simon
- University of Washington Department of Bioengineering
| | | | | | | | | | - Marta Scatena
- University of Washington Department of Bioengineering
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8
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Pojero F, Gervasi F, Fiore SD, Aiello A, Bonacci S, Caldarella R, Attanzio A, Candore G, Caruso C, Ligotti ME, Procopio A, Restivo I, Tesoriere L, Allegra M, Accardi G. Anti-Inflammatory Effects of Nutritionally Relevant Concentrations of Oleuropein and Hydroxytyrosol on Peripheral Blood Mononuclear Cells: An Age-Related Analysis. Int J Mol Sci 2023; 24:11029. [PMID: 37446206 DOI: 10.3390/ijms241311029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 06/26/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Immunosenescence and inflammaging facilitate the insurgence of chronic diseases. The Mediterranean diet is a non-invasive intervention to improve the chronic low-grade inflammatory status associated with aging. Olive oil oleuropein (OLE) and hydroxytyrosol (HT) demonstrated a controversial modulatory action on inflammation in vitro when tested at concentrations exceeding those detectable in human plasma. We studied the potential anti-inflammatory effects of OLE and HT at nutritionally relevant concentrations on peripheral blood mononuclear cells (PBMCs) as regards cell viability, frequency of leukocyte subsets, and cytokine release, performing an age-focused analysis on two groups of subjects: Adult (age 18-64 years) and Senior (age ≥ 65 years). OLE and HT were used alone or as a pre-treatment before challenging PBMCs with lipopolysaccharide (LPS). Both polyphenols had no effect on cell viability irrespective of LPS, but 5 µM HT had an LPS-like effect on monocytes, reducing the intermediate subset in Adult subjects. OLE and HT had no effect on LPS-triggered release of TNF-α, IL-6 and IL-8, but 5 µM HT reduced IL-10 secretion by PBMCs from Adult vs. Senior group. In summary, nutritionally relevant concentrations of OLE and HT elicit no anti-inflammatory effect and influence the frequency of immune cell subsets with age-related different outcomes.
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Affiliation(s)
- Fanny Pojero
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Francesco Gervasi
- Specialistic Oncology Laboratory Unit, ARNAS Hospitals Civico Di Cristina e Benfratelli, 90127 Palermo, Italy
| | - Salvatore Davide Fiore
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Anna Aiello
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Sonia Bonacci
- Department of Health Sciences, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosalia Caldarella
- Department of Laboratory Medicine, "P. Giaccone" University Hospital, 90127 Palermo, Italy
| | - Alessandro Attanzio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Giuseppina Candore
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Calogero Caruso
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Mattia Emanuela Ligotti
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
| | - Antonio Procopio
- Department of Health Sciences, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Ignazio Restivo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Luisa Tesoriere
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Mario Allegra
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, 90123 Palermo, Italy
| | - Giulia Accardi
- Laboratory of Immunopathology and Immunosenescence, Department of Biomedicine, Neurosciences and Advanced Technologies, University of Palermo, 90133 Palermo, Italy
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9
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Bacon B, Repin M, Shuryak I, Wu HC, Santella RM, Terry MB, Brenner DJ, Turner HC. High-throughput measurement of double strand break global repair phenotype in peripheral blood mononuclear cells after long-term cryopreservation. Cytometry A 2023; 103:575-583. [PMID: 36823754 PMCID: PMC10680149 DOI: 10.1002/cyto.a.24725] [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: 08/18/2022] [Revised: 01/02/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023]
Abstract
Peripheral blood mononuclear cells (PBMCs) are a useful model for biochemical assays, particularly for etiological studies. We describe here a method for measuring DNA repair capacity (DRC) in archival cryogenically preserved PBMCs. To model DRC, we measured γ-H2AX repair kinetics in thawed PBMCs after irradiation with 3 Gy gamma rays. Time-dependent fluorescently labeled γ-H2AX levels were measured at five time points from 1 to 20 h, yielding an estimate of global DRC repair kinetics as well as a measure of unrepaired double strand breaks at 20 h. While γ-H2AX levels are traditionally measured by either microscopy or flow-cytometry, we developed a protocol for imaging flow cytometry (IFC) that combines the detailed information of microscopy with the statistical power of flow methods. The visual imaging component of the IFC allows for monitoring aspects such as cellular health and apoptosis as well as fluorescence localization of the γ-H2AX signal, which ensures the power and significance of this technique. Application of a machine-learning based image classification improved flow cytometry fluorescent measurements by identifying apoptotic cells unable to undergo DNA repair. We present here DRC repair parameters from 18 frozen archival PBMCs and 28 fresh blood samples collected from a demographically diverse cohort of women measured in a high-throughput IFC format. This thaw method and assay can be used alone or in conjunction with other assays to measure etiological phenotypes in cryogenic biobanks of PBMCs.
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Affiliation(s)
- Bezalel Bacon
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY)
| | - Mikhail Repin
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY)
| | - Igor Shuryak
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY)
| | - Hui-Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
| | - Regina M. Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center
- Department of Epidemiology, Mailman School of Public Health, Columbia University, Irving Medical Center, New York
| | - David J. Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY)
| | - Helen C. Turner
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY)
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10
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Wong YY, Harbison JE, Hope CM, Gundsambuu B, Brown KA, Wong SW, Brown CY, Couper JJ, Breen J, Liu N, Pederson SM, Köhne M, Klee K, Schultze J, Beyer M, Sadlon T, Barry SC. Parallel recovery of chromatin accessibility and gene expression dynamics from frozen human regulatory T cells. Sci Rep 2023; 13:5506. [PMID: 37016052 PMCID: PMC10073253 DOI: 10.1038/s41598-023-32256-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 03/24/2023] [Indexed: 04/06/2023] Open
Abstract
Epigenetic features such as DNA accessibility dictate transcriptional regulation in a cell type- and cell state- specific manner, and mapping this in health vs. disease in clinically relevant material is opening the door to new mechanistic insights and new targets for therapy. Assay for Transposase Accessible Chromatin Sequencing (ATAC-seq) allows chromatin accessibility profiling from low cell input, making it tractable on rare cell populations, such as regulatory T (Treg) cells. However, little is known about the compatibility of the assay with cryopreserved rare cell populations. Here we demonstrate the robustness of an ATAC-seq protocol comparing primary Treg cells recovered from fresh or cryopreserved PBMC samples, in the steady state and in response to stimulation. We extend this method to explore the feasibility of conducting simultaneous quantitation of chromatin accessibility and transcriptome from a single aliquot of 50,000 cryopreserved Treg cells. Profiling of chromatin accessibility and gene expression in parallel within the same pool of cells controls for cellular heterogeneity and is particularly beneficial when constrained by limited input material. Overall, we observed a high correlation of accessibility patterns and transcription factor dynamics between fresh and cryopreserved samples. Furthermore, highly similar transcriptomic profiles were obtained from whole cells and from the supernatants recovered from ATAC-seq reactions. We highlight the feasibility of applying these techniques to profile the epigenomic landscape of cells recovered from cryopreservation biorepositories.
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Affiliation(s)
- Ying Y Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jessica E Harbison
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Christopher M Hope
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | | | - Katherine A Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Soon W Wong
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Cheryl Y Brown
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jennifer J Couper
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Jimmy Breen
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Ning Liu
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Stephen M Pederson
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Maren Köhne
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Kathrin Klee
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Joachim Schultze
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Marc Beyer
- German Center for Neurodegenerative Diseases, University of Bonn, Bonn, Germany
| | - Timothy Sadlon
- Robinson Research Institute, University of Adelaide, Adelaide, Australia
- Women's and Children's Hospital, North Adelaide, Australia
| | - Simon C Barry
- Robinson Research Institute, University of Adelaide, Adelaide, Australia.
- Women's and Children's Hospital, North Adelaide, Australia.
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11
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Thébault P, Cailhier JF, Lapointe R. Blood Sample Processing and Banking for Functional and Molecular Analyses. Methods Mol Biol 2023; 2614:37-46. [PMID: 36587117 DOI: 10.1007/978-1-0716-2914-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Immune monitoring of circulating immune cells in the blood provides insight into a patient's own immune response over the course of a treatment or disease progression. Information such as whether immune cells are functional or non-functional and what specific proteins they express or secrete can be essential to understand if (and how) a treatment is working or a disease is progressing. To do so, it requires careful handling and storage of precious biological samples with the goals of obtaining a large amount of information from limited samples and minimizing future research costs by the use of banked samples. Many factors, including blood sample types, time of collection, containers used, preservatives and other additives, transport means, and length of transit time, all affect the quality of the samples and the stability of biomarkers and must be considered at the initial collection stage. An efficient study design includes provisions for further processing of the original samples, such as cryopreservation of isolated cells, purification of DNA and RNA, and preparation of specimens for genomic, immunological, and biochemical analyses. Development of standard operating procedures and quality control plans is a safeguard of the samples' quality and of the validity of the results. Here, we focus on the collection and processing of blood suitable for plasma and peripheral blood mononuclear cell (PBMC) banking, including collection, processing, and storage of samples, based on our experience.
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Affiliation(s)
- Paméla Thébault
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada
| | - Jean-François Cailhier
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada.,Institut du cancer de Montréal, Montréal, QC, Canada.,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada
| | - Réjean Lapointe
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, QC, Canada. .,Institut du cancer de Montréal, Montréal, QC, Canada. .,Faculté de Médecine, Département de Médecine, Université de Montréal, Montréal, QC, Canada.
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