1
|
Phongpreecha T, Mathi K, Cholerton B, Fox EJ, Sigal N, Espinosa C, Reincke M, Chung P, Hwang LJ, Gajera CR, Berson E, Perna A, Xie F, Shu CH, Hazra D, Channappa D, Dunn JE, Kipp LB, Poston KL, Montine KS, Maecker HT, Aghaeepour N, Montine TJ. Single-cell peripheral immunoprofiling of lewy body and Parkinson's disease in a multi-site cohort. Mol Neurodegener 2024; 19:59. [PMID: 39090623 PMCID: PMC11295553 DOI: 10.1186/s13024-024-00748-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/22/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Multiple lines of evidence support peripheral organs in the initiation or progression of Lewy body disease (LBD), a spectrum of neurodegenerative diagnoses that include Parkinson's Disease (PD) without or with dementia (PDD) and dementia with Lewy bodies (DLB). However, the potential contribution of the peripheral immune response to LBD remains unclear. This study aims to characterize peripheral immune responses unique to participants with LBD at single-cell resolution to highlight potential biomarkers and increase mechanistic understanding of LBD pathogenesis in humans. METHODS In a case-control study, peripheral mononuclear cell (PBMC) samples from research participants were randomly sampled from multiple sites across the United States. The diagnosis groups comprise healthy controls (HC, n = 159), LBD (n = 110), Alzheimer's disease dementia (ADD, n = 97), other neurodegenerative disease controls (NDC, n = 19), and immune disease controls (IDC, n = 14). PBMCs were activated with three stimulants (LPS, IL-6, and IFNa) or remained at basal state, stained by 13 surface markers and 7 intracellular signal markers, and analyzed by flow cytometry, which generated 1,184 immune features after gating. RESULTS The model classified LBD from HC with an AUROC of 0.87 ± 0.06 and AUPRC of 0.80 ± 0.06. Without retraining, the same model was able to distinguish LBD from ADD, NDC, and IDC. Model predictions were driven by pPLCγ2, p38, and pSTAT5 signals from specific cell populations under specific activation. The immune responses characteristic for LBD were not associated with other common medical conditions related to the risk of LBD or dementia, such as sleep disorders, hypertension, or diabetes. CONCLUSIONS AND RELEVANCE Quantification of PBMC immune response from multisite research participants yielded a unique pattern for LBD compared to HC, multiple related neurodegenerative diseases, and autoimmune diseases thereby highlighting potential biomarkers and mechanisms of disease.
Collapse
Affiliation(s)
- Thanaphong Phongpreecha
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Kavita Mathi
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | | | - Eddie J Fox
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Natalia Sigal
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Camilo Espinosa
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Momsen Reincke
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Philip Chung
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
| | - Ling-Jen Hwang
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | - Eloise Berson
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Amalia Perna
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Feng Xie
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Chi-Hung Shu
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Debapriya Hazra
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Divya Channappa
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Jeffrey E Dunn
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Lucas B Kipp
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Kathleen L Poston
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | | | - Holden T Maecker
- Institute for Immunity, Transplantation and Infection, Stanford University, Stanford, CA, USA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
2
|
Schade R, Butler DSC, McKenna JA, Di Luccia B, Shokoohi V, Hamblin M, Pham THM, Monack DM. Transcriptional profiling links unique human macrophage phenotypes to the growth of intracellular Salmonella enterica serovar Typhi. Sci Rep 2024; 14:12811. [PMID: 38834738 PMCID: PMC11150401 DOI: 10.1038/s41598-024-63588-6] [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: 03/29/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Macrophages provide a crucial environment for Salmonella enterica serovar Typhi (S. Typhi) to multiply during typhoid fever, yet our understanding of how human macrophages and S. Typhi interact remains limited. In this study, we delve into the dynamics of S. Typhi replication within human macrophages and the resulting heterogeneous transcriptomic responses of macrophages during infection. Our study reveals key factors that influence macrophage diversity, uncovering distinct immune and metabolic pathways associated with different stages of S. Typhi intracellular replication in macrophages. Of note, we found that macrophages harboring replicating S. Typhi are skewed towards an M1 pro-inflammatory state, whereas macrophages containing non-replicating S. Typhi exhibit neither a distinct M1 pro-inflammatory nor M2 anti-inflammatory state. Additionally, macrophages with replicating S. Typhi were characterized by the increased expression of genes associated with STAT3 phosphorylation and the activation of the STAT3 transcription factor. Our results shed light on transcriptomic pathways involved in the susceptibility of human macrophages to intracellular S. Typhi replication, thereby providing crucial insight into host phenotypes that restrict and support S. Typhi infection.
Collapse
Affiliation(s)
- Ruth Schade
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Daniel S C Butler
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Joy A McKenna
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Blanda Di Luccia
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Vida Shokoohi
- Stanford Functional Genomics Facility, Stanford University, Stanford, CA, USA
| | - Meagan Hamblin
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Trung H M Pham
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Denise M Monack
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
3
|
Manohar SM. Shedding Light on Intracellular Proteins using Flow Cytometry. Cell Biochem Biophys 2024:10.1007/s12013-024-01338-1. [PMID: 38831173 DOI: 10.1007/s12013-024-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2024] [Indexed: 06/05/2024]
Abstract
Intracellular protein abundance is routinely measured in mammalian cells using population-based techniques such as western blotting which fail to capture single cell protein levels or using fluorescence microscopy which is although suitable for single cell protein detection but not for rapid analysis of large no. of cells. Flow cytometry offers rapid, high-throughput, multiparameter-based analysis of intracellular protein expression in statistically significant no. of cells at single cell resolution. In past few decades, customized assays have been developed for flow cytometric detection of specific intracellular proteins. This review discusses the scope of flow cytometry for intracellular protein detection in mammalian cells along with specific applications. Technological advancements to overcome the limitations of traditional flow cytometry for the same are also discussed.
Collapse
Affiliation(s)
- Sonal M Manohar
- Department of Biological Sciences, Sunandan Divatia School of Science, SVKM's NMIMS (Deemed-to-be) University, Vile Parle (West), Mumbai, 400056, India.
| |
Collapse
|
4
|
Thirman HL, Hayes MJ, Brown LE, Porco JA, Irish JM. Single Cell Profiling Distinguishes Leukemia-Selective Chemotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.591362. [PMID: 38826485 PMCID: PMC11142275 DOI: 10.1101/2024.05.01.591362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
A central challenge in chemical biology is to distinguish molecular families in which small structural changes trigger large changes in cell biology. Such families might be ideal scaffolds for developing cell-selective chemical effectors - for example, molecules that activate DNA damage responses in malignant cells while sparing healthy cells. Across closely related structural variants, subtle structural changes have the potential to result in contrasting bioactivity patterns across different cell types. Here, we tested a 600-compound Diversity Set of screening molecules from the Boston University Center for Molecular Discovery (BU-CMD) in a novel phospho-flow assay that tracked fundamental cell biological processes, including DNA damage response, apoptosis, M-phase cell cycle, and protein synthesis in MV411 leukemia cells. Among the chemotypes screened, synthetic congeners of the rocaglate family were especially bioactive. In follow-up studies, 37 rocaglates were selected and deeply characterized using 12 million additional cellular measurements across MV411 leukemia cells and healthy peripheral blood mononuclear cells. Of the selected rocaglates, 92% displayed significant bioactivity in human cells, and 65% selectively induced DNA damage responses in leukemia and not healthy human blood cells. Furthermore, the signaling and cell-type selectivity were connected to structural features of rocaglate subfamilies. In particular, three rocaglates from the rocaglate pyrimidinone (RP) structural subclass were the only molecules that activated exceptional DNA damage responses in leukemia cells without activating a detectable DNA damage response in healthy cells. These results indicate that the RP subset should be extensively characterized for anticancer therapeutic potential as it relates to the DNA damage response. This single cell profiling approach advances a chemical biology platform to dissect how systematic variations in chemical structure can profoundly and differentially impact basic functions of healthy and diseased cells.
Collapse
Affiliation(s)
- Hannah L. Thirman
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
- Chemical & Physical Biology Program, Vanderbilt University, Nashville, TN, USA
| | - Madeline J. Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Lauren E. Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - John A. Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, Boston, MA, USA
| | - Jonathan M. Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
- Vanderbilt Center for Immunobiology, Vanderbilt University Medical Center, Nashville, TN, USA
| |
Collapse
|
5
|
De Biasi S, Gigan JP, Borella R, Santacroce E, Lo Tartaro D, Neroni A, Paschalidis N, Piwocka K, Argüello RJ, Gibellini L, Cossarizza A. Cell metabolism: Functional and phenotypic single cell approaches. Methods Cell Biol 2024; 186:151-187. [PMID: 38705598 DOI: 10.1016/bs.mcb.2024.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Several metabolic pathways are essential for the physiological regulation of immune cells, but their dysregulation can cause immune dysfunction. Hypermetabolic and hypometabolic states represent deviations in the magnitude and flexibility of effector cells in different contexts, for example in autoimmunity, infections or cancer. To study immunometabolism, most methods focus on bulk populations and rely on in vitro activation assays. Nowadays, thanks to the development of single-cell technologies, including multiparameter flow cytometry, mass cytometry, RNA cytometry, among others, the metabolic state of individual immune cells can be measured in a variety of samples obtained in basic, translational and clinical studies. Here, we provide an overview of different single-cell approaches that are employed to investigate both mitochondrial functions and cell dependence from mitochondria metabolism. Moreover, besides the description of the appropriate experimental settings, we discuss the strengths and weaknesses of different approaches with the aim to suggest how to study cell metabolism in the settings of interest.
Collapse
Affiliation(s)
- Sara De Biasi
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy.
| | - Julien Paul Gigan
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Rebecca Borella
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Elena Santacroce
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Domenico Lo Tartaro
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Anita Neroni
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Katarzyna Piwocka
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Rafael José Argüello
- Aix Marseille University, CNRS, INSERM, CIML, Centre d'Immunologie de Marseille-Luminy, Marseille, France
| | - Lara Gibellini
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Andrea Cossarizza
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| |
Collapse
|
6
|
Toney NJ, Schlom J, Donahue RN. Phosphoflow cytometry to assess cytokine signaling pathways in peripheral immune cells: potential for inferring immune cell function and treatment response in patients with solid tumors. J Exp Clin Cancer Res 2023; 42:247. [PMID: 37741983 PMCID: PMC10517546 DOI: 10.1186/s13046-023-02802-1] [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: 06/07/2023] [Accepted: 08/17/2023] [Indexed: 09/25/2023] Open
Abstract
Tumor biopsy is often not available or difficult to obtain in patients with solid tumors. Investigation of the peripheral immune system allows for in-depth and dynamic profiling of patient immune response prior to and over the course of treatment and disease. Phosphoflow cytometry is a flow cytometry‒based method to detect levels of phosphorylated proteins in single cells. This method can be applied to peripheral immune cells to determine responsiveness of signaling pathways in specific immune subsets to cytokine stimulation, improving on simply defining numbers of populations of cells based on cell surface markers. Here, we review studies using phosphoflow cytometry to (a) investigate signaling pathways in cancer patients' peripheral immune cells compared with healthy donors, (b) compare immune cell function in peripheral immune cells with the tumor microenvironment, (c) determine the effects of agents on the immune system, and (d) predict cancer patient response to treatment and outcome. In addition, we explore the use and potential of phosphoflow cytometry in preclinical cancer models. We believe this review is the first to provide a comprehensive summary of how phosphoflow cytometry can be applied in the field of cancer immunology, and demonstrates that this approach holds promise in exploring the mechanisms of response or resistance to immunotherapy both prior to and during the course of treatment. Additionally, it can help identify potential therapeutic avenues that can restore normal immune cell function and improve cancer patient outcome.
Collapse
Affiliation(s)
- Nicole J Toney
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Schlom
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Renee N Donahue
- Center for Immuno-Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
7
|
Garcia C, Dejean S, Savy N, Bordet JC, Series J, Cadot S, Ribes A, Voisin S, Rugeri L, Payrastre B, Sié P. Multicolor flow cytometry in clinical samples for platelet signaling assessment. Res Pract Thromb Haemost 2023; 7:100180. [PMID: 37538502 PMCID: PMC10394564 DOI: 10.1016/j.rpth.2023.100180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 05/01/2023] [Accepted: 05/05/2023] [Indexed: 08/05/2023] Open
Abstract
Background Availability of multichannel cytometers and specific commercial antibodies makes flow cytometry a new option to simultaneously assess multiple intracellular platelet signaling pathways for clinical purposes, in small volume of blood or low platelet count. Objectives To describe a multicolor flow cytometry with fluorescent barcoding technique for screening signaling pathways downstream membrane receptors of major platelet agonists (adenosine diphosphate, thrombin, thromboxane, and collagen). Methods By comparison with immunoblotting, we first selected the target phosphoproteins, AKT, P38MAPK, LIMK, and SPL76; the times of stimulation; and phosphoflow barcoding conditions. We then performed a clinical study on whole blood of patients without evidence of blood platelet disorder on standard biological screening, consulting for trivial or occasionally provoked bleeds without familial antecedent (bleeding of unknown origin, n = 23) or type-1 von Willebrand disease (n = 9). In addition, we included a small group of patients with definite platelet disorders (Glanzmann thrombasthenia, δ-storage pool deficiency, and immune glycoprotein VI-related disease with granule secretion defect). Results The range, kinetics, and distribution of fluorescence intensity were established for each agonist-target protein combination. Principal component analysis indicates a correlation in response to a target phosphoprotein (AKT and P38MAPK) to different agonists but no correlation in the response of different target phosphoproteins to the same agonist. The heterogeneity of individual responses in the whole population displayed was analyzed using clustering algorithm. Patients with platelet storage pool deficiency were positioned as lowest responders on the heatmap. Conclusion In complement of functional tests, this study introduces a new approach for rapid platelet signaling profiling in clinical practice.
Collapse
Affiliation(s)
- Cedric Garcia
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Sebastien Dejean
- Université Paul Sabatier Toulouse III, Institut de Mathématiques, CNRS UMR 5219, Toulouse, France
| | - Nicolas Savy
- Université Paul Sabatier Toulouse III, Institut de Mathématiques, CNRS UMR 5219, Toulouse, France
| | - Jean-Claude Bordet
- Laboratoire d’Hématologie, Hospices Civiles de Lyon, Lyon, France
- EA 4609-Hémostase et Cancer, Université Claude Bernard Lyon 1, Lyon, France
| | - Jennifer Series
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Sarah Cadot
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
| | - Agnès Ribes
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Faculté de Médecine, Université Paul Sabatier Toulouse III, Toulouse, France
| | - Sophie Voisin
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
| | - Lucia Rugeri
- Laboratoire d’Hématologie, Hospices Civiles de Lyon, Lyon, France
- Hospices Civils de Lyon, Unité d’Hémostase clinique, Bron, France
| | - Bernard Payrastre
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Faculté de Médecine, Université Paul Sabatier Toulouse III, Toulouse, France
| | - Pierre Sié
- CHU de Toulouse, Laboratoire d’Hématologie, Toulouse, France
- Institut des Maladies Métaboliques et Cardiovasculaires INSERM U1048, Université de Toulouse, Toulouse, France
- Université Paul Sabatier Toulouse III, Faculté de Pharmacie, Toulouse, France
| |
Collapse
|
8
|
Sputum analysis by flow cytometry; an effective platform to analyze the lung environment. PLoS One 2022; 17:e0272069. [PMID: 35976857 PMCID: PMC9385012 DOI: 10.1371/journal.pone.0272069] [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: 04/08/2022] [Accepted: 07/12/2022] [Indexed: 11/19/2022] Open
Abstract
Low dose computed tomography (LDCT) is the standard of care for lung cancer screening in the United States (US). LDCT has a sensitivity of 93.8% but its specificity of 73.4% leads to potentially harmful follow-up procedures in patients without lung cancer. Thus, there is a need for additional assays with high accuracy that can be used as an adjunct to LDCT to diagnose lung cancer. Sputum is a biological fluid that can be obtained non-invasively and can be dissociated to release its cellular contents, providing a snapshot of the lung environment. We obtained sputum from current and former smokers with a 30+ pack-year smoking history and who were either confirmed to have lung cancer or at high risk of developing the disease. Dissociated sputum cells were counted, viability determined, and labeled with a panel of markers to separate leukocytes from non-leukocytes. After excluding debris and dead cells, including squamous epithelial cells, we identified reproducible population signatures and confirmed the samples’ lung origin. In addition to leukocyte and epithelial-specific fluorescent antibodies, we used the highly fluorescent meso-tetra(4-carboxyphenyl) porphyrin (TCPP), known to preferentially stain cancer (associated) cells. We looked for differences in cell characteristics, population size and fluorescence intensity that could be useful in distinguishing cancer samples from high-risk samples. We present our data demonstrating the feasibility of a flow cytometry platform to analyze sputum in a high-throughput and standardized matter for the diagnosis of lung cancer.
Collapse
|
9
|
Honke N, Wiest CJ, Pongratz G. β2-Adrenergic Receptor Expression and Intracellular Signaling in B Cells Are Highly Dynamic during Collagen-Induced Arthritis. Biomedicines 2022; 10:biomedicines10081950. [PMID: 36009497 PMCID: PMC9406045 DOI: 10.3390/biomedicines10081950] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/07/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
The sympathetic nervous system (SNS) has either a pro-inflammatory or anti-inflammatory effect, depending on the stage of arthritis. In the past, treatment of arthritic B cells with a β2-adrenergic receptor (β2-ADR) agonist has been shown to attenuate arthritis. In this study, the expression and signaling of β2-ADR in B cells during collagen-induced arthritis (CIA) were investigated to provide an explanation of why only B cells from arthritic mice are able to improve CIA. Splenic B cells were isolated via magnetic-activated cell sorting (MACS). Adrenergic receptors on B cells and intracellular β2-ADR downstream molecules (G protein-coupled receptor kinase 2 (GRK-2), β-Arrestin 2, p38 MAPK, extracellular signal-regulated kinase 1/2 (ERK1/2) and cAMP response element-binding protein (CREB)) were analyzed at different time points in naïve and arthritic B cells with and without stimulation of β2-ADR agonist terbutaline by flow cytometry. β2-ADR-expressing B cells increase during CIA without a change in receptor density. Moreover, we observed a profound downregulation of GRK-2 shortly after induction of arthritis and an increase in β-Arrestin 2 only at late stage of arthritis. The second messengers studied (p38, ERK1/2 and CREB) followed a biphasic course, characterized by a reduction at onset and an increase in established arthritis. Stimulation of CIA B cells with the β-ADR agonist terbutaline increased pp38 MAPK independent of the timepoint, while pERK1/2 and pCREB were enhanced only in the late phase of arthritis. The phosphorylation of p38 MAPK, ERK1/2 and CREB in the late phase of arthritis was associated with increased IL-10 produced by B10 cells. The change of β2-ADR expression and signaling during sustained inflammation might be an integral part of the switch from pro- to anti-inflammatory action of sympathetic mechanisms in late arthritis.
Collapse
Affiliation(s)
- Nadine Honke
- Department of Rheumatology, Hiller Research Center Rheumatology, University Hospital Düsseldorf, 40225 Düsseldorf, Germany
- Correspondence: (N.H.); (G.P.); Tel.: +49-(0)-2118106149 (N.H.); +49-(0)-9405-18-1078 (G.P.)
| | - Clemens J. Wiest
- Department of Internal Medicine II, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Georg Pongratz
- Department of Rheumatology, Hiller Research Center Rheumatology, University Hospital Düsseldorf, 40225 Düsseldorf, Germany
- Center for Rheumatologic Rehabilitation, Asklepios Clinic, 93077 Bad Abbach, Germany
- Medical Faculty of the University of Regensburg, 93053 Regensburg, Germany
- Correspondence: (N.H.); (G.P.); Tel.: +49-(0)-2118106149 (N.H.); +49-(0)-9405-18-1078 (G.P.)
| |
Collapse
|
10
|
Tan J, Li H, Ji C, Zhang L, Zhao C, Tang L, Zhang C, Sun Z, Tan W, Yuan Q. Electron transfer-triggered imaging of EGFR signaling activity. Nat Commun 2022; 13:594. [PMID: 35105871 PMCID: PMC8807759 DOI: 10.1038/s41467-022-28213-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023] Open
Abstract
In vivo electron transfer processes are closely related to the activation of signaling pathways, and, thus, affect various life processes. Indeed, the signaling pathway activation of key molecules may be associated with certain diseases. For example, epidermal growth factor receptor (EGFR) activation is related to the occurrence and development of tumors. Hence, monitoring the activation of EGFR-related signaling pathways can help reveal the progression of tumor development. However, it is challenging for current detection methods to monitor the activation of specific signaling pathways in complex biochemical reactions. Here we designed a highly sensitive and specific nanoprobe that enables in vivo imaging of electronic transfer over a broad range of spatial and temporal scales. By using the ferrocene-DNA polymer “wire”, the electrons transferred in a biochemical reaction can flow to persistent luminescent nanoparticles and change their electron distribution, thereby altering the optical signal of the particles. This electron transfer-triggered imaging probe enables mapping the activation of EGFR-related signaling pathways in a temporally and spatially precise manner. By offering precise visualization of signaling activity, this approach may offer a general platform not only for understanding molecular mechanisms in various biological processes but also for promoting disease therapies and drug evaluation. Here, the authors design a nanoprobe for in vivo imaging of electronic transfer, consisting of a ferrocene-DNA polymer to transfer electrons to luminescent nanoparticles, changing their optical signal. Using this probe, they map activation of EGFR signalling during tumour treatment.
Collapse
Affiliation(s)
- Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Hao Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China
| | - Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Chenxuan Zhao
- Department of Chemistry, ZJU-NHU United R&D Center, Zhejiang University, Hangzhou, 310027, P. R. China
| | - Liming Tang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Caixin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China
| | - Zhijun Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China.
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, School of Physics and Electronics, Hunan University, Changsha, 410082, China. .,The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Bio-medicine Ministry of Education, School & Hospital of Stomatology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, China.
| |
Collapse
|
11
|
Krzyzosiak A, Pitera AP, Bertolotti A. An Overview of Methods for Detecting eIF2α Phosphorylation and the Integrated Stress Response. Methods Mol Biol 2022; 2428:3-18. [PMID: 35171470 DOI: 10.1007/978-1-0716-1975-9_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Phosphorylation of the translation initiation factor eIF2α is an adaptive signaling event that is essential for cell and organismal survival from yeast to humans. It is central to the integrated stress response (ISR) that maintains cellular homeostasis in the face of threats ranging from viral infection, amino acid, oxygen, and heme deprivation to the accumulation of misfolded proteins in the endoplasmic reticulum. Phosphorylation of eIF2α has broad physiological, pathological, and therapeutic relevance. However, despite more than two decades of research and growing pharmacological interest, phosphorylation of eIF2α remains difficult to detect and quantify, because of its transient nature and because substoichiometric amounts of this modification are sufficient to profoundly reshape cellular physiology. This review aims to provide a roadmap for facilitating a robust evaluation of eIF2α phosphorylation and its downstream consequences in cells and organisms.
Collapse
|
12
|
Wagner A, Teufl M, Gold L, Lehner M, Obinger C, Sykacek P, Traxlmayr MW. PhosphoFlowSeq - A High-throughput Kinase Activity Assay for Screening Drug Resistance Mutations in EGFR. J Mol Biol 2021; 433:167210. [PMID: 34499921 DOI: 10.1016/j.jmb.2021.167210] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/29/2021] [Accepted: 08/14/2021] [Indexed: 12/30/2022]
Abstract
Drug resistance poses a major challenge for targeted cancer therapy. To be able to functionally screen large randomly mutated target gene libraries for drug resistance mutations, we developed a biochemically defined high-throughput assay termed PhosphoFlowSeq. Instead of selecting for proliferation or resistance to apoptosis, PhosphoFlowSeq directly analyzes the enzymatic activities of randomly mutated kinases, thereby reducing the dependency on the signaling network in the host cell. Moreover, simultaneous analysis of expression levels enables compensation for expression-based biases on a single cell level. Using EGFR and its kinase inhibitor erlotinib as a model system, we demonstrate that the clinically most relevant resistance mutation T790M is reproducibly detected at high frequencies after four independent PhosphoFlowSeq selection experiments. Moreover, upon decreasing the selection pressure, also mutations which only confer weak resistance were identified, including T854A and L792H. We expect that PhosphoFlowSeq will be a valuable tool for the prediction and functional screening of drug resistance mutations in kinases.
Collapse
Affiliation(s)
- Anja Wagner
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria; Department of Biotechnology, Institute of Molecular Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Magdalena Teufl
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Lukas Gold
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Manfred Lehner
- St. Anna Children's Cancer Research Institute, Vienna, Austria; Department of Pediatrics, St. Anna Kinderspital, Medical University of Vienna, Vienna, Austria
| | - Christian Obinger
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Peter Sykacek
- Department of Biotechnology, Institute for Computational Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Michael W Traxlmayr
- Department of Chemistry, Institute of Biochemistry, University of Natural Resources and Life Sciences, Vienna, Austria.
| |
Collapse
|
13
|
Roe CE, Hayes MJ, Barone SM, Irish JM. Training Novices in Generation and Analysis of High-Dimensional Human Cell Phospho-Flow Cytometry Data. ACTA ACUST UNITED AC 2021; 93:e71. [PMID: 32250555 DOI: 10.1002/cpcy.71] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
This article presents a single experiment designed to introduce a trainee to multiple advanced bench and analysis techniques, including high-dimensional cytometry, profiling cell signaling networks, functional assays with primary human tissue, and single-cell analysis with machine learning tools. The trainee is expected to have only minimal laboratory experience and is not required to have any prior training in flow cytometry, immunology, or data science. This article aims to introduce the advanced research areas with a design that is robust enough that novice trainees will succeed, flexible enough to allow some project customization, and fundamental enough that the skills and knowledge gained will provide a template for future experiments. For advanced users, the updated phospho-flow protocol and the established controls, best practices, and expected outcomes presented here also provide a framework for adapting these tools in new areas with unexplored biology. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Phospho-protein stimulation and mass cytometry data collection Support Protocol: Analysis of signaling mass cytometry data.
Collapse
Affiliation(s)
- Caroline E Roe
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Madeline J Hayes
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sierra M Barone
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jonathan M Irish
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee.,Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| |
Collapse
|
14
|
Sayed N, Huang Y, Nguyen K, Krejciova-Rajaniemi Z, Grawe AP, Gao T, Tibshirani R, Hastie T, Alpert A, Cui L, Kuznetsova T, Rosenberg-Hasson Y, Ostan R, Monti D, Lehallier B, Shen-Orr SS, Maecker HT, Dekker CL, Wyss-Coray T, Franceschi C, Jojic V, Haddad F, Montoya JG, Wu JC, Davis MM, Furman D. An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. ACTA ACUST UNITED AC 2021; 1:598-615. [PMID: 34888528 PMCID: PMC8654267 DOI: 10.1038/s43587-021-00082-y] [Citation(s) in RCA: 208] [Impact Index Per Article: 69.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
While many diseases of aging have been linked to the immunological system, immune metrics capable of identifying the most at-risk individuals are lacking. From the blood immunome of 1,001 individuals aged 8-96 years, we developed a deep-learning method based on patterns of systemic age-related inflammation. The resulting inflammatory clock of aging (iAge) tracked with multimorbidity, immunosenescence, frailty and cardiovascular aging, and is also associated with exceptional longevity in centenarians. The strongest contributor to iAge was the chemokine CXCL9, which was involved in cardiac aging, adverse cardiac remodeling and poor vascular function. Furthermore, aging endothelial cells in human and mice show loss of function, cellular senescence and hallmark phenotypes of arterial stiffness, all of which are reversed by silencing CXCL9. In conclusion, we identify a key role of CXCL9 in age-related chronic inflammation and derive a metric for multimorbidity that can be utilized for the early detection of age-related clinical phenotypes.
Collapse
|
15
|
Tracey LJ, An Y, Justice MJ. CyTOF: An Emerging Technology for Single-Cell Proteomics in the Mouse. Curr Protoc 2021; 1:e118. [PMID: 33887117 DOI: 10.1002/cpz1.118] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The ability to analyze the proteome of single cells is critical for the advancement of studies of steady-state and pathological processes. Mass cytometry, or CyTOF, combines principles of mass spectrometry and flow cytometry to enable single-cell analysis of protein expression. CyTOF can simultaneously assess DNA content and proteins and has the capacity to measure 40 to 100 parameters in each cell. Applying this technology to tissues or cells on slides, termed imaging mass cytometry (IMC), allows for visualization of normal and diseased tissues in situ. The high-dimensional proteomic analysis that can be undertaken with CyTOF and IMC has the potential to enhance our understanding of complex and heterogeneous developmental and disease pathways. This article will describe the CyTOF experimental workflow, including reagent selection, sample preparation, and data analysis. CyTOF is compared to flow cytometry, focusing on the strengths and weaknesses of these powerful techniques. Importantly, we review key studies in mouse models of human disease that highlight the strength of CyTOF and IMC to drive discovery research and therapeutic advancement. © 2021 Wiley Periodicals LLC.
Collapse
Affiliation(s)
- Lauren J Tracey
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yeji An
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Monica J Justice
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
16
|
Abstract
IL-4 production is associated with low-avidity, poorly cytotoxic T cell induction that contributes to viral immune evasion and the failure of T cell-based vaccines. Yet, the precise mechanisms that regulate IL-4 signalling in T cells remain elusive. Mounting evidence indicates that cells can dynamically alter their IL-4/IL-13 receptor signature to modulate downstream immune outcomes upon pathogen encounter. Here, we describe how naïve (CD62L+CD44lo-mid) CD4 and CD8 T cells distinctly engage both STAT6 and STAT3 in response to IL-4. We further show that IL-4R⍺ expression is both time- and IL-4 concentration-dependent. Remarkably, our findings reveal that STAT3 inhibition can ablate IL-4R⍺ and affect transcriptional expression of other Stat and Jak family members. By extension, the loss of STAT3 lead to aberrant STAT6 phosphorylation, revealing an inter-regulatory relationship between the two transcription factors. Moreover, IL-4 stimulation down-regulated TGF-β1 and IFN-γR1 expression on naïve T cells, possibly signifying the broad regulatory implications of IL-4 in conditioning lineage commitment decisions during early infection. Surprisingly, naïve T cells were unresponsive to IL-13 stimulation, unlike dendritic cells. Collectively, these findings could be exploited to inform more efficacious vaccines, as well as design treatments against IL-4/IL-13-associated disease conditions.
Collapse
|
17
|
Koenig A, Charmetant X, Barba T, Sicard A, Espi M, Dussurgey S, Thaunat O. Improved cell signaling analysis by biofunctionalized nanospheres and imaging flow cytometry. Cytometry A 2021; 99:1079-1090. [PMID: 33866668 DOI: 10.1002/cyto.a.24354] [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: 12/11/2020] [Revised: 03/16/2021] [Accepted: 04/07/2021] [Indexed: 11/11/2022]
Abstract
The analysis of immune cell signaling is critical for the understanding of the biology and pathology of the immune system, and thus a mandatory step for the development of efficient biomarkers and targeted therapies. Phosflow, which has progressively replaced the traditional western blot approach, relies on flow cytometry to analyze various signaling pathways at a single-cell level. This technique however suffers a lack of sensitivity largely due to the low signal/noise ratio that characterizes cell signaling analysis. In this study, we describe a new technique, which combines the use of biofunctionalized nanospheres (i.e., synthetic particulate antigens, SPAg) to stimulate the immune cells in suspension and imaging flow cytometry to identify homogenously-stimulated cells and quantify the activity of the chosen signaling pathway in selected subcellular regions of interest. Using BCR signaling as model, we demonstrate that SIBERIAN (SPAg-assIsted suB-cEllulaR sIgnaling ANalysis) allows assessing immune cell signaling with unprecedented sensitivity and specificity.
Collapse
Affiliation(s)
- Alice Koenig
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Xavier Charmetant
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Thomas Barba
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Antoine Sicard
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Maxime Espi
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| | - Sébastien Dussurgey
- University of Lyon, ENS de Lyon, Inserm, CNRS SFR Biosciences US8 UMS3444, UCBL, Lyon, France
| | - Olivier Thaunat
- CIRI, INSERM U1111, Université Claude Bernard Lyon I, CNRS UMR5308, Ecole Normale Supérieure de Lyon, University of Lyon, Lyon, France.,Department of Transplantation, Nephrology and Clinical Immunology, Hospices Civils de Lyon, Edouard Herriot Hospital, Lyon, France.,Lyon-Est Medical Faculty, Claude Bernard University (Lyon 1), Lyon, France
| |
Collapse
|
18
|
Flanagan SP, Fogel R, Edkins AL, Ho LSJ, Limson J. Nonspecific nuclear uptake of anti-MUC1 aptamers by dead cells: the role of cell viability monitoring in aptamer targeting of membrane-bound protein cancer biomarkers. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:1191-1203. [PMID: 33605950 DOI: 10.1039/d0ay01878c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Most aptamers targeting cell-expressed antigens are intended for in vivo application, however, these sequences are commonly generated in vitro against synthetic oligopeptide epitopes or recombinant proteins. As these in vitro analogues frequently do not mimic the in vivo target within an endogenous environment, the evolved aptamers are often prone to nonspecific binding. The presence of dead cells and cellular debris further complicate aptamer targeting, due to their high nonspecific affinities to single-stranded DNA. Despite these known limitations, assessment of cell viability and/or the removal of dead cells is rarely applied as part of the methodology during in vivo testing of aptamer binding. Furthermore, the extent and route(s) by which dead cells uptake existing aptamers remains to be determined in the literature. For this purpose, the previously reported aptamer sequences 5TR1, 5TR4, 5TRG2 and S22 - enriched against the MUC1 tumour marker of the mucin glycoprotein family - were used as model sequences to evaluate the influence of cell viability and the presence of nontarget cell-expressed protein on aptamer binding to the MUC1 expressing human cancer cell lines MCF-7, Hs578T, SW480, and SW620. From fluorescence microscopy analysis, all tested aptamers demonstrated extensive nonspecific uptake within the nuclei of dead cells with compromised membrane integrities. Using fluorescent-activated cell sorting (FACS), the inclusion of excess double-stranded DNA as a blocking agent showed no effect on nonspecific aptamer uptake by dead cells. Further nonspecific binding to cell-membrane bound and intracellular protein was evident for each aptamer sequence, as assessed by southwestern blotting and FACS. These factors likely contributed to the ∼120-fold greater binding response of the 5TR1 aptamer to dead MCF-7 cells over equivalent live cell populations. The identification of dead cells and cellular debris using viability stains and the subsequent exclusion of these cells from FACS analysis was identified as an essential requirement for the evaluation of aptamer binding specificity to live cell populations of the cancer cell lines MCF-7, Hs578T and SW480. The research findings stress the importance of dead cell uptake and more comprehensive cell viability screening to validate novel aptamer sequences for diagnostic and therapeutic application.
Collapse
|
19
|
Abstract
Flow cytometry (FCM) is a sophisticated technique that works on the principle of light scattering and fluorescence emission by the specific fluorescent probe-labeled cells as they pass through a laser beam. It offers several unique advantages as it allows fast, relatively quantitative, multiparametric analysis of cell populations at the single cell level. In addition, it also enables physical sorting of the cells to separate the subpopulations based on different parameters. In this constantly evolving field, innovative technologies such as imaging FCM, mass cytometry and Raman FCM are being developed in order to address limitations of traditional FCM. This review explains the general principles, main applications and recent advances in the field of FCM.
Collapse
|
20
|
Märcher A, Palmfeldt J, Nisavic M, Gothelf KV. A Reagent for Amine‐Directed Conjugation to IgG1 Antibodies. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202013911] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Anders Märcher
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine Aarhus University Brendstrupgårdsvej 21A 8200 Aarhus N Denmark
| | - Marija Nisavic
- Department of Chemistry and Department of Clinical Medicine Aarhus University Brendstrupgårdsvej 21A 8200 Aarhus N Denmark
| | - Kurt V. Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| |
Collapse
|
21
|
Märcher A, Palmfeldt J, Nisavic M, Gothelf KV. A Reagent for Amine‐Directed Conjugation to IgG1 Antibodies. Angew Chem Int Ed Engl 2021; 60:6539-6544. [DOI: 10.1002/anie.202013911] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/28/2020] [Indexed: 01/24/2023]
Affiliation(s)
- Anders Märcher
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| | - Johan Palmfeldt
- Department of Clinical Medicine Aarhus University Brendstrupgårdsvej 21A 8200 Aarhus N Denmark
| | - Marija Nisavic
- Department of Chemistry and Department of Clinical Medicine Aarhus University Brendstrupgårdsvej 21A 8200 Aarhus N Denmark
| | - Kurt V. Gothelf
- Department of Chemistry and Interdisciplinary Nanoscience Centre (iNANO) Aarhus University Gustav Wieds Vej 14 8000 Aarhus Denmark
| |
Collapse
|
22
|
Wang L, Hu Z, Wu S, Pan J, Xu X, Niu X. A peroxidase-mimicking Zr-based MOF colorimetric sensing array to quantify and discriminate phosphorylated proteins. Anal Chim Acta 2020; 1121:26-34. [DOI: 10.1016/j.aca.2020.04.073] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/17/2020] [Accepted: 04/27/2020] [Indexed: 02/08/2023]
|
23
|
Bonaccorso P, Bugarin C, Buracchi C, Fazio G, Biondi A, Lo Nigro L, Gaipa G. Single‐cell profiling of pediatric T‐cell acute lymphoblastic leukemia: Impact of
PTEN
exon 7 mutation on
PI3K
/
Akt
and
JAK–STAT
signaling pathways. CYTOMETRY PART B-CLINICAL CYTOMETRY 2020; 98:491-503. [DOI: 10.1002/cyto.b.21882] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Paola Bonaccorso
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
- Center of Pediatric Hematology Oncology Azienda Policlinico‐OVE, University of Catania Catania Italy
| | - Cristina Bugarin
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
| | - Chiara Buracchi
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
| | - Grazia Fazio
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
| | - Andrea Biondi
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
- Pediatric Clinic University of Milano Bicocca, Fondazione MBBM/Ospedale San Gerardo Monza Italy
| | - Luca Lo Nigro
- Center of Pediatric Hematology Oncology Azienda Policlinico‐OVE, University of Catania Catania Italy
| | - Giuseppe Gaipa
- M. Tettamanti Research Center University of Milano‐Bicocca, San Gerardo Hospital Monza Italy
| |
Collapse
|
24
|
Rip J, de Bruijn MJW, Kaptein A, Hendriks RW, Corneth OBJ. Phosphoflow Protocol for Signaling Studies in Human and Murine B Cell Subpopulations. THE JOURNAL OF IMMUNOLOGY 2020; 204:2852-2863. [PMID: 32253241 DOI: 10.4049/jimmunol.1901117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 03/16/2020] [Indexed: 11/19/2022]
Abstract
BCR signaling, involving phosphorylation of various downstream molecules, including kinases, lipases, and linkers, is crucial for B cell selection, survival, proliferation, and differentiation. Phosphoflow cytometry (phosphoflow) is a single-cell-based technique to measure phosphorylated intracellular proteins, providing a more quantitative read-out than Western blotting. Recent advances in phosphoflow basically allow simultaneous analysis of protein phosphorylation in B cell (sub)populations, without prior cell sorting. However, fixation and permeabilization procedures required for phosphoflow often affect cell surface epitopes or mAb conjugates, precluding the evaluation of the phosphorylation status of signaling proteins across different B cell subpopulations present in a single sample. In this study, we report a versatile phosphoflow protocol allowing extensive staining of B cell subpopulations in human peripheral blood or various anatomical compartments in the mouse, starting from freshly isolated or frozen cell suspensions. Both human and mouse B cell subpopulations showed different basal and BCR stimulation-induced phosphorylation levels of downstream signaling proteins. For example, peritoneal B-1 cells and splenic marginal zone B cells exhibited significantly increased basal (ex vivo) signaling and increased responsiveness to in vitro BCR stimulation compared with peritoneal B-2 cells and splenic follicular B cells, respectively. In addition, whereas stimulation with anti-IgM or anti-Igκ L chain Abs resulted in strong pCD79a and pPLCγ2 signals, IgD stimulation only induced CD79a but not pPLCγ2 phosphorylation. In summary, the protocol is user friendly and quantifies BCR-mediated phosphorylation with high sensitivity at the single-cell level, in combination with extensive staining to identify individual B cell development and differentiation stages.
Collapse
Affiliation(s)
- Jasper Rip
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, NL 3000 CA Rotterdam, the Netherlands; and
| | - Marjolein J W de Bruijn
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, NL 3000 CA Rotterdam, the Netherlands; and
| | | | - Rudi W Hendriks
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, NL 3000 CA Rotterdam, the Netherlands; and
| | - Odilia B J Corneth
- Department of Pulmonary Medicine, Erasmus MC Rotterdam, NL 3000 CA Rotterdam, the Netherlands; and
| |
Collapse
|
25
|
Mu T, Toyoda H, Kimura Y, Yamada M, Utoh R, Umeno D, Seki M. Laborless, Automated Microfluidic Tandem Cell Processor for Visualizing Intracellular Molecules of Mammalian Cells. Anal Chem 2020; 92:2580-2588. [PMID: 31822057 DOI: 10.1021/acs.analchem.9b04288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Visualization and quantification of intracellular molecules of mammalian cells are crucial steps in clinical diagnosis, drug development, and basic biological research. However, conventional methods rely mostly on labor-intensive, centrifugation-based manual operations for exchanging the cell carrier medium and have limited reproducibility and recovery efficiency. Here we present a microfluidic cell processor that can perform four-step exchange of carrier medium, simply by introducing a cell suspension and fluid reagents into the device. The reaction time period for each reaction step, including fixation, membrane permeabilization, and staining, was tunable in the range of 2 to 15 min by adjusting the volume of the reaction tube connecting the neighboring exchanger modules. We double-stained the cell nucleus and cytoskeleton (F-actin) using the presented device with an overall reaction period of ∼30 min, achieving a high recovery ratio and high staining efficiency. Additionally, intracellular cytokine (IL-2) was visualized for T cells to demonstrate the feasibility of the device as a pretreatment system for downstream flow-cytometric analysis. The presented approach would facilitate the development of laborless, automated microfluidic systems that integrate cell processing and analysis operations and would pave a new path to high-throughput biological experiments.
Collapse
Affiliation(s)
- Tinglin Mu
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Hajime Toyoda
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Yuki Kimura
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Masumi Yamada
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Rie Utoh
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Daisuke Umeno
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| | - Minoru Seki
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering , Chiba University , 1-33 Yayoi-cho , Inage-ku , Chiba 263-8522 , Japan
| |
Collapse
|
26
|
Whole blood preservation methods alter chemokine receptor detection in mass cytometry experiments. J Immunol Methods 2020; 476:112673. [DOI: 10.1016/j.jim.2019.112673] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Revised: 09/19/2019] [Accepted: 09/19/2019] [Indexed: 12/21/2022]
|
27
|
Abramczyk H, Imiela A, Brożek-Płuska B, Kopeć M, Surmacki J, Śliwińska A. Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers. Cancers (Basel) 2019; 11:E2017. [PMID: 31847192 PMCID: PMC6966530 DOI: 10.3390/cancers11122017] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/03/2019] [Accepted: 12/11/2019] [Indexed: 12/30/2022] Open
Abstract
(1) Background: Novel methods are required for analysing post-translational modifications of protein phosphorylation by visualizing biochemical landscapes of proteins in human normal and cancerous tissues and cells. (2) Methods: A label-free Raman method is presented for detecting spectral changes that arise in proteins due to phosphorylation in the tissue of human breasts, small intestines, and brain tumours, as well as in the normal human astrocytes and primary glioblastoma U-87 MG cell lines. Raman spectroscopy and Raman imaging are effective tools for monitoring and analysing the vibrations of functional groups involved in aberrant phosphorylation in cancer without any phosphorecognition of tag molecules. (3) Results: Our results based on 35 fresh human cancer and normal tissues prove that the aberrant tyrosine phosphorylation monitored by the unique spectral signatures of Raman vibrations is a universal characteristic in the metabolic regulation in different types of cancers. Overexpressed tyrosine phosphorylation in the human breast, small intestine and brain tissues and in the human primary glioblastoma U-87 MG cell line was monitored by using Raman biomarkers. (4) We showed that the bands at 1586 cm-1 and 829 cm-1, corresponding to phosphorylated tyrosine, play a pivotal role as a Raman biomarker of the phosphorylation status in aggressive cancers. We found that the best Raman biomarker of phosphorylation is the 1586/829 ratio showing the statistical significance at p Values of ≤ 0.05. (5) Conclusions: Raman spectroscopy and imaging have the potential to be used as screening functional assays to detect phosphorylated target proteins and will help researchers to understand the role of phosphorylation in cellular processes and cancer progression. The abnormal and excessive high level of tyrosine phosphorylation in cancer samples compared with normal samples was found in the cancerous human tissue of breasts, small intestines and brain tumours, as well as in the mitochondria and lipid droplets of the glioblastoma U-87 MG cell line. Detailed insights are presented into the intracellular oncogenic metabolic pathways mediated by phosphorylated tyrosine.
Collapse
Affiliation(s)
- Halina Abramczyk
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Anna Imiela
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Beata Brożek-Płuska
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Monika Kopeć
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Jakub Surmacki
- Laboratory of Laser Molecular Spectroscopy, Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, 93-590 Lodz, Poland; (A.I.); (B.B.-P.); (M.K.); (J.S.)
| | - Agnieszka Śliwińska
- Faculty of Medicine, Medical University of Lodz, Chair of Department of Nucleic Acids Biochemistry, Pomorska 251, 92-213 Lodz, Poland;
| |
Collapse
|
28
|
Sharma R, Sharma A, Kumar A, Jaganathan BG. Phospho-protein Analysis in Adherent Cells Using Flow Cytometry. Bio Protoc 2019; 9:e3395. [PMID: 33654896 DOI: 10.21769/bioprotoc.3395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 11/02/2022] Open
Abstract
Protein phosphorylation is one of the most important post-translational modifications, which acts as a reversible on or off switch for the activity of a large number of proteins. Analyzing the phosphorylation status of different proteins can reveal the alterations in the state of the cells in response to cellular damage, cancer and pharmaceutical drugs. Techniques such as mass spectrometry, radiolabeling, 2D-gel electrophoresis and western blotting are used to quantify protein phosphorylation. These assays can quantify phosphorylation in the bulk population of cells, however, flow cytometry can couple cell surface marker expression data with phosphorylation data to understand differential signaling in a sub-population within a heterogeneous population of cells. Our protocol describes the use of flow-cytometry for rapid and single cell-based quantification of intracellular phospho-protein with the help of anti-phospho protein specific antibody.
Collapse
Affiliation(s)
- Renu Sharma
- Stem Cells and Cancer Biology Group, Department of Biosciences and Bioengineering, Guwahati, India
| | - Amit Sharma
- Stem Cells and Cancer Biology Group, Department of Biosciences and Bioengineering, Guwahati, India
| | - Atul Kumar
- Stem Cells and Cancer Biology Group, Department of Biosciences and Bioengineering, Guwahati, India
| | - Bithiah Grace Jaganathan
- Stem Cells and Cancer Biology Group, Department of Biosciences and Bioengineering, Guwahati, India
| |
Collapse
|
29
|
Kuczera D, Assolini JP, Tomiotto-Pellissier F, Pavanelli WR, Silveira GF. Highlights for Dengue Immunopathogenesis: Antibody-Dependent Enhancement, Cytokine Storm, and Beyond. J Interferon Cytokine Res 2019; 38:69-80. [PMID: 29443656 DOI: 10.1089/jir.2017.0037] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Infection with dengue virus (DENV) can lead to a wide spectrum of clinical presentations, ranging from asymptomatic infection to death. It is estimated that the disease manifests only in 90 million cases out of the total 390 million yearly infections. Even though research has not yet elucidated which are the precise pathophysiological mechanisms that trigger severe forms of dengue, the infection elicits a critical immune response significant for dengue pathogenesis development. Understanding how the immune response to DENV is established and how it can resolve the infection or turn into an immunopathology is of great importance in DENV research. Currently, studies have extensively debated 2 hypotheses involving immune response: antibody-dependent enhancement and cytokine storm. However, despite its undeniable importance in severe forms of the disease, these 2 hypotheses are based on a primed immune status resulting from previous heterologous infection, abstaining them from explaining the severe forms of dengue in naive immune subjects, for example. Thus, it seems that a more intricate arrangement of causes and conditions must be achieved to severe dengue to occur. Among them, the cytokine network signature elicited, in association with viral aspects deserves special attention regarding the establishment of infection and evolution to pathogenesis. In this work, we intend to shed light on how those elements contribute to severe dengue development.
Collapse
Affiliation(s)
- Diogo Kuczera
- 1 Laboratório de Virologia Molecular, Instituto Carlos Chagas , ICC/Fiocruz/PR, Curitiba, Brazil
| | - João Paulo Assolini
- 2 Departamento de Ciências Patológicas, Centro de Ciências Biológicas , Universidade Estadual de Londrina, Londrina, Brazil
| | - Fernanda Tomiotto-Pellissier
- 2 Departamento de Ciências Patológicas, Centro de Ciências Biológicas , Universidade Estadual de Londrina, Londrina, Brazil
| | - Wander Rogério Pavanelli
- 2 Departamento de Ciências Patológicas, Centro de Ciências Biológicas , Universidade Estadual de Londrina, Londrina, Brazil
| | | |
Collapse
|
30
|
Vazquez J, Ong IM, Stanic AK. Single-cell technologies in reproductive immunology. Am J Reprod Immunol 2019; 82:e13157. [PMID: 31206899 PMCID: PMC6697222 DOI: 10.1111/aji.13157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/06/2019] [Accepted: 06/07/2019] [Indexed: 11/29/2022] Open
Abstract
The maternal-fetal interface represents a unique immune privileged site that maintains the ability to defend against pathogens while orchestrating the necessary tissue remodeling required for placentation. The recent discovery of novel cellular families (innate lymphoid cells, tissue-resident NK cells) suggests that our understanding of the decidual immunome is incomplete. To understand this complex milieu, new technological developments allow reproductive immunologists to collect increasingly complex data at a cellular resolution. Polychromatic flow cytometry allows for greater resolution in the identification of novel cell types by surface and intracellular protein. Single-cell RNA-seq coupled with microfluidics allows for efficient cellular transcriptomics. The extreme dimensionality and size of data sets generated, however, requires the application of novel computational approaches for unbiased analysis. There are now multiple dimensionality reduction (tSNE, SPADE) and visualization tools (SPICE) that allow researchers to efficiently analyze flow cytometry data. Development of computational tools has also been extended to RNA-seq data (including scRNA-seq), which requires specific analytical tools. Here, we provide an overview and a brief primer for the reproductive immunology community on data acquisition and computational tools for the analysis of complex flow cytometry and RNA-seq data.
Collapse
Affiliation(s)
- Jessica Vazquez
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
| | - Irene M Ong
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
- Division of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI
| | - Aleksandar K. Stanic
- Division of Reproductive Sciences, University of Wisconsin-Madison, Madison, WI
- Division of Reproductive Endocrinology and Infertility, Departments of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI
| |
Collapse
|
31
|
Civelekoglu O, Wang N, Boya M, Ozkaya-Ahmadov T, Liu R, Sarioglu AF. Electronic profiling of membrane antigen expression via immunomagnetic cell manipulation. LAB ON A CHIP 2019; 19:2444-2455. [PMID: 31199420 DOI: 10.1039/c9lc00297a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Membrane antigens control cell function by regulating biochemical interactions and hence are routinely used as diagnostic and prognostic targets in biomedicine. Fluorescent labeling and subsequent optical interrogation of cell membrane antigens, while highly effective, limit expression profiling to centralized facilities that can afford and operate complex instrumentation. Here, we introduce a cytometry technique that computes surface expression of immunomagnetically labeled cells by electrically tracking their trajectory under a magnetic field gradient on a microfluidic chip with a throughput of >500 cells per min. In addition to enabling the creation of a frugal cytometry platform, this immunomagnetic cell manipulation-based measurement approach allows direct expression profiling of target subpopulations from non-purified samples. We applied our technology to measure epithelial cell adhesion molecule expression on human breast cancer cells. Once calibrated, surface expression and size measurements match remarkably well with fluorescence-based measurements from a commercial flow cytometer. Quantitative measurements of biochemical and biophysical cell characteristics with a disposable cytometer have the potential to impact point of care testing of clinical samples particularly in resource limited settings.
Collapse
Affiliation(s)
- Ozgun Civelekoglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | - Ningquan Wang
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | - Mert Boya
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | - Tevhide Ozkaya-Ahmadov
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | - Ruxiu Liu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
| | - A Fatih Sarioglu
- School of Electrical and Computer Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. and Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA and Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| |
Collapse
|
32
|
Chu KL, Batista NV, Wang KC, Zhou AC, Watts TH. GITRL on inflammatory antigen presenting cells in the lung parenchyma provides signal 4 for T-cell accumulation and tissue-resident memory T-cell formation. Mucosal Immunol 2019; 12:363-377. [PMID: 30487647 DOI: 10.1038/s41385-018-0105-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 10/02/2018] [Accepted: 10/27/2018] [Indexed: 02/07/2023]
Abstract
T-cell responses in the lung are critical for protection against respiratory pathogens. TNFR superfamily members play important roles in providing survival signals to T cells during respiratory infections. However, whether these signals take place mainly during priming in the secondary lymphoid organs and/or in the peripheral tissues remains unknown. Here we show that under conditions of competition, GITR provides a T-cell intrinsic advantage to both CD4 and CD8 effector T cells in the lung tissue, as well as for the formation of CD4 and CD8 tissue-resident memory T cells during respiratory influenza infection in mice. In contrast, under non-competitive conditions, GITR has a preferential effect on CD8 over CD4 T cells. The nucleoprotein-specific CD8 T-cell response partially compensated for GITR deficiency by expansion of higher affinity T cells; whereas, the polymerase-specific response was less flexible and more GITR dependent. Following influenza infection, GITR is expressed on lung T cells and GITRL is preferentially expressed on lung monocyte-derived inflammatory antigen presenting cells. Accordingly, we show that GITR+/+ T cells in the lung parenchyma express more phosphorylated-ribosomal protein S6 than their GITR-/- counterparts. Thus, GITR signaling within the lung tissue critically regulates effector and tissue-resident memory T-cell accumulation.
Collapse
Affiliation(s)
- Kuan-Lun Chu
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | | | - Kuan Chung Wang
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Angela C Zhou
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Tania H Watts
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
| |
Collapse
|
33
|
Davies R, Sarkar I, Hammenfors D, Bergum B, Vogelsang P, Solberg SM, Gavasso S, Brun JG, Jonsson R, Appel S. Single Cell Based Phosphorylation Profiling Identifies Alterations in Toll-Like Receptor 7 and 9 Signaling in Patients With Primary Sjögren's Syndrome. Front Immunol 2019; 10:281. [PMID: 30846988 PMCID: PMC6393381 DOI: 10.3389/fimmu.2019.00281] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 02/01/2019] [Indexed: 11/13/2022] Open
Abstract
Primary Sjögren's syndrome (pSS) is associated with polymorphisms and mRNA expression profiles that are indicative of an exaggerated innate and type I IFN immune response. Excessive activation potential of signaling pathways may play a role in this profile, but the intracellular signaling profile of the disease is not well characterized. To gain insights into potentially dysfunctional intracellular signaling profiles of pSS patients we conducted an exploratory analysis of MAPK/ERK and JAK/STAT signaling networks in peripheral blood mononuclear cells (PBMC) from 25 female pSS patients and 25 female age-matched healthy donors using phospho-specific flow cytometry. We analyzed unstimulated samples, as well as samples during a 4 h time period following activation of Toll-like receptor (TLR) 7 and 9. Expression levels of MxA, IFI44, OAS1, GBP1, and GBP2 in PBMC were analyzed by real-time PCR. Cytokine levels in plasma were determined using a 25-plex Luminex-assay. Principal component analysis (PCA) showed that basal phosphorylation profiles could be used to differentiate pSS patients from healthy donor samples by stronger intracellular signaling pathway activation in NK and T cells relative to B cells. Stimulation of PBMC with TLR7 and -9 ligands showed significant differences in the phosphorylation profiles between samples from pSS patients and healthy donors. Including clinical parameters such as extraglandular manifestations (EGM), we observed stronger responses of NF-κB and STAT3 S727 in B cells from EGM-negative patients compared to EGM-positive patients and healthy controls. Plasma cytokine levels were correlated to the basal phosphorylation levels in these patients. In addition, 70% of the patients had a positive IFN score. These patients differed from the IFN score negative patients regarding their phosphorylation profiles and their plasma cytokine levels. In conclusion, we here report increased signaling potentials in peripheral B cells of pSS patients in response to TLR7 and -9 stimulation through STAT3 S727 and NF-κB that correlate with a type I IFN signature. Induction of these pathways could contribute to the generation of a type I IFN signature in pSS. Patients displaying elevated potentiation of STAT3 S727 and NF-κB signaling could therefore benefit from therapies targeting these pathways.
Collapse
Affiliation(s)
- Richard Davies
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Irene Sarkar
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Daniel Hammenfors
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Brith Bergum
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Petra Vogelsang
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Silje M Solberg
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Dermatology, Haukeland University Hospital, Bergen, Norway
| | - Sonia Gavasso
- Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Johan G Brun
- Department of Rheumatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Roland Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - Silke Appel
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| |
Collapse
|
34
|
Kumar S, Sharma SK, Kaushik G, Avti PK, Pandey SK, Sarma P, Medhi B, Khanduja KL. Therapeutic potential of arachidonyl trifluromethyl ketone, a cytosolic phospholipaseA 2 IVA specific inhibitor, in cigarette smoke condensate-induced pathological conditions in alveolar type I & II epithelial cells. Toxicol In Vitro 2019; 54:215-223. [PMID: 30253184 DOI: 10.1016/j.tiv.2018.09.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/07/2018] [Accepted: 09/19/2018] [Indexed: 11/18/2022]
Abstract
Cigarette smoke is responsible for multiple disorders and causes almost 10 million annual deaths globally but underlying mechanisms are still underexplored. Continuous exposure of Cigarette smoke condensate (CSC) leads to cytosolic phospholipase A2 (cPLA2) mediated high free radicals where cPLA2s seems to play crucial role in generated various patho-physiological conditions such as chronic inflammation, oxidative stress and cancer. In this view, we assessed the therapeutic potential of arachidonyl trifluromethyl ketone (ATK), a cPLA2 inhibitor, via pharmacological inhibition of most expressible CSC-induced cPLA2 group IVA in type-I and type-II alveolar epithelial cells. The In Vitro inhibitory effect of ATK on CSC-induced PLA2 activity and its cellular role were assessed in terms of cell viability, fluorescein diacetate (FDA) dye uptake assay for membrane integrity, reactive oxygen species (ROS)/reactive nitrogen species (RNS) levels and pro apoptotic as well as anti apoptosis markers via flow cytometry, along with extracellular signal-regulated kinases (ERK) levels using enzyme-linked immunosorbent assay (ELISA). The experimental findings demonstrated that ATK acts as potent inhibitor of cPLA2 activity and shown its effectiveness as therapeutic agent by significantly mimicking CSC-induced levels of free radicals, primary apoptosis, ratio of pro-apoptotic/apoptotic proteins and levels of ERK whereas protected cells from loss of cell viability and membrane integrity. Thus, this study is an important step towards the opening up of avenues for the applicability of the cPLA2 isoform specific inhibitors such as ATK for pre-clinical and clinical studies and could be beneficial during smoking-induced lung pathological conditions.
Collapse
Affiliation(s)
- Subodh Kumar
- Department of Biophysics, PGIMER, Chandigarh 160012, India.
| | - Sanjeev Kumar Sharma
- Department of Biophysics, PGIMER, Chandigarh 160012, India; Rajiv Gandhi Cancer Institute & Research Centre (RGCIRC), Rohini, New Delhi 110085, India
| | - Gaurav Kaushik
- Department of Biophysics, PGIMER, Chandigarh 160012, India; Surgery, School of Medicine, KU Medical Center (KUMC), Kansas City KS-66160, USA
| | | | - Satish Kumar Pandey
- Central Scientific Instruments Organisation (CSIO), Chandigarh 160030, India
| | - Phulen Sarma
- Present address: Department of Pharmacology, PGIMER, Chandigarh 160012, India
| | - Bikash Medhi
- Present address: Department of Pharmacology, PGIMER, Chandigarh 160012, India
| | | |
Collapse
|
35
|
An Analysis of the Intracellular Signal Transduction of Peripheral Blood Leukocytes in Animal Models of Diabetes Using Flow Cytometry. Methods Mol Biol 2018. [PMID: 30535695 DOI: 10.1007/978-1-4939-8994-2_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Various complications of diabetes are induced by the augmentation of chronic inflammation and attenuation of immunity. Leukocytes, which play major roles in inflammation and immune responses, are affected by the glycemic status and blood insulin level. In this chapter, we explain a method for analyzing the signal transduction pathway of leukocytes in peripheral blood. This method using flow cytometry can analyze a small amount of blood (50-100 μL/sample) without leukocyte purification. Thus, this procedure is useful for experiments using small-animal models of diabetes, such as mice and rats. We also introduce a new method for classifying intracellular signal transduction by combining the dispersibility level and the activation level of the signaling molecules.
Collapse
|
36
|
Hermansen JU, Tjønnfjord GE, Munthe LA, Taskén K, Skånland SS. Cryopreservation of primary B cells minimally influences their signaling responses. Sci Rep 2018; 8:17651. [PMID: 30518828 PMCID: PMC6281576 DOI: 10.1038/s41598-018-36121-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023] Open
Abstract
Phospho flow is a powerful approach to detect cell signaling aberrations, identify biomarkers and assess pharmacodynamics, and can be performed using cryopreserved samples. The effects of cryopreservation on signaling responses and the reproducibility of phospho flow measurements are however unknown in many cell systems. Here, B lymphocytes were isolated from healthy donors and patients with the B cell malignancy chronic lymphocytic leukemia and analyzed by phospho flow using phospho-specific antibodies targeting 20 different protein epitopes. Cells were analyzed both at basal conditions and after activation of cluster of differentiation 40 (CD40) or the B cell receptor. Pharmacodynamics of the novel pathway inhibitor ibrutinib was also assessed. At all conditions, fresh cells were compared to cryopreserved cells. Minimal variation between fresh and frozen samples was detected. Reproducibility was tested by running samples from the same donors in different experiments. The results demonstrate reproducibility across different phospho flow runs and support the use of cryopreserved samples in future phospho flow studies of B lymphocytes.
Collapse
Affiliation(s)
- Johanne U Hermansen
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Geir E Tjønnfjord
- Department of Haematology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway
| | - Ludvig A Munthe
- K. G. Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway.,Department of Immunology, Oslo University Hospital, Oslo, Norway
| | - Kjetil Taskén
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,K. G. Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway.,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway.,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Sigrid S Skånland
- Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway. .,K. G. Jebsen Centre for B Cell Malignancies, University of Oslo, Oslo, Norway. .,K. G. Jebsen Centre for Cancer Immunotherapy, University of Oslo, Oslo, Norway. .,Department of Cancer Immunology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| |
Collapse
|
37
|
Peña FJ, Ortiz Rodriguez JM, Gil MC, Ortega Ferrusola C. Flow cytometry analysis of spermatozoa: Is it time for flow spermetry? Reprod Domest Anim 2018; 53 Suppl 2:37-45. [DOI: 10.1111/rda.13261] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/06/2018] [Accepted: 05/01/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Fernando J. Peña
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
| | - Jose M. Ortiz Rodriguez
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
| | - María C. Gil
- Laboratory of Equine Reproduction and Spermatology; University of Extremadura; Cáceres Spain
| | | |
Collapse
|
38
|
Lim SY, Rizos H. Immune cell profiling in the age of immune checkpoint inhibitors: implications for biomarker discovery and understanding of resistance mechanisms. Mamm Genome 2018; 29:866-878. [PMID: 29968076 PMCID: PMC6267680 DOI: 10.1007/s00335-018-9757-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 06/28/2018] [Indexed: 12/27/2022]
Abstract
Immunotherapy has changed the landscape of cancer treatment. The introduction of immune checkpoint inhibitors has seen tremendous success in improving overall survival of patients with advanced metastatic cancers and has now become the standard of care for multiple tumor types. However, efficacy of immune checkpoint blockade appears to be limited to immunogenic cancers, and even amongst immune-reactive cancers, response rates are low and variable between patients. Recent data have also demonstrated the rapid emergence of resistance to immune checkpoint inhibitors, with some patients progressing on treatment within one year. Significant research efforts are now directed at identifying predictive biomarkers and mechanisms of resistance to immune checkpoint blockade. These studies are underpinned by comprehensive and detailed profiling of the immune milieu. In this review, we discuss the utility and efficacy of immune cell profiling to uncover biomarkers of response and mechanisms of resistance to immune checkpoint inhibitors.
Collapse
Affiliation(s)
- Su Yin Lim
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia. .,Melanoma Institute Australia, Sydney, NSW, Australia.
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, Sydney, NSW, Australia
| |
Collapse
|
39
|
Aarebrot AK, Solberg SM, Davies R, Bader LI, Holmes TD, Gavasso S, Bryceson YT, Jonsson R, Sandvik LF, Appel S. Phosphorylation of intracellular signalling molecules in peripheral blood cells from patients with psoriasis on originator or biosimilar infliximab. Br J Dermatol 2018; 179:371-380. [PMID: 29274242 DOI: 10.1111/bjd.16269] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND Psoriasis vulgaris is a chronic, inflammatory skin disease characterized by a dysregulated immune response and it is associated with substantial systemic comorbidities. Biological drugs such as tumour necrosis factor (TNF)-α inhibitors can ameliorate the disease but are expensive. Biosimilar drugs have the same amino-acid sequence as the originator, but differences in manufacturing can affect biological activity, efficacy and tolerability. OBJECTIVES To explore potential differences in intracellular phosphorylation of signalling molecules in peripheral blood cells from patients with psoriasis treated with the TNF-α inhibitor infliximab compared with healthy controls, and to investigate if the phosphorylation pattern was influenced by switching from the originator infliximab to the biosimilar CT-P13. METHODS By flow cytometry, we measured phosphorylation of nuclear factor kappa B, extracellular signal-regulated kinase 1/2, p38 mitogen-activated protein kinase and signal transducer and activator of transcription 3, before and after TNF-α stimulation in monocytes and T, B, natural killer and CD3+ CD56+ cells from 25 patients with psoriasis treated with infliximab and 19 healthy controls. RESULTS At inclusion, phosphorylation levels of peripheral blood mononuclear cells (PBMCs) were increased in patients with psoriasis compared with healthy controls, even though clinical remission had already been achieved. Phosphorylation levels declined in patients on both originator infliximab and biosimilar during continued treatment. No significant differences were detected between the two medications after 12 months. CONCLUSIONS Patients with psoriasis on infliximab have higher activation levels of PBMCs than do healthy controls, possibly reflecting systemic inflammation. Switching from the originator infliximab to biosimilar CT-P13 did not affect phosphorylation levels or clinical parameters, suggesting that CT-P13 is a noninferior treatment alternative to the originator infliximab.
Collapse
Affiliation(s)
- A K Aarebrot
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - S M Solberg
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Dermatology, Haukeland University Hospital, Bergen, Norway
| | - R Davies
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - L I Bader
- Bergen Group of Epidemiology and Biomarkers in Rheumatic Disease (BEaBiRD), Department of Rheumatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - T D Holmes
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - S Gavasso
- Neuroimmunology Laboratory, Department of Neurology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Y T Bryceson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Centre for Hematology and Regenerative Medicine, Department of Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - R Jonsson
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway.,Bergen Group of Epidemiology and Biomarkers in Rheumatic Disease (BEaBiRD), Department of Rheumatology, Haukeland University Hospital, Bergen, Norway
| | - L F Sandvik
- Department of Dermatology, Haukeland University Hospital, Bergen, Norway.,Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - S Appel
- Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, Bergen, Norway
| |
Collapse
|
40
|
New Technologies for Vaccine Development: Harnessing the Power of Human Immunology. J Indian Inst Sci 2018. [DOI: 10.1007/s41745-018-0064-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
41
|
Canto E, Isobe N, Didonna A, Hauser SL, Oksenberg JR. Aberrant STAT phosphorylation signaling in peripheral blood mononuclear cells from multiple sclerosis patients. J Neuroinflammation 2018. [PMID: 29514694 PMCID: PMC5840794 DOI: 10.1186/s12974-018-1105-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Background Multiple sclerosis (MS) is characterized by increased activation of peripheral blood mononuclear cells (PBMCs), linked to perturbations in the phosphorylation of signaling proteins. Methods We developed a phosphoflow cytometry protocol to assess the levels of 11 phosphorylated nuclear proteins at baseline conditions and after cell activation in distinct PBMC populations from 41 treatment-naïve relapsing-remitting (RR) MS subjects and 37 healthy controls, and in a second cohort of 9 untreated RRMS patients and 10 secondary progressive (SP) MS patients. Levels of HLA-ABC, HLA-E, and HLA-DR were also assessed. Phosphorylation levels of selected proteins were also assessed in mouse splenocytes isolated from myelin oligodendrocyte glycoprotein (MOG)35–55-induced experimental autoimmune encephalomyelitis (EAE). Results Modest differences were observed at baseline between patients and controls, with general lower phosphorylation levels in cells from affected individuals. Conversely, a dramatic increase in phosphorylated p38MAPK and STAT proteins was observed across all cell types in MS patients compared to controls after in vitro activation. A similar phosphorylation profile was observed in mouse lymphocytes primed in vivo with MOG. Furthermore, levels of all p-STAT proteins were found directly correlated with HLA expression in monocytes. Levels of phosphorylated proteins did not differ between relapsing-remitting and secondary progressive MS patients either in baseline conditions or after stimulation. Lastly, phosphorylation levels appear to be independent of the genotype. Conclusion The response to IFN-α through STAT proteins signaling is strongly dysregulated in MS patients irrespective of disease stage. These findings suggest that the aberrant activation of this pathway could lead to changes in the expression of HLA molecules in antigen presenting cells, which are known to play important roles in the regulation of the immune response in health and disease. Electronic supplementary material The online version of this article (10.1186/s12974-018-1105-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Ester Canto
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, Nelson Rising Lane, San Francisco, CA, 94158, USA
| | - Noriko Isobe
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, Nelson Rising Lane, San Francisco, CA, 94158, USA
| | - Alessandro Didonna
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, Nelson Rising Lane, San Francisco, CA, 94158, USA
| | | | - Stephen L Hauser
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, Nelson Rising Lane, San Francisco, CA, 94158, USA
| | - Jorge R Oksenberg
- Department of Neurology and Weill Institute for Neurosciences, University of California at San Francisco, Nelson Rising Lane, San Francisco, CA, 94158, USA.
| |
Collapse
|
42
|
Imaging flow cytometry: A method for examining dynamic native FOXO1 localization in human lymphocytes. J Immunol Methods 2018; 454:59-70. [DOI: 10.1016/j.jim.2018.01.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/28/2017] [Accepted: 01/08/2018] [Indexed: 12/11/2022]
|
43
|
How Nanotechnology and Biomedical Engineering Are Supporting the Identification of Predictive Biomarkers in Neuro-Oncology. MEDICINES 2018; 5:medicines5010023. [PMID: 29495368 PMCID: PMC5874588 DOI: 10.3390/medicines5010023] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 02/12/2018] [Accepted: 02/22/2018] [Indexed: 01/26/2023]
Abstract
The field of neuro-oncology is rapidly progressing and internalizing many of the recent discoveries coming from research conducted in basic science laboratories worldwide. This systematic review aims to summarize the impact of nanotechnology and biomedical engineering in defining clinically meaningful predictive biomarkers with a potential application in the management of patients with brain tumors. Data were collected through a review of the existing English literature performed on Scopus, MEDLINE, MEDLINE in Process, EMBASE, and/or Cochrane Central Register of Controlled Trials: all available basic science and clinical papers relevant to address the above-stated research question were included and analyzed in this study. Based on the results of this systematic review we can conclude that: (1) the advances in nanotechnology and bioengineering are supporting tremendous efforts in optimizing the methods for genomic, epigenomic and proteomic profiling; (2) a successful translational approach is attempting to identify a growing number of biomarkers, some of which appear to be promising candidates in many areas of neuro-oncology; (3) the designing of Randomized Controlled Trials will be warranted to better define the prognostic value of those biomarkers and biosignatures.
Collapse
|
44
|
Richardson AM, Moyer AM, Hasadsri L, Abraham RS. Diagnostic Tools for Inborn Errors of Human Immunity (Primary Immunodeficiencies and Immune Dysregulatory Diseases). Curr Allergy Asthma Rep 2018; 18:19. [PMID: 29470720 DOI: 10.1007/s11882-018-0770-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
PURPOSE OF REVIEW The purpose of this review is to provide an overview of diagnostic testing in primary immunodeficiency and immune dysregulatory disorders (PIDDs), particularly focusing on flow cytometry and genetic techniques, utilizing specific examples of PIDDs. RECENT FINDINGS Flow cytometry remains a vital tool in the diagnosis and monitoring of immunological diseases. Its utility ranges from cellular analysis and specific protein quantitation to functional assays and signaling pathway analysis. Mass cytometry combines flow cytometry and mass spectrometry to dramatically increase the throughput of multivariate single-cell analysis. Next-generation sequencing in combination with other molecular techniques and processing algorithms has become more widely available and identified the diverse and heterogeneous genetic underpinnings of these disorders. As the spectrum of disease is further clarified by increasing immunological, genetic, and epigenetic knowledge, the careful application of these diagnostic tools and bioinformatics will assist not only in our understanding of these complex disorders, but also enable the implementation of personalized therapeutic approaches for disease management.
Collapse
Affiliation(s)
- Annely M Richardson
- Division of Allergic Diseases, Department of Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M Moyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Linda Hasadsri
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Roshini S Abraham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
| |
Collapse
|
45
|
Abstract
Cancer immunotherapy fights against cancer by modulating the immune response and is delivering encouraging results in clinical treatments. However, it is challenging to achieve durable response in all cancer patients during treatment due to the diversity and dynamic nature of immune system as well as inter- and intratumor heterogeneity. A comprehensive assessment of system immunity and tumor microenvironment is crucial for effective and safe cancer therapy, which can potentially be resolved by single-cell proteomic analysis. Single-cell proteomic technologies enable system-wide profiling of protein levels in a number of single cells within the immune system and tumor microenvironment, and thereby provide direct assessment of the functional state of the immune cells and tumor-immune interaction that could be used to evaluate efficacy of immunotherapy and to improve clinical outcome. In this chapter, we summarized current single-cell proteomic technologies and their applications in cancer immunotherapy.
Collapse
|
46
|
Barteneva NS, Vorobjev IA. Heterogeneity of Metazoan Cells and Beyond: To Integrative Analysis of Cellular Populations at Single-Cell Level. Methods Mol Biol 2018; 1745:3-23. [PMID: 29476460 DOI: 10.1007/978-1-4939-7680-5_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
In this paper, we review some of the recent advances in cellular heterogeneity and single-cell analysis methods. In modern research of cellular heterogeneity, there are four major approaches: analysis of pooled samples, single-cell analysis, high-throughput single-cell analysis, and lately integrated analysis of cellular population at a single-cell level. Recently developed high-throughput single-cell genetic analysis methods such as RNA-Seq require purification step and destruction of an analyzed cell often are providing a snapshot of the investigated cell without spatiotemporal context. Correlative analysis of multiparameter morphological, functional, and molecular information is important for differentiation of more uniform groups in the spectrum of different cell types. Simplified distributions (histograms and 2D plots) can underrepresent biologically significant subpopulations. Future directions may include the development of nondestructive methods for dissecting molecular events in intact cells, simultaneous correlative cellular analysis of phenotypic and molecular features by hybrid technologies such as imaging flow cytometry, and further progress in supervised and non-supervised statistical analysis algorithms.
Collapse
Affiliation(s)
- Natasha S Barteneva
- PCMM-Harvard Medical School, Boston Children's Hospital, Boston, MA, USA.
- Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana, Kazakhstan.
| | - Ivan A Vorobjev
- Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana, Kazakhstan
| |
Collapse
|
47
|
Sadanand A, Janardhanan A, Vanisree AJ, Pavai T. Neurotrophin Expression in Lymphocytes: a Powerful Indicator of Degeneration in Parkinson's Disease, Amyotrophic Lateral Sclerosis and Ataxia. J Mol Neurosci 2017; 64:224-232. [PMID: 29247376 DOI: 10.1007/s12031-017-1014-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 12/03/2017] [Indexed: 10/18/2022]
Abstract
Deregulated neurotrophin is an etiological factor in the pathology of neurodegenerative diseases (ND) that are clinically different entities but characterised by similar limb dysfunction. Earlier validation of peripheral biomarkers can provide significant translational benefit to ND patients. We analysed brain-derived neurotrophic factor (BDNF)-tropomyosin possessing tyrosine-related kinase (Trk B) and its key downstream proteins which are implicated in ND such as Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and ataxia. Blood from ND patients with PD, ALS and Ataxia with movement dysfunctions were obtained to analyse mRNA and protein expressions of the above mentioned factors in lymphocytes. The mRNA and protein expression of BDNF-Trk B and its key downstream molecules showed a significant variation when compared to control and among NDs. The study intends to show that on identifying the variation of these key molecules in the blood samples of patients with ND can serve as early diagnostic candidates. Thus by intervening, the neurotrophins and their pathways can help in early diagnosis and optimising levels of diagnostic certainty.
Collapse
Affiliation(s)
- Anjana Sadanand
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai, Tamil Nadu, -600025, India
| | - Anjali Janardhanan
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai, Tamil Nadu, -600025, India
| | - A J Vanisree
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai, Tamil Nadu, -600025, India.
| | - Thamil Pavai
- Department of Neurology and Neurosurgery, Madras Medical College, Chennai, Tamil Nadu, -600003, India
| |
Collapse
|
48
|
Kim H, Brooks KM, Tang CC, Wakim P, Blake M, Brooks SR, Montealegre Sanchez GA, de Jesus AA, Huang Y, Tsai WL, Gadina M, Prakash A, Janes JM, Zhang X, Macias WL, Kumar P, Goldbach-Mansky R. Pharmacokinetics, Pharmacodynamics, and Proposed Dosing of the Oral JAK1 and JAK2 Inhibitor Baricitinib in Pediatric and Young Adult CANDLE and SAVI Patients. Clin Pharmacol Ther 2017; 104:364-373. [PMID: 29134648 DOI: 10.1002/cpt.936] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/03/2017] [Accepted: 11/05/2017] [Indexed: 12/19/2022]
Abstract
Population pharmacokinetic (popPK) modeling was used to characterize the PK profile of the oral Janus kinase (JAK)1/JAK2 inhibitor, baricitinib, in 18 patients with Mendelian interferonopathies who are enrolled in a compassionate use program. Patients received doses between 0.1 to 17 mg per day. Covariates of weight and renal function significantly influenced volume-of-distribution and clearance, respectively. The half-life of baricitinib in patients less than 40 kg was substantially shorter than in adult populations, requiring the need for dosing up to 4 times daily. On therapeutic doses, the mean area-under-the-concentration-vs.-time curve was 2,388 nM*hr, which is 1.83-fold higher than mean baricitinib exposures in adult patients with rheumatoid arthritis receiving doses of 4 mg once-daily. Dose-dependent decreases in interferon (IFN) biomarkers confirmed an in vivo effect of baricitinib on type-1 IFN signaling. PopPK and pharmacodynamic data support a proposal for a weight- and estimated glomerular filtration rate-based dosing regimen in guiding baricitinib dosing in patients with rare interferonopathies.
Collapse
Affiliation(s)
- Hanna Kim
- Lawrence Shulman Scholar, Office of the Clinical Director, and Pediatric Translational Research Branch, NIAMS, NIH, Bethesda, Maryland, USA
| | - Kristina M Brooks
- Clinical Pharmacokinetics Research Unit, Pharmacy Department, NIH Clinical Center, Bethesda, Maryland, USA
| | | | - Paul Wakim
- Biostatistics and Clinical Epidemiology Service, NIH Clinical Center, Bethesda, Maryland, USA
| | - Mary Blake
- Translational Immunology Section, Office of Science and Technology, NIAMS, NIH, Bethesda, Maryland, USA
| | - Stephen R Brooks
- Biodata Mining and Discovery Section, Office of Science and Technology, NIAMS, NIH, Bethesda, Maryland, USA
| | | | - Adriana A de Jesus
- Translational Autoinflammatory Disease Studies, NIAID, NIH, Bethesda, Maryland, USA
| | - Yan Huang
- Translational Autoinflammatory Disease Studies, NIAID, NIH, Bethesda, Maryland, USA
| | - Wanxia Li Tsai
- Translational Immunology Section, Office of Science and Technology, NIAMS, NIH, Bethesda, Maryland, USA
| | - Massimo Gadina
- Translational Immunology Section, Office of Science and Technology, NIAMS, NIH, Bethesda, Maryland, USA
| | | | | | - Xin Zhang
- Eli Lilly and Co, Indianapolis, Indiana, USA
| | | | - Parag Kumar
- Clinical Pharmacokinetics Research Unit, Pharmacy Department, NIH Clinical Center, Bethesda, Maryland, USA
| | | |
Collapse
|
49
|
Lyons YA, Wu SY, Overwijk WW, Baggerly KA, Sood AK. Immune cell profiling in cancer: molecular approaches to cell-specific identification. NPJ Precis Oncol 2017; 1:26. [PMID: 29872708 PMCID: PMC5871917 DOI: 10.1038/s41698-017-0031-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/10/2017] [Accepted: 07/24/2017] [Indexed: 01/22/2023] Open
Abstract
The immune system has many important regulatory roles in cancer development and progression. Given the emergence of effective immune therapies against many cancers, reliable predictors of response are needed. One method of determining response is by evaluating immune cell populations from treated and untreated tumor samples. The amount of material obtained from tumor biopsies can be limited; therefore, gene-based or protein-based analyses may be attractive because they require minimal tissue. Cell-specific signatures are being analyzed with use of the latest technologies, including NanoString’s nCounter technology, intracellular staining flow cytometry, cytometry by time-of-flight, RNA-Seq, and barcoding antibody-based protein arrays. These signatures provide information about the contributions of specific types of immune cells to bulk tumor samples. To date, both tumor tissue and immune cells have been analyzed for molecular expression profiles that can assess genes and proteins that are specific to immune cells, yielding results of varying specificity. Here, we discuss the importance of profiling tumor tissue and immune cells to identify immune-cell-associated genes and proteins and specific gene profiles of immune cells. We also discuss the use of these signatures in cancer treatment and the challenges faced in molecular expression profiling of immune cell populations.
Collapse
Affiliation(s)
- Yasmin A Lyons
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Sherry Y Wu
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Willem W Overwijk
- 2Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Keith A Baggerly
- 3Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| | - Anil K Sood
- 1Department of Gynecologic Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA.,4Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA.,5Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas 77030 USA
| |
Collapse
|
50
|
Ortega-Ferrusola C, Gil MC, Rodríguez-Martínez H, Anel L, Peña FJ, Martín-Muñoz P. Flow cytometry in Spermatology: A bright future ahead. Reprod Domest Anim 2017; 52:921-931. [DOI: 10.1111/rda.13043] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022]
Affiliation(s)
- C Ortega-Ferrusola
- Reproduction and Obstetrics Department of Animal Medicine and Surgery; University of León; León Spain
| | - MC Gil
- Laboratory of Equine Reproduction and Equine Spermatology; Veterinary Teaching Hospital; University of Extremadura; Cáceres Spain
| | - H Rodríguez-Martínez
- Department of Clinical and Experimental Medicine; Faculty of Health Sciences Linköping University; Linköping Sweden
| | - L Anel
- Reproduction and Obstetrics Department of Animal Medicine and Surgery; University of León; León Spain
| | - FJ Peña
- Laboratory of Equine Reproduction and Equine Spermatology; Veterinary Teaching Hospital; University of Extremadura; Cáceres Spain
| | - P Martín-Muñoz
- Laboratory of Equine Reproduction and Equine Spermatology; Veterinary Teaching Hospital; University of Extremadura; Cáceres Spain
| |
Collapse
|