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Simon Davis DA, Ritchie M, Hammill D, Garrett J, Slater RO, Otoo N, Orlov A, Gosling K, Price J, Yip D, Jung K, Syed FM, Atmosukarto II, Quah BJC. Identifying cancer-associated leukocyte profiles using high-resolution flow cytometry screening and machine learning. Front Immunol 2023; 14:1211064. [PMID: 37600768 PMCID: PMC10435879 DOI: 10.3389/fimmu.2023.1211064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 06/26/2023] [Indexed: 08/22/2023] Open
Abstract
Background Machine learning (ML) is a valuable tool with the potential to aid clinical decision making. Adoption of ML to this end requires data that reliably correlates with the clinical outcome of interest; the advantage of ML is that it can model these correlations from complex multiparameter data sets that can be difficult to interpret conventionally. While currently available clinical data can be used in ML for this purpose, there exists the potential to discover new "biomarkers" that will enhance the effectiveness of ML in clinical decision making. Since the interaction of the immune system and cancer is a hallmark of tumor establishment and progression, one potential area for cancer biomarker discovery is through the investigation of cancer-related immune cell signatures. Hence, we hypothesize that blood immune cell signatures can act as a biomarker for cancer progression. Methods To probe this, we have developed and tested a multiparameter cell-surface marker screening pipeline, using flow cytometry to obtain high-resolution systemic leukocyte population profiles that correlate with detection and characterization of several cancers in murine syngeneic tumor models. Results We discovered a signature of several blood leukocyte subsets, the most notable of which were monocyte subsets, that could be used to train CATboost ML models to predict the presence and type of cancer present in the animals. Conclusions Our findings highlight the potential utility of a screening approach to identify robust leukocyte biomarkers for cancer detection and characterization. This pipeline can easily be adapted to screen for cancer specific leukocyte markers from the blood of cancer patient.
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Affiliation(s)
- David A. Simon Davis
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Melissa Ritchie
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Dillon Hammill
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Jessica Garrett
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Robert O. Slater
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Naomi Otoo
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Anna Orlov
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Katharine Gosling
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
| | - Jason Price
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Desmond Yip
- Australian National University, Canberra, ACT, Australia
- Department of Medical Oncology, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Kylie Jung
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Farhan M. Syed
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
| | - Ines I. Atmosukarto
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Division of Genome Sciences & Cancer, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Ben J. C. Quah
- Irradiation Immunity Interaction Lab, Australian National University, Canberra, ACT, Australia
- Radiation Oncology Department, Canberra Hospital & Health Services, Canberra, ACT, Australia
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Acute T-Cell-Driven Inflammation Requires the Endoglycosidase Heparanase-1 from Multiple Cell Types. Int J Mol Sci 2022; 23:ijms23094625. [PMID: 35563015 PMCID: PMC9105945 DOI: 10.3390/ijms23094625] [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: 03/14/2022] [Revised: 04/13/2022] [Accepted: 04/14/2022] [Indexed: 12/10/2022] Open
Abstract
It has been accepted for decades that T lymphocytes and metastasising tumour cells traverse basement membranes (BM) by deploying a battery of degradative enzymes, particularly proteases. However, since many redundant proteases can solubilise BM it has been difficult to prove that proteases aid cell migration, particularly in vivo. Recent studies also suggest that other mechanisms allow BM passage of cells. To resolve this issue we exploited heparanase-1 (HPSE-1), the only endoglycosidase in mammals that digests heparan sulfate (HS), a major constituent of BM. Initially we examined the effect of HPSE-1 deficiency on a well-characterised adoptive transfer model of T-cell-mediated inflammation. We found that total elimination of HPSE-1 from this system resulted in a drastic reduction in tissue injury and loss of target HS. Subsequent studies showed that the source of HPSE-1 in the transferred T cells was predominantly activated CD4+ T cells. Based on bone marrow chimeras, two cellular sources of HPSE-1 were identified in T cell recipients, one being haematopoiesis dependent and the other radiation resistant. Collectively our findings unequivocally demonstrate that an acute T-cell-initiated inflammatory response is HPSE-1 dependent and is reliant on HPSE-1 from at least three different cell types.
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Toribio-Fernandez R, Zorita V, Herrero-Fernandez B, Gonzalez-Granado JM. An In Vivo Mouse Model to Measure Naïve CD4 T Cell Activation, Proliferation and Th1 Differentiation Induced by Bone Marrow-derived Dendritic Cells. J Vis Exp 2018. [PMID: 30199029 DOI: 10.3791/58118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Quantification of naïve CD4 T cell activation, proliferation, and differentiation to T helper 1 (Th1) cells is a useful way to assess the role played by T cells in an immune response. This protocol describes the in vitro differentiation of bone marrow (BM) progenitors to obtain granulocyte macrophage colony-stimulating factor (GM-CSF) derived-dendritic cells (DCs). The protocol also describes the adoptive transfer of ovalbumin peptide (OVAp)-loaded GM-CSF-derived DCs and naïve CD4 T cells from OTII transgenic mice in order to analyze the in vivo activation, proliferation, and Th1 differentiation of the transferred CD4 T cells. This protocol circumvents the limitation of purely in vivo methods imposed by the inability to specifically manipulate or select the studied cell population. Moreover, this protocol allows studies in an in vivo environment, thus avoiding alterations to functional factors that may occur in vitro and including the influence of cell types and other factors only found in intact organs. The protocol is a useful tool for generating changes in DCs and T cells that modify adaptive immune responses, potentially providing important results to understand the origin or development of numerous immune associated diseases.
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Affiliation(s)
| | - Virginia Zorita
- LamImSys Lab, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC)
| | | | - Jose M Gonzalez-Granado
- LamImSys Lab, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC); LamImSys Lab, Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12); CIBER de Enfermedades Cardiovasculares;
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Haymaker CL, Hailemichael Y, Yang Y, Nurieva R. In Vivo Assay for Detection of Antigen-specific T-cell Cytolytic Function Using a Vaccination Model. J Vis Exp 2017. [PMID: 29286361 DOI: 10.3791/56255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Current methodologies for antigen-specific killing are limited to in vitro use or utilized in infectious disease models. However, there is not a protocol specifically intended to measure antigen-specific killing without an infection. This protocol is designed and describes methods to overcome these limitations by allowing for the detection of antigen-specific killing of a target cell by CD8+ T cells in vivo. This is accomplished by merging a vaccination model with a traditional CFSE-labeled target killing assay. This combination allows the researcher to assess the antigen-specific CTL potential directly and quickly as the assay is not dependent upon tumor growth or infection. In addition, the readout is based on flow cytometry and so should be readily accessible to most researchers. The major limitation of the study is identifying the timeline in vivo that is appropriate to the hypothesis being tested. Variations in antigen strength and mutations in the T cells that may result in differential cytolytic function need to be carefully assessed to determine the optimal time for cell harvest and assessment. The appropriate concentration of peptide for vaccination has been optimized for hgp10025-33 and OVA257-264, but further validation would be needed for other peptides that may be more appropriate to a given study. Overall, this protocol allows a quick assessment of killing function in vivo and can be adapted to any given antigen.
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Affiliation(s)
- Cara L Haymaker
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center
| | - Yared Hailemichael
- Department of Melanoma Medical Oncology, University of Texas MD Anderson Cancer Center
| | - Yi Yang
- Department of Immunology, University of Texas MD Anderson Cancer Center; Department of Radiation Oncology, The Second Hospital of Jilin University
| | - Roza Nurieva
- Department of Immunology, University of Texas MD Anderson Cancer Center;
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Ochando J, Conde P. Functional Characterization of Regulatory Macrophages That Inhibit Graft-reactive Immunity. J Vis Exp 2017. [PMID: 28654060 DOI: 10.3791/54242] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Macrophage accumulation in transplanted organs has long been recognized as a feature of allograft rejection1. Immunogenic monocytes infiltrate the allograft early after transplantation, mount a graft reactive response against the transplanted organ, and initiate organ rejection2. Recent data suggest that suppressive macrophages facilitate successful long-term transplantation3 and are required for the induction of transplantation tolerance4. This suggests a multidimensional concept of macrophage ontogeny, activation, and function, which demands a new roadmap for the isolation and analysis of macrophage function5. Due to the plasticity of macrophages, it is necessary to provide a methodology to isolate and characterize macrophages, depending on the tissue environment, and to define their functions according to different scenarios. Here, we describe a protocol for immune characterization of graft-infiltrating macrophages and the methods we used to functionally evaluate their capacity to inhibit CD8+ T proliferation and to promote CD4+Foxp3+ Treg expansion in vitro.
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Affiliation(s)
- Jordi Ochando
- Department of Medicine, Icahn School of Medicine at Mount Sinai; Immunología de Trasplantes, Centro Nacional de Microbiología, Instituto de Salud Carlos III
| | - Patricia Conde
- Department of Medicine, Icahn School of Medicine at Mount Sinai; Immunología de Trasplantes, Centro Nacional de Microbiología, Instituto de Salud Carlos III;
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Tomusange K, Wijesundara D, Gummow J, Garrod T, Li Y, Gray L, Churchill M, Grubor-Bauk B, Gowans EJ. A HIV-Tat/C4-binding protein chimera encoded by a DNA vaccine is highly immunogenic and contains acute EcoHIV infection in mice. Sci Rep 2016; 6:29131. [PMID: 27358023 PMCID: PMC4928126 DOI: 10.1038/srep29131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 06/15/2016] [Indexed: 12/22/2022] Open
Abstract
DNA vaccines are cost-effective to manufacture on a global scale and Tat-based DNA vaccines have yielded protective outcomes in preclinical and clinical models of human immunodeficiency virus (HIV), highlighting the potential of such vaccines. However, Tat-based DNA vaccines have been poorly immunogenic, and despite the administration of multiple doses and/or the addition of adjuvants, these vaccines are not in general use. In this study, we improved Tat immunogenicity by fusing it with the oligomerisation domain of a chimeric C4-binding protein (C4b-p), termed IMX313, resulting in Tat heptamerisation and linked Tat to the leader sequence of tissue plasminogen activator (TPA) to ensure that the bulk of heptamerised Tat is secreted. Mice vaccinated with secreted Tat fused to IMX313 (pVAX-sTat-IMX313) developed higher titres of Tat-specific serum IgG, mucosal sIgA and cell-mediated immune (CMI) responses, and showed superior control of EcoHIV infection, a surrogate murine HIV challenge model, compared with animals vaccinated with other test vaccines. Given the crucial contribution of Tat to HIV-1 pathogenesis and the precedent of Tat-based DNA vaccines in conferring some level of protection in animal models, we believe that the virologic control demonstrated with this novel multimerised Tat vaccine highlights the promise of this vaccine candidate for humans.
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Affiliation(s)
- Khamis Tomusange
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Danushka Wijesundara
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Jason Gummow
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Tamsin Garrod
- Royal Australasian College of Surgeons, Adelaide, South Australia, Australia
| | - Yanrui Li
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Lachlan Gray
- Centre for Biomedical Research, Burnet Institute, Melbourne VIC, Australia
- Department of Infectious Diseases, Monash University, Melbourne VIC, Australia
| | - Melissa Churchill
- Centre for Biomedical Research, Burnet Institute, Melbourne VIC, Australia
| | - Branka Grubor-Bauk
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
| | - Eric J. Gowans
- Virology Laboratory, Basil Hetzel Institute, Discipline of Surgery, University of Adelaide, Adelaide, South Australia, Australia
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Ochyl LJ, Moon JJ. Whole-animal imaging and flow cytometric techniques for analysis of antigen-specific CD8+ T cell responses after nanoparticle vaccination. J Vis Exp 2015:e52771. [PMID: 25992469 PMCID: PMC4541589 DOI: 10.3791/52771] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Traditional vaccine adjuvants, such as alum, elicit suboptimal CD8+ T cell responses. To address this major challenge in vaccine development, various nanoparticle systems have been engineered to mimic features of pathogens to improve antigen delivery to draining lymph nodes and increase antigen uptake by antigen-presenting cells, leading to new vaccine formulations optimized for induction of antigen-specific CD8+ T cell responses. In this article, we describe the synthesis of a "pathogen-mimicking" nanoparticle system, termed interbilayer-crosslinked multilamellar vesicles (ICMVs) that can serve as an effective vaccine carrier for co-delivery of subunit antigens and immunostimulatory agents and elicitation of potent cytotoxic CD8+ T lymphocyte (CTL) responses. We describe methods for characterizing hydrodynamic size and surface charge of vaccine nanoparticles with dynamic light scattering and zeta potential analyzer and present a confocal microscopy-based procedure to analyze nanoparticle-mediated antigen delivery to draining lymph nodes. Furthermore, we show a new bioluminescence whole-animal imaging technique utilizing adoptive transfer of luciferase-expressing, antigen-specific CD8+ T cells into recipient mice, followed by nanoparticle vaccination, which permits non-invasive interrogation of expansion and trafficking patterns of CTLs in real time. We also describe tetramer staining and flow cytometric analysis of peripheral blood mononuclear cells for longitudinal quantification of endogenous T cell responses in mice vaccinated with nanoparticles.
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Affiliation(s)
- Lukasz J Ochyl
- Department of Pharmaceutical Sciences, University of Michigan; Biointerfaces Institute, University of Michigan
| | - James J Moon
- Department of Pharmaceutical Sciences, University of Michigan; Biointerfaces Institute, University of Michigan; Department of Biomedical Engineering, University of Michigan;
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Viral semaphorin inhibits dendritic cell phagocytosis and migration but is not essential for gammaherpesvirus-induced lymphoproliferation in malignant catarrhal fever. J Virol 2015; 89:3630-47. [PMID: 25589653 DOI: 10.1128/jvi.03634-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
UNLABELLED Viral semaphorins are semaphorin 7A (sema7A) mimics found in pox- and herpesviruses. Among herpesviruses, semaphorins are encoded by gammaherpesviruses of the Macavirus genus only. Alcelaphine herpesvirus 1 (AlHV-1) is a macavirus that persistently infects wildebeest asymptomatically but induces malignant catarrhal fever (MCF) when transmitted to several species of susceptible ruminants and the rabbit model. MCF is caused by the activation/proliferation of latently infected T lymphocytes. Viral semaphorins have been suggested to mediate immune evasion mechanisms and/or directly alter host T cell function. We studied AlHV-sema, the viral semaphorin encoded by the A3 gene of AlHV-1. Phylogenetic analyses revealed independent acquisition of pox- and herpesvirus semaphorins, suggesting that these proteins might have distinct functions. AlHV-sema showed a predicted three-dimensional structure very similar to sema7A and conserved key residues in sema7A-plexinC1 interaction. Expression analyses revealed that AlHV-sema is a secreted 93-kDa glycoprotein expressed during the early phase of virus replication. Purified AlHV-sema was able to bind to fibroblasts and dendritic cells and induce F-actin condensation and cell retraction through a plexinC1 and Rho/cofilin-dependent mechanism. Cytoskeleton rearrangement was further associated with inhibition of phagocytosis by dendritic cells and migration to the draining lymph node. Next, we generated recombinant viruses and demonstrated that the lack of A3 did not significantly affect virus growth in vitro and did not impair MCF induction and associated lymphoproliferative lesions. In conclusion, AlHV-sema has immune evasion functions through mechanisms similar to poxvirus semaphorin but is not directly involved in host T cell activation during MCF. IMPORTANCE Whereas most poxviruses encode viral semaphorins, semaphorin-like genes have only been identified in few gammaherpesviruses belonging to the Macavirus genus. Alcelaphine herpesvirus 1 (AlHV-1) is a macavirus carried asymptomatically by wildebeest but induces a latency-associated lymphoproliferative disease of T lymphocytes in various ruminant species, namely, malignant catarrhal fever (MCF). Viral semaphorins have been hypothesized to have immune evasion functions and/or be involved in activating latently infected T cells. We present evidence that the viral semaphorin AlHV-sema inhibits dendritic cell phagocytosis and migration to the draining lymph node, both being indispensable mechanisms for protective antiviral responses. Next, we engineered recombinant viruses unable to express AlHV-sema and demonstrated that this protein is dispensable for the induction of MCF. In conclusion, this study suggests that herpesvirus and poxvirus semaphorins have independently evolved similar functions to thwart the immune system of the host while AlHV-sema is not directly involved in MCF-associated T-cell activation.
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