scholarly journals Single-cell mass cytometry on peripheral blood identifies immune cell subsets associated with primary biliary cholangitis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jin Sung Jang ◽  
Brian D. Juran ◽  
Kevin Y. Cunningham ◽  
Vinod K. Gupta ◽  
Young Min Son ◽  
...  
2020 ◽  
Author(s):  
Jin Sung Jang ◽  
Brian Juran ◽  
Kevin Y. Cunningham ◽  
Vinod K. Gupta ◽  
YoungMin Son ◽  
...  

AbstractThe relationship between Primary Biliary Cholangitis (PBC), a chronic cholestatic autoimmune liver disease, and the peripheral immune system remains to be fully understood. Herein, we performed the first mass cytometry (CyTOF)-based, immunophenotyping analysis of the peripheral immune system in PBC at single-cell resolution. CyTOF was performed on peripheral blood mononuclear cells (PBMCs) from PBC patients (n=33) and age-/sex-matched healthy controls (n=33) to obtain immune cell abundance and marker expression profiles. Hiearchical clustering methods were applied to identify immune cell types and subsets significantly associated with PBC. Subsets of gamma-delta T cells (CD3+TCRgd+), CD8+ T cells (CD3+CD8+CD161+PD1+), and memory B cells (CD3-CD19+CD20+CD24+CD27+) were found to have lower abundance in PBC than in control. In contrast, higher abundance of subsets of monocytes and naïve B cells were observed in PBC compared to control. Furthermore, several naïve B cell (CD3-CD19+CD20+CD24-CD27-) subsets were significantly higher in PBC patients with cirrhosis (indicative of late-stage disease) than in those without cirrhosis. Alternatively, subsets of CD8+CD161+ T cells and memory B cells were lower in abundance in cirrhotic relative to non-cirrhotic PBC patients. Future immunophenotyping investigations could lead to better understanding of PBC pathogenesis and progression, and also to the discovery of novel biomarkers and treatment strategies.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 1859-1859 ◽  
Author(s):  
Yongxian Hu ◽  
Zhang Yanlei ◽  
Guoqing Wei ◽  
Chang alex Hong ◽  
He Huang

Background BCMA CAR-T cells have demonstrated substantial clinical activity against relapsed/refractory multiple myeloma (RRMM). In different clinical trials, the overall response rate (ORR) varied from 50% to 100%. Complete remission (CR) rate varied from 20% to 80%. Here we developed a BCMA CAR-T cell product manufactured via lentiviral vector-mediated transduction of activated T cells to express a second-generation CAR with 4-1BB costimulatory domain and evaluated the efficacy and safety, moreover, dynamics of immune cell subsets using single-cell mass cytometry during treatment were analyzed. Methods Our trial (ChiCTR1800017404) is a phase 1, single-arm, open-label single center study to evaluate the safety and efficacy of autologous BCMA CAR-T treatment for RRMM. Patients were subjected to a lymphodepleting regimen with Flu and Cy prior to CAR-T infusion. BCMA CAR-T cells were administered as a single infusion at a median dose of 3.5 (1 to 6) ×106/kg. MM response assessment was conducted according to the International Uniform Response Criteria. Cytokine-release syndrome (CRS) was graded as Lee DW et al described (Blood.2014;124(2):188-195). Phenotypic analysis of peripheral blood mononuclear cells (PBMCs), frozen BCMA CAR-T aliquots, phenotype and in vivo kinetics of immune cell subsets after CAR-T infusion were performed by single-cell mass cytometry. Results As of the data cut-off date (August 1st, 2019), 33 patients, median age 62.5 (49 to 75) years old were infused with BCMA CAR-T cells. The median observation period is 8.0 (0.7 to 18) months. ORR was 100% (The patient who died of infection at 20 days after CAR-T infusion were excluded). All the 32 patients achieved MRD negative in bone marrow by flow cytometry in 2 weeks after CAR-T infusion. Partial response (4 PR, 12.1%), VGPR (7 VGPR, 21.2%), and complete response (21 CR, 63.6%) within 12 weeks post CAR-T infusion were achieved. Durable responses from 4 weeks towards the data cut-off date were found in 28/33 patients (84.8%) (Figure 1a). All patients had detectable CAR-T expansion by flow cytometry from Day 3 post CAR-T cell infusion. The peak CAR-T cell expansion in CD3+ lymphocytes of peripheral blood (PB) varied from 35% to 95% with a median percentage of 82.9%. CRS was reported in all the 33 patients, including 4 with Grade 1, 13 with Grade 2 and 16 with Grade 3. During follow-up, 1-year progression-free survival (PFS) was 70.7% (Figure 1b) and overall survival (OS) was 71.7% (Figure 1c). Multivariate analysis of patients with PR and patients with CR+VGPR revealed that factors including extramedullary infiltration, age>60 years old, high-risk cytogenetics, late stage and CAR-T cell dose were not associated with clinical response (P>0.05). Single-cell mass cytometry revealed that the frequency of total T cells, CD8+ T cells, NK cells and CD3+CD56+ NKT cells in PB was not associated with BCM CAR-T expansion or clinical response. CD8+ Granzyme B+ Ki-67+ CAR-T cells expanded prominently in CRS period. As serum cytokines increased during CRS, non-CAR-T immune cell subsets including PD1+ NK cells, CD8+ Ki-67+ ICOS+ T cells expanded dominantly implying that non-CAR-T cells were also activated after CAR-T treatment. After CRS, stem cell like memory CAR-T cells (CD45RO+ CCR7- CD28- CD95+) remain the main subtype of CAR-T cells (Figure 1d). Conclusions Our data showed BCMA CAR-T treatment is safe with prominent efficacy which can overcome the traditional high-risk factors. We also observed high expansion level and long-term persistence of BCMA CAR-T cells contribute to potent anti-myeloma activity. Stem cell like memory CAR-T cells might be associated with long-term persistence of BCMA CAR-T cells. These initial data provide strong evidence to support the further development of this anti-myeloma cellular immunotherapy. Figure 1. Disclosures No relevant conflicts of interest to declare.


2014 ◽  
Vol 6 (255) ◽  
pp. 255ra131-255ra131 ◽  
Author(s):  
Brice Gaudillière ◽  
Gabriela K. Fragiadakis ◽  
Robert V. Bruggner ◽  
Monica Nicolau ◽  
Rachel Finck ◽  
...  

Delayed recovery from surgery causes personal suffering and substantial societal and economic costs. Whether immune mechanisms determine recovery after surgical trauma remains ill-defined. Single-cell mass cytometry was applied to serial whole-blood samples from 32 patients undergoing hip replacement to comprehensively characterize the phenotypic and functional immune response to surgical trauma. The simultaneous analysis of 14,000 phosphorylation events in precisely phenotyped immune cell subsets revealed uniform signaling responses among patients, demarcating a surgical immune signature. When regressed against clinical parameters of surgical recovery, including functional impairment and pain, strong correlations were found with STAT3 (signal transducer and activator of transcription), CREB (adenosine 3′,5′-monophosphate response element–binding protein), and NF-κB (nuclear factor κB) signaling responses in subsets of CD14+ monocytes (R = 0.7 to 0.8, false discovery rate <0.01). These sentinel results demonstrate the capacity of mass cytometry to survey the human immune system in a relevant clinical context. The mechanistically derived immune correlates point to diagnostic signatures, and potential therapeutic targets, that could postoperatively improve patient recovery.


2020 ◽  
Author(s):  
Julia Casado ◽  
Oskari Lehtonen ◽  
Ville Rantanen ◽  
Katja Kaipio ◽  
Luca Pasquini ◽  
...  

AbstractMotivationSingle-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single cell resolution. These large amounts of data, however, require dedicated, interactive tools for translating the data into knowledge.ResultsWe present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automatizes the use of of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood as well as cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples.AvailabilityThe method is available as a Docker container at https://hub.docker.com/r/anduril/cyto and the user guide and source code are available at https://bitbucket.org/anduril-dev/[email protected] informationSupplementary material is available and FCS files are hosted at flowrepository.org/id/FR-FCM-Z2LW


2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A698-A698
Author(s):  
Todd Bartkowiak ◽  
Sierra Barone ◽  
Madeline Hayes ◽  
Allison Greenplate ◽  
Justine Sinnaeve ◽  
...  

BackgroundGlioblastomas make up more than 60% of adult primary brain tumors and carry a median survival of less than 15 months despite aggressive therapy. Immunotherapy, now standard of care for many peripheral solid tumors, offers an appealing alternative platform that may improve survival outcomes for patients with glioblastoma; however, predictive features that could inform responsiveness to different immunotherapeutic modalities remains to be elucidated. Recent studies have demonstrated that patients whose tumors show radiographic contact with the lateral ventricle have diminished survival outcomes compared to patients whose tumors do not contact the lateral ventricle. While greater immune infiltrate correlates with more favorable outcomes and more effectual responses to immunotherapy, the anti-tumor immune response in the ventricle is unknown. We hypothesized that ventricle contact may provide a uniquely immunosuppressive microenvironment within the brain that promotes tumor growth by suppressing anti-tumor immunity, that may be overcome with appropriate targeting strategies.MethodsPrimary glioblastoma tumors obtained in accordance with the Declaration of Helsinki and with institutional IRB approval (#131870) were disaggregated into single-cell suspensions. Radiographic contact with the LV was identified by MRI imaging and confirmed by a trained neurosurgeon. Multi-dimensional single-cell mass cytometry (CyTOF) then measured >30 immune parameters in thirteen immune subpopulations infiltrating human glioblastomas, including T cells, natural killer cells, B cells, microglia, peripheral macrophages, and myeloid-derived suppressors cells (MDSC). Computational machine-learning pipelines including Citrus, t-SNE, FlowSOM, and MEM identified key differences in the abundance and phenotypes of immune infiltrates.ResultsOn the basis of glioblastoma contact with the ventricle, we computationally identified consequential distinctions in the abundance of T cell, macrophage, and microglia subsets constituting five immunotype signatures among glioblastoma patients. Immunotypes associated with CD69+CD32+CD44+ peripheral macrophages and PD-1+TIGIT+ CD8 T cells correlated with ventricle contact, whereas immunotypes associated with enriched γδ T cells, B, NK cell, and tissue-resident microglial cells correlated with tumors distal to the ventricle. Further, immune infiltration in the tumor microenvironment correlated with patient outcome, with higher lymphocyte infiltrates correlating with more favorable outcomes, and immune exhaustion correlating with less favorable outcomes.ConclusionsSingle-cell mass cytometry in conjunction with the machine learning tools identified key differences in immune cell abundance between lateral ventricle contacting and non-contacting glioblastomas. These results provide key insights into the immune microenvironment of glioblastomas and elucidate several clinically actionable immunotherapeutic targets that may be used to optimize treatment strategies for glioblastomas based on ventricle contact status.Ethics ApprovalThis study was approved by Vanderbilt University’s Institutional Ethics Board, approval number 131870


Author(s):  
Julia Casado ◽  
Oskari Lehtonen ◽  
Ville Rantanen ◽  
Katja Kaipio ◽  
Luca Pasquini ◽  
...  

Abstract Motivation Single-cell proteomics technologies, such as mass cytometry, have enabled characterization of cell-to-cell variation and cell populations at a single-cell resolution. These large amounts of data, require dedicated, interactive tools for translating the data into knowledge. Results We present a comprehensive, interactive method called Cyto to streamline analysis of large-scale cytometry data. Cyto is a workflow-based open-source solution that automates the use of state-of-the-art single-cell analysis methods with interactive visualization. We show the utility of Cyto by applying it to mass cytometry data from peripheral blood and high-grade serous ovarian cancer (HGSOC) samples. Our results show that Cyto is able to reliably capture the immune cell sub-populations from peripheral blood and cellular compositions of unique immune- and cancer cell subpopulations in HGSOC tumor and ascites samples. Availabilityand implementation The method is available as a Docker container at https://hub.docker.com/r/anduril/cyto and the user guide and source code are available at https://bitbucket.org/anduril-dev/cyto. Supplementary information Supplementary data are available at Bioinformatics online.


Author(s):  
Wen Shi ◽  
Xiuxing Liu ◽  
Qiqi Cao ◽  
Pengjuan Ma ◽  
Wenqing Le ◽  
...  

Coronavirus disease 2019 (COVID-19), driven by SARS-CoV-2, is now declared a global pandemic. Pathogenic T cells and inflammatory monocytes are regarded as the central drivers of the cytokine storm associated with the severity of COVID-19. In this study, we explored the characteristic peripheral cellular profiles of patients with COVID-19 in both acute and convalescent phases by single-cell mass cytometry (CyTOF). Using a combination of algorithm-guided data analyses, we identified peripheral immune cell subsets in COVID-19, and revealed CD4+ T cell depletion, T cell differentiation, plasma cell expansion, and the reduced antigen presentation capacity of innate immunity. Notably, COVID-19 induces a dysregulation in the balance of monocyte populations by the expansion of the monocyte subsets. Collectively, our results represent a high-dimensional single-cell profile of the peripheral immune response to SARS-CoV-2 infection.


2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Christos Nikolaou ◽  
Kerstin Muehle ◽  
Stephan Schlickeiser ◽  
Alberto Sada Japp ◽  
Nadine Matzmohr ◽  
...  

An amendment to this paper has been published and can be accessed via the original article.


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