CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

Nowicka, Małgorzata; Krieg, Carsten; Crowell, Helena L.; Weber, Lukas M.; Hartmann, Felix J.; Guglietta, Silvia; Levesque, Mitchell P.; Robinson, Mark D.

doi:10.12688/f1000research.11622.4

Cited by 29 publications

(25 citation statements)

References 54 publications

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“…Then, data from 5000 CD4 + T cells and 2500 CD8 + T cells per sample were exported for further analysis in R, by following a script that makes use of Bioconductor libraries and R statistical packages (CATALYST 1.10.1). The script is available at: https://github.com/ HelenaLC/CATALYST) 52 . The selection of cofactor for data transformation was checked on Cytobank premium version (see: cytobank.org).…”

Section: Methodsmentioning

confidence: 99%

Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

et al. 2020

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The immune system of patients infected by SARS-CoV-2 is severely impaired. Detailed investigation of T cells and cytokine production in patients affected by COVID-19 pneumonia are urgently required. Here we show that, compared with healthy controls, COVID-19 patients' T cell compartment displays several alterations involving naïve, central memory, effector memory and terminally differentiated cells, as well as regulatory T cells and PD1 + CD57 + exhausted T cells. Significant alterations exist also in several lineage-specifying transcription factors and chemokine receptors. Terminally differentiated T cells from patients proliferate less than those from healthy controls, whereas their mitochondria functionality is similar in CD4 + T cells from both groups. Patients display significant increases of proinflammatory or anti-inflammatory cytokines, including T helper type-1 and type-2 cytokines, chemokines and galectins; their lymphocytes produce more tumor necrosis factor (TNF), interferon-γ, interleukin (IL)-2 and IL-17, with the last observation implying that blocking IL-17 could provide a novel therapeutic strategy for COVID-19.

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Section: Methodsmentioning

confidence: 99%

Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

et al. 2020

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“…Based on a 40% assignment probability cutoff and a 20% delta cutoff, 98% of the cells were retained in the analysis. To visualize the high-dimensional data in two dimensions, the t-SNE algorithm was applied on data from a maximum of 1,000 randomly selected cells from each sample, with a perplexity set to 80, using the implementation of t-SNE available in CATALYST (Nowicka et al , 2019). Channels which were not relevant for these cell subsets or which were affected by different background stainings across batches were excluded (CD15, CD66ace, CD3, CD45, CD8a, CD20, CXCR2, GranzymeB).…”

Section: Methodsmentioning

confidence: 99%

“…Channels which were not relevant for these cell subsets or which were affected by different background stainings across batches were excluded (CD15, CD66ace, CD3, CD45, CD8a, CD20, CXCR2, GranzymeB). Data were displayed using the ggplot2 R package or the plotting functions of CATALYST (Nowicka et al , 2019).…”

Section: Methodsmentioning

confidence: 99%

A distinct innate immune signature marks progression from mild to severe COVID-19

Chevrier

Zurbuchen

Cervia

et al. 2020

Preprint

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Coronavirus disease 2019 (COVID-19) manifests with a range of severities, but immune signatures of mild and severe disease are still not fully understood. Excessive inflammation has been postulated to be a major factor in the pathogenesis of severe COVID-19 and innate immune mechanisms are likely to be central in the inflammatory response. We used 40-plex mass cytometry and targeted serum proteomics to profile innate immune cell populations from peripheral blood of patients with mild or severe COVID-19 and healthy controls. Sampling at different stages of COVID-19 allowed us to reconstruct a pseudo-temporal trajectory of the innate immune response. Despite the expected patient heterogeneity, we identified consistent changes during the course of the infection. A rapid and early surge of CD169+ monocytes associated with an IFNy+MCP-2+ signature quickly followed symptom onset; at symptom onset, patients with mild and severe COVID-19 had a similar signature, but over the course of the disease, the differences between patients with mild and severe disease increased. Later in the disease course, we observed a more pronounced re-appearance of intermediate/non-classical monocytes and mounting systemic CCL3 and CCL4 levels in patients with severe disease. Our data provide new insights into the dynamic nature of the early inflammatory response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and identifies sustained pathological innate immune responses as a likely key mechanism in severe COVID-19, further supporting investigation of targeted anti-inflammatory interventions in severe COVID-19.

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“…The pre-gated data was exported as an FCS file and then imported into RStudio. We used the package CATALYST ( 32 ) to arcsine transform marker intensities with a cofactor of 5 and performed subsequent analysis. Unsupervised clustering was performed using FlowSOM ( 33 ), data representation was performed using the R package ggplot2, and marker enrichment modeling (MEM) ( 34 ) was used to characterize different clusters.…”

Section: Methodsmentioning

confidence: 99%

Clinical and Immunological Features of Human BCL10 Deficiency

et al. 2021

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The CARD-BCL10-MALT1 (CBM) complex is critical for the proper assembly of human immune responses. The clinical and immunological consequences of deficiencies in some of its components such as CARD9, CARD11, and MALT1 have been elucidated in detail. However, the scarcity of BCL10 deficient patients has prevented gaining detailed knowledge about this genetic disease. Only two patients with BCL10 deficiency have been reported to date. Here we provide an in-depth description of an additional patient with autosomal recessive complete BCL10 deficiency caused by a nonsense mutation that leads to a loss of expression (K63X). Using mass cytometry coupled with unsupervised clustering and machine learning computational methods, we obtained a thorough characterization of the consequences of BCL10 deficiency in different populations of leukocytes. We showed that in addition to the near absence of memory B and T cells previously reported, this patient displays a reduction in NK, γδT, Tregs, and TFH cells. The patient had recurrent respiratory infections since early childhood, and showed a family history of lethal severe infectious diseases. Fortunately, hematopoietic stem-cell transplantation (HSCT) cured her. Overall, this report highlights the importance of early genetic diagnosis for the management of BCL10 deficient patients and HSCT as the recommended treatment to cure this disease.

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CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets

Cited by 29 publications

References 54 publications

Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

Marked T cell activation, senescence, exhaustion and skewing towards TH17 in patients with COVID-19 pneumonia

A distinct innate immune signature marks progression from mild to severe COVID-19

Clinical and Immunological Features of Human BCL10 Deficiency

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