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A topic modeling approach reveals the dynamic T cell composition of peripheral blood during cancer immunotherapy.


ABSTRACT: We present TopicFlow, a computational framework for flow cytometry data analysis of patient blood samples for the identification of functional and dynamic topics in circulating T cell population. This framework applies a Latent Dirichlet Allocation (LDA) model, adapting the concept of topic modeling in text mining to flow cytometry. To demonstrate the utility of our method, we conducted an analysis of ∼17 million T cells collected from 138 peripheral blood samples in 51 patients with melanoma undergoing treatment with immune checkpoint inhibitors (ICIs). Our study highlights three latent dynamic topics identified by LDA: a T cell exhaustion topic that independently recapitulates the previously identified LAG-3+ immunotype associated with ICI resistance, a naive topic and its association with immune-related toxicity, and a T cell activation topic that emerges upon ICI treatment. Our approach can be broadly applied to mine high-parameter flow cytometry data for insights into mechanisms of treatment response and toxicity.

SUBMITTER: Peng X 

PROVIDER: S-EPMC10475788 | biostudies-literature | 2023 Aug

REPOSITORIES: biostudies-literature

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A topic modeling approach reveals the dynamic T cell composition of peripheral blood during cancer immunotherapy.

Peng Xiyu X   Lee Jasme J   Adamow Matthew M   Maher Colleen C   Postow Michael A MA   Callahan Margaret K MK   Panageas Katherine S KS   Shen Ronglai R  

Cell reports methods 20230802 8


We present TopicFlow, a computational framework for flow cytometry data analysis of patient blood samples for the identification of functional and dynamic topics in circulating T cell population. This framework applies a Latent Dirichlet Allocation (LDA) model, adapting the concept of topic modeling in text mining to flow cytometry. To demonstrate the utility of our method, we conducted an analysis of ∼17 million T cells collected from 138 peripheral blood samples in 51 patients with melanoma un  ...[more]

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