Genome Biol 2020 Jun 22; 21(1):150
Sputum induction is a non-invasive method to evaluate the airway environment, particularly for asthma. RNA sequencing (RNA-seq) of sputum samples can be challenging to interpret due to the complex and heterogeneous mixtures of human cells and exogenous (microbial) material. In this study, we develop a pipeline that integrates dimensionality reduction and statistical modeling to grapple with the heterogeneity. LDA(Latent Dirichlet allocation)-link connects microbes to genes using reduced-dimensionality LDA topics. We validate our method with single-cell RNA-seq and microscopy and then apply it to the sputum of asthmatic patients to find known and novel relationships between microbes and genes.
Spakowicz, Daniel; Lou, Shaoke; Barron, Brian; Gomez, Jose L; Li, Tianxiao; Liu, Qing; Grant, Nicole; Yan, Xiting; Hoyd, Rebecca; Weinstock, George M.; Chupp, Geoffrey L; and Gerstein, Mark, "Approaches for integrating heterogeneous RNA-seq data reveal cross-talk between microbes and genes in asthmatic patients." (2020). Faculty Research 2020. 103.