@article{eb3ca1fd818a4caa8f0cfb61629bb434,
title = "Gene set predictor for post-treatment Lyme disease",
abstract = "Lyme disease (LD) is tick-borne disease whose post-treatment sequelae are not well understood. For this study, we enrolled 152 individuals with symptoms of post-treatment LD (PTLD) to profile their peripheral blood mononuclear cells (PBMCs) with RNA sequencing (RNA-seq). Combined with RNA-seq data from 72 individuals with acute LD and 44 uninfected controls, we investigated differences in differential gene expression. We observe that most individuals with PTLD have an inflammatory signature that is distinguished from the acute LD group. By distilling gene sets from this study with gene sets from other sources, we identify a subset of genes that are highly expressed in the cohorts but are not already established as biomarkers for inflammatory response or other viral or bacterial infections. We further reduce this gene set by feature importance to establish an mRNA biomarker set capable of distinguishing healthy individuals from those with acute LD or PTLD as a candidate for translation into an LD diagnostic.",
author = "Clarke, {Daniel J.B.} and Rebman, {Alison W.} and Jinshui Fan and Soloski, {Mark J.} and Aucott, {John N.} and Avi Ma'ayan",
note = "Funding Information: The project was partially supported by funds from the Cohen Lyme & Tickborne Disease Initiative and NIH grant P30AR070254 . We would like to thank Ting Yang from JHU for depositing the data into dbGAP. Funding Information: The project was partially supported by funds from the Cohen Lyme & Tickborne Disease Initiative and NIH grant P30AR070254. We would like to thank Ting Yang from JHU for depositing the data into dbGAP. D.J.B.C. performed the analysis, created the figures, and contributed to the writing of the manuscript; A.W.R. provided information about the clinical component of the study and contributed to the writing of the manuscript; J.F. processed the and annotated the samples; M.J.S. and J.N.A. designed the study, oversaw the analysis and interpretations of the results, and contributed to the writing of the manuscript; A.M. oversaw and contributed to the analysis and led the writing of the manuscript. The authors have applied for patents covering some aspects of the study. The authors support inclusive, diverse, and equitable conduct of research. Publisher Copyright: {\textcopyright} 2022 The Author(s)",
year = "2022",
month = nov,
day = "15",
doi = "10.1016/j.xcrm.2022.100816",
language = "English",
volume = "3",
journal = "Cell Reports Medicine",
issn = "2666-3791",
publisher = "Cell Press",
number = "11",
}