AmpliSeq transcriptome analysis of human alveolar and monocyte-derived macrophages over time in response to Mycobacterium tuberculosis infection

PloS One
Audrey C PappWolfgang Sadee

Abstract

Human alveolar macrophages (HAM) are primary bacterial niche and immune response cells during Mycobacterium tuberculosis (M.tb) infection, and human blood monocyte-derived macrophages (MDM) are a model for investigating M.tb-macrophage interactions. Here, we use a targeted RNA-Seq method to measure transcriptome-wide changes in RNA expression patterns of freshly obtained HAM (used within 6 h) and 6 day cultured MDM upon M.tb infection over time (2, 24 and 72 h), in both uninfected and infected cells from three donors each. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) uses primers targeting 18,574 mRNAs and 2,228 non-coding RNAs (ncRNAs) for a total of 20,802 transcripts. AmpliSeqTM yields highly precise and reproducible gene expression profiles (R2 >0.99). Taking advantage of AmpliSeq's reproducibility, we establish well-defined quantitative RNA expression patterns of HAM versus MDM, including significant M.tb-inducible genes, in networks and pathways that differ in part between MDM and HAM. A similar number of expressed genes are detected at all time-points between uninfected MDM and HAM, in common pathways including inflammatory and immune functions, but canonical pathway differences also exist. In par...Continue Reading

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Citations

Sep 13, 2019·The Journal of Immunology : Official Journal of the American Association of Immunologists·William P LafuseLarry S Schlesinger
Apr 9, 2020·Frontiers in Immunology·Anu GoenkaTracy Hussell
Aug 9, 2020·International Journal of Molecular Sciences·Jungho KimHyeyoung Lee
Feb 28, 2021·Annual Review of Immunology·Mariëtta M Ravesloot-ChávezSarah A Stanley

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Methods Mentioned

BETA
AmpliSeq
bronchoalveolar lavage
PCR
chip
RNA-Seq
Infection
chips
RNA assay

Software Mentioned

edgeR
Ion Torrent Mapping Alignment Program ( TMAP )
TMAP
dbGAP
AmpliSeq
R package edgeR
GENCODE
IPA

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