title: High-resolution transcriptome of human macrophages.
abstract: Macrophages are dynamic cells integrating signals from their microenvironment to develop specific functional responses. Although, microarray-based transcriptional profiling has established transcriptional reprogramming as an important mechanism for signal integration and cell function of macrophages, current knowledge on transcriptional regulation of human macrophages is far from complete. To discover novel marker genes, an area of great need particularly in human macrophage biology but also to generate a much more thorough transcriptome of human M1- and M1-like macrophages, we performed RNA sequencing (RNA-seq) of human macrophages. Using this approach we can now provide a high-resolution transcriptome profile of human macrophages under classical (M1-like) and alternative (M2-like) polarization conditions and demonstrate a dynamic range exceeding observations obtained by previous technologies, resulting in a more comprehensive understanding of the transcriptome of human macrophages. Using this approach, we identify important gene clusters so far not appreciated by standard microarray techniques. In addition, we were able to detect differential promoter usage, alternative transcription start sites, and different coding sequences for 57 gene loci in human macrophages. Moreover, this approach led to the identification of novel M1-associated (CD120b, TLR2, SLAMF7) as well as M2-associated (CD1a, CD1b, CD93, CD226) cell surface markers. Taken together, these data support that high-resolution transcriptome profiling of human macrophages by RNA-seq leads to a better understanding of macrophage function and will form the basis for a better characterization of macrophages in human health and disease.
authors.affiliation: Genomics and Immunoregulation, LIMES-Institute, University of Bonn, Bonn, Germany.
authors.forename: Marc
authors.initials: M
authors.lastname: Beyer
authors.forename: Michael R
authors.initials: MR
authors.lastname: Mallmann
authors.forename: Jia
authors.initials: J
authors.lastname: Xue
authors.forename: Andrea
authors.initials: A
authors.lastname: Staratschek-Jox
authors.forename: Daniela
authors.initials: D
authors.lastname: Vorholt
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Krebs
authors.forename: Daniel
authors.initials: D
authors.lastname: Sommer
authors.forename: Jil
authors.initials: J
authors.lastname: Sander
authors.forename: Christina
authors.initials: C
authors.lastname: Mertens
authors.forename: Andrea
authors.initials: A
authors.lastname: Nino-Castro
authors.forename: Susanne V
authors.initials: SV
authors.lastname: Schmidt
authors.forename: Joachim L
authors.initials: JL
authors.lastname: Schultze
mesh_terms: D017398:Alternative Splicing; D016000:Cluster Analysis; D059472:Exome; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D006801:Humans; D016130:Immunophenotyping; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D018950:Lipopolysaccharide Receptors / Q000378:metabolism; D008264:Macrophages / Q000378:metabolism*; D059467:Transcriptome
chemical_list: D018950:Lipopolysaccharide Receptors