A modular analysis of microglia gene expression, insights into the aged phenotype

BMC Genomics
Christine E ChoFredrik Kamme

Abstract

Microglia are multifunctional cells that are key players in brain development and homeostasis. Recent years have seen tremendous growth in our understanding of the role microglia play in neurodegeneration, CNS injury, and developmental disorders. Given that microglia show diverse functional phenotypes, there is a need for more precise tools to characterize microglial states. Here, we experimentally define gene modules as the foundation for describing microglial functional states. In an effort to develop a comprehensive classification scheme, we profiled transcriptomes of mouse microglia in a stimulus panel with 96 different conditions. Using the transcriptomic data, we generated fine-resolution gene modules that are robustly preserved across datasets. These modules served as the basis for a combinatorial code that we then used to characterize microglial activation under various inflammatory stimulus conditions. The microglial gene modules described here were robustly preserved, and could be applied to in vivo as well as in vitro conditions to dissociate the signaling pathways that distinguish acutely inflamed microglia from aged microglia. The microglial gene modules presented here are a novel resource for classifying and chara...Continue Reading

References

Oct 12, 2000·Proceedings of the National Academy of Sciences of the United States of America·A J ButteI S Kohane
Jan 22, 2004·Nature Reviews. Genetics·Albert-László Barabási, Zoltán N Oltvai
May 3, 2005·Nature Reviews. Immunology·Leonidas C Platanias
Mar 25, 2006·The Journal of Clinical Investigation·Oleg ButovskyMichal Schwartz
Jul 25, 2006·Trends in Neurosciences·Wolfgang J Streit
Aug 29, 2006·PLoS Genetics·Anatole GhazalpourSteve Horvath
Nov 15, 2006·Proceedings of the National Academy of Sciences of the United States of America·Michael C OldhamDaniel H Geschwind
Dec 7, 2007·Journal of Neuroscience Research·Jeppe FalsigMarcel Leist
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Mar 16, 2011·Journal of Alzheimer's Disease : JAD·Angela Marie Floden, Colin Kelly Combs
Oct 26, 2011·Brain Research Bulletin·Joshua A SmithNaren L Banik
Feb 14, 2012·Current Opinion in Virology·John W Schoggins, Charles M Rice
Mar 26, 2013·Nature Neuroscience·Masaki UenoToshihide Yamashita
Dec 10, 2013·Nature Neuroscience·Oleg ButovskyHoward L Weiner
Mar 19, 2014·Nature Reviews. Neurology·V Hugh Perry, Clive Holmes
Apr 22, 2014·Nature Methods·Dominic GrünAlexander van Oudenaarden
Jul 25, 2014·PLoS Computational Biology·Rekin's JankyStein Aerts
Sep 26, 2014·F1000Research·Jason MontojoQuaid Morris
Jan 19, 2016·Nature Neuroscience·Kathleen GrabertBarry W McColl
Feb 18, 2016·Proceedings of the National Academy of Sciences of the United States of America·Mariko L BennettBen A Barres
Apr 22, 2016·Nucleic Acids Research·Jüri ReimandJaak Vilo
Dec 3, 2016·Nucleic Acids Research·UNKNOWN The Gene Ontology Consortium
Mar 7, 2017·Nature Methods·Rob PatroCarl Kingsford
Aug 2, 2017·The Journal of Clinical Investigation·Inge R HoltmanChristopher K Glass
Sep 9, 2017·Nature Medicine·Michael W Salter, Beth Stevens
Nov 2, 2017·Nucleic Acids Research·Paul Julian KerseyAndrew Yates

❮ Previous
Next ❯

Citations

Dec 6, 2019·Frontiers in Cellular Neuroscience·Cai-Yun LiuHong-Liang Zhang
Jul 30, 2020·The European Journal of Neuroscience·Thaís Cristina Galdino de OliveiraCristovam Wanderley Picanço-Diniz
May 23, 2021·Mechanisms of Ageing and Development·Jéssica CostaAna L Cardoso
Jun 30, 2021·Neurochemistry International·Ivan A LindhoutAndis Klegeris

❮ Previous
Next ❯

Methods Mentioned

BETA
Magnet Activated Cell Sorting
flow cytometry

Software Mentioned

Salmon
GeneMANIA
Ensembl
Weighted Gene Correlation Network Analysis ( WGCNA )
iRegulon
gProfiler
Gene Ontology Enrichment Analysis
Cytoscape
cutreeDynamic
WGCNA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.