Untangling the brain's neuroinflammatory and neurodegenerative transcriptional responses.
A common approach to understanding neurodegenerative disease is comparing gene expression in diseased versus healthy tissues. We illustrate that expression profiles derived from whole tissue RNA highly reflect the degenerating tissues' altered cellular composition, not necessarily transcriptional regulation. To accurately understand transcriptional changes that accompany neuropathology, we acutely purify neurons, astrocytes and microglia from single adult mouse brains and analyse their transcriptomes by RNA sequencing. Using peripheral endotoxemia to establish the method, we reveal highly specific transcriptional responses and altered RNA processing in each cell type, with Tnfr1 required for the astrocytic response. Extending the method to an Alzheimer's disease model, we confirm that transcriptomic changes observed in whole tissue are driven primarily by cell type composition, not transcriptional regulation, and identify hundreds of cell type-specific changes undetected in whole tissue RNA. Applying similar methods to additional models and patient tissues will transform our understanding of aberrant gene expression in neurological disease.
Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Karpagam
K
Srinivasan
Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Brad A
BA
Friedman
Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Jessica L
JL
Larson
Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Benjamin E
BE
Lauffer
Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.|Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Leonard D
LD
Goldstein
Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Laurie L
LL
Appling
Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Jovencio
J
Borneo
Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Chungkee
C
Poon
Department of Immunology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Terence
T
Ho
Department of Diagnostics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Fang
F
Cai
Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Pascal
P
Steiner
Department of Diagnostics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Marcel P
MP
van der Brug
Department of Molecular Biology, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Zora
Z
Modrusan
Department of Bioinformatics, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
Joshua S
JS
Kaminker
Department of Neuroscience, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, USA.
David V
http://orcid.org/0000-0001-9679-7189
DV
Hansen
D000328:Adult; D000544:Alzheimer Disease / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D000818:Animals; D001253:Astrocytes / Q000187:drug effects / Q000378:metabolism* / Q000473:pathology; D002531:Cerebellum / Q000187:drug effects / Q000378:metabolism / Q000473:pathology; D004195:Disease Models, Animal; D019446:Endotoxemia / Q000139:chemically induced / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D005625:Frontal Lobe / Q000187:drug effects / Q000378:metabolism / Q000473:pathology; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D008070:Lipopolysaccharides / Q000494:pharmacology; D051379:Mice; D017628:Microglia / Q000187:drug effects / Q000378:metabolism* / Q000473:pathology; D009419:Nerve Tissue Proteins / Q000235:genetics / Q000378:metabolism; D009474:Neurons / Q000187:drug effects / Q000378:metabolism* / Q000473:pathology; D009928:Organ Specificity; D047888:Receptors, Tumor Necrosis Factor, Type I / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D059467:Transcriptome
D008070:Lipopolysaccharides; D009419:Nerve Tissue Proteins; D047888:Receptors, Tumor Necrosis Factor, Type I; C506236:Tnfrsf1a protein, mouse