Biology and Bias in Cell Type-Specific RNAseq of Nucleus Accumbens Medium Spiny Neurons.
Hope KronmanFelix RichterBenoit LabontéRamesh ChandraShan ZhaoGabriel E HoffmanMary Kay LoboEric E SchadtEric J NestlerPublished in: Scientific reports (2019)
Subcellular RNAseq promises to dissect transcriptional dynamics but is not well characterized. Furthermore, FACS may introduce bias but has not been benchmarked genome-wide. Finally, D1 and D2 dopamine receptor-expressing medium spiny neurons (MSNs) of the nucleus accumbens (NAc) are fundamental to neuropsychiatric traits but have only a short list of canonical surface markers. We address these gaps by systematically comparing nuclear-FACS, whole cell-FACS, and RiboTag affinity purification from D1- and D2-MSNs. Using differential expression, variance partitioning, and co-expression, we identify the following trade-offs for each method. RiboTag-seq best distinguishes D1- and D2-MSNs but has the lowest transcriptome coverage. Nuclear-FACS-seq generates the most differentially expressed genes and overlaps significantly with neuropsychiatric genetic risk loci, but un-annotated genes hamper interpretation. Whole cell-FACS is more similar to nuclear-FACS than RiboTag, but captures aspects of both. Using pan-method approaches, we discover that transcriptional regulation is predominant in D1-MSNs, while D2-MSNs tend towards cytosolic regulation. We are also the first to find evidence for moderate sexual dimorphism in these cell types at baseline. As these results are from 49 mice (nmale = 39, nfemale = 10), they represent generalizable ground-truths. Together, these results guide RNAseq methods selection, define MSN transcriptomes, highlight neuronal sex differences, and provide a baseline for D1- and D2-MSNs.
Keyphrases
- genome wide
- single cell
- dna methylation
- rna seq
- copy number
- cell therapy
- gene expression
- transcription factor
- poor prognosis
- metabolic syndrome
- stem cells
- uric acid
- mental health
- insulin resistance
- brain injury
- subarachnoid hemorrhage
- affordable care act
- heat shock protein
- mass spectrometry
- binding protein
- skeletal muscle
- heat stress
- genome wide identification
- bone marrow
- health insurance