A translational profiling approach for the molecular characterization of CNS cell types
Open accessAbstract
The cellular heterogeneity of the brain confounds efforts to elucidate the biological properties of distinct neuronal populations. Using bacterial artificial chromosome (BAC) transgenic mice that express EGFP-tagged ribosomal protein L10a in defined cell populations, we have developed a methodology for affinity purification of polysomal mRNAs from genetically defined cell populations in the brain. The utility of this approach is illustrated by the comparative analysis of four types of neurons, revealing hundreds of genes that distinguish these four cell populations. We find that even two morphologically indistinguishable, intermixed subclasses of medium spiny neurons display vastly different translational profiles and present examples of the physiological significance of such differences. This genetically targeted translating ribosome affinity purification (TRAP) methodology is a generalizable method useful for the identification of molecular changes in any genetically defined cell type in response to genetic alterations, disease, or pharmacological perturbations.
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Canonical SPN marker expression indicates eSPNs may be molecularly camouflaged, including in mouse studies using Drd1- and Adora2a-driven transgenes to label or manipulate dSPNs/iSPNs.
“Expression of markers associated with canonical SPNs suggests eSPNs have been molecularly “camouflaged,” including in studies using mice that have employed Drd1 and Adora2a driven–transgenes to label and manipulate dSPNs or iSPNs (Heiman et al., 2008; Kozorovitskiy et al., 2012; Kravitz et al., 2012).”
From Molecular diversity and specializations among the cells of the adult mouse brain (2018) · cites this paper as Heiman et al., 2008
In Results (“The BACarray approach and methodology”; page unavailable), Heiman et al. describe D1-driven BAC transgenic mice used to identify striatonigral neurons. Results (“BACarray profiling of striatonigral and striatopallidal MSNs”; page unavailable) identify Adora2a as a striatopallidal marker, but the study uses D2—not Adora2a—to drive its striatopallidal transgene. It does not establish the cited example of Adora2a-driven transgenes used to label or manipulate those neurons; the molecular-camouflage inference is the citing authors’ framing. (LLM, conf=0.85)
Experimental — accuracy not yet measuredCrossing these mice to microglia-specific Cre mice allows for the isolation of ribosome-associated mRNAs in a cell-type-specific fashion using eGFP-based immunoaffinity purification.
“Crossing these mice to microglia-specific Cre mice allows for the isolation of ribosome-associated mRNAs in a cell-type-specific fashion using eGFP-based immunoaffinity purification28,91,93.”
From Lymphoid gene expression supports neuroprotective microglia function (2025) · cites this paper as [91]
The Introduction and Results describe cell-type-specific isolation of ribosome-associated mRNAs using EGFP-L10a and anti-EGFP immunoaffinity purification. They do not describe crossing the mice with microglia-specific Cre mice; the reported targeting uses BAC transgenes in neuronal populations. No page numbers are available in our copy. (LLM, conf=0.85)
Experimental — accuracy not yet measuredThe TRAP approach relies on the genetic labelling of the ribosomal protein L10a with the enhanced green fluorescent protein (eGFP) using Eef1a1LSL.eGFPL10a/+ mice.
“The TRAP approach91,92 relies on the genetic labelling of the ribosomal protein L10a with the enhanced green fluorescent protein (eGFP) using Eef1a1LSL.eGFPL10a/+ mice60.”
From Lymphoid gene expression supports neuroprotective microglia function (2025) · cites this paper as [91]
Nucleus accumbens medium spiny neurons are defined by transcriptional profiles including dopamine receptor 1 versus dopamine receptor 2 expression, substance P, enkephalin, and other enriched genes.
“These neurons are defined by their transcriptional profiles, including dopamine receptor 1 (D1) vs. dopamine receptor 2 (D2) expression, substance P and enkephalin, and other enriched genes (16–18).”
From Emerging Role for Nucleus Accumbens Medium Spiny Neuron Subtypes in Depression (2017) · cites this paper as [18]
Electron-microscopic images from sucrose gradient fractions after puromycin runoff in the IVT-EBP system showed complexes containing multiple ribosomes.
“These fractions harbor complexes containing multiple ribosomes (Figure 7A) identified as such by immuno-EM on the same gradient fraction prepared from a transgenic mouse expressing the tagged ribosomal protein EGFP-rpL10a (Heiman et al., 2008; Doyle et al., 2008) (Figure 7B).”
From FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism (2011) · cites this paper as Heiman et al., 2008
TRAP/Ribo-tag, which overexpresses an epitope-tagged ribosomal protein under a cell-type-specific promoter, allows purification by immunoprecipitation of transcripts bound by polyribosomes in desired cells.
“overexpression of an epitope-tagged ribosomal protein (referred to as ‘TRAP’ or ‘Ribo-tag’ methods) under the control of one such cell-type-specific promoter allows purification by immunoprecipitation of the transcripts bound by the polyribosome in the desired cells58”
From Decoding neuroproteomics: integrating the genome, translatome and functional anatomy (2014) · cites this paper as [58]
The sample sizes used in the study were similar to those reported in previous publications.
“No statistical methods were used to pre-determine sample sizes but our sample sizes are similar to those reported in previous publications19,31,95,99,108.”
From Epigenetic regulation of brain region-specific microglia clearance activity (2018) · cites this paper as [19]
The bacTRAP technology enabled assaying Alzheimer's disease-relevant neuronal cell types with genome-wide coverage, measuring transcripts ex vivo, and specifically capturing actively translated genes.
“The bacTRAP technology enabled us to assay AD-relevant neuronal cell types with genome-wide coverage, measure transcripts ex vivo (as opposed to postmortem), and specifically capture actively translated (rather than all transcribed) genes.”
From Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis (2020) · cites this paper as Heiman et al., 2008
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- Authors
- Heiman, M., Schaefer, A., Gong, S., Peterson, J. D., Day, M., Ramsey, K. E., Suárez-Fariñas, M., Schwarz, C., Stephan, D. A., Surmeier, D. J., Greengard, P., & Heintz, N.
- Affiliations
- Rockefeller University (US)
- Northwestern University (US)
- Translational Genomics Research Institute (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Heintz, Nathaniel
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2008-11
- Volume
- 135
- Issue
- 4
- Pages
- 738-748
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2696821
- OpenAlex
- W2150626351
- Cited by
- 1,134
- References
- 59
- Citations by year
- 2026: 28 · 2025: 61 · 2024: 57 · 2023: 65 · 2022: 55 · 2021: 60 · 2020: 79 · 2019: 76 · 2018: 93 · 2017: 76 · 2016: 70 · 2015: 70 · 2014: 97 · 2013: 70 · 2012: 55
- FWCI
- 16.44
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1755 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (1f32da021487-01)
- National Institute on Aging (AG09464, P01AG009464)
- National Institute of Mental Health (MH-074866, P50MH074866)
- National Institute on Drug Abuse (5F32DA021487, DA10044, P01DA010044, F32 DA021487)
- National Institute of Neurological Disorders and Stroke (NS 34696, R01NS034696, R37NS034696)
- National Center for Research Resources (UL1RR024143)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Neuroscience › Cellular and Molecular Neuroscience › Neuroscience and Neuropharmacology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- translating ribosome affinity purification, polysomal mRNA, neuronal cell types, medium spiny neurons, translational profiling, BAC transgenic mice, cell type-specific gene expression
- MeSH terms
- Animals, Brain, Central Nervous System, Cocaine, Genetic Techniques, Immunohistochemistry, Mice, Transgenic, Models, Biological, Neurons, Ribosomes, Protein Biosynthesis, Dopamine Uptake Inhibitors, Chromosomes, Artificial, Bacterial, Green Fluorescent Proteins, Mice
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