Drug targets: single-cell transcriptomics hastens unbiased discovery

doi:10.1016/j.tips.2011.09.006

Trends in Pharmacological Sciences

Volume 33, Issue 1, January 2012, Pages 9-16

https://doi.org/10.1016/j.tips.2011.09.006 Get rights and content

Drug discovery in neuro- and psychopharmacology is lagging, and the most commonly mentioned cause is the scarcity of drug targets. Using NextGen ‘sequencing based single-cell transcriptomics’ (SBSCT), several hundred different receptors and channels can be identified in individual neurons, and the functional gene product can subsequently be validated. The use of single-cell transcriptome data to reveal the entire receptor repertoire is crucial, as the copy numbers of mRNAs encoding receptors are low, and when cells are pooled dilution of rare mRNAs leads to loss of signal. These overlooked receptors on key neurons often mediate robust effects that may be therapeutically useful. SBSCT also enables the identification of orphan receptors and can provide strong evidence for receptor heterodimers. Here, we compare SBSCT to other single-cell profiling methods. We argue that the unbiased nature of SBSCT makes it a powerful tool for the identification of new drug targets.

Section snippets

Single-cell profiling is important for drug discovery

A key to modern drug discovery is the availability of high quality, new drug targets. Some therapeutic areas such as oncology and inflammation/immunity are rich in drug targets, whereas psychiatry and neurology are, currently, poor in good drug targets 1, 2, 3. The identification of promising drug targets in neuropsychiatry is essential for further drug development and will also help us to better understand underlying illnesses. During the past 30 years, a confluence of techniques such as

SBSCT compared with other methods of single-cell profiling

The advantages of single-cell transcriptomics over pooled cells or tissue sample transcriptomics have been discussed many times previously. The advantages of single-cell methodologies lie in their higher sensitivity, higher specificity and colocalization within the same cell type of information leading to the discovery of which mRNAs are indeed expressed in the same cell. This provides a basis for the study of whether the gene products of multiple targets may directly associate through the

The neurons

Currently, many important neurons in key circuits can be recognized by morphological markers, by being tagged with promoter-driven green fluorescent protein (GFP) expression in transgenic animals [29] or by identification of their specific activity profile. Once individual, active neurons are recognizable in tissue slice or in vivo, whole-cell patch clamp recordings can be made from them. This mode of electrophysiological characterization also opens the way for physically sampling the cell for

Discovery of orphan receptors is accelerated by SBSCT

The localization of orphan receptor mRNAs to a given neuron has been previously achieved by a set of methods that each has biases and limitations overcome by SBSCT: ISH, PCR analysis and microarray. ISH studies are unbiased but often have low resolution for transcripts under scrutiny. Of the 21 orphan receptors we identified in the WSNs [14], we could only find 60% in the Allen Brain Atlas. Furthermore, we would not have known whether these are expressed in warm-sensitive or insensitive cells

Concluding remarks

Our studies on the WSNs in the mouse hypothalamus 14, 33, 34, 35 and on pyramidal cells in rat hippocampus [43] using SBSCT have shown that most CNS neurons express mRNAs encoding 200–500 or more receptors, although in highly varying copy number per cell. The SBSCT and validation results show that the neuronal transcriptome (the RNA complement of a cell) and proteome (the protein complement of a cell) are usually in good concordance with each other, and thus the 200–500 receptor proteins are

Acknowledgments

This work was funded in part by Health Research Formula Funds (HRFF) from the Commonwealth of Pennsylvania and MH88849, DP10D004117 and AG9900 to J.E. and by funds from The Skaggs Institute for Chemical Biology, The Harold L. Dorris Neurological Research Institute, and the National Institute of Mental Health (NIMH) to T.B. We thank members of our labs and our collaborators for helpful and insightful discussions. This is TSRI manuscript number 21212.

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Trends in Pharmacological Sciences

OpinionDrug targets: single-cell transcriptomics hastens unbiased discovery

Section snippets

Single-cell profiling is important for drug discovery

SBSCT compared with other methods of single-cell profiling

The neurons

Discovery of orphan receptors is accelerated by SBSCT

Concluding remarks

Acknowledgments

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Neuroscience

Cell Stem Cell

Brain Res. Bull.

J. Biol. Chem.

Cytokine

Parkinsonism Relat. Disord.

Adv. Pharmacol.

Neuron

Pharmacol. Ther.

Single-cell gene expression analysis: implications for neurodegenerative and neuropsychiatric disorders

Neurochem. Res.

Antipsychotic drug development

Curr. Top Behav. Neurosci.

Schizophrenia from a neural circuitry perspective: advancing toward rational pharmacological therapies

J. Clin. Invest.

Imaging the glutamate system in humans: relevance to drug discovery for schizophrenia

Curr. Pharm. Des.

Analysis of gene expression in single live neurons

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Opinion
Drug targets: single-cell transcriptomics hastens unbiased discovery