Applications of single-cell RNA sequencing in drug discovery and development

Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods, together with associated computational tools and the growing availability of public data resources, are transforming drug discovery and development. New opportunities are emerging in target identification owing to improved disease understanding through cell subtyping, and highly multiplexed functional genomics screens incorporating scRNA-seq are enhancing target credentialling and prioritization. ScRNA-seq is also aiding the selection of relevant preclinical disease models and providing new insights into drug mechanisms of action. In clinical development, scRNA-seq can inform decision-making via improved biomarker identification for patient stratification and more precise monitoring of drug response and disease progression. Here, we illustrate how scRNA-seq methods are being applied in key steps in drug discovery and development, and discuss ongoing challenges for their implementation in the pharmaceutical industry.

A scalable SCENIC workflow for single-cell gene regulatory network analysis

This protocol explains how to perform a fast SCENIC analysis alongside standard best practices steps on single-cell RNA-sequencing data using software containers and Nextflow pipelines. SCENIC reconstructs regulons (i.e., transcription factors and their target genes) assesses the activity of these discovered regulons in individual cells and uses these cellular activity patterns to find meaningful clusters of cells. Here we present an improved version of SCENIC with several advances. SCENIC has been refactored and reimplemented in Python (pySCENIC), resulting in a tenfold increase in speed, and has been packaged into containers for ease of use. It is now also possible to use epigenomic track databases, as well as motifs, to refine regulons. In this protocol, we explain the different steps of SCENIC: the workflow starts from the count matrix depicting the gene abundances for all cells and consists of three stages. First, coexpression modules are inferred using a regression per-target approach (GRNBoost2). Next, the indirect targets are pruned from these modules using cis-regulatory motif discovery (cisTarget). Lastly, the activity of these regulons is quantified via an enrichment score for the regulon's target genes (AUCell). Nonlinear projection methods can be used to display visual groupings of cells based on the cellular activity patterns of these regulons. The results can be exported as a loom file and visualized in the SCope web application. This protocol is illustrated on two use cases: a peripheral blood mononuclear cell data set and a panel of single-cell RNA-sequencing cancer experiments. For a data set of 10,000 genes and 50,000 cells, the pipeline runs in <2 h.

Male-specific fruitless isoforms target neurodevelopmental genes to specify a sexually dimorphic nervous system

Background

In Drosophila, male courtship behavior is regulated in large part by the gene fruitless (fru). fru encodes a set of putative transcription factors that promote male sexual behavior by controlling the development of sexually dimorphic neuronal circuitry. Little is known about how Fru proteins function at the level of transcriptional regulation or the role that isoform diversity plays in the formation of a male-specific nervous system.

Results

To characterize the roles of sex-specific Fru isoforms in specifying male behavior, we generated novel isoform-specific mutants and used a genomic approach to identify direct Fru isoform targets during development. We demonstrate that all Fru isoforms directly target genes involved in the development of the nervous system, with individual isoforms exhibiting unique binding specificities. We observe that fru behavioral phenotypes are specified by either a single isoform or a combination of isoforms. Finally, we illustrate the utility of these data for the identification of novel sexually dimorphic genomic enhancers and novel downstream regulators of male sexual behavior.

Conclusions

These findings suggest that Fru isoform diversity facilitates both redundancy and specificity in gene expression, and that the regulation of neuronal developmental genes may be the most ancient and conserved role of fru in the specification of a male-specific nervous system.

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Isoform-specific fru mutants reveal both functional redundancy and specificity

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Fru isoform-specific genomic occupancy is characterized in the Drosophila nervous system

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All Fru isoforms directly target neuronal morphogenesis genes

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Isoform-specific motifs are associated with specific Fru isoform occupancy

Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

The identification of transcription factor binding sites, enhancers, and transcriptional target genes often relies on the integration of gene expression profiling and computational cis-regulatory sequence analysis. Methods for the prediction of cis-regulatory elements can take advantage of comparative genomics to increase signal-to-noise levels. However, gene expression data are usually derived from only one species. Here we investigate tissue-specific cross-species gene expression profiling by high-throughput sequencing, combined with cross-species motif discovery. First, we compared different methods for expression level quantification and cross-species integration using Tag-seq data. Using the optimal pipeline, we derived a set of genes with conserved expression during retinal determination across Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis. These genes are enriched for binding sites of eye-related transcription factors including the zinc-finger Glass, a master regulator of photoreceptor differentiation. Validation of predicted Glass targets using RNA-seq in homozygous glass mutants confirms that the majority of our predictions are expressed downstream from Glass. Finally, we tested nine candidate enhancers by in vivo reporter assays and found eight of them to drive GFP in the eye disc, of which seven colocalize with the Glass protein, namely, scrt, chp, dpr10, CG6329, retn, Lim3, and dmrt99B. In conclusion, we show for the first time the combined use of cross-species expression profiling with cross-species motif discovery as a method to define a core developmental program, and we augment the candidate Glass targetome from a single known target gene, lozenge, to at least 62 conserved transcriptional targets.

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

The field of regulatory genomics today is characterized by the generation of high-throughput data sets that capture genome-wide transcription factor (TF) binding, histone modifications, or DNAseI hypersensitive regions across many cell types and conditions. In this context, a critical question is how to make optimal use of these publicly available datasets when studying transcriptional regulation. Here, we address this question in Drosophila melanogaster for which a large number of high-throughput regulatory datasets are available. We developed i-cisTarget (where the 'i' stands for integrative), for the first time enabling the discovery of different types of enriched 'regulatory features' in a set of co-regulated sequences in one analysis, being either TF motifs or 'in vivo' chromatin features, or combinations thereof. We have validated our approach on 15 co-expressed gene sets, 21 ChIP data sets, 628 curated gene sets and multiple individual case studies, and show that meaningful regulatory features can be confidently discovered; that bona fide enhancers can be identified, both by in vivo events and by TF motifs; and that combinations of in vivo events and TF motifs further increase the performance of enhancer prediction.

Comparison of bandwidths in the inferior colliculus and the auditory nerve. I. Measurement using a spectrally manipulated stimulus

A defining feature of auditory systems across animal divisions is the ability to sort different frequency components of a sound into separate neural frequency channels. Narrowband filtering in the auditory periphery is of obvious advantage for the representation of sound spectrum and manifests itself pervasively in human psychophysical studies as the critical band. Peripheral filtering also alters coding of the temporal waveform, so that temporal responses in the auditory periphery reflect both the stimulus waveform and peripheral filtering. Temporal coding is essential for the measurement of the time delay between waveforms at the two ears-a critical component of sound localization. A number of human psychophysical studies have shown a wider effective critical bandwidth with binaural stimuli than with monaural stimuli, although other studies found no difference. Here we directly compare binaural and monaural bandwidths (BWs) in the anesthetized cat. We measure monaural BW in the auditory nerve (AN) and binaural BW in the inferior colliculus (IC) using spectrally manipulated broadband noise and response metrics that reflect spike timing. The stimulus was a pair of noise tokens that were interaurally in phase for all frequencies below a certain flip frequency (f(flip)) and that had an interaural phase difference of pi above f(flip). The response was measured as a function of f(flip) and, using a separate stimulus protocol, as a function of interaural correlation. We find that both AN and IC filter BW depend on characteristic frequency, but that there is no difference in mean BW between the AN and IC.

Binaural and cochlear disparities

Binaural auditory neurons exhibit "best delays" (BDs): They are maximally activated at certain acoustic delays between sounds at the two ears and thereby signal spatial sound location. BDs arise from delays internal to the auditory system, but their source is controversial. According to the classic Jeffress model, they reflect pure time delays generated by differences in axonal length between the inputs from the two ears to binaural neurons. However, a relationship has been reported between BDs and the frequency to which binaural neurons are most sensitive (the characteristic frequency), and this relationship is not predicted by the Jeffress model. An alternative hypothesis proposes that binaural neurons derive their input from slightly different places along the two cochleas, which induces BDs by virtue of the slowness of the cochlear traveling wave. To test this hypothesis, we performed a coincidence analysis on spiketrains of pairs of auditory nerve fibers originating from different cochlear locations. In effect, this analysis mimics the processing of phase-locked inputs from each ear by binaural neurons. We find that auditory nerve fibers that innervate different cochlear sites show a maximum number of coincidences when they are delayed relative to each other, and that the optimum delays decrease with characteristic frequency as in binaural neurons. These findings suggest that cochlear disparities make an important contribution to the internal delays observed in binaural neurons.