Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity

Thank you for sending your work entitled “Transcriptional profiling at whole population and single cell levels reveals somatosensory neuron molecular diversity” for consideration at eLife. Your article has been favorably evaluated by a Senior editor, Jeremy Nathans (Reviewing editor), and 3 reviewers, one of whom, Lee Henry, has agreed to share his identity.

The Reviewing editor and the other reviewers discussed their comments before we reached this decision, and the Reviewing editor has assembled the following comments to help you prepare a revised submission.

All of the reviewers were impressed with the thoroughness of your experiments and the accompanying analysis. We believe that this data set will be of substantial interest to neuroscientists working on DRG development and function, and that it will also be of interest to a broad community of scientists who are working with single cell transcriptome approaches.

Four major points to address are listed below:

1) One issue with the data is that the expression pattern of Kcnq4 seems inconsistent between microarray and qRT-PCR. Kcnq4 has previously been found to be expressed in low-threshold mechanoreceptors, but not nociceptors or proprioceptors (Heidenreich, et al., 2012). In the population RNA seq data presented in the Excel files, Kcnq4 is shown to be highly expressed in SNS-Cre+ neurons, but not detectable in Parv-Cre+ neurons, which is inconsistent with the previous publication. However, in Figure 12, Kcnq4 is identified as a transcript specifically expressed in Group VII, which contains the Parv-Cre+ population. The authors should address why this transcript is enriched in one population by microarray, but another by quantitative RT-PCR.

2) In Figure 3–figure supplement 2 the authors present their data as 'transcript fold differences'. This is a valid means of comparing multiple samples, however, it doesn't speak to the purity of the samples being compared. For example, if the profiled cell populations are enriched rather than highly pure, you would expect to recover differences in any pairwise comparison, however, the magnitude of those differences would be depressed if a sufficient number of non-target cells contribute to the individual profiles. It is clear that the experiments are highly reproducible (Figure 3–figure supplement 2), however, it would be useful if the authors could show in a more absolute (not comparative) manner that their samples do not express genes that should not be in these cell types.

3) The data presented in Figure 12 is impressive, however, a common problem associated with single cell studies is amplification-based noise. The authors could address this issue by showing the expression of the 'ubiquitous' markers that they describe in the text (Scn10a, Scn11a, Kcnc1, Kcnv1, Trpv1 and Trpa1). This could be done in a second part of Figure 12 or in the supplement to the figure.

4) The authors should mention possible limitations to their analysis, since I assume the profiles were obtained from a single (postnatal?) time point and from sensory neurons taken from a single (lumbar?) level. The authors should clarify at the beginning of the results the age and rostrocaudal position of the DRG being analyzed. Genes relevant to establishing proper circuitry may include those that are only transiently expressed during embryogenesis, are expressed on only at certain levels (as a consequence of intrinsic positional identities, or target dependent gene regulation).

1) One issue with the data is that the expression pattern of Kcnq4 seems inconsistent between microarray and qRT-PCR. Kcnq4 has previously been found to be expressed in low-threshold mechanoreceptors, but not nociceptors or proprioceptors (Heidenreich, et al., 2012). In the population RNA seq data presented in the Excel files, Kcnq4 is shown to be highly expressed in SNS-Cre+ neurons, but not detectable in Parv-Cre+ neurons, which is inconsistent with the previous publication. However, in Figure 12, Kcnq4 is identified as a transcript specifically expressed in Group VII, which contains the Parv-Cre+ population. The authors should address why this transcript is enriched in one population by microarray, but another by quantitative RT-PCR.

We thank the reviewers for reviewing our expression data in detail and finding that Kcnq4 showed a mismatched expression pattern between the whole population microarray data and the single cell qRT-PCR datasets. In reanalyzing our qRT-PCR dataset, we found that we had made an error in labeling gene names for neuronal Group VII, where “Spp1” was incorrectly labeled as “Kcnq4”, which is the underlying reason for this discrepancy. We apologize for this error and we are grateful that reviewers spotted it.

We have now reanalyzed all single cell neuronal expression data to ensure accuracy of all the subgroup-enriched markers. In the newly added Figure 12–figure supplement 2, we show plots of all characteristic markers of the two neuronal subgroups that have the most significantly enriched transcripts in our dataset, Group I (Grik1, Scn11a, Mrgprd, Agtr1a, St6gal2, Pde11a, Ggta1, Prkcq, A3galt2, Ptgdr, P2rx3, Lpar5, Mmp25, Lpar3, Casz1, Slc16a12, Lypd1, Moxd1, Wnt2b) and Group VII (Pvalb, Car2, Spp1, Ndst4, Etv1, Gprc5b, Ano1, Pth1r, Runx3, Kcnc1, Wnt7a, Cdh12). These transcripts are presented in order from highest to lowest expression levels normalized to Gapdh. In this re-analysis, we found that Group I enriched transcripts Pde11a and Lypd1 were not originally reported in our manuscript. We have now made changes to Figure 12 and added supplemental figure 1 to correct this. For gene expression markers described for Groups II, IV, V, and VI, underlying plots of gene expression are shown in Figures 14, and supplements 1, 2.

As the reviewers point out, our Kcnq4 population-level data and the published literature (Heidenreich et al, 2012) show enrichment in IB4^-SNS-Cre⁺ neurons (Figure 6, Tables 2, 6). Our single cell qRT-PCR data for Kcnq4, however, is inconclusive (Figure 12–figure supplement 2). This may be due to the Taqman probeset used, and we thus do not make further conclusions about its single cell expression. By contrast, Spp1, which we had originally mislabeled as Kcnq4, is definitively enriched in Group VII at high levels compared to other neuronal groups (Figure 12–figure supplement 2).

The following specific corrections have been made to the manuscript: “Kcnq4” has been relabeled to “Spp1” in Figure 12 and in the manuscript text. Pde11a and Lypd1 are now added as Group I characteristics in Figure 12.

2) In Figure 3–figure supplement 2 the authors present their data as 'transcript fold differences'. This is a valid means of comparing multiple samples, however, it doesn't speak to the purity of the samples being compared. For example, if the profiled cell populations are enriched rather than highly pure, you would expect to recover differences in any pairwise comparison, however, the magnitude of those differences would be depressed if a sufficient number of non-target cells contribute to the individual profiles. It is clear that the experiments are highly reproducible (figure supplement 2), however, it would be useful if the authors could show in a more absolute (not comparative) manner that their samples do not express genes that should not be in these cell types.

We appreciate the point that relative fold-differences does not demonstrate purity as well as absolute values. We have now re-plotted all myelin associated transcripts, nociceptor associated transcripts, and proprioceptor associated transcripts as absolute robust multi-array average (RMA) normalized expression levels (new Figure 3–figure supplement 2). These data show significant decreases in myelin associated transcript expression in FACS purified samples relative to whole DRG samples (p<0.001 by One-way ANOVA) and increases in neuronal transcript expression levels (p<0.001 by One-way ANOVA). Overall signal intensity was higher for some microarray probesets, which may reflect greater probeset sensitivity or nonspecific background. For example, low level expression of certain transcripts were found in sorted samples (Mpz, Mbp), while other transcripts were not detected at all (Pmp2, Mag). Based on these data, our sorting methodology strongly enriches for neurons compared to whole DRG tissue, but we cannot rule out the presence of small numbers of non-neuronal cells. Thus, these data confirm the advantage of FACS sorting of neuronal subsets vs. whole DRG tissue analysis.

3) The data presented in Figure 12 is impressive, however, a common problem associated with single cell studies is amplification-based noise. The authors could address this issue by showing the expression of the 'ubiquitous' markers that they describe in the text (Scn10a, Scn11a, Kcnc1, Kcnv1, Trpv1 and Trpa1). This could be done in a second part of Figure 12 or in the supplement to the figure.

We thank the reviewers for pointing out potential issues with amplification-based noise. We now show the presence of these neuronal markers, as the reviewer requests (new Figure 12–figure supplement 1). Specifically, we show the expression patterns of the ligand-gated ion channels (Trpv1, Trpa1), voltage-gated ion channels (Scn10a, Scn11a), Kcnc1, Kcnv1), and Pvalb (proprioceptive neuron marker) across the 334 single cell dataset. Single cell samples show expression of at least one of these transcripts in each of the cells, indicating their neuronal nature, as these ion channels or markers are strongly associated with neuron-specific functions. These data also demonstrates that amplification-based noise does not obscure the specific enrichment of specific neuronal transcripts in particular subsets as defined by Fluidigm qRT-PCR.

4) The authors should mention possible limitations to their analysis, since I assume the profiles were obtained from a single (postnatal?) time point and from sensory neurons taken from a single (lumbar?) level. The authors should clarify at the beginning of the results the age and rostrocaudal position of the DRG being analyzed. Genes relevant to establishing proper circuitry may include those that are only transiently expressed during embryogenesis, are expressed on only at certain levels (as a consequence of intrinsic positional identities, or target dependent gene regulation).

We have now added the requested clarification of our analysis at the beginning of the Results section on FACS purification and transcriptional profiling analysis. The details of these methodologies are also in the Method section under “Flow Cytometry of Neurons”. The limitations of our study are also discussed in the new manuscript in relation to other studies in the Discussion.

Our population level and single cell sorting was conducted postnatally on dorsal root ganglion neurons isolated from 7-20 week old mice (both males and females). For microarray whole transcriptome analysis, 100 ng RNA was required for reverse transcription, cDNA preparation using the Ambion WT Expression kit, which is a standard protocol in Genechip hybridization facilities. We actively chose to avoid performing pre-amplification steps using kits prior to this step, which often introduces transcript signal biases. As a result, sufficient RNA was more difficult to obtain from sorted populations, in particular Parv-Cre/TdTomato⁺ neurons, which make up only 12.5±1.7% of DRG neurons). Thus, in order to obtain sufficient RNA for analysis without introducing amplification biases, we pooled cervical (C1-C8), thoracic (T1-T13), and lumbar DRGs (L1-L6). This is a limitation of our study, as certain anatomical regions are potentially more enriched for particular transcripts (e.g. lumbar vs. certical). To minimize technical variability, SNS-Cre/TdTomato (total, IB4⁺, IB4^-) and Parv-Cre/TdTomato neurons were sorted on the same day. As the reviewer points out, developmental timepoint certainly influences gene expression, as distinct embryonic stage-dependent expression patterns likely determine specification of each subset. Preliminary analysis of neonatal SNS-Cre/TdTomato⁺ neurons (P2) show significant differences compared to our adult purified neurons (Data not shown). We discuss these imitations in the Discussion, and point out that more specific and targeted analysis will be important future studies.

While preparing the revisions to this manuscript, three papers performing expression profiling of postnatal adult sensory neurons were published: one of which was mentioned by Reviewer #1 (Goswani et al, 2014;Thakur et al, 2014; Usokin et al, 2014). We have added a new paragraph in our manuscript discussing how our study’s approach and findings relate to these papers. In particular comparison to Usokin et al, we have some similar findings, including our Group VI pruriceptive neurons (IL31ra⁺). However, our analysis showed higher definition of Group I and Group VII neurons (distinctly more markers), as well as Group IV neurons which they did not detect. We note that each of these studies utilized distinct methodologies: two performed analysis of one neuronal population each (Goswani et al, 2014; Thakur et al, 2014), and one performed single cell RNA-seq but not population analysis (Usokin et al, 2014). We believe that our study possesses certain advantages as well as limitations in relation to these studies but remains a unique and important contribution.

In brief summary: a) Goswami et al profiled Trpv1 lineage neurons compared to Trpv1-DTA whole DRG tissues. b) Thakur et al performed magnetic bead selection to remove DRG non-neuronal cells, leaving neurons for a population RNA-seq analysis. c) Usokin et al performed single cell RNA-seq on hundreds of DRG neurons that were robotically picked in an unbiased fashion. In our study, we performed whole population analysis of 3 major DRG subsets, which we followed by single cell granular profiling of hundreds of cells from the same populations. We believe one advantage of our study is beginning with differential analysis of well-defined and functionally relevant populations. The two published population level studies did not perform comparative analysis with other distinct populations. We then further define each of our populations in detail using the single cell strategy, which gives us high-resolution analysis of functionally defined groups of cells. The same advantages of a population based strategy is also a caveat, in that it could introduce pre-determined bias, which Usokin et al purposely avoids by randomly picking single DRG neurons as a starting point. We note that our analysis is the only one to utilize parallel qRT-PCR of single cells, which we demonstrate is able to detect log-scale differences in expression (Figure 11), and we believe may have better detection sensitivities compared to single cell RNA-seq. As genomic technologies and single cell sorting methodologies evolve, the limitations (e.g. RNA quantity) will be overcome and future analysis of thousands of single cells from distinct anatomical locations, developmental time-points, or following injury/inflammation will begin to reveal even more critical information about the somatosensory system. We believe that our study and these recently published papers are a critical foundation for such future analysis.