Spatial transcriptomics in adult Drosophila reveals new cell types in the brain and identifies subcellular mRNA patterns in muscles
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eLife assessment
This study presents a valuable method to visualize the location of the cell types discovered through single-cell RNA sequencing. The evidence supporting the claims is solid, but the inclusion of a larger number of samples would strengthen the study. It would also be helpful to have the methods explained in more detail. The work will be of interest to those seeking to identify new cell types from scRNA-seq and snRNA-seq data.
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Abstract
Recently, we have achieved a significant milestone with the creation of the Fly Cell Atlas. This single-nuclei atlas encompasses the entire fly, covering the entire head and body, in addition to all major organs. This atlas catalogs hundreds to thousands of cell types, of which we annotated 250. This still leaves many clusters to be fully characterized, in particular in the brain. Furthermore, with single-nuclei sequencing, all information about the spatial location of the cells and of the mRNAs within these cells is lost. Here, we provide a solution to this problem. In a proof of concept study, we have applied spatial transcriptomics using a selected gene panel to pinpoint the locations of 150 mRNA species in the adult fly. This enabled us to map unknown cell types identified in the Fly Cell Atlas to their spatial locations in the brain. Additionally, spatial transcriptomics discovered interesting principles of mRNA localization in large crowded muscle cells that may spark future mechanistic investigations. Furthermore, we present a set of computational tools that will allow for easier integration of spatial transcriptomics and single-cell datasets.
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Author Response
eLife assessment
This study presents a valuable method to visualize the location of the cell types discovered through single-cell RNA sequencing. The evidence supporting the claims is solid, but the inclusion of a larger number of samples would strengthen the study. It would also be helpful to have the methods explained in more detail. The work will be of interest to those seeking to identify new cell types from scRNA-seq and snRNA-seq data.
Response: We are surprised about the editor’s assessment of our paper as a “valuable” method. This is the first Drosophila adult spatial transcriptomics paper. Hence, we would at least consider this being an “important” method. Spatial transcriptomics has thus far only been done in embryos, which are easy to process for FISH for many decades. Integration with single-cell data is …
Author Response
eLife assessment
This study presents a valuable method to visualize the location of the cell types discovered through single-cell RNA sequencing. The evidence supporting the claims is solid, but the inclusion of a larger number of samples would strengthen the study. It would also be helpful to have the methods explained in more detail. The work will be of interest to those seeking to identify new cell types from scRNA-seq and snRNA-seq data.
Response: We are surprised about the editor’s assessment of our paper as a “valuable” method. This is the first Drosophila adult spatial transcriptomics paper. Hence, we would at least consider this being an “important” method. Spatial transcriptomics has thus far only been done in embryos, which are easy to process for FISH for many decades. Integration with single-cell data is also new. We are further surprised that this assessment does not mention the identification of subcellular mRNA patterns in adult muscles as an “important” biological finding of this paper. We are not aware that any localized mRNAs in Drosophila muscles were known prior to our study. This shows the advantage of spatial transcriptomics over single-cell techniques.
The work indeed does not represent a full spatial fly adult atlas – however, a proof of principle study covering both the head and body that we consider at least “important”.
Public Reviews:
Reviewer #1 (Public Review):
Summary:
In this manuscript, Janssens et al. addressed the challenge of mapping the location of transcriptionally unique cell types identified by single nuclei sequencing (snRNA-seq) data available through the Fly Cell Atlas. They identified 100 transcripts for head samples and 50 transcripts for fly body samples allowing the identification of every unique cell type discovered through the Fly Cell Atlas. To map all of these cell types, the authors divided the fly body into head and body samples and used the Molecular Cartography (Resolve Biosciences) method to visualize these transcripts. This approach allowed them to build spatial tissue atlases of the fly head and body, to identify the location of previously unknown cell types and the subcellular localization of different transcripts. By combining snRNA-seq data from the Fly Cell Atlas with their spatially resolved transcriptomics (SRT) data, they demonstrated an automated cell type annotation strategy to identify unknown clusters and infer their location in the fly body. This manuscript constitutes a proof-of-principle study to map the location of the cells identified by ever-growing single-cell transcriptomic datasets generated by others.
Strengths:
The authors used the Molecular Cartography (Resolve Biosciences) method to visualize 100 transcripts for head samples and 50 transcripts for fly body samples in high resolution. This method achieves high resolution by multiplexing a large number of transcript visualization steps and allows the authors to map the location of unique cell types identified by the Fly Cell Atlas.
Response: We thank the reviewer for their comment, but are surprised that this assessment does not mention the identification of subcellular mRNA patterns in adult muscles as an important biological finding of this paper. This might be due to the visualization problem that this reviewer was facing with a greyscale version of the PDF as mentioned in the comments below. We do not know what caused the technical problem for this reviewer (the PDF figures are in color on the eLife website and on bioRxiv). We are surprised that the eLife discussion session did not resolve this issue.
Weaknesses:
Combining single-nuclei sequencing (snRNA-seq) data with spatially resolved transcriptomics (SRT) data is challenging, and the methods used by the authors in this study cannot reliably distinguish between cells, especially in brain regions where the processes of different neurons are clustered, such as in neuropils. This means that a grid that the authors mark as a unique cell may actually be composed of processes from multiple cells.
Response: The size of the fly is one of the most challenging aspects of performing spatial transcriptomics. The small size of the samples led to detachment from the slides, which we solved by coating the slides with gelatin. While the resolution of Molecular Cartography is high (<200nm), in the brain challenges remain as noted by the reviewer. Drosophila neuronal nuclei are notoriously small and cannot be easily resolved with current techniques. We agree that for a full atlas either expansion microscopy, 3D techniques or even higher resolution will be required.
Reviewer #2 (Public Review):
Summary:
The landmark publication of the "Fly Atlas" in 2022 provided a single cell/nuclear transcriptomic dataset from 15 individually dissected tissues, the entire head, and the body of male and female flies. These data led to the annotation of more than 250 cell types. While certainly a powerful and data-rich approach, a significant step forward relies on mapping these data back to the organism in time and space. The goal of this manuscript is to map 150 transcripts defined by the Fly Atlas by FISH and in doing so, provide, for the first time, a spatial transcriptomic dataset of the adult fly. Using this approach (Molecular Cartography with Resolve Biosciences), the authors, furthermore, distinguish different RNA localizations within a cell type. In addition, they seek to use this approach to define previously unannotated clusters found in the Fly Atlas. As a resource for the community at large interested in the computational aspects of their pipeline, the authors compare the strengths and weaknesses of their approach to others currently being performed in the field.
Strengths:
- The authors use Resolve Biosciences and a novel bioinformatics approach to generate a FISH-based spatial transcriptomics map. To achieve this map, they selected 150 genes (50 body; 100 head) that were highly expressed in the single nuclear RNA sequencing dataset and were used in the 2022 paper to annotate specific cell types; moreover, the authors chose several highly expressed genes characteristic of unannotated cell types. Together, the approach and generated data are important next steps in translating the transcriptomic data to spatial data in the organism.
Response: We thank the reviewer for this comment but would like to add that the statement that we selected “150 genes (50 body; 100 head) that were highly expressed in the single nuclear RNA sequencing dataset” is not correct. We have chosen genes with widely differing expression levels (log-scale range of 3.95 in body, 5.76 in head). Many of the chosen genes are also transcription factors. In fact, the here introduced method is more sensitive than the single cell atlas: the tinman positive cells were readily located (even non-heart cells were found to express tinman), whereas in the single cell FCA data tinman expression is often not detected in the cardiomyocytes (Tinman is detected in 273 cells in the entire FCA (mean expression of 1.44 UMI in positive cells), and in 71 cells out of 273 cardial cells (26%)).
Author response image 1.
Density plots for body (left) and head (right) showing levels of gene expression detected in scRNA-seq (body: Fly Cell Atlas, Li et al. 2022, head: Pech et al. (2023)). Blue: all genes, red: genes used in the spatial study.
- Working with Resolve, the authors developed a relatively high throughput approach to analyze the location of transcripts in Drosophila adults. This approach confirmed the identification of particular cell types suggested by the FlyAtlas as well as revealed interesting subcellular locations of the transcripts within the cell/tissue type. In addition, the authors used co-expression of different RNAs to unbiasedly identify "new cell types". This pipeline and data provide a roadmap for additional analyses of other time points, female flies, specific mutants, etc.
- The authors show that their approach reveals interesting patterns of mRNA distribution (e.g alpha- and beta-Trypsin in apical and basal regions of gut enterocytes or striped patterns of different sarcomeric proteins in body muscle). These observations are novel and reveal unexpected patterns. Likewise, the authors use their more extensive head database to identify the location of cells in the brain. They report the resolution of 23 clusters suggested by the single-cell sequencing data, given their unsupervised clustering approach. This identification supports the use of spatial cell transcriptomics to characterize cell types (or cell states).
- Lastly, the authors compare three different approaches --- their own described in this manuscript, Tangram, and SpaGE - which allow integration of single cell/nuclear RNA-seq data with spatial localization FISH. This was a very helpful section as the authors compared the advantages and disadvantages (including practical issues, like computational time).
Weaknesses:
- Experimental setup. It is not clear how many and, for some of the data, the sex of the flies that were analyzed. It appears that for the body data, only one male was analyzed. For the heads, methods say male and female heads, but nothing is annotated in the figures. As such, it remains unclear how robust these data are, given such a limited sample from one sex. As such, the claims of a spatial atlas of the entire fly body and its head ("a rosetta stone") are overstated. Also, the authors should clearly state in the main text and figure legends the sex, the age, how many flies, and how many replicates contributed to the data presented (not just the methods). What also adds to the confusion is the use of "n" in para 2 of the results. " ... we performed coronal sections at different depths in the head (n=13)..." 13 sections in total from 1 head or sections from 13 heads? Based on the body and what is shown in the figure, one assumes 13 sections from one head. Please clarify.
Response: While we agree that sex differences present indeed an interesting opportunity to study with spatial transcriptomics, our goal was not to define male/female differences but rather to establish the technology to go into this detail if wanted in the future. In the revised version, we will provide a more detailed description of the sections, including their sex/genotype/age. We would like to point out that we verified the specificity of our FISH method on all the body sections (Figure 2A, TpnC4 & Act88F) and not only on one. Furthermore, we also would like to state that the idea of “a rosetta stone” was mentioned as a future prospect. We will rewrite the discussion to make this more clear.
- Probes selected: Information from the methods section should be put into the main text so that it is clear what and why the gene lists were selected. The current main text is confusing. If the authors want others to use their approach, then some testing or, at the very least, some discussion of lower expressed genes should be added. How useful will this approach be if only highly expressed genes can be resolved? In addition, while it is understood that the company has a propriety design algorithm for the probes, the authors should comment on whether the probes for individual genes detect all isoforms or subsets (exons and introns?), given the high level of splicing in tissues such as muscle.
Response: As stated above, while there is a slight bias to higher expressed genes (as expected for marker genes), we have also used very low expressed genes like tinman (body) or sens (head). This shows that our method is more sensitive than single-cell data, as ALL cardiomyocytes can be identified by tinman expression and not only some are positive, as is the case in the FCA data. In fact, the method can’t resolve too highly expressed genes due to optical crowding of the signal leading to a worse quantification. For this reason, ninaE was removed from the analysis (as mentioned in Spatial transcriptomics allows the localization of cell types in the head and brain and in Methods).
As mentioned in the Methods, the probes are designed on gene level targeting all isoforms, but favoring principal isoforms (weighted by APPRIS level). The high level of splicing is indeed interesting and we expect that in the future spatial transcriptomics can help to generate more insight in this.
- Imaging: it isn't clear from the text whether the repeated rounds of imaging impacted data collection. In many of what appear to be "stitched" images, there are gradients of signal (eg, figure 2F); please comment. Also, since this a new technique, could a before and after comparison of the original images and the segmented images be shown in the supplemental data so that the reader can better appreciate how the authors assessed/chose/thresholded their data? More discussion of the accuracy of spot detection would be helpful.
Response: Any high-resolution imaging (pixel size = 138 nm) of a large field of view (>1mm) uses a stitching method to combine several individual images to reconstruct a large field of view. This does not generate signal gradients, apart from lower signal at the extreme edges of each of the individual images. The spot detection algorithm was written and used by Resolve Biosciences and benchmarked for human (Hela) and mouse (NIH-3T3) cell lines in Groiss et al. 2021 (Highly resolved spatial transcriptomics for detection of rare events in cells, biorxiv). The specificity of the decoded probes was found to lie between 99.45 and 99.9% here, matching the results we found for TpnC4 and Act88F (99.4 and 99.8%). We will add their analysis to our discussion.
- The authors comment on how many RNAs they detected (first paragraph of results). How do these numbers compare to the total mRNA present as detected by single-cell or single-nuclear sequencing?
Response: The total number of mRNAs detected per spatial transcriptomics experiment is much higher for the body samples compared to single-cell experiments (FCA data). In the head it is slightly lower, but here it is important to note that not all cell types are present in each slice in the head (while they are all present in the head scRNA experiments). A comparison on the cell-type level would be more meaningful, and we will investigate this for the revision.
Author response image 2.
Barplots showing total number of mRNA molecules detected in Molecular Cartography (Resolve, spatial spots) and in snRNA-seq data from the Fly Cell Atlas (10x Genomics, UMIs). Individual black dots show individual experiments, counts are only shown for the chosen gene panel for each sample. Bar shows the mean, with error bars representing the standard error.
- Using this higher throughput method of spatial transcriptomics, the authors discern different cell types and different localization patterns within a tissue/cell type.
a. The authors should comment on the resolution provided by this approach, in terms of the detection of populations of mRNAs detected by low throughput methods, for example, in glia, motor neuron axons, and trachea that populate muscle tissue. Are these found in the images? Please show.
Response: We did not add any markers for trachea in our gene panel, but we do detect sparse spots of repo (glia) and elav/VGlut in the muscle tissues (Gad1/VAChT are hardly detected in the muscle tissue). This is consistent with the glutamatergic nature of motor neurons in Drosophila as described previously (Schuster CM (2006) Glutamatergic synapses of Drosophila neuromuscular junctions: a high-resolution model for the analysis of experience-dependent potentiation. Cell Tissue Res 326: 287–299.)
Author response image 3.
Molecular Cartography zoomed in on indirect flight muscle. Segmented nuclei are shown in white (based on DAPI), scalebars represent 100 μm).
b. The authors show interesting localization patterns in muscle tissue for different sarcomere protein-coding mRNAs, including enrichment of sls in muscle nuclei located near the muscle-tendon attachment sites. As this high throughput approach is newly being applied to the adult fly, it would increase confidence in these data, if the authors would confirm these data using a low throughput FISH technique. For example, do the authors detect such alternating "stripes" ( Act 88F, TpnC4, and Mhc) or enriched localization (sls) using FISH that doesn't rely on the repeated colorization, imaging, decolorization of the probes?
Response: We thank the reviewer for their interest in the localization patterns in muscle tissue. We could confirm localized mRNA in all the sections analyzed, in flight muscles as well as in leg muscles. We furthermore show that Act 88F, TpnC4 are not detected outside of flight muscle cells (99.4% and 99.8% of the single molecular signal in flight muscles only). Hence, we already show the specificity test in a much more quantitative way compared to traditional FISH, which often includes amplification.
- The authors developed an unbiased method to identify "new cell types" which relies on co-expression of different transcripts. Are these new cell types or a cell state? While expression is a helpful first step, without any functional data, the significance of what the authors found is diminished. The authors need to soften their statements.
Response: The term “new cell types” only appears in the title. We agree that with the current spatial map we cannot be sure to have found “new cell types”, instead we have shown where unannotated clusters from scRNA-seq map, based on gene expression. Therefore, we will tone down the title in the revised version and thank the reviewer for this valuable suggestion.
Appraisal:
The authors' goal is to map single cell/nuclear RNAseq data described in the 2022 Fly Atlas paper spatially within an organism to achieve a spatial transcriptomic map of the adult fly; no doubt, this is a critical next step in our use of 'omics approaches. While this manuscript does the hard work of trying to take this next step, including developing and testing a new pipeline for high throughput FISH and its analysis, it falls short, in its present form, in achieving this goal. The authors discuss creating a robust spatial map, based on one male fly. Moreover, they do not reveal principles of mRNA localization, as stated in the abstract; they show us patterns, but nothing about the logic or function of these patterns. This same criticism can be said of the identification of "new cell types, just based on RNA colocalization. In both cases (mRNA subcellular localization or cell type identification), further data in the form of validation with traditional low throughput FISH and genetic manipulations to assess the relation to cell function are required for the authors to make such claims.
Response: We have indeed used one male fly for the adult male body data. This is mainly due to the cost of the sample processing. We used 12 individuals for the head samples (from 1 individual we acquired 2 sections, a total of 13 sections). We show that the body samples show a high correlation with each other, while the head samples cover multiple depths of the head. Still, even in the head, we find that sections at similar depths show a high similarity to each other in terms of gene-gene co-expression and expression patterns. Although obtaining more sections would be valuable, we don’t believe it to be necessary for the current goals. Additional replicates beyond the ones we already provide would require significant amounts of extra time and budget, while they would produce similar results as we already show. We are therefore reluctant to repeat the effort again.
The usage of the term “new cell types” is indeed ambiguous and we will tone this down in the revised version. Instead, we meant that unannotated clusters could be mapped to their location. In the text, we further specify that this means that now we only have inferred the location of the nuclei and that for neurons their function/processes are still unknown. As such, our data provides a starting point to identify new cell types since their marker genes and nuclear location are inferred. The next step to identify “new cell types” would indeed be to acquire genetic access to the cell types and characterize them in more detail. This is currently beyond our goals, and therefore we will tone down the title in the revised version and thank the reviewer for this valuable suggestion.
Discussion of likely impact:
If revised, these data, and importantly the approach, would impact those working on Drosophila adults as well as those working in other model systems where single cell/nuclear sequencing is being translated to the spatial localization within the organism. The subcellular localization data - for example, the size of transcripts and how that relates to localization or the patterns of sarcomeric protein localization in muscle - are intriguing, and would likely impact our thinking on RNA localization, transport, etc if confirmed. Lastly, the authors compare their computational approaches to those available in the field; this is valuable as this is a rapidly evolving field and such considerations are critical for those wishing to use this type of approach.
Response: We believe that our manuscript as it stands now is already an “important” paper that will strongly impact the Drosophila community (and beyond the spatial transcriptomics community). As it stands, it provides the groundwork for a full Drosophila adult spatial atlas, similar to how early scRNA-seq datasets provided a framework for the Fly Cell Atlas. In the manuscript we provide both experimental information on how to successfully perform spatial transcriptomics (treating slides for optimal attachment) and the data serves as a benchmark for future experiments to improve upon (similar to how early Drop-seq datasets were compared to later 10x datasets in single-cell transcriptomics). In addition, it also provides proof of principle methods on how to integrate the FCA data with these spatial data and it identifies localized mRNA species in large adult muscle cells, showing the complementarity of spatial techniques with single-cell RNA-seq. To conclude, this is the first spatial adult Drosophila transcriptomics paper, locating 150 mRNA species with easy data access in our user portal (https://spatialfly.aertslab.org/).
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eLife assessment
This study presents a valuable method to visualize the location of the cell types discovered through single-cell RNA sequencing. The evidence supporting the claims is solid, but the inclusion of a larger number of samples would strengthen the study. It would also be helpful to have the methods explained in more detail. The work will be of interest to those seeking to identify new cell types from scRNA-seq and snRNA-seq data.
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Reviewer #1 (Public Review):
Summary:
In this manuscript, Janssens et al. addressed the challenge of mapping the location of transcriptionally unique cell types identified by single nuclei sequencing (snRNA-seq) data available through the Fly Cell Atlas. They identified 100 transcripts for head samples and 50 transcripts for fly body samples allowing the identification of every unique cell type discovered through the Fly Cell Atlas. To map all of these cell types, the authors divided the fly body into head and body samples and used the Molecular Cartography (Resolve Biosciences) method to visualize these transcripts. This approach allowed them to build spatial tissue atlases of the fly head and body, to identify the location of previously unknown cell types and the subcellular localization of different transcripts. By combining …Reviewer #1 (Public Review):
Summary:
In this manuscript, Janssens et al. addressed the challenge of mapping the location of transcriptionally unique cell types identified by single nuclei sequencing (snRNA-seq) data available through the Fly Cell Atlas. They identified 100 transcripts for head samples and 50 transcripts for fly body samples allowing the identification of every unique cell type discovered through the Fly Cell Atlas. To map all of these cell types, the authors divided the fly body into head and body samples and used the Molecular Cartography (Resolve Biosciences) method to visualize these transcripts. This approach allowed them to build spatial tissue atlases of the fly head and body, to identify the location of previously unknown cell types and the subcellular localization of different transcripts. By combining snRNA-seq data from the Fly Cell Atlas with their spatially resolved transcriptomics (SRT) data, they demonstrated an automated cell type annotation strategy to identify unknown clusters and infer their location in the fly body. This manuscript constitutes a proof-of-principle study to map the location of the cells identified by ever-growing single-cell transcriptomic datasets generated by others.Strengths:
The authors used the Molecular Cartography (Resolve Biosciences) method to visualize 100 transcripts for head samples and 50 transcripts for fly body samples in high resolution. This method achieves high resolution by multiplexing a large number of transcript visualization steps and allows the authors to map the location of unique cell types identified by the Fly Cell Atlas.Weaknesses:
Combining single-nuclei sequencing (snRNA-seq) data with spatially resolved transcriptomics (SRT) data is challenging, and the methods used by the authors in this study cannot reliably distinguish between cells, especially in brain regions where the processes of different neurons are clustered, such as in neuropils. This means that a grid that the authors mark as a unique cell may actually be composed of processes from multiple cells. -
Reviewer #2 (Public Review):
Summary:
The landmark publication of the "Fly Atlas" in 2022 provided a single cell/nuclear transcriptomic dataset from 15 individually dissected tissues, the entire head, and the body of male and female flies. These data led to the annotation of more than 250 cell types. While certainly a powerful and data-rich approach, a significant step forward relies on mapping these data back to the organism in time and space. The goal of this manuscript is to map 150 transcripts defined by the Fly Atlas by FISH and in doing so, provide, for the first time, a spatial transcriptomic dataset of the adult fly. Using this approach (Molecular Cartography with Resolve Biosciences), the authors, furthermore, distinguish different RNA localizations within a cell type. In addition, they seek to use this approach to define …Reviewer #2 (Public Review):
Summary:
The landmark publication of the "Fly Atlas" in 2022 provided a single cell/nuclear transcriptomic dataset from 15 individually dissected tissues, the entire head, and the body of male and female flies. These data led to the annotation of more than 250 cell types. While certainly a powerful and data-rich approach, a significant step forward relies on mapping these data back to the organism in time and space. The goal of this manuscript is to map 150 transcripts defined by the Fly Atlas by FISH and in doing so, provide, for the first time, a spatial transcriptomic dataset of the adult fly. Using this approach (Molecular Cartography with Resolve Biosciences), the authors, furthermore, distinguish different RNA localizations within a cell type. In addition, they seek to use this approach to define previously unannotated clusters found in the Fly Atlas. As a resource for the community at large interested in the computational aspects of their pipeline, the authors compare the strengths and weaknesses of their approach to others currently being performed in the field.Strengths:
1. The authors use Resolve Biosciences and a novel bioinformatics approach to generate a FISH-based spatial transcriptomics map. To achieve this map, they selected 150 genes (50 body; 100 head) that were highly expressed in the single nuclear RNA sequencing dataset and were used in the 2022 paper to annotate specific cell types; moreover, the authors chose several highly expressed genes characteristic of unannotated cell types. Together, the approach and generated data are important next steps in translating the transcriptomic data to spatial data in the organism.
2. Working with Resolve, the authors developed a relatively high throughput approach to analyze the location of transcripts in Drosophila adults. This approach confirmed the identification of particular cell types suggested by the FlyAtlas as well as revealed interesting subcellular locations of the transcripts within the cell/tissue type. In addition, the authors used co-expression of different RNAs to unbiasedly identify "new cell types". This pipeline and data provide a roadmap for additional analyses of other time points, female flies, specific mutants, etc.
3. The authors show that their approach reveals interesting patterns of mRNA distribution (e.g alpha- and beta-Trypsin in apical and basal regions of gut enterocytes or striped patterns of different sarcomeric proteins in body muscle). These observations are novel and reveal unexpected patterns. Likewise, the authors use their more extensive head database to identify the location of cells in the brain. They report the resolution of 23 clusters suggested by the single-cell sequencing data, given their unsupervised clustering approach. This identification supports the use of spatial cell transcriptomics to characterize cell types (or cell states).
4. Lastly, the authors compare three different approaches --- their own described in this manuscript, Tangram, and SpaGE - which allow integration of single cell/nuclear RNA-seq data with spatial localization FISH. This was a very helpful section as the authors compared the advantages and disadvantages (including practical issues, like computational time).Weaknesses:
1. Experimental setup. It is not clear how many and, for some of the data, the sex of the flies that were analyzed. It appears that for the body data, only one male was analyzed. For the heads, methods say male and female heads, but nothing is annotated in the figures. As such, it remains unclear how robust these data are, given such a limited sample from one sex. As such, the claims of a spatial atlas of the entire fly body and its head ("a rosetta stone") are overstated. Also, the authors should clearly state in the main text and figure legends the sex, the age, how many flies, and how many replicates contributed to the data presented (not just the methods). What also adds to the confusion is the use of "n" in para 2 of the results. " ... we performed coronal sections at different depths in the head (n=13)..." 13 sections in total from 1 head or sections from 13 heads? Based on the body and what is shown in the figure, one assumes 13 sections from one head. Please clarify.
2. Probes selected: Information from the methods section should be put into the main text so that it is clear what and why the gene lists were selected. The current main text is confusing. If the authors want others to use their approach, then some testing or, at the very least, some discussion of lower expressed genes should be added. How useful will this approach be if only highly expressed genes can be resolved? In addition, while it is understood that the company has a propriety design algorithm for the probes, the authors should comment on whether the probes for individual genes detect all isoforms or subsets (exons and introns?), given the high level of splicing in tissues such as muscle.
3. Imaging: it isn't clear from the text whether the repeated rounds of imaging impacted data collection. In many of what appear to be "stitched" images, there are gradients of signal (eg, figure 2F); please comment. Also, since this a new technique, could a before and after comparison of the original images and the segmented images be shown in the supplemental data so that the reader can better appreciate how the authors assessed/chose/thresholded their data? More discussion of the accuracy of spot detection would be helpful.
4. The authors comment on how many RNAs they detected (first paragraph of results). How do these numbers compare to the total mRNA present as detected by single-cell or single-nuclear sequencing?
5. Using this higher throughput method of spatial transcriptomics, the authors discern different cell types and different localization patterns within a tissue/cell type.
a. The authors should comment on the resolution provided by this approach, in terms of the detection of populations of mRNAs detected by low throughput methods, for example, in glia, motor neuron axons, and trachea that populate muscle tissue. Are these found in the images? Please show.
b. The authors show interesting localization patterns in muscle tissue for different sarcomere protein-coding mRNAs, including enrichment of sls in muscle nuclei located near the muscle-tendon attachment sites. As this high throughput approach is newly being applied to the adult fly, it would increase confidence in these data, if the authors would confirm these data using a low throughput FISH technique. For example, do the authors detect such alternating "stripes" ( Act 88F, TpnC4, and Mhc) or enriched localization (sls) using FISH that doesn't rely on the repeated colorization, imaging, decolorization of the probes?
6. The authors developed an unbiased method to identify "new cell types" which relies on co-expression of different transcripts. Are these new cell types or a cell state? While expression is a helpful first step, without any functional data, the significance of what the authors found is diminished. The authors need to soften their statements.Appraisal:
The authors' goal is to map single cell/nuclear RNAseq data described in the 2022 Fly Atlas paper spatially within an organism to achieve a spatial transcriptomic map of the adult fly; no doubt, this is a critical next step in our use of 'omics approaches. While this manuscript does the hard work of trying to take this next step, including developing and testing a new pipeline for high throughput FISH and its analysis, it falls short, in its present form, in achieving this goal. The authors discuss creating a robust spatial map, based on one male fly. Moreover, they do not reveal principles of mRNA localization, as stated in the abstract; they show us patterns, but nothing about the logic or function of these patterns. This same criticism can be said of the identification of "new cell types, just based on RNA colocalization. In both cases (mRNA subcellular localization or cell type identification), further data in the form of validation with traditional low throughput FISH and genetic manipulations to assess the relation to cell function are required for the authors to make such claims.Discussion of likely impact:
If revised, these data, and importantly the approach, would impact those working on Drosophila adults as well as those working in other model systems where single cell/nuclear sequencing is being translated to the spatial localization within the organism. The subcellular localization data - for example, the size of transcripts and how that relates to localization or the patterns of sarcomeric protein localization in muscle - are intriguing, and would likely impact our thinking on RNA localization, transport, etc if confirmed. Lastly, the authors compare their computational approaches to those available in the field; this is valuable as this is a rapidly evolving field and such considerations are critical for those wishing to use this type of approach. -
