Shared and distinct transcriptomic cell types across neocortical areas

In the citing paper

“We also observed that the NP–CT–L6b-like (NP, near-projecting; CT, corticothalamic; L6b, layer 6b) subclasses emerge as a group highly distinct from the IT–ET-like (IT, intratelencephalic; ET, extratelencephalic) subclasses13,23,26,27, forming two distinct classes, IT–ET Glut and NP–CT–L6b Glut.”

In the citing paper

“One exception is cortical GABAergic cell types, which are shared across all cortical areas as we previously reported23,26”

In the citing paper

“While we found that different t-types had different preferred morphologies (Extended Data Table 1), they showed substantial overlap, in agreement with the L5 Pvalb t-types themselves not having clear boundaries4 (Fig. 1d).”

In the citing paper

“We chose to focus on SST neurons in the brain because this population is known to be diverse and to be composed of several relatively rare subpopulations (Muñoz et al., 2017; Tasic et al., 2018; Tasic et al., 2016), and thus might serve as a good test case.”

In the citing paper

“We assessed Loki Decompose on our in-house triple-negative breast cancer (TNBC) dataset, a human colorectal cancer dataset48 and a brain dataset49,50.”

In the citing paper

“Notably, the prediction of GABAergic subclasses and their spatial location in both directions appears to have more confusions, especially in the Subpallium-GABA neighbourhood, consistent with the more widespread distribution across multiple cortical areas of many GABAergic cell types23,26.”

In the citing paper

“Clustering for both 10xv2 and 10xv3 datasets was performed independently using the in-house developed R package scrattch.bigcat (v0.0.5, available via github https://github.com/AllenInstitute/scrattch.bigcat), which is a scaled-up version of R package scrattch.hicat23,26 to deal with the increased size of datasets.”

In the citing paper

“The anatomical distribution of the marker genes selective for specific t- or met-types have been characterized in a recent MERFISH study in the mouse primary motor cortex (MOp) (Zhang et al., 2020); they may be similarly distributed in the visual cortex since GABAergic t-types are shared across cortical areas (Tasic et al., 2018).”

In the citing paper

“Recent studies have defined taxonomies of mouse neocortical cell types by single-cell RNA-seq transcriptomic profiling of isolated neurons and glia12–14.”

In the citing paper

“An important caveat to these findings is that most analyses performed in these studies are performed on populations of neurons.”

In the citing paper

“Loki Decompose accurately predicted the distribution of VLMCs, astrocytes, neurons from L2/3, L4/5 and L6 and oligodendrocytes, aligning closely with brain anatomic ref. 49.”

In the citing paper

“VLMCs and astrocytes are concentrated near the cortical surface and pial borders (for example, layer 1), while oligodendrocytes are more prevalent in deeper layers and within white matter tracts49.”

In the citing paper

“High-throughput single-cell sequencing techniques have identified dozens of types of neuron on the basis of their transcriptional profiles3,4,14,15, but linking transcriptomically defined cell types (t-types) to their phenotypes has remained a major challenge16.”

In the citing paper

“Similarly, cortical studies have identified many intermediate cells with uncertain t-type assignments3,4.”

In the citing paper

“Within-type distributions of soma depths (Fig. 1b) agreed well with previous data4 and with the layer-specific nomenclature of excitatory t-types, confirming the validity of our t-type assignment.”

In the citing paper

“In summary, different transcriptomic families had largely distinct morpho-electric phenotypes, in agreement with them being well separated in the transcriptomic space4.”

In the citing paper

“We observed the same in the Sst subclass, which is known to be transcriptomically4 and morpho-electrically29,30,33 diverse in L5. Here we also found that morpho-electric properties varied continuously across the transcriptomic landscape, with neighbouring t-types consistently showing similar morphologies and similar rebound values (Fig. 4b).”

In the citing paper

“the three large transcriptomic groups (CGE-derived interneurons, MGE-derived interneurons, and excitatory neurons) that are perfectly separated from each other with no transcriptomically intermediate cells4.”

In the citing paper

“transcriptomically-defined types of GABAergic interneurons are more readily conserved across cortical brain areas”

In the citing paper

“Recent advances in the collection and analysis of single cell RNA-sequencing (scRNAseq) data provide a promising new way to define cell types and how they relate to one another”

In the citing paper

“the number of VISp GABAergic “t-types” (60) and “me-types” (26) - differs by more than a factor of two”

In the citing paper

“Even in transcriptomic data from isolated cells, continuous variations were frequently observed (Stanley et al., 2020; Harris et al., 2018; Tasic et al., 2018).”

In the citing paper

“Based on gene expression, Sncg neurons have been linked to Vip+/Cck + basket cells (Tasic et al., 2018).”

In the citing paper

“Glutamatergic neuron types are distinct between visual and motor cortical areas whereas GABAergic neuron types are shared between the two areas (Tasic et al., 2018).”

In the citing paper

“The current CTX-HPF GABAergic taxonomy is largely consistent with previous transcriptomic taxonomies derived from cortical areas VISp-ALM (Tasic et al., 2018) and MOp (Yao et al., 2020) at the supertype level but exhibits notable ambiguity at the type/cluster level”

In the citing paper

“These studies demonstrate the validity and power of using the highly scalable scRNA-seq approach to generate a comprehensive census of cell types as a foundation for further structural and functional studies of brain circuits.”

In the citing paper

“most clusters are shared by all isocortical areas, consistent with our previous observations (Tasic et al., 2018), and also by RHP regions”

In the citing paper

“Previously, we analyzed single-cell transcriptomes to define 133 cell types in two isocortical areas, primary visual cortex (VISp) and anterolateral motor cortex (ALM), in mice (Tasic et al., 2018) and found that they have shared GABAergic interneuron types but distinct glutamatergic neuron types.”

In the citing paper

“The three ALM L5 PT types previously identified (Economo et al., 2018; Tasic et al., 2018) correspond to cluster #248 (thalamus-projecting cells) in the Npnt supertype and clusters #249 and #252 (medulla-projecting cells) in the Cdh13 supertype, respectively”

In the citing paper

“This difference in developmental origins may be the underlying reason for the dichotomy between the extensive regional diversity of glutamatergic types and the sharing of a common set of GABAergic types across isocortical regions”

In the citing paper

“In addition to the classical single-cell clustering processing steps provided by other tools such as Seurat (Butler et al., 2018), this package features automatic iterative clustering while ensuring all pairs of clusters, even at the finest level, are separable by fairly stringent differential gene expression criteria (Tasic et al., 2018).”

In the citing paper

“Across all isocortical areas, most glutamatergic cell types are shared among multiple areas (Fig. 3B, S2), contrary to what we found in our previous study of two distantly located cortical areas, VISp and ALM”

In the citing paper

“This suggests that Sst Calb2 Pdlim is a MC type, in agreement with the conclusions of Tasic et al.25 based on the data from Paul et al.46, and that Sst Hpse Cbln4 is a NMC type, in agreement with Naka et al.47.”

In the citing paper

“The quality of the mapping was equally good for V1 and S1 cells (Supplementary Fig. 7), suggesting that the V1 + ALM dataset is a reasonable reference for S1 interneurons, in agreement with the idea that inhibitory transcriptomic cell types are shared across cortical regions25,26.”

In the citing paper

“Recent large-scale studies of transcriptomic cell types in mouse and human cortex showed that most interneuron types are shared between cortical areas while the excitatory types are predominantly area-specific25,26.”

In the citing paper

“We did not encounter any labeled NGCs in PV-Cre, SST-Cre, or VIP-Cre lines, suggesting that they belonged to the Lamp5 transcriptomic family25.”

In the citing paper

“Using Patch-seq, we showed that SOM+ MCs in V1 L4 and SOM+ NMCs in S1 L4 correspond to two different transcriptomic cell types (Sst Calb2 Pdlim and Sst Hpse Cbln4 respectively) previously identified in a large-scale transcriptomic cell atlas25.”

In the citing paper

“Tasic et al.25 showed that the majority of transcriptomic inhibitory types are shared between two very different cortical areas (V1 and ALM).”

In the citing paper

“the transcriptomic reference dataset25 contained many V1 cells from the Sst Hpse Cbln4 type”

In the citing paper

“A subsequent large-scale study of ~23,800 cells incorporating multiple transgenic lines targeting neuronal subpopulations suggested 113 cortical cell types; these include ~60 GABAergic types conserved between visual and frontal cortex and 56 glutamatergic types that are mostly distinct between these two areas23 (Fig. 1).”

In the citing paper

“This landmark data set represents the most comprehensive survey of cortical transcriptional types, establishing a scaffold for transcriptome-based classification and a working draft of cortical cell taxonomy, including GABAergic interneuron taxonomy.”

In the citing paper

“The ~60 ‘atomic’ GABAergic t-types at the base of the hierarchy23 are probably fluidic and may well be modified by future scRNAseq and orthogonal data sets.”

In the citing paper

“For example, the number of Sst transcriptional clusters can vary by a factor of 2 depending on the stringency of clustering (30 when less stringent and 15 when more stringent)23.”

In the citing paper

“Unexpectedly, a group of Lamp5 subclass interneurons with prominent Lhx6 and Nkx2.1 expression were classified as CGE-derived putative neurogliaform cells (NGFCs)23.”

In the citing paper

“The same large-scale analysis of adult mouse visual cortex36 used 28 Cre driver lines to enable broad coverage, selective targeting of rare populations and linking to previous single-cell transcriptomic data sets23 — the intrinsic properties of >1,900 neurons (928 spiny and 1,010 sparsely spiny) were analysed and the morphologies of 461 neurons (254 spiny and 207 aspiny) were partially”

In the citing paper

“Thus, the extent to which the 60 t-types23 correspond to the 17 e-types and 38 m-types and 46 me-types36 is currently not well established.”

In the citing paper

“Recent studies using transcriptomic characterization based on single-cell RNA-sequencing techniques performed unsupervised classification to generate a taxonomy of transcriptomic types in the mouse neocortex12–14.”

In the citing paper

“A diverse set of transgenic mouse lines14–18 were used to ensure broad coverage of excitatory and inhibitory classes across all cortical layers, to enable selective targeting of rare cell populations, and to link our study with other experimental approaches, such as transcriptomic characterization19.”

In the citing paper

“We note that we are not yet able to establish clear links to the recently described Sncg inhibitory subclass14”

In the citing paper

“In L1-L4, the line is associated mostly with the Pvalb-Vipr2 type (expected to be chandelier cells14) and the Pvalb-Tpbg type (Fig. 7i).”

In the citing paper

“It is known that individual t-types can exhibit substantial continuous variation within a type14”

In the citing paper

“these cells are expected to have the Sst-Chodl t-type, linked to deep long-range projecting interneurons12,14,36,37 (Fig. 7h).”

In the citing paper

“The recent finding of shared t-types among inhibitory cells but different t-types among excitatory cells from separate cortical areas14”

In the citing paper

“Large-scale transcriptomic studies have provided informative taxonomies of cortical cell types12–14.”

In the citing paper

“The application of single-cell RNA sequencing (scRNA-seq) to the neocortex and other brain regions has revealed a complex but tractable hierarchical organization of transcriptomic cell types that are consistent overall with knowledge from decades of anatomical, physiological and developmental studies but with an unmatched level of granularity7–11.”

In the citing paper

“MY-projecting neurons showed clear enrichment for L5 ET cluster 0 (Fig. 4e, Extended Data Fig. 3b), in agreement with scRNA-seq data for anterolateral motor cortex (ALM), part of MOs9,53.”

In the citing paper

“MERFISH data showed that L4/5 IT and L5 IT cells occupied distinct layers in MOp, and the L4/5 IT type expressed Rspo1 (Fig. 7c), a L4 cell-type marker in sensory cortical areas identified in previous studies9.”

In the citing paper

“Compared with the previous VISp–ALM transcriptomic taxonomy9, mouse MOp L5 ET_1 type corresponded to the ALM MY-projecting type, whereas MOp L5 ET_2-4 types corresponded to the ALM TH-projecting types37.”

In the citing paper

“MERFISH data showed that L4/5 IT and L5 IT cells occupied distinct layers in MOp, and the L4/5 IT type expressed Rspo1 (Fig. 7c), a L4 cell-type marker in sensory cortical areas identified in previous studies9.”

In the citing paper

“In this context, another important finding, consistent with and building on multiple other studies9,11,68,69, is the coexistence of discrete and continuous variations of cell features across modalities at the lower branch level.”

In the citing paper

“Substantiating previous studies9,10, our multimodal cross-species study of the primary motor cortex suggests that a general principle of cortical cell-type organization is its hierarchical relationship, whereby high-level classes linked by major branches comprise progressively finer subpopulations connected by minor branches.”

In the citing paper

“Recent scRNA-seq studies sampled >20,000–750,000 cells in individual mouse brain regions (Kozareva et al., 2020; Shekhar et al., 2016; Tasic et al., 2018; Yao et al., 2020a).”

In the citing paper

“A recurring theme from single-cell studies of the brain is the greater diversity of glutamatergic vs. GABAergic neurons across brain regions (Tasic et al., 2018; Yao et al., 2020b; Zeisel et al., 2015) or species (Bakken et al., 2020; Lake et al., 2016).”

In the citing paper

“Some cells, such as cortical layer 5 pyramidal tract neurons, may be more likely to die during cell isolation for scRNA-seq (Tasic et al., 2018).”

In the citing paper

“By infecting axon terminals in a defined brain region with a retrograde virus, the cell bodies of source neurons projecting to that region can be labeled, sorted, and their transcriptomes measured by sc/snRNA-seq (Retro-seq) (Tasic et al., 2018).”

In the citing paper

“As a result, high-throughput multi-omics studies in mouse cerebral cortex identified 9–22 cell types (Chen et al., 2019b; Zhu et al., 2019), compared with over 100 cell types found using scRNA-seq (Tasic et al., 2018; Yao et al., 2020a, 2020b).”

In the citing paper

“gene-expression patterns for these conserved types differed by cortical region in marmosets”

In the citing paper

“which suggests that the genes that encode these markers stably delineate a core repertoire of neocortical interneuron types in these species11,15,18”

In the citing paper

“for example, somatostatin-expressing cortical interneurons comprise several anatomically, electrophysiologically, and molecularly defined cell types whose dysfunction is associated with neuropsychiatric and neurological disorders (Jiang et al., 2015; Muñoz et al., 2017; Tasic et al., 2018).”

In the citing paper

“the subclasses of excitatory neurons in different layers of cortex (ITL23GL, Cortex L2/3; ITL4GL, Cortex L4; ITL5GL, Cortex L5; PTGL, Cortex PT; NPGL, Cortex NP; ITL6GL, Cortex L6; CTGL, Cortex CT; and L6bGL, Cortex L6b) were clearly identified31”

In the citing paper

“These studies have also shown the ubiquity of neuron types that have the genetic constituents required for the release of more than one neurotransmitter.6,7,9,40,131”

In the citing paper

“and are likely the remaining non-MGE origin cells (arising from CGE and/or POA)14–16”

In the citing paper

“Prior studies indicate that inhibitory neurons show uniform molecular features even between distant cortical areas14.”