Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity

  1. Catarina Catela
  2. Yihan Chen
  3. Yifei Weng
  4. Kailong Wen
  5. Paschalis Kratsios  Is a corresponding author
  1. Department of Neurobiology, University of Chicago, United States
  2. University of Chicago Neuroscience Institute, United States

Abstract

Spinal motor neurons (MNs) constitute cellular substrates for several movement disorders. Although their early development has received much attention, how spinal MNs become and remain terminally differentiated is poorly understood. Here, we determined the transcriptome of mouse MNs located at the brachial domain of the spinal cord at embryonic and postnatal stages. We identified novel transcription factors (TFs) and terminal differentiation genes (e.g. ion channels, neurotransmitter receptors, adhesion molecules) with continuous expression in MNs. Interestingly, genes encoding homeodomain TFs (e.g. HOX, LIM), previously implicated in early MN development, continue to be expressed postnatally, suggesting later functions. To test this idea, we inactivated Hoxc8 at successive stages of mouse MN development and observed motor deficits. Our in vivo findings suggest that Hoxc8 is not only required to establish, but also maintain expression of several MN terminal differentiation markers. Data from in vitro generated MNs indicate Hoxc8 acts directly and is sufficient to induce expression of terminal differentiation genes. Our findings dovetail recent observations in Caenorhabditis elegans MNs, pointing toward an evolutionarily conserved role for Hox in neuronal terminal differentiation.

Editor's evaluation

This manuscript will be of interest to developmental geneticists interested in neuroscience, and how spinal motor neurons maintain their unique identities in adulthood after fate decisions are made in the embryo. The work here demonstrates that a Hox transcription factor acts as a terminal selector to control motor neuron identity, thus mirroring recent studies in C. elegans, and thus pointing towards this type of gene regulation as important in building diverse nervous systems.

https://doi.org/10.7554/eLife.70766.sa0

Introduction

Motor neurons (MNs) represent the main output of our central nervous system. They control both voluntary and involuntary movement and are cellular substrates for several degenerative disorders (Arora and Khan, 2021). Due to their stereotypic cell body position, easily identifiable axons and highly precise synaptic connections with well-defined muscles, MNs are exceptionally well characterized in all major model systems. Extensive research over the past decades in worms, flies, and mice has focused on the early steps of MN development, thereby advancing our understanding of the molecular mechanisms controlling specification of progenitor cells and young postmitotic MNs, as well as motor circuit assembly (Osseward and Pfaff, 2019, Philippidou and Dasen, 2013; Sagner and Briscoe, 2019; Thor and Thomas, 2002). In the vertebrate spinal cord, progenitor cell specification critically depends on morphogenetic signals, whereas initial fate determination of postmitotic MNs relies on combinatorial activity of different classes of transcription factors (TFs) (di Sanguinetto et al., 2008, Jessell, 2000; Lee and Pfaff, 2001; Stifani, 2014). The focus in early development, however, has left poorly explored the molecular mechanisms that control the final steps of MN differentiation. Once MNs are born and specified, how do they acquire their terminal differentiation features, such as neurotransmitter (NT) phenotype, electrical, and signaling properties? And perhaps most important, what are the mechanisms that ensure maintenance of such features throughout life?

The terminal differentiation features of every neuron type are determined by the expression of specific sets of proteins, such as NT biosynthesis components, NT receptors, ion channels, neuropeptides, signaling molecules, transmembrane receptors, and adhesion molecules (Hobert, 2008). The genes coding for these proteins (‘terminal differentiation genes’) are continuously expressed from development through adulthood, thereby determining the functional and phenotypic properties of individual neuron types (Hobert, 2008; Hobert, 2011). Therefore, the challenge of understanding how MNs acquire and maintain their functional features lies in understanding how the expression of MN terminal differentiation genes is regulated over time. Importantly, defects in expression of such genes constitute one of the earliest molecular signs of MN disease (Nutini et al., 2011; Shibuya et al., 2011). However, the regulatory mechanisms that induce and maintain expression of terminal differentiation genes in spinal MNs are poorly defined. In part, this is due to: (a) a scarcity of temporally controlled gene inactivation studies that remove the activity of MN-expressed regulatory factors (e.g. TF, chromatin factor) at different life stages, and (b) a paucity of terminal differentiation markers for spinal MNs. Although recent RNA-Sequencing (RNA-Seq) studies have begun to address the latter (Blum et al., 2021; Delile et al., 2019; Alkaslasi et al., 2021), most genetic and molecular profiling studies on spinal MNs are not conducted in a longitudinal fashion, i.e., at embryonic and postnatal stages. Hence, how these cells become and remain terminally differentiated remains unclear.

To elucidate the molecular mechanisms that enable spinal MNs to acquire and maintain their terminal differentiation features, we took advantage of the orderly anatomical relationship between MN cell body location and muscle innervation, referred to as ‘topography’ (Dasen and Jessell, 2009). In the spinal cord, this topographic relationship is mostly evident along the rostrocaudal axis, where MN populations located in different spinal cord domains (e.g. brachial, thoracic, lumbar, sacral) innervate different muscles. In this study, we focused on the brachial domain, where postmitotic MNs are organized into two columns: (a) the lateral motor column (LMC) contains limb-innervating MNs necessary for reaching, grasping, and locomotion, and (b) the medial motor column (MMC) contains axial muscle-innervating MNs required for postural control (Philippidou and Dasen, 2013). Through a longitudinal RNA-Seq approach, we identified multiple terminal differentiation markers and novel TFs with continuous expression in embryonic and postnatal brachial MNs. Interestingly, we also found that several homeodomain TFs (HOX, LIM) that were previously implicated in the early steps of brachial MN development (e.g. initial specification, circuit assembly) (Philippidou and Dasen, 2013; Stifani, 2014) continue to be expressed in postnatal MNs. We therefore hypothesized that some of these TFs play additional roles in later steps of brachial MN development.

To test this hypothesis, we focused on Hox proteins because recent findings in the ventral nerve cord (equivalent to mouse spinal cord) of the nematode Caenorhabditis elegans identified Hox proteins as critical regulators of cholinergic MN terminal differentiation (Feng et al., 2020; Kratsios et al., 2017). Among the seven Hox genes retrieved from our RNA-Seq, Hoxc8 is highly expressed both in embryonic and postnatal brachial MNs. A previous study showed that Hoxc8 acts early to establish brachial MN connectivity (Catela et al., 2016). Here, we report a new role for Hoxc8 in later stages of mouse MN development. By inactivating Hoxc8 at successive developmental stages, we found that it is necessary for the establishment and maintenance of select terminal differentiation features of brachial MNs. Mechanistically, Hoxc8 acts directly to induce expression of terminal differentiation genes. Similar to our observations in brachial MNs, we identified additional Hox genes with continuous expression in thoracic and lumbar MNs, suggesting maintained Hox expression in MNs is a broadly applicable theme to other rostrocaudal domains of the spinal cord. Because Hox genes are also expressed in the mouse and human brain during embryonic and postnatal stages (Lizen et al., 2017; Takahashi et al., 2004; Hutlet et al., 2016; Krumlauf, 2016), similar Hox-based mechanisms to the one described here may be widely used in the nervous system for the control of neuronal terminal differentiation.

Results

Molecular profiling of mouse brachial MNs at embryonic and postnatal stages

We first sought to define the molecular profile of brachial MNs at embryonic and postnatal stages with the goal of identifying putative terminal differentiation markers for these cells. This longitudinal approach focused on postmitotic MNs at embryonic day 12 (e12) and postnatal day 8 (p8). We chose e12 because: (i) spinal e12 MNs begin to acquire their terminal differentiation features, such as NT phenotype (Martinez et al., 2012), and (ii) MN axons at e12 have exited the spinal cord (Catela et al., 2016). We chose p8 because: (i) these are several days after neuromuscular synapse formation (Gautam et al., 1996), and (ii) pups at p8 become more active, indicating spinal MN functionality. To genetically label e12 MNs, we used the Mnx1-GFP (green fluorescent protein) reporter mouse (Wichterle et al., 2002) as it primarily labels embryonic MNs at e12 (Amin et al., 2015; Hanley et al., 2016; Sawai et al., 2022; Wichterle et al., 2002; Figure 1A). Due to low expression of Mnx1-GFP at postnatal stages, we turned to an alternative labeling strategy and crossed ChatIRESCre mice (Rossi et al., 2011) with the Ai9 Cre-responder line (Rosa26-CAGpromoter-loxP-STOP-loxP-tdTomato) (Madisen et al., 2010). At p8, we observed fluorescent labeling of spinal MNs with tdTomato (Figure 1A, Figure 1—figure supplement 1). Taking advantage of the topographic MN organization along the rostrocaudal axis, we followed a region-specific approach focused on the brachial region (segments C4-T1) that contains MNs of the MMC and LMC. Upon precise microdissection of this region (see Materials and methods), we used fluorescence-activated cell sorting (FACS) to isolate GFP-labeled brachial MNs from e12 Mnx1-GFP mice and tdTomato-labeled brachial MNs from p8 ChatIRESCre::Ai9 mice (Figure 1A). Through RNA-Seq, we obtained and compared the molecular profile of these cells (see Materials and methods). We identified differentially expressed transcripts (>fourfold, p<0.05) in the e12 (3715 transcripts) and p8 (3209 transcripts) dataset (Figure 1B, Supplementary file 1), suggesting gene expression profiles of embryonic and postnatal brachial MNs differ. Two factors that could contribute to these transcriptional differences between the e12 and p8 datasets are: (1) different levels of gene expression (see next section), and (2) a small fraction of the FACS-sorted cells are not MNs. Indeed, Mnx1 and Chat, in addition to MNs, are also expressed in small, nonoverlapping neuronal populations in the spinal cord (Wilson et al., 2005; Zagoraiou et al., 2009; Wichterle et al., 2002; Figure 1—figure supplement 1).

Figure 1 with 2 supplements see all
Molecular profiling of mouse brachial motor neurons (MNs) at embryonic and postnatal stages.

(A) Schematic representation of the workflow used in the comparison of embryonic and postnatal transcriptomes. The brachial domain (C4–T1) of Mnx1-GFP (in green) and ChatIRESCre::Ai9 (in red) mice was microdissected. Brachial GFP+ (at e12.5, scale bar: 20 μm) and tdTomato+ (at p8, scale bar: 100 μm) MNs were fluorescence-activated cell sorted and processed for RNA-sequencing. Spinal cord is outlined with white dashed line. (B) MA plot of differentially expressed genes. Green and red dots represent individual genes that are significantly (p<0.05) expressed (fourfold and/or higher) in embryonic and postnatal MNs, respectively. (C) Graphs showing fold enrichment for genes involved in specific biological processes. (D) Gene onthology analysis comparing protein class categories of highly expressed genes in embryonic (e12.5) and postnatal (p8) MNs. Green and red bars represent embryonic and postnatal genes, respectively.

Subsequent gene ontology (GO) analysis on proteins from embryonically enriched (e12) transcripts revealed an overrepresentation of molecules associated with neuronal development, such as regionalization, dendrite formation, and axon guidance (Figure 1C, Supplementary file 2). Notably, the most enriched class of proteins in the e12 dataset is TFs, many of which are known to control MN development (Figure 1D, see next section). On the other hand, GO analysis on proteins from postnatally enriched (p8) transcripts uncovered an overrepresentation of molecules associated with cell metabolism, such as ATP synthesis, oxidative phosphorylation, and energy-coupled proton transport (Figure 1C–D, Supplementary file 2), perhaps indicative of the higher metabolic demands of p8 MNs compared to their embryonic (e12) counterparts.

To identify terminal differentiation markers with continuous expression in brachial MNs, we leveraged our e12 RNA-Seq dataset (Figure 1D, Supplementary file 1). We arbitrarily selected eight genes coding for NT receptors, ion channels, and signaling molecules (Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2, Cldn1, Cacna1g) and evaluated their expression at different life stages. Through RNA ISH, we found six genes (Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2) with continuous expression in putative brachial MNs at embryonic (e12) and early postnatal (p8) stages (Table 1, Supplementary file 1). Available RNA ISH data from the Allen Brain Atlas also confirmed their expression at p56 (Table 1). The ventrolateral location of the cells expressing these six genes in the spinal cord strongly suggests they constitute terminal differentiation markers for brachial MNs.

Table 1
Summary of candidate and unbiased approaches to reveal Hoxc8 target genes in mouse brachial MNs.
Gene nameExpression in WT brachial MNsHoxc8 dependency
e12p8p56 Allen Brain ISHp60snRNA-Seq datasetHoxc8 MNΔ early miceHoxc8 MNΔ late mice
Candidate approachSlc10a4++++NoN.D
Nrg1++++YesYes
Nyap2++N.D+NoN.D
Sncg++++NoN.D
Ngfr+++NoN.D
Glra2++++NoYes
Cldn1N.DN.DN.DN.D
Cacna1gN.D++N.DN.D
RNA-Seq approachSlc44a5++++NoN.D
Mcam++++YesYes
Pappa++++YesYes
Sema5a++N.D+YesN.D
Pex14++N.D+NoN.D
Tagln2+++NoN.D
Cldn19N.DN.DN.D
Wwc2N.D++N.DN.D
Septin1N.DN.DN.DN.DN.D
Irx2+++N.DN.D
Irx5+++N.DN.D
Irx6+++N.DN.D
Known Hoxc8 targetsRet++N.D+YesNo
Gfra3+YesN.D
  1. Expression in p56 brachial MNs was determined using the Allen Brain Map (http://portal.brain-map.org). We also interrogated the single nucleus (sn) RNA-seq datasets of p60 spinal MNs from http://spinalcordatlas.org/.

  2. N.D: Not determined; + denotes expression; – denotes no expression.

  3. RNA-Seq: RNA-sequencing.

Developmental transcription factors continue to be expressed in spinal MNs at postnatal stages

Two simple, but not mutually exclusive mechanisms can be envisioned for the continuous expression of terminal differentiation genes (e.g. Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2) in brachial MNs. Their embryonic initiation and maintenance could be controlled by separate mechanisms involving distinct combinations of TFs solely dedicated to either initiation or maintenance. Alternatively, initiation and maintenance can be achieved through the activity of the same, continuously expressed TF (or combinations thereof). Recent invertebrate and vertebrate studies on various neuron types support the latter mechanism (Deneris and Hobert, 2014; Hobert and Kratsios, 2019). We therefore sought to identify TFs with continuous expression, from embryonic to postnatal stages, in mouse brachial MNs.

First, we examined whether TFs from our embryonic (e12) RNA-Seq dataset continue to be expressed at postnatal stages (Figure 1D). We initially focused on 14 TFs from various families (e.g. LIM, Hox) with previously known embryonic expression and function in brachial MNs (Ebf2, Islet1, Islet2, Hb9, Foxp1, Lhx3, Runx1, Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7, Hoxc8) (Arber et al., 1999; Catela et al., 2019; Catela et al., 2016; Dasen et al., 2008; Ericson et al., 1992; Philippidou and Dasen, 2013; Sharma et al., 1998; Stifani et al., 2008; Thaler et al., 1999; Thaler et al., 2004; Thaler et al., 2002; Tsuchida et al., 1994). Through RNA ISH or antibody staining, we detected robust expression in brachial MNs at e12 for all 14 factors. Notably, 13 of these TFs continue to be expressed albeit at lower levels - in brachial MNs at p8 (Figure 2A, Table 2), suggesting these proteins - in addition to their known roles during early MN development - may exert other functions at later developmental and/or postnatal stages. Seven of these 13 proteins are TFs of the Hox family (Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7, Hoxc8) known to be expressed in brachial MNs at embryonic stages (Philippidou and Dasen, 2013), confirming the regional specificity of our RNA-Seq approach (Figure 2A). Moreover, our strategy is sensitive as it captured TFs with known expression in small populations of brachial MNs (e.g. MMC neurons), such as Ebf2 and Lhx3 (Figure 2A; Catela et al., 2019; Sharma et al., 1998).

Known and novel transcription factors (TFs) are continuously expressed in brachial motor neurons (MNs) during embryonic and postnatal stages.

(A) The expression of TFs with previously published roles in MN development was assessed in embryonic (e12.5) and postnatal (p8) spinal cords (N = 4) with RNA ISH (Ebf2, Runx1, Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7, Hoxc8) and immunohistochemistry (Islet1/2, Mnx1 [Hb9], Lhx3, Foxp1). Zoomed area of one side of the ventral spinal cord is shown below each image. (B) The expression of novel TFs was assessed in embryonic (e12.5) and postnatal (p8) spinal cords with RNA ISH (N = 4). Scale bar for e12.5 images: 50 μm; scale bar for p8 images: 250 μm.

Table 2
Validation of transcription factor expression in brachial MNs.
TFTypeNovel TF with MN expressione12 MNsp8 MNsp56 MNsISH Allen Brainp60snRNA-Seq datasetExpression in other spinal cells at e12
Ebf2Ebf/COENo++
Islet1LIM HDNo+++N.D+
Islet2LIM HDNo+++N.D+
Hb9HDNo+++N.D+
Foxp1FOXNo+++
Lhx3LIM HDNo++N.D+
Runx1RUNXNo+++
Hoxc4HOXNo+++++
Hoxa5HOXNo++N.D+
Hoxc5HOXNo+++++
Hoxa6HOXNo+++
Hoxc6HOXNo++N.D+
Hoxa7HOXNo++++
Hoxc8HOXNo++N.D+
Irx1IRO HDYes++++
Irx2IRO HDYes++++
Irx3IRO HDYes+++
Irx5IRO HDYes+++
Irx6IRO HDYes+++
Creb5CREYes++++
EsrrgNHRYes++++
FosFOSYes++++
Arid5aARIDYes+++
Irf1IRFYes+++
Irf8IRFYes+++
Klf6KLFYes+++
Tshz1C2H2 ZnYes+++++
Zfp296ZFPYes++++
Neurod6bHLHN.AN.DDorsal interneurons
Arid5bARIDN.AN.D+Dorsal interneurons
Pou3f3POUN.AN.D+Dorsal interneurons
MafbbZIPN.AN.DN.DVentral interneurons
Zfhx4Zn HDN.AN.D+Ventral interneurons
Elk3ETSN.AN.D+Vasculature
Epas1HIFN.AN.DVasculature
HeylbHLHN.AN.DVasculature
  1. Expression in p60 brachial MNs was determined using the Allen Brain Map (http://portal.brain-map.org). We also interrogated the single nucleus (sn) RNA-seq datasets of p60 spinal MNs from http://spinalcordatlas.org/. + denotes expression; – denotes no expression; N. D: Not determined; N. A: Not applicable.

  2. RNA-Seq: RNA-sequencing.

We next sought to identify novel TFs with maintained expression in brachial MNs. We arbitrarily selected 22 genes from different TF families (15 TFs from the e12 dataset [Irx1, Irx2, Irx3, Irx5, Irx6, Creb5, Esrrg, Neurod6, Arid5b, Pou3f3, MafB, Zfhx4, Elk3, Epas1, Heyl] and 7 TFs from the p8 dataset [Fos, Arid5a, Irf1, Irf8, Klf6, Tshz1, Zfp296]). We detected persistent expression for 14 of these TFs in the embryonic (e12) and early postnatal (p8) brachial spinal cord. Expression was evident at the ventrolateral region, which is populated by MNs (Figure 2B, Table 2).

In conclusion, the expression of 13 TFs, with known roles in early MN development (e.g. cell specification, motor circuit assembly), is persistent at early postnatal stages (p8). Moreover, we identified 14 novel TFs from different families with expression in embryonic and postnatal (p8) brachial MNs (Figure 2B, Table 2). The continuous expression of all these factors suggests they may exert various functions in postmitotic MNs at different life stages. Consistent with this notion, some of these TFs are also expressed at later postnatal (p56, p60) stages in brachial MNs (Table 2).

Hoxc8 controls expression of several terminal differentiation genes in e12 brachial MNs

In mice, Hox genes play critical roles during the early steps of spinal cord development, such as MN specification and circuit assembly (Dasen et al., 2008; Dasen et al., 2003; Dasen et al., 2005; Philippidou and Dasen, 2013). We found that several Hox genes (Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7, Hoxc8) are continuously expressed - from embryonic to postnatal stages - in brachial MNs (Figure 2A), but their function during later stages of MN development is largely unknown. This pattern of continuous Hox gene expression is reminiscent of recent observations in C. elegans nerve cord MNs (Feng et al., 2020; Kratsios et al., 2017). Importantly, C. elegans Hox genes are required not only to establish but also maintain at later stages the expression of multiple terminal differentiation genes (e.g. NT receptors, ion channels, signaling molecules) in nerve cord MNs (Feng et al., 2020).

Motivated by these findings in C. elegans, we sought to test the hypothesis that, in mice, Hox proteins control expression of terminal differentiation genes in spinal MNs. We focused on Hoxc8 because it is expressed in the majority of brachial MNs (segments C6-T2) (Figure 2A; Catela et al., 2016). Hoxc8 is not required for the overall organization of brachial MNs into columns, but - during early development (e12) - it controls forelimb muscle innervation by regulating Gfrα3 and Ret expression in brachial MNs (Catela et al., 2016). However, whether Hoxc8 is involved in additional processes, such as the control of MN terminal differentiation, remains unclear.

To test this, we removed Hoxc8 gene activity in brachial MNs. Because Hoxc8 is also expressed in other spinal neurons (Baek et al., 2019; Shin et al., 2020; Figure 2A), we crossed Hoxc8 fl/fl mice to Olig2Cre mice that enable Cre recombinase expression specifically in MN progenitors (Figure 3A; Zawadzka et al., 2010). This genetic strategy effectively removed Hoxc8 protein from postmitotic brachial MNs by e12 (Figure 3B). Because e12 is an early stage of MN differentiation (postmitotic MNs are generated between e9 and e11) (Sims and Vaughn, 1979), we will refer to the Olig2Cre::Hoxc8 fl/fl mice as Hoxc8 MNΔearly. Of note, the total number of brachial MNs (Mnx1+[HB9+] Isl1/2+) is unaffected in these animals at e12 (Figure 3C).

Figure 3 with 1 supplement see all
Early Hoxc8 gene inactivation in brachial motor neurons (MNs) affects the expression of terminal differentiation genes.

(A) Diagram illustrating genetic approach for Hoxc8 gene inactivation during early MN development (Hoxc8 MNΔ early mice). (B) Immunohistochemistry showing that Hoxc8 protein (green) is not detected in Foxp1+ MNs (red, indicated with dashed ellipse) of Hoxc8 MNΔearly spinal cords at e12.5. Images of one side of the spinal cord are shown (boxed region in schematic at left). Scale bar: 50 μm. (C) Quantification of Mnx1+(Hb9+) Isl1/2+ MNs in e12.5 brachial spinal cords of Hoxc8 MNΔearly and control (Hoxc8fl/fl) embryos (N = 4). (D) Heatmap showing upregulated and downregulated genes detected by RNA-Seq in control (Hoxc8 fl/fl) and Hoxc8 MNΔearly e12.5 MNs. Green and red colors, respectively, represent lower and higher gene expression levels. (E) Graphical percentage (%) representation of protein classes of the downregulated genes in Hoxc8 MNΔearly spinal cords. (F) RNA ISH showing downregulation of Nrg1, Mcam, Pappa, and Sema5a mRNAs in brachial MNs of e12.5 Hoxc8 MNΔearly spinal cords (N = 4). Spinal cord is outlined with a white dotted line. Scale bar: 50 μm. (G) RNA FISH for Sema5a coupled with antibody staining against Foxp1 (LMC marker) shows reduced Sema5a mRNA expression in Foxp1 +MNs of e12.5 Hoxc8 MNΔearly spinal cords (N = 4). Images of a cross-section of the entire e12.5 spinal cord are shown. Scale bar: 40 μm.

To test whether Hoxc8 controls expression of terminal differentiation genes, we initially followed a candidate approach. At e12, spinal MNs begin to acquire their terminal differentiation features, evident by the induction of genes coding for acetylcholine (ACh) biosynthesis proteins (Slc18a3 [VAChT], Slc5a7[ChT1]) (Martinez et al., 2012). Consistently, Slc18a3 and Slc5a7 transcripts were captured in our e12 RNA-Seq dataset (Figure 1D). However, Slc18a3 and Slc5a7 expression was not affected in brachial MNs of Hoxc8 MNΔ early mice (Figure 1—figure supplement 2). Next, we tested the six newly identified terminal differentiation markers (Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2) summarized in Table 1. We found that expression of Neuregulin 1 (Nrg1), a molecule required for neuromuscular synapse maintenance and neurotransmission (Mei and Xiong, 2008; Wolpowitz et al., 2000), is reduced (but not eliminated) in e12 brachial MNs of Hoxc8 MNΔ early mice (Figure 3F), likely due to the existence of additional factors that partially compensate for loss of Hoxc8 gene activity. However, expression of the remaining five genes was unaffected in these animals (Figure 1—figure supplement 2), prompting us to devise an unbiased strategy to identify Hoxc8 targets.

We performed RNA-Seq on FACS-sorted brachial MNs from Hoxc8 MNΔ early::Mnx1-GFP and control mice at e12 (see Materials and methods). We found dozens of significantly (p<0.05) upregulated (55) and downregulated (84) transcripts in MNs lacking Hoxc8 (Figure 3D). To test the hypothesis of Hoxc8 being necessary to activate expression of MN terminal differentiation genes, we specifically focused on the list of 84 downregulated transcripts, which included two known Hoxc8 target genes (Ret, Gfrα3) (Catela et al., 2016) and Hoxc8 itself (Supplementary file 3). GO analysis (see Materials and methods) on these 84 transcripts identified several putative Hoxc8 target genes encoding proteins from various classes (Figure 3E, Supplementary file 3). We focused on ion channels, transmembrane proteins, cell adhesion, and signaling molecules, as these constitute putative terminal differentiation markers (Hobert, 2008; Hobert, 2011). We selected nine genes (Slc44a5, Mcam, Pappa, Sema5a, Pex14, Tagln2, Cldn19, Wwc2, Septin1) and evaluated their expression with RNA ISH in brachial MNs at different stages. Five of these genes (Slc44a5, Mcam, Pappa, Pex14, Tagln2) are continuously expressed in brachial MNs at embryonic and postnatal stages (Table 1, Figure 1—figure supplement 2). Importantly, RNA ISH showed that expression of Mcam, a transmembrane cell adhesion molecule of the Immunoglobulin superfamily (Gu et al., 2015; Taira et al., 2004), and Pappa, a secreted molecule involved in skeletal muscle development (Rehage et al., 2007), is reduced at e12 in brachial MNs of Hoxc8 MNΔ early mice (Figure 3F–G, Figure 1—figure supplement 2). Similar results for Mcam and Pappa were obtained with an RNA FISH method (Figure 3—figure supplement 1). In addition, we observed that Sema5a is expressed in embryonic (e12) but not postnatal brachial MNs, and this embryonic expression depends on Hoxc8 (Table 1, Figure 3F–G). Because Sema5a encodes a transmembrane protein of the Semaphorin protein family involved in axon guidance (Duan et al., 2014; Hilario et al., 2009; Lin et al., 2009), its dependency on Hoxc8 could, at least partially, account for the previously reported MN axonal defects of Hoxc8 MNΔ early mice (Catela et al., 2016).

Altogether, this analysis identified 11 terminal differentiation genes with continuous expression in brachial MNs (Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2, Slc44a5, Mcam, Pappa, Pex14, Tagln2), 3 of which (Nrg1, Mcam, Pappa) constitute Hoxc8 targets (Table 1). Although additional, yet-to-be identified TFs (potential Hoxc8 collaborators) must regulate the remaining eight genes, our findings do suggest Hoxc8 is involved in MN terminal differentiation. This new role for Hox in vertebrate MN development is consistent with recent studies in the C. elegans nerve cord, where Hox genes also control MN terminal differentiation (Feng et al., 2020; Kratsios et al., 2017).

Hoxc8 is required to maintain expression of terminal differentiation genes in brachial MNs

Our analysis of Hoxc8 MNΔ early mice at e12 suggests Hoxc8 controls the early expression of select terminal differentiation genes (Nrg1, Mcam, Pappa) in brachial MNs. However, the persistent expression of Hoxc8 both in embryonic and early postnatal MNs raises the intriguing possibility of a continuous requirement (Figures 2A4, Figure 4—figure supplement 1). Is Hoxc8 required at later stages to maintain expression of terminal differentiation genes and thereby ensure the functionality of brachial MNs?

Figure 4 with 1 supplement see all
Late Hoxc8 gene inactivation in brachial motor neurons (MNs) affects expression of terminal differentiation genes.

(A) Diagram illustrating genetic approach for Hoxc8 gene inactivation during late MN development. Hoxc8 conditional mice were crossed with the ChatIRESCre mouse line (Hoxc8 MNΔlate). (B) Immunohistochemistry showing that Hoxc8 protein (green) is not detected in ChAT-exprressing MNs (red) of Hoxc8 MNΔ late spinal cords at e14.5 (N = 4). MN location is indicated with white dashed line. Hoxc8 is also expressed in other cell types outside the MN territory. Images of one side of the spinal cord are shown (boxed region in schematic at left). Scale bar: 100 μm. (C) RNA ISH showing reduced expression of Pappa, Mcam, Glra2, and Nrg1 in Hoxc8 MNΔlate spinal cords at p8 (N = 4). Scale bar: 200 μm. (D) Ret expression is comparable between control and Hoxc8 MNΔlate spinal cords at p8 (N = 4). Scale bar: 200 μm. (E) Representative images and quantification of TdTomato-labeled MNs in p8 control (Hoxc8fl/fl::Ai9) and Hoxc8 MNΔ late (Hoxc8fl/fl::ChatIRESCre::Ai9) spinal cords (N = 4). Scale bar: 200 μm. (F) Schematic summarizing Hoxc8 target genes in brachial MNs. Asterisks indicate previously known Hoxc8 target genes.

To address this, we crossed the Hoxc8fl/fl mice with the ChatIRESCre mouse line, which enables efficient gene inactivation in postmitotic MNs around e13.5–e14.5 (Philippidou et al., 2012; Figure 4A). Given that postmitotic MNs are generated between e9.5 and e11.5 (Sims and Vaughn, 1979), this genetic strategy preserves Hoxc8 expression in MNs at least for 2 days after their generation. Consistent with a previous study that used this ChatIRESCre line (Philippidou et al., 2012), we observed Hoxc8 protein depletion in brachial MNs at e14.5 and later stages (Figure 4B, Figure 4—figure supplement 1). We will therefore refer to the ChatIRESCre::Hoxc8fl/fl animals as Hoxc8 MNΔ late because Hoxc8 depletion in MNs occurs later compared to Hoxc8 MNΔ early mice (Figure 4A). Interestingly, expression of the same terminal differentiation genes (Nrg1, Mcam, Pappa) we found affected in Hoxc8 MNΔ early mice is also reduced in brachial MNs of Hoxc8 MNΔ late mice at p8 (Figure 4C). This reduction is not due to secondary events affecting MN generation or survival because similar numbers of brachial MNs were observed in control and Hoxc8 MNΔ late spinal cords at p8 (Figure 4E). Taken together, our findings on Hoxc8 MNΔ early and Hoxc8 MNΔ late mice strongly suggest a continuous requirement - Hoxc8 is required to establish and maintain at later developmental stages the expression of several terminal differentiation genes in brachial MNs (Figure 4F).

In brachial MNs, Hoxc8 partially modifies the suite of its target genes across different life stages

In the context of C. elegans MNs, our previous work revealed ‘temporal modularity’ in TF function (Li et al., 2020). That is, the suite of target genes of a continuously expressed TF, in the same cell type (e.g. MNs), is partially modified across different life stages. Here, we provide evidence for temporal modularity in Hoxc8 function. We found that the terminal differentiation gene coding for the glycine receptor subunit alpha-2 (Glra2) (Young-Pearse et al., 2006) is affected in brachial MNs of Hoxc8 MNΔ late mice at p8 (Figure 4C). No effect was observed in MNs of Hoxc8 MNΔ early mice at e12 (Figure 1—figure supplement 2), indicating a selective Hoxc8 requirement for maintenance of Glra2. Conversely, the expression of Ret, a known Hoxc8 target gene involved in MN axon guidance (Bonanomi et al., 2012), is selectively reduced in brachial MNs of Hoxc8 MNΔ early animals at e12 (Catela et al., 2016), but remains unaffected in Hoxc8 MNΔ late animals at p8 (Figure 4D), suggesting Hoxc8 is only required for early Ret expression. Lastly, Hoxc8 can only activate expression of Sema5a (member of Semaphorin family) at embryonic stages (Figure 3F–G, Table 1). Contrary to these stage-specific Hoxc8 dependencies (Hoxc8 controls Ret and Sema5a at e12 and Glra2 at p8), we also found that Hoxc8 is continuously required (both at e12 and p8) for expression of several terminal differentiation genes (Nrg1, Mcam, Pappa) (Figures 3F and 4C).

Altogether, these findings suggest that, in brachial MNs, Hoxc8 modifies the suite of its target genes at different developmental stages (Figure 4F). In Discussion, we elaborate on the functional significance of this phenomenon (temporal modularity).

Hoxc8 is sufficient to induce its target genes and acts directly

To gain mechanistic insights, we analyzed recently published RNA-Seq and chromatin immunoprecipitation-sequencing (ChIP-seq) datasets on MNs derived from mouse embryonic stem cells (ESC), in which Hoxc8 expression was induced with doxycycline (Bulajić et al., 2020). Our RNA-Seq analysis showed that induction of Hoxc8 (iHox8) resulted in upregulation of previously known (Ret, Pou3f1 [Scip]) and new (Pappa, Glra2, Sema5a) Hoxc8 target genes (Figure 5A). Moreover, ChIP-Seq for Hoxc8 in the context of these iHoxc8 ESC-derived MNs revealed binding in the cis-regulatory region of all these genes (Figure 5B), suggesting Hoxc8 acts directly to activate their expression. This in vitro data together with the in vivo findings in Hoxc8 MNΔ early and Hoxc8 MNΔ late mice (Figure 3F–G, Figure 3—figure supplement 1, Figure 4C) suggest that Hoxc8 is both necessary and sufficient for the expression of several of its target genes in spinal MNs.

Figure 5 with 1 supplement see all
Hoxc8 sufficiency and direct mode of action.

(A) Analysis of RNA-sequencing (RNA-Seq) data from control and iHoxc8 motor neurons (MNs) shows Hoxc8 is sufficient to induce the expression of previously known (Ret, Pou3f1[Scip]) and new (Pappa, Glra2, Sema5a) Hoxc8 target genes. GEO accession numbers: Control (GSM4226469, GSM4226470, GSM4226471) and iHoxc8 (GSM4226475, GSM4226476, GSM4226477). (B) Analysis of chromatin immunoprecipitation-sequencing (ChIP-Seq) data from iHoxc8 MNs shows Hoxc8 directly binds to the cis-regulatory region of its target genes (Ret, Mcam, Pappa, Glra2, Sema5a). GEO accession numbers: Input (GSM4226461) and iHoxc8 replicates (GSM4226436, GSM4226437). Snapshots of each gene locus were generated with Integrative Genomics Viewer (IGV, Broad Institute).

Importantly, not all Hoxc8 target genes (e.g. Nrg1, Mcam) we identified in vivo are upregulated in iHoxc8 ESC-derived MNs (Figure 5—figure supplement 1). This is likely due to the lack of Hoxc8 collaborating factors in these in vitro generated MNs. A putative collaborator is Hoxc6 because (a) Hoxc6 and Hoxc8 are coexpressed in embryonic brachial MNs (Catela et al., 2016), (b) animals lacking either Hoxc6 or Hoxc8 in brachial MNs display similar axon guidance defects (Catela et al., 2016), and (c) Hoxc6 and Hoxc8 control the expression of the same axon guidance molecule (Ret) in brachial MNs (Catela et al., 2016). Supporting the notion of collaboration, our analysis of available ChIP-seq data for Hoxc6 and Hoxc8 from iHoxc6 and iHoxc8 ESC-derived MNs (Bulajić et al., 2020), respectively, showed that these Hox proteins bind directly on the cis-regulatory region of previously known (Ret, Gfra3) and new (Mcam, Pappa, Nrg1, Sema5a) Hoxc8 target genes (Figure 5—figure supplement 1).

Hoxc8 gene activity is necessary for brachial motor neuron function

We next sought to assess any potential behavioral defects in adult Hoxc8 MNΔ early and Hoxc8 MNΔ late animals by evaluating their motor coordination (Deacon, 2013), forelimb grip strength (Takeshita et al., 2017), and treadmill performance (Wozniak et al., 2019). No defects were observed in Hoxc8 MNΔ early and Hoxc8 MNΔ late mice during the rotarod performance test (Figure 6—figure supplement 1), suggesting balance and motor coordination are normal in these animals. Next, we evaluated forelimb grip strength because brachial MNs innervate forelimb muscles. We found a statistically significant defect in Hoxc8 MNΔearly mice, but not in Hoxc8 MNΔlate mice (Figure 6A–B). Lastly, we tested these animals for their ability to run on a treadmill for a period of 30 s. At a low speed (15 cm/s), we observed statistically significant defects in Hoxc8 MNΔearly mice. That is, 64.28% of Hoxc8 MNΔearly mice fell off the treadmill in the first 5 s of the trial compared to 28.57% of control mice (p=0.0108) (Figure 6C, Figure 6—videos 1; 2). Moreover, 0% of Hoxc8 MNΔearly mice were able to stay longer than 20 s on the treadmill compared to 42.85% of control mice (Figure 6C). On the other hand, statistically significant defects were observed in Hoxc8 MNΔlate mice only when the treadmill speed was increased to 25 cm/s (Figure 6C–D). That is, 43.33% of Hoxc8 MNΔ late mice fell off the treadmill in the first 5 s of the trial compared to 17.39% of control mice (p=0.0461) (Figure 6D, Figure 6—videos 3; 4). Together, these data show that Hoxc8 MNΔlate mice display a milder behavioral phenotype compared to Hoxc8 MNΔearly mice. This is likely due to the fact that Hoxc8 MNΔearly mice display a composite phenotype i.e. defects in early MN specification and axon guidance (Catela et al., 2016) combined with terminal differentiation defects (this study), whereas the Hoxc8 MNΔlate mice only display terminal differentiation defects (this study). Although we cannot exclude the possibility that the terminal differentiation defects of Hoxc8 MNΔearly mice are a consequence of their early MN specification defects, this is unlikely as Hoxc8 binds directly to the cis-regulatory region of terminal differentiation genes (Mcam, Pappa, Glra2) (Figure 5B).

Figure 6 with 6 supplements see all
Brachial motor neuron (MN) function is impaired upon Hoxc8 depletion.

(A) Forelimb grip strength analysis on control (Hoxc8 fl/fl, N = 7) and Hoxc8 MNΔ early (N = 8) adult mice. See Methods for details. (B) Forelimb grip strength analysis on control (Hoxc8 fl/fl, N = 7) and Hoxc8 MNΔ late (N = 8) adult mice. (C). Treadmill analysis (at 15 cm/s speed) on control (Hoxc8 fl/fl, N = 7) and Hoxc8 MNΔ early (N = 8) adult mice, as well as on control (Hoxc8 fl/fl, N = 8) and Hoxc8 MNΔ late (N = 10) adult mice. See Methods for details. Asterisk (*) indicates p=0.0108. Experiment repeated twice. (D). Treadmill analysis (at 25 cm/s speed) on control (Hoxc8 fl/fl, N = 8) and Hoxc8 MNΔ late (N = 10) adult mice. Treadmill speed at 25 cm/s. Asterisk (*) indicates p=0.0461. Experiment repeated three times. The 30-s long videos were analyzed and data were binned into four categories based on the duration of each mouse’s stay on the treadmill (category 1 [black]: <5 s; category 2 [blue]: 5–10 s; category 3 [gray]: 10–15 s; category 4 [red]: >20 s).

Hox gene expression is maintained in thoracic and lumbar MNs at postnatal stages

In brachial MNs, we found that the expression of multiple Hox genes (Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7, Hoxc8) is maintained from embryonic to early postnatal stages (Figure 2A). We wondered whether sustained Hox gene expression in MNs is a broadly applicable theme to other rostrocaudal domains of the spinal cord. We therefore performed RNA-Seq on thoracic and lumbar FACS-isolated MNs from ChATIRESCre::Ai9 mice at p8 (see Materials and methods) (Figure 6—figure supplement 2). Our analysis indeed revealed that, similar to our observations in the brachial domain, additional Hox genes are expressed postnatally (p8) in thoracic (Hoxd9) and lumbar (Hoxa10, Hoxc10, Hoxa11) MNs (Figure 6—figure supplement 2A-C). We further confirmed these findings with RNA ISH (Figure 6—figure supplement 2D). While the functions of some of these Hox genes are known during the early steps of MN development (Philippidou and Dasen, 2013), their continuous expression suggests additional roles at later embryonic and postnatal stages. Genetic inactivation of these genes at successive developmental stages will determine whether they function in a manner similar to Hoxc8, suggesting a more general Hox-based strategy for the control of spinal MN terminal differentiation.

Discussion

Somatic MNs in the spinal cord innervate hundreds of skeletal muscles and control a variety of motor behaviors, such as locomotion, skilled movement, and postural control. Although we are beginning to understand the molecular programs that control the early steps of spinal MN development (Osseward and Pfaff, 2019, Philippidou and Dasen, 2013; Stifani, 2014), how these clinically relevant cells acquire and maintain their terminal differentiation features (e.g. NT phenotype, electrical, and signaling properties) remains poorly understood. In this study, we focused on the brachial region of the mouse spinal cord and determined the molecular profile of postmitotic MNs at a developmental and a postnatal stage. This longitudinal approach identified genes with continuous expression in brachial MNs, encoding novel TFs and effector molecules critical for neuronal terminal differentiation (e.g. ion channels, NT receptors, signaling proteins, adhesion molecules). Interestingly, we also found that most TFs, previously implicated in the early steps of brachial MN development (e.g. initial specification, axon guidance, circuit assembly), such as LIM- and Hox-type TFs (di Sanguinetto et al., 2008, Philippidou and Dasen, 2013; Stifani, 2014), continue to be expressed in these cells postnatally (p8). Such maintained expression suggested additional roles for these factors during later developmental stages. To test this idea, we focused on Hoxc8, identified its target genes, and uncovered a continuous requirement for Hoxc8 in the establishment and maintenance of select MN terminal differentiation features. Our findings dovetail recent Hox studies in the C. elegans nervous system (Feng et al., 2020; Kratsios et al., 2017; Zheng et al., 2015) and suggest an evolutionarily conserved role for Hox proteins in the control of neuronal terminal differentiation.

Hoxc8 partially modifies the suite of its target genes to control multiple aspects of brachial MN development

Despite their fundamental roles in patterning the vertebrate hindbrain and spinal cord (Krumlauf, 2016; Parker and Krumlauf, 2017; Philippidou and Dasen, 2013), the downstream targets of Hox proteins in the nervous system remain poorly defined. In this study, we uncovered several Hoxc8 target genes encoding different classes of proteins (Sema5a - axon guidance molecule; Glra2, Nrg1, Mcam, Pappa - terminal differentiation genes) (Figures 3E and 4F), suggesting Hoxc8 controls different aspects of brachial MN development through the regulation of these genes.

In mice, Hoxc8 is expressed in MNs of the MMC and LMC columns between segments C6 and T1 of the spinal cord (Catela et al., 2016; Tiret et al., 1998), herein referred to as ‘brachial MNs’. Previous studies using either global Hoxc8 knock-out or Hoxc8 MNΔ early mice reported aberrant connectivity of forelimb muscles (Catela et al., 2016; Tiret et al., 1998). It was proposed that this early developmental phenotype likely arises due to reduced expression of axon guidance molecules, such as Ret and Gfrα3, in brachial MNs of Hoxc8 MNΔ early mice (Catela et al., 2016). Another early developmental defect previously observed in Hoxc8 MNΔ early mice is the reduced expression of MN pool-specific markers (Pou3f1 [Scip], Etv4 [Pea3]) within the LMC (Figure 4F), albeit the overall organization of brachial MNs into MMC and LMC columns appears normal (Catela et al., 2016). Although these findings implicate Hoxc8 in the early steps of brachial MN development, it remained unclear whether Hoxc8 controls additional aspects of MN development during later stages.

In this study, we propose that Hoxc8 controls select features of brachial MN terminal differentiation, such as the expression of the glycine receptor subunit Glra2, the cell adhesion molecule Mcam, the secreted signaling protein Pappa, and a molecule associated with neurotransmission and neuromuscular synapse maintenance (Nrg1). We found that all these molecules are expressed continuously in embryonic and postnatal (p8) brachial MNs. By removing Hoxc8 gene activity either at an early (Hoxc8 MNΔ early mice) or late (Hoxc8 MNΔ late mice) developmental stage, we uncovered a continuous Hoxc8 requirement for the initial expression and maintenance of Mcam, Pappa, and Nrg1. Intriguingly, we also found evidence for temporal modularity in Hoxc8 function, that is, the suite of Hoxc8 targets in brachial MNs is partially modified at different developmental stages. Two lines of evidence support this notion: (a) expression of the terminal differentiation gene Glra2 is only affected in Hoxc8 MNΔ late mice, indicating a selective Hoxc8 requirement for Glra2 maintenance in MNs, and (b) expression of two axon guidance molecule (Sema5a, Ret) is only affected in MNs of Hoxc8 MNΔ early mice.

What is the purpose of such temporal modularity? We propose that Hoxc8 partially modifies the suite of its target genes at different life stages to control different facets of brachial MN development, such as early MN specification, axon guidance, and terminal differentiation (Figure 4F). During early development, Hoxc8 controls early specification markers (Etv4 [Pea3], Pou3f1[Scip]), as well as axon guidance molecules, such as Ret (Bonanomi et al., 2012; Catela et al., 2016) and Sema5a (this study) in order to ensure proper MN-muscle connectivity. Consistent with this idea, similar axon guidance defects occur in Hoxc8 and Ret mutant mice (Catela et al., 2016). During late development, Hoxc8 maintains the expression of the glycine receptor subunit Glra2, a terminal differentiation marker necessary for glycinergic input to brachial MNs (Young-Pearse et al., 2006). Apart from Hoxc8, temporal modularity has been recently described for two other TFs: UNC-3 in C. elegans MNs and Pet-1 in mouse serotonergic neurons (Li et al., 2020; Wyler et al., 2016). Like Hoxc8, UNC-3 and Pet-1 control various aspects of C. elegans motor and mouse serotonergic neurons (e.g. axon guidance, terminal differentiation) (Donovan et al., 2019; Kratsios et al., 2011, Liu et al., 2010; Prasad et al., 1998). Although the mechanistic basis of such modularity remains poorly understood, a possible scenario is the employment of transient enhancers – a mechanism recently proposed for maintenance of gene expression in in vitro differentiated spinal MNs (Rhee et al., 2016). We surmise that temporal modularity in TF function may be a broadly applicable mechanism enabling a single TF to control different, temporally segregated ‘tasks/processes’ within the same neuron type.

A new role for Hox in the mouse nervous system: establishment and maintenance of neuronal terminal differentiation

Much of our current understanding of Hox protein function in the nervous system stems from studies in the vertebrate hindbrain and spinal cord, as well as the Drosophila ventral nerve cord (Baek et al., 2013; Baek et al., 2019; Estacio-Gómez and Díaz-Benjumea, 2014; Estacio-Gómez et al., 2013; Karlsson et al., 2010; Mendelsohn et al., 2017; Miguel-Aliaga and Thor, 2004; Moris-Sanz et al., 2015; Parker and Krumlauf, 2017; Philippidou and Dasen, 2013). This large body of work has established Hox proteins as critical regulators of the early steps of neuronal development including cell specification, migration, survival, axonal path finding, and circuit assembly. However, the functions of Hox proteins in later steps of nervous system development remain poorly understood. Recent work on invertebrate Hox genes has begun to address this knowledge gap. In Drosophila MNs necessary for feeding, Deformed (Dfd) is required to maintain neuromuscular synapses (Friedrich et al., 2016). In C. elegans touch receptor neurons, the anterior (ceh-13) and posterior (egl-5) Hox genes control the expression levels of the LIM homeodomain protein MEC-3, which in turn controls touch receptor terminal differentiation (Zheng et al., 2015). In the C. elegans ventral nerve cord, midbody (lin-39, mab-5) and posterior (egl-5) Hox genes control distinct terminal differentiation features of midbody and posterior MNs, respectively (Kratsios et al., 2017). LIN-39 binds to the cis-regulatory region of multiple terminal differentiation genes (e.g. ion channels, NT receptors, signaling molecules) and is required for their maintained expression in MNs during postembryonic stages (Feng et al., 2020).

Our Hoxc8 findings in mice support the hypothesis that Hox-mediated control of later aspects of neuronal development (e.g. terminal differentiation) is evolutionarily conserved from invertebrates to mammals. Similar to C. elegans Hox genes, mouse Hoxc8 is continuously expressed in brachial MNs from embryonic to early postnatal stages, and sustained Hoxc8 gene activity is required to establish and maintain at later developmental stages the expression of several terminal differentiation genes. This noncanonical, late function of Hoxc8 may be shared by other Hox genes in the mouse nervous system. In the spinal cord, we found several other Hox genes (Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7) to be continuously expressed in brachial MNs, potentially acting as Hoxc8 collaborators. We made similar observations in thoracic (Hoxd9) and lumbar (Hoxc10, Hoxa11) MNs (Figure 6—figure supplement 2). Moreover, expression of multiple Hox genes has been observed in the adult mouse and human brain, leading to the hypothesis that maintained Hox gene expression is necessary for activity-dependent synaptic pruning and maturation (Hutlet et al., 2016; Takahashi et al., 2004). To date, the functional significance of maintained Hox gene expression in the CNS remains largely unknown, and temporally controlled genetic approaches are required to fully elucidate the late functions of this remarkable class of highly conserved TFs.

The quest for terminal selectors of spinal motor neuron identity

Numerous genetic studies in the nematode C. elegans support the idea that continuously expressed TFs (termed ‘terminal selectors’) establish during development and maintain throughout postembryonic life the identity and function of individual neuron types by activating the expression of terminal differentiation genes (e.g. NT biosynthesis components, ion channels, adhesion, and signaling molecules) (Deneris and Hobert, 2014; Hobert, 2008; Hobert, 2016). Multiple cases of terminal selectors for various neuron types have already been described in flies, cnidarians, marine chordates, and mice, suggesting deep conservation for this type of regulators (Allan and Thor, 2015; Deneris and Hobert, 2014; Hobert, 2008; Hobert, 2016; Hobert and Kratsios, 2019; Tournière et al., 2020). However, it remains unclear whether spinal MNs in vertebrates employ a terminal selector type of mechanism to acquire and maintain their terminal differentiation features. Addressing this knowledge gap could aid the development of in vitro protocols for the generation of mature and terminally differentiated spinal MNs, a much anticipated goal in the field of MN disease modeling (Sances et al., 2016).

Three lines of evidence implicate Hoxc8 in the control of MN terminal differentiation. First, Hoxc8 is expressed continuously, from embryonic to early postnatal stages, in brachial MNs. Second, our in vivo data and in vitro analysis suggest Hoxc8 is both necessary and sufficient for the expression of several of its target genes in MNs - such mode of action is reminiscent of terminal selectors (Flames and Hobert, 2009; Kratsios et al., 2011). Third, both early and late removal of Hoxc8 in brachial MNs affected the expression of several terminal differentiation genes, suggesting a continuous requirement. However, Hoxc8 does not act alone - loss of Hoxc8 did not completely eliminate the expression of its target genes (Figures 3F–G4C). This residual expression indicates that additional TFs are necessary to control brachial MN terminal differentiation. As mentioned in Results, one such factor is Hoxc6, which is coexpressed with Hoxc8 in brachial MNs during embryonic and postnatal stages (Catela et al., 2016; Figure 2A). Importantly, Hoxc6 and Hoxc8 bind directly on the cis-regulatory regions of the same terminal differentiation genes in the context of mouse ESC-derived MNs (Figure 5—figure supplement 1). Another putative Hoxc8 collaborator is the LIM homeodomain protein Islet1 (Isl1), which is required for early induction of genes necessary for ACh biosynthesis in mouse spinal MNs and the in vitro generation of MNs from human pluripotent stem cells (Cho et al., 2014; Qu et al., 2014; Rhee et al., 2016). Interestingly, Isl1 is expressed continuously in brachial MNs (Figure 2) and amplifies its own expression (Erb et al., 2017) - both defining features of a terminal selector gene. In addition to Hoxc6 and Isl1, our expression analysis revealed multiple TFs from different families (e.g. Hox, Irx, LIM) with continuous expression in brachial MNs (Figure 2, Table 2). In the future, temporally controlled gene inactivation studies are needed to determine whether these TFs participate in the control of spinal MN terminal differentiation. Intriguingly, the majority of the TFs with continuous expression in brachial MNs belong to the homeodomain family. Homeodomain TFs are overrepresented in the current list of C. elegans and mouse terminal selectors (Deneris and Hobert, 2014; Reilly et al., 2020; Serrano-Saiz et al., 2013), suggesting an ancient role for this family of regulatory factors in the control of neuronal terminal differentiation.

Materials and methods

Key resources table
Reagent type (species) or resourceDesignationSource or referenceIdentifiersAdditional information
Genetic reagent (Mus musculus)Mnx1-GFPPMID:12176325Not availableNot available
Genetic reagent (M. musculus)Ai9PMID:20023653MGI: J:155,793Not available
Genetic reagent (M. musculus)Hoxc8 fl/flPMID:19621436Not availableNot available
Genetic reagent (M. musculus)Olig2CrePMID:18046410MGI: 3774124Not available
Genetic reagent (M. musculus)ChatIRESCrePMID:21284986MGI: J:169,562Not available
Antibodyanti-ChAT(Goat polyclonal)MilliporeCat# AB144P, RRID:AB_2079751IF (1:100)
Antibodyanti-FoxP1 (Rabbit polyclonal)Dasen labCU1025IF(1:32000)
Antibodyanti-RFP (Rabbit polyclonal)RocklandCat# 600-401-379S, RRID:AB_11182807IF(1:500)
Antibodyanti-Alexa 488-Hoxc8 (mouse monoclonal)Dasen labNot applicableIF(1:1500)
Antibodyanti-GFAP (Chicken polyclonal)MilliporeCat# AB5541, RRID:AB_177521IF(1:200)
Antibodyanti-CD11b (Rat monoclonal)Bio-RadCat# MCA711, RRID:AB_321292IF(1:50)
Antibodyanti-mPea3 (Rabbit polyclonal)Dasen labNot applicableIF(1:32000)
Antibodyanti-Digoxigenin-POD, Fab fragments (Sheep polyclonal)Roche Diagnostics Deutschland GmbHCat# 11207733910IF(1:3000)
AntibodyCy3 AffiniPure anti-Goat IgG (Donkey polyclonal)Jackson ImmunoResearch LabsCat# 705-165-147, RRID:AB_2307351IF(1:800)
AntibodyAlexa Fluor 488 anti-Rabbit IgG (Donkey)Thermo Fisher ScientificCat# A-21206, RRID:AB_2535792IF(1:1000)
AntibodyCy3 AffiniPure anti- Rabbit IgG (Donkey polyclonal)Jackson ImmunoResearch LabsCat# 711-165-152, RRID:AB_2307443IF(1:800)
AntibodyAlexa Fluor 488 anti-Goat IgG (Donkey polyclonal)Thermo Fisher ScientificCat# A-11055, RRID:AB_2534102IF(1:1000)
AntibodyAlexa Fluor 488 anti-mouse IgG (Donkey polyclonal)Thermo Fisher ScientificCat# A-21202, RRID:AB_141607IF(1:1000)
AntibodyAlexa Fluor 488 anti-Chicken IgY (Goat polyclonal)Thermo Fisher ScientificCat# A32931, RRID:AB_2762843IF(1:1000)
AntibodyAlexa Fluor 488 anti-Rat IgG (Goat polyclonal)Thermo Fisher ScientificCat# A-11006, RRID:AB_2534074IF(1:1000)
Software, algorithmZENZEISSRRID: SCR_013672Version 2.3.69.1000, Blue edition
Software, algorithmFijiImage JRRID: SCR_003070Version 1.52i

Mouse husbandry and genetics

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All mouse procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of the University of Chicago (Protocol No. 72463). The generation of Hoxc8 floxed/floxed (Blackburn et al., 2009), Olig2Cre (Dessaud et al., 2007), Mnx1-GFP (Wichterle et al., 2002), ChAT-IRES-Cre (Rossi et al., 2011), and Ai9 (Madisen et al., 2010) mice has been previously described. Mendelian ratios at weaning stage for Hoxc8 MNΔ early and Hoxc8 MNΔ late animals are provided in Supplementary file 4.

Fluorescence-activated cell sorting and RNA-Seq of brachial motor neurons

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For the analysis shown in Figure 1, spinal cord segments C4-T1 of e12.5 Mnx1-GFP and p8 ChatIRESCre::Ai9 animals were microdissected using the dorsal root ganglia as reference. For the analysis shown in Figure 3, segments C7-T2 were used. The spinal cord tissue was dissociated using papain and filtered (using 50 μm filters) for sorting. A GFP negative spinal cord was also included as a negative control for the FACS setup. DAPI staining was used to exclude dead cells from the sorting. FACS-sorted MNs were collected into Arcturus Picopure extraction buffer and immediately processed for RNA isolation. RNA was extracted from purified MNs, using the Arcturus Picopure RNA isolation kit (Arcturus, #KIT0204). For the RNA-Seq analysis on e12.5 Mnx1-GFP embryos, three biological replicates were used; five to six spinal cords were pooled per replicate. For the RNA-Seq analysis on p8 ChatIRESCre::Ai9 animals, three biological replicates were used; three spinal cords were pooled per replicate. RNA quality and quantity were measured with an Agilent Picochip (Agilent 2100 Bioanalyzer). All samples had high quality scores between 9 and 10 RIN. After cDNA library preparation, RNA-Seq was performed using an Illumina HiSeq 4000 sequencer (50-nucleotide single-end reads, University of Chicago Genomics Core facility).

RNA-Seq analysis

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Raw sequence data were subjected to quality control using the FastQC algorithm (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). Unique reads were aligned into the mouse genome (GRCm38/mm10) using the HISET2 alignment program Kim et al., 2015 followed by transcript counting with the featureCounts program (Liao et al., 2014). Differential gene expression analysis was performed with the DESeq2 program (Love et al., 2014). All analyses were performed using the open source, web-based Galaxy platform (https://usegalaxy.org). The heatmaps were generated using the Morpheus program developed by the Broad Institute (https://software.broadinstitute.org/morpheus). Gene hierarchical clustering was performed using a Pearson’s correlation calculation.

RNA in situ hybridization

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E12.5 embryos and p8 spinal cords were fixed in 4% paraformaldehyde for 1.5–2  hr and overnight, respectively, placed in 30% sucrose overnight (4 °C) and embedded in optimal cutting temperature compound. Cryosections were generated and processed for ISH or immunohistochemistry as previously described (Dasen et al., 2005; De Marco Garcia and Jessell, 2008).

Fluorescent RNA ISH coupled with antibody staining

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Cryosections were postfixed in 4% paraformaldehyde, washed in PBS, endogenous peroxidase was blocked with a 0.1% H2O2 solution and permeabilized in PBS/0.1% Triton-X100. Upon hybridization with DIG-labeled RNA probe overnight at 72°C and washes in SSC, the anti-DIG antibody conjugated with peroxidase (Roche) and primary antibody against Foxp1 (rabbit anti-Foxp1, Dr. Jeremy Dasen) were applied overnight (4 °C) to the sections. The next day, the sections were incubated with the secondary antibody (Alexa 488 donkey anti-rabbit IgG, Life Technologies, A21206), and detection of RNA was performed using a Cy3 Tyramide Amplification system (Perkin Elmer). Images were obtained with a high-power fluorescent microscope (Zeiss Imager V2) and analyzed with Fiji software (Schindelin et al., 2012).

Immunohistochemistry

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Fluorescence staining on cryosections was performed as previously described (Catela et al., 2016).

Gene ontology analysis

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Protein classification was performed using the Panther Classification System Version 15.0 (http://www.pantherdb.org). Embryonic (1381 out of 2904) and postnatal (1348 out of 2699) MN genes were categorized into protein classes using the algorithms built into Panther (Mi et al., 2013; Thomas et al., 2003).

Rotarod performance test

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Female mice were trained on an accelerating rotarod for 5 days. The experimenter was blind to the genotypes. For the Hoxc8 MNΔ early analysis, seven control (Hoxc8fl/fl) and seven (Olig2Cre::Hoxc8fl/fl) mice were used at the age of 4–5 months. For the Hoxc8 MNΔ late analysis, 8 control (Hoxc8fl/fl) and 10 (ChatIRESCre::Hoxc8fl/fl) mice were used at the age of 2–5 months. A computer-controlled rotarod apparatus (Rotamex-5, Columbus Instruments, Columbus, OH, USA) with a rat rod (7-cm diameter) was set to accelerate from 4 to 40 revolutions per minute (rpm) over 300 s, and recorded time to fall. Mice received five consecutive trials per session, one session per day (about 60 s between trials).

Forelimb grip strength test

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The forelimb strength of female mice was measured using a grip strength meter from Bioseb (model BIO-GS3). For the Hoxc8 MNΔ early analysis, seven control (Hoxc8fl/fl) and seven (Olig2Cre::Hoxc8fl/fl) mice were used at the age of 4–5 months. For the Hoxc8 MNΔ late analysis, 8 control (Hoxc8fl/fl) and 10 (ChatIRESCre::Hoxc8fl/fl) mice were used at the age of 2–5 months. We followed the manufacturer’s protocol. In brief, the meter was positioned horizontally on a heavy metal shelf (provided by the manufacturer), assembled with a grip grid. Mice were held by the tail and lowered toward the apparatus. The mice were allowed to grasp the metal grid only with their forelimbs and were then pulled backward in the horizontal plane. The maximum force of grip was measured, and we used the average of six measurements for analysis. Force was measured in Newton and Grams. The experimenter was blind to the genotypes.

Treadmill test

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The treadmill test was conducted on female mice by using the DigiGait system (MouseSpecifics, Inc), which is equipped with a motorized transparent treadmill belt and a high-speed digital camera that provides images of the ventral side of the mouse (Figure 6—videos 1–4). For the Hoxc8 MNΔ early analysis, seven control (Hoxc8fl/fl) and seven (Olig2Cre::Hoxc8fl/fl fl) mice at the age of 4–5 months were placed onto the walking compartment. The treadmill was turned on at a speed of 15 cm/s. For the Hoxc8 MNΔ late analysis, 8 control (Hoxc8fl/fl) and 10 (ChatIRESCre::Hoxc8fl/fl) mice at the age of 2–5 months were placed onto the walking compartment. The treadmill test was conducted at two different speeds (15 cm/s and 25 cm/s). The 30-s long videos were obtained for each mouse. Videos were analyzed and data were binned into four categories based on the duration of each mouse’s stay on the treadmill (category 1: <5 s; category 2: 5–10 s; category 3: 10–15 s; category 4: >20 s).

Statistical analysis

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For data quantification, graphs show values expressed as mean ± SEM. With the exception of the rotarod and treadmill experiments, all other statistical analyses were performed using the unpaired t-test (two-tailed). Differences with p<0.05 were considered significant. For the rotarod performance test, two-way ANOVA was performed (Prism Software). For the treadmill experiment, we used Fisher’s exact test.

Data availability

Sequencing data have been deposited in GEO under accession code GSE174709. All data generated or analyzed in this study are included in the manuscript and supporting files.

The following data sets were generated
    1. Catela C
    2. Kratsios P
    (2021) NCBI Gene Expression Omnibus
    ID GSE174709. New roles for Hoxc8 in the establishment and maintenance of motor neuron identity.
The following previously published data sets were used
    1. Mahony S
    (2020) NCBI Gene Expression Omnibus
    ID GSE142379. Diversification of posterior Hox patterning by graded ability to engage inaccessible chromatin.

References

  1. Book
    1. Arora RD
    2. Khan YS
    (2021)
    Motor Neuron Disease StatPearls
    StatPearls Publishing LLC.

Decision letter

  1. Ishmail Abdus-Saboor
    Reviewing Editor; Columbia University, United States
  2. Piali Sengupta
    Senior Editor; Brandeis University, United States
  3. Aaron D Gitler
    Reviewer; Stanford University School of Medicine, United States

Our editorial process produces two outputs: i) public reviews designed to be posted alongside the preprint for the benefit of readers; ii) feedback on the manuscript for the authors, including requests for revisions, shown below. We also include an acceptance summary that explains what the editors found interesting or important about the work.

Decision letter after peer review:

Thank you for submitting your article "Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity" for consideration by eLife. Your article has been reviewed by 3 peer reviewers, one of whom is a member of our Board of Reviewing Editors, and the evaluation has been overseen by Piali Sengupta as the Senior Editor. The following individual involved in review of your submission has agreed to reveal their identity: Aaron D Gitler (Reviewer #2).

The reviewers have discussed their reviews with one another, and the Reviewing Editor has drafted this to help you prepare a revised submission.

Essential revisions:

The reviewers are in agreement that this is a very interesting study, addressing a fundamental topic in developmental genetics, with important implications for the field. Nonetheless, the reviewers have coalesced around several items that need to be addressed before we can consider this paper for publication.

1. The behavioral data is potentially important to this study, but not robustly performed. The N numbers need to be increased and additional behavioral tests should be added. Moreover, deleting Hoxc8 expression earlier in these studies, as was done for other experiments, would be useful.

2. The quality of many of the RNA in situ experiments was not good, making it hard for reviewers to easily assess the data. The authors should repeat the in situs where necessary or even consider newer, more quantitative RNA in situ approaches.

3. Authors should clarify their conclusions about the role of Hoxc8 in brachial motor neuron differentiation because at least from the data presented it does not seem to have a very significant role, and the authors should consider the potential involvement of other collaborating factors.

4. Authors should clarify the potential caveats by using two different methods for labeling MNs at the two time points and possibly coming up with a better method or way to normalize the data.

Reviewer #1 (Recommendations for the authors):

1. My major concern with this paper is the lack of specificity for the findings and ease in building a cohesive story. The paper is largely centered around RNAseq and RNA in situ (that is sometimes hard to interpret, see comment below). I appreciate the large amount of effort put into this study, but it would be nice to know how many of these gene regulatory networks are direct (ie. TF binding to consensus motifs in promoter regions). I was unable to follow a clear logic as to why certain genes were chosen for follow up, or to focus large parts of the story on.

2. In regards to Figure 1, how specific are HB9::GFP and Chat::Ai9 to motor neurons, or neurons in general. Authors should co-stain for other neuronal and glial markers. Also, why not use a reporter from one of the identified terminal differentiation factors which is on early and late, so that a single reporter is used?

3. The RNA in situs in Figures3A, 4E, 5B and some of the supplemental images are not of the highest quality and one has to read the manuscript to know what to conclude. Perhaps newer approaches like RNAscope, or similar probes, would be more quantitative and easier to interpret. Also some images have white dotted circles around them cells of interest and other images do not – please be consistent.

4. Although sympathetic to the need to use the Hoxc8 late mice for behavioral experiments due to perinatal lethality with the Hoxc8 early mice, these experiments demonstrate there is no phenotype and the author's assertion that mutant mice "tend" to perform worse is an unfair stretch. Moreover, with an N number of 3 and 5 mice on some of the experiments, its hard to make conclusions. The authors should consider consulting with or collaborating with a more behavior focused lab to do these experiments in a more robust manner, adding more tests and mice, or consider leaving the behavior experiments out of this paper.

Reviewer #2 (Recommendations for the authors):

We have the following comments and suggestions for the authors to consider:

1) Hox factors are known to control motor neuron subtype/pool specification (e.g. Dasen et al., 2005). It would be helpful to know if Hoxc8 early or late deletions change motor neuron subtype/pool identity rather than their maturation, which could be the reason for the differential gene expression This could be confirmed with co-labeling of reporter and subtype/pool markers, as in the Irx experiments.

2) Based on Figure 4F, the authors seem to distinguish terminal differentiation genes (e.g. neurotransmitters, synapse molecules) from axon guidance molecules and transcription factors. However, there are times when these seem to be treated interchangeably (e.g. discussion of Sema5a and Ret on page 12). The authors should more clearly and consistently state what they consider terminal differentiation markers in the text.

3) It would be worthwhile to have co-labeling with reporter (Hb9-GFP vs ChAT-tdTom) for at least some of the selected genes (e.g. in Figure 3G) to see if there is specific reduction in the cells of interest rather than just through correlation based on spatial pattern.

4) The Irx2 knockout experiments suggest that this downstream target of Hoxc8 may be involved in specification of limb-generating motor neurons, but not in the expression of terminal differentiation markers regulated by Hoxc8. This result seems tangential to the paper as 1) the knockouts are performed very early (prior to cell specification) and therefore does not provide any additional information about how Hoxc8 regulates motor neuron development past specification stage and 2) do not a clear functional link between Hoxc8 and terminal differentiation regulation.

5) It is unclear what the C. elegans Irx2 (fosmid) experiments add to this paper. The loss of MNs entirely seems to detract from the overall point of this paper, which is that Hoxc8 helps to establish/maintain brachial motor neuron identity/maturation.

6) It is unclear what the behavioral experiments add to the paper since would be very difficult to attribute any phenotype to a specific cause. Also, unclear why the experiments were performed only in late Hoxc8 deletion and not the early deletion as well.

7) The quality of some of the in situs should be improved (e.g. Glra2 in Figure 4E)

8) It might be of interest to overexpress Hoxc8 in other regions of the spinal cord (e.g. cervical or thoracic) using chick electroporation for example to see if it can lead to overexpression of some of these terminal differentiation genes. This gain-of-function experiment may lend additional support to the proposal that Hoxc8 is required to maintain expression of these genes, although I am not sure that this is a requirement for distinguishing terminal selectors.

Reviewer #3 (Recommendations for the authors):

1. The authors used two different genetic systems to label brachial MNs at embryonic day 12 (e12) and postnatal day 8 (p8) as it was not possible for them to label MNs with just a single genetic system. Using these reagents they conclude that Hoxc8 regulates some of the same and some different targets. But can they rule out that some of these results is a consequence of using two different labeling systems? Are they certain that the cells labeled at both time points are the same cells? Perhaps using a lineage tracing tool and/or normalizing with some of the genes they discover in their RNA-seq experiments may be a way add confidence in the similarities and differences that they find in the RNAseq datasets are accurate.

2. Along the same lines, the RNA ISH of Hoxc8 at e12 looks dense, suggesting that all MNs in LMC and MMC regions express Hoxc8. On the other hand, expression of Hoxc8 seems sparse at p8, suggesting few Hoxc8+ MNs at p8 compared to e12 stage. Performing dual RNA ISH with Hoxc8 and endogenous genes of interest would provide greater confidence that the same number of Hoxc8+ MNs are present at two different time points.

3. The authors state that Hoxc8 MN late mutants perform worse in rotarod performance test and forelimb grip strength in 3-month old mice. However, the statistical analysis suggests there is no significant change. It was unclear why the authors chose such a late time point for these assays, when the mice potentially have time to compensate for a compromised motor system. Redoing this experiment at earlier time points, such as with 1 month old mice (there is precedence for this in the literature), might reveal significant differences.

https://doi.org/10.7554/eLife.70766.sa1

Author response

Essential revisions:

The reviewers are in agreement that this is a very interesting study, addressing a fundamental topic in developmental genetics, with important implications for the field. Nonetheless, the reviewers have coalesced around several items that need to be addressed before we can consider this paper for publication.

1. The behavioral data is potentially important to this study, but not robustly performed. The N numbers need to be increased and additional behavioral tests should be added. Moreover, deleting Hoxc8 expression earlier in these studies, as was done for other experiments, would be useful.

We completely agree. In the revised manuscript, we have included new data on three behavioral tests (forelimb grip strength, treadmill, rotarod). We increased the number of animals (N) and also included in the analysis two sets of mice with conditional Hoxc8 manipulations: 1) Hoxc8 MNΔearly mice in which Olig2-Cre is active in motor neuron (MN) progenitors, and 2) Hoxc8 MNΔlate mice in which ChAT-IRES-Cre is active in post-mitotic MNs.

We have added the following paragraph in Results that summarizes our findings:

“Hoxc8 gene activity is necessary for brachial motor neuron function

We next sought to assess any potential behavioral defects in adult Hoxc8 MNΔ early and Hoxc8 MNΔ late animals by evaluating their motor coordination (Deacon, 2013), forelimb grip strength (Takeshita et al., 2017) and treadmill performance(Wozniak et al., 2019). No defects were observed in Hoxc8 MNΔ early and Hoxc8 MNΔ late mice during the rotarod performance test (Figure 6 —figure supplement 1), suggesting balance and motor coordination are normal in these animals. Next, we evaluated forelimb grip strength because brachial MNs innervate forelimb muscles. We found a statistically significant defect in Hoxc8 MNΔearly mice, but not in Hoxc8 MNΔlate mice (Figure 6A-B). Lastly, we tested these animals for their ability to run on a treadmill for a period of 30 seconds (sec). At a low speed (15 cm/sec), we observed statistically significant defects in Hoxc8 MNΔearly mice. That is, 64.28% of Hoxc8 MNΔearly mice fell off the treadmill in the first 5 sec of the trial compared to 28.57% of control mice (p = 0.0108) (Figure 6C, Figure 6 – videos 1-2). Moreover, 0% of Hoxc8 MNΔearly mice were able to stay longer than 20 sec on the treadmill compared to 42.85% of control mice (Figure 6C). On the other hand, statistically significant defects were observed in Hoxc8 MNΔlate mice only when the treadmill speed was increased to 25 cm/sec (Figure 6C-D). That is, 43.33% of Hoxc8 MNΔ late mice fell off the treadmill in the first 5 sec of the trial compared to 17.39% of control mice (p = 0.0461) (Figure 6D, Figure 6 – videos 3-4). Together, these data show that Hoxc8 MNΔlate mice display a milder behavioral phenotype compared to Hoxc8 MNΔearly mice. This is likely due to the fact that Hoxc8 MNΔearly mice display a composite phenotype i.e., defects in early MN specification and axon guidance (Catela et al., 2016) combined with terminal differentiation defects [this study], whereas the Hoxc8 MNΔlate mice only display terminal differentiation defects (this study). Although we cannot exclude the possibility that the terminal differentiation defects of MNΔearly mice are a consequence of their early MN specification defects, this is unlikely as Hoxc8 binds directly to the cis-regulatory region of terminal differentiation genes (Mcam, Pappa, Glra2) (Figure 5B).”

2. The quality of many of the RNA in situ experiments was not good, making it hard for reviewers to easily assess the data. The authors should repeat the in situs where necessary or even consider newer, more quantitative RNA in situ approaches.

We conducted new RNA fluorescent ISH (FISH) experiments coupled with a MN-specific marker (Foxp1). These new data corroborate our original conclusion: Hoxc8 controls the expression of several target genes in brachial MNs (new Figure 3G, new Figure 3 —figure supplement 1). To complement these in vivo findings, we now provide evidence in in vitro generated MNs that Hoxc8 is sufficient to induce the expression of the same target genes (e.g., Pappa, Glra2, Sema5a) we identified in vivo (new Figure 5A).

3. Authors should clarify their conclusions about the role of Hoxc8 in brachial motor neuron differentiation because at least from the data presented it does not seem to have a very significant role, and the authors should consider the potential involvement of other collaborating factors.

We completely agree. Our new molecular analysis and behavioral data suggest Hoxc8 does not act alone in the context of brachial motor neuron terminal differentiation. We have clarified our conclusions and further highlighted the involvement of other collaborating factors in multiple places in Results and Discussion. The most significant changes to address this important point are summarized below.

In Results:

“We found that expression of Neuregulin 1 (Nrg1), a molecule required for neuromuscular synapse maintenance and neurotransmission(Mei and Xiong, 2008, Wolpowitz et al., 2000), is reduced (but not eliminated) in e12 brachial MNs of Hoxc8 MNΔ early mice (Figure 3F), likely due to the existence of additional factors that partially compensate for loss of Hoxc8 gene activity.”

“Importantly, not all Hoxc8 target genes (e.g., Nrg1, Mcam) we identified in vivo are upregulated in iHoxc8 ESC-derived MNs (Figure 5 —figure supplement 1). This is likely due to the lack of Hoxc8 collaborating factors in these in vitro generated MNs. A putative collaborator is Hoxc6 because (a) Hoxc6 and Hoxc8 are co-expressed in embryonic brachial MNs (Catela et al., 2016), (b) animals lacking either Hoxc6 or Hoxc8 in brachial MNs display similar axon guidance defects (Catela et al., 2016), and (c) Hoxc6 and Hoxc8 control the expression of the same axon guidance molecule (Ret) in brachial MNs (Catela et al., 2016). Supporting the notion of collaboration, our analysis of available ChIP-seq data for Hoxc6 and Hoxc8 from iHoxc6 and iHoxc8 ESC-derived MNs(Bulajic et al., 2020), respectively, showed that these Hox proteins bind directly on the cis-regulatory region of previously known (Ret, Gfra3) and new (Mcam, Pappa, Nrg1, Sema5a) Hoxc8 target genes (Figure 5 —figure supplement 1).”

In Discussion:

“In the spinal cord, we found several other Hox genes (Hoxc4, Hoxa5, Hoxc5, Hoxa6, Hoxc6, Hoxa7) to be continuously expressed in brachial MNs, potentially acting as Hoxc8 collaborators.”

“This residual expression indicates that additional TFs are necessary to control brachial MN terminal differentiation. As mentioned in Results, one such factor is Hoxc6, which is co-expressed with Hoxc8 in brachial MNs during embryonic and postnatal stages (Catela et al., 2016) (Figure 2A). Importantly, Hoxc6 and Hoxc8 bind directly on the cis-regulatory regions of the same terminal differentiation genes in the context of mouse ESC-derived MNs (Figure 5 —figure supplement 1). Another putative Hoxc8 collaborator is the LIM homeodomain protein Islet1 (Isl1), which is required for early induction of genes necessary for ACh biosynthesis in mouse spinal MNs and the in vitro generation of MNs from human pluripotent stem cells(Cho et al., 2014, Qu et al., 2014, Rhee et al., 2016).”

4. Authors should clarify the potential caveats by using two different methods for labeling MNs at the two time points and possibly coming up with a better method or way to normalize the data.

We completely agree. The potential caveat is that our FACS-sorted cells also include a minority of cells that are not motor neurons. We acknowledge this possibility in Results:

“Two factors that could contribute to these transcriptional differences between the e12 and p8 datasets are: (1) different levels of gene expression (see next Section), and (2) a small fraction of the FACS-sorted cells are not MNs. Indeed, Hb9 (Mnx1) and ChAT, in addition to MNs, are also expressed in small, non-overlapping neuronal populations in the spinal cord (Wilson et al., 2005, Zagoraiou et al., 2009, Wichterle et al., 2002) (Figure 1 —figure supplement 1).”

However, we believe this caveat is not of a major concern for the following reasons:

(a) The end goal of using these two different methods for labeling brachial MNs was to identify genes (transcription factors, terminal differentiation markers) that are expressed continuously in these cells. Our extensive validation of RNA-Seq results with RNA ISH suggests we met this goal (Figure 2-4, Figure 1 —figure supplement 2, new Figure 3 —figure supplement 1).

(b) As we mention in our reply to Reviewer 1 (please see R1 – Response 2), we conducted additional experiments to test the specificity of our genetic labeling approach (new Figure 1 —figure supplement 1).

(c) As we mention in Results, the RNA-Seq of genetically labeled brachial MNs was: (a) sensitive because it identified genes expressed in subtypes of brachial MNs (Ebf2, Lhx3, Irx), and (b) region-specific because it identified specific Hox genes, known to be expressed only in brachial MNs

Reviewer #1 (Recommendations for the authors):

1. My major concern with this paper is the lack of specificity for the findings and ease in building a cohesive story. The paper is largely centered around RNAseq and RNA in situ (that is sometimes hard to interpret, see comment below). I appreciate the large amount of effort put into this study, but it would be nice to know how many of these gene regulatory networks are direct (ie. TF binding to consensus motifs in promoter regions). I was unable to follow a clear logic as to why certain genes were chosen for follow up, or to focus large parts of the story on.

We regret that in some parts the original version of the manuscript lacked cohesion. To address this, we have now made significant changes in Results and also removed all data on Irx transcription factors, as suggested by Reviewers 1 and 2. We hope the revised manuscript is now more focused and communicates effectively its main conclusion, i.e., sustained Hoxc8 activity is necessary for brachial motor neuron terminal differentiation.

To address the comment on lack of specificity, we have now performed RNA fluorescent in situ hybridization (FISH) coupled with a motor neuron-specific marker (FoxP1). These new findings (presented in Figure 3G and Figure 3 —figure supplement 1) corroborate the initial results reported in this paper.

Motivated by the reviewer’s comment to identify direct Hoxc8 target genes, we analyzed recently published RNA-Seq and ChIP-seq datasets from motor neurons derived from ES cells (ESC-MNs) in which Hoxc8 expression can be induced upon doxycycline treatment (Bulajic et al., 2020). Our analysis showed that the same Hoxc8 target genes (e.g., Pappa, Glra2) we found downregulated in brachial motor neurons of Hoxc8 MNΔ early and Hoxc8 MNΔ late mice are upregulated in motor neurons derived from ES cells (ESC-MNs), in which Hoxc8 expression is induced (Bulajic et al., 2020) (Figure 5A). Lastly, we found that Hoxc8 binds directly at the cis-regulatory region of the terminal differentiation genes (e.g., Mcam, Pappa, Glra2) we identified in vivo, and is sufficient to induce their expression in the context of ESC-MNs (Figure 5B, Figure 5 —figure supplement 1).

2. In regards to Figure 1, how specific are HB9::GFP and Chat::Ai9 to motor neurons, or neurons in general. Authors should co-stain for other neuronal and glial markers.

To our knowledge, the HB9::GFP mouse line is the best available tool to genetically label mouse embryonic motor neurons. This mouse line has been used by several recent studies for the same purpose and at the same time point with us: to isolate mouse spinal MNs at e12.5 with FACS and then conduct RNA-Sequencing (Sawai et al., eLife, 2022, PMID: 34994686; Hanley et al., Neuron, 2016, PMID: 27568519; Amin et al., Science, 2015, PMID: 26680198). However, we cannot exclude the possibility that a very small population of the HB9::GFP+ cells we isolated at e12.5 are spinal interneurons. The original paper (Wichterle et al., Cell, 2002, PMID: 12176325) describing the generation of HB9::GFP mice notes: “GFP expression was found in motor neuron cell bodies, dendrites, and axons in HB9::GFP embryos. In this line a very low level of expression (10- to 20-fold lower than in motor neurons) was detected in DRG neurons and a subset of ventral interneurons at e10.5, but not later”.

It is also unlikely that we isolated any glia at e12.5 with the HB9::GFP line – mature oligodendrocytes are not present at e12.5 in the spinal cord, as the peak of myelination in mice occurs at postnatal day 21 (p21). Moreover, the aforementioned studies (PMID: 34994686, PMID: 27568519, PMID: 26680198) have not reported any HB9::GFP expression in glia.

Prompted by the reviewer’s suggestion, we conducted additional experiments to evaluate the specificity of labeling spinal motor neurons at p8 with the ChAT::IRES::Cre; Ai9 [Rosa26-CAGpromoter-loxP-STOP-loxP-tdTomato] mouse line. Double immunofluorescence staining using antibodies against ChAT (cholinergic motor neuron marker) and tdTomato (expressed in cells in which Cre is/was active) revealed robust co-localization of ChAT with tdTomato in most (if not all) spinal motor neurons (Figure 1 —figure supplement 1).

We also observed sparse tdTomato expression, but not ChAT, in a few cells (5-10 cells per section) located more dorsally and medially in the spinal cord, which are not motor neurons (Figure 1 —figure supplement 1). A recent study that used the same ChAT::IRES::Cre line reported similar observations and suggested that this is likely due to earlier Cre expression in the lineage of these tdTomato positive cells (PMID: 33931636).

At p8, there are many astrocytes present in the spinal cord but few mature oligodendrocytes (myelination peaks at p21). We therefore stained against the astrocyte marker GFAP (Millipore, AB5541, 1:200) and found no colocalization with tdTomato-expressing cells in ChAT::IRES::Cre; Ai9 spinal cords at p8 (Figure 1 —figure supplement 1). We also attempted to stain for a microglia marker CD11b (Bio-Rad, MCA711, 1:50), but we did not detect any staining likely due to technical reasons. Altogether, these new data suggest that the tdTomato-expressing cells we isolated at p8 by FACS are mostly spinal motor neurons. Please, see also ER- Response 4 (page 3 of this document).

Also, why not use a reporter from one of the identified terminal differentiation factors which is on early and late, so that a single reporter is used?

This is a great suggestion but it would require the generation and characterization of new mouse lines, as well as redoing the RNA-Seq experiments at e12 and p8. Such endeavor will take 4-5 years to complete judging from the amount of time it took to complete the current study. However, we are planning on generating in the future new reporter/Cre lines based on the terminal differentiation markers identified from this study.

3. The RNA in situs in Figures3A, 4E, 5B and some of the supplemental images are not of the highest quality and one has to read the manuscript to know what to conclude. Perhaps newer approaches like RNAscope, or similar probes, would be more quantitative and easier to interpret. Also some images have white dotted circles around them cells of interest and other images do not – please be consistent.

We conducted new RNA fluorescent ISH (FISH) experiments coupled with a MN-specific marker (Foxp1). These new data corroborate our original conclusion: Hoxc8 controls the expression of several target genes in brachial MNs (new Figure 3G, new Figure 3 —figure supplement 1). To complement these in vivo findings, we now provide evidence in in vitro generated MNs that Hoxc8 is sufficient to induce the expression of the same target genes (e.g., Pappa, Glra2, Sema5a) we identified in vivo (new Figure 5A). Lastly, we are now consistent with the white dotted circles. We only use them when we show Hoxc8 antibody staining or Hoxc8 RNA ISH data because Hoxc8 is also expressed in other cells of the spinal cord. We decided against using white dotted circles in all figures in order to be minimally invasive and avoid excessive drawing on top of our microscopy images. There is, however, a spinal cord schematic next to each image to orient the reader on what part of the spinal cord is actually shown.

4. Although sympathetic to the need to use the Hoxc8 late mice for behavioral experiments due to perinatal lethality with the Hoxc8 early mice, these experiments demonstrate there is no phenotype and the author's assertion that mutant mice "tend" to perform worse is an unfair stretch. Moreover, with an N number of 3 and 5 mice on some of the experiments, its hard to make conclusions. The authors should consider consulting with or collaborating with a more behavior focused lab to do these experiments in a more robust manner, adding more tests and mice, or consider leaving the behavior experiments out of this paper.

Thank you for this excellent suggestion. By expanding our mouse colony, we have now conducted behavioral experiments both on Hoxc8 MNΔearly and Hoxc8 MNΔlate mice and increased N (new Figure 6, new Figure 6—figure supplement 1). Prompted by Reviewers 1 and 3, we have added a new test (treadmill analysis) on both Hoxc8 MNΔearly and Hoxc8 MNΔlate mice. Please see our detailed answer in ER – Response 1 (page 1 of this document).

Reviewer #2 (Recommendations for the authors):

We have the following comments and suggestions for the authors to consider:

1) Hox factors are known to control motor neuron subtype/pool specification (e.g. Dasen et al., 2005). It would be helpful to know if Hoxc8 early or late deletions change motor neuron subtype/pool identity rather than their maturation, which could be the reason for the differential gene expression This could be confirmed with co-labeling of reporter and subtype/pool markers, as in the Irx experiments.

This is an excellent point that we now clarified by text changes and new experiments.

A previous study (Catela et al., Cell Reports, 2016, PMID: 26904955) found that the overall organization of brachial MNs into columns is normal in Hoxc8 MNΔearly mice. However, the same study found that the expression of two motor neuron pool markers (Scip, Pea3) at e12.5 is partially affected, suggesting defects in motor neuron pool specification when Hoxc8 is deleted early. In the current manuscript, we report that brachial motor neurons are generated in normal numbers in Hoxc8 MNΔearly mice (Figure 3C), but the expression of terminal differentiation genes (e.g., Nrg1, Mcam, Pappa) is affected in these mice (Figure 3F-G). Moreover, Hoxc8 binds directly on the cis-regulatory region of these genes (new Figure 5B, new Figure 5—figure supplement 1).

For the Hoxc8 MNΔlate mice, we attempted to stain brachial motor neurons with the motor neuron pool markers (Scip, Pea3) at e14.5 because at 14.5 we detect robust Hoxc8 depletion in these mice (new Figure 4B). However, these markers are transiently expressed and become downregulated in wildtype samples after e12.5. This prevented us from evaluating their expression at e14.5 in Hoxc8 MNΔlate spinal cords. Taken together, our analyses show that the expression of several terminal differentiation markers (e.g., Nrg1, Mcam, Pappa, Glra2) is affected in brachial MNs of Hoxc8 MNΔlate mice, which could explain their milder behavioral phenotype when compared to the Hoxc8 MNΔearly mice (new Figure 6, Figure 6 – videos 1 – 4).

In Results, we mention: “Together, these data show that Hoxc8 MNΔlate mice display a milder behavioral phenotype compared to Hoxc8 MNΔearly mice. This is likely due to the fact that Hoxc8 MNΔearly mice display a composite phenotype (i.e., defects in early MN specification and axon guidance (Catela et al., 2016) combined with terminal differentiation defects [this study], whereas the Hoxc8 MNΔlate mice only display terminal differentiation defects (this study). Although we cannot exclude the possibility that the terminal differentiation defects of MNΔearly mice are a consequence of their early MN specification defects, this is unlikely as Hoxc8 binds directly to the cis-regulatory region of terminal differentiation genes (Mcam, Pappa, Glra2) (Figure 5B).”

2) Based on Figure 4F, the authors seem to distinguish terminal differentiation genes (e.g. neurotransmitters, synapse molecules) from axon guidance molecules and transcription factors. However, there are times when these seem to be treated interchangeably (e.g. discussion of Sema5a and Ret on page 12). The authors should more clearly and consistently state what they consider terminal differentiation markers in the text.

Thanks, we recognize the confusion and have modified the text accordingly in several occasions:

“Two simple, but not mutually exclusive mechanisms can be envisioned for the continuous expression of terminal differentiation genes (e.g., Slc10a4, Nrg1, Nyap2, Sncg, Ngfr, Glra2) in brachial MNs.”

“Lastly, Hoxc8 can only activate expression of Sema5a (member of Semaphorin family) at embryonic stages (Figure 3F-G, Table 1).”

“In this study, we uncovered several Hoxc8 target genes encoding different classes of proteins (Sema5a – axon guidance molecule; Glra2, Nrg1, Mcam, Pappa – terminal differentiation genes) (Figure 3E, Figure 4F), suggesting Hoxc8 controls different aspects of brachial MN development through the regulation of these genes.”

3) It would be worthwhile to have co-labeling with reporter (Hb9-GFP vs ChAT-tdTom) for at least some of the selected genes (e.g. in Figure 3G) to see if there is specific reduction in the cells of interest rather than just through correlation based on spatial pattern.

To address this important point, we coupled RNA fluorescence in situ (FISH) with antibody staining for FoxP1 (marker of LMC column in brachial region) on spinal cords of Hoxc8 MNΔearly mice. Consistent with what we originally reported, these experiments showed that the expression of several Hoxc8 target genes (Sema5a, Mcam, Pappa) is affected in brachial motor neurons (new Figure 3G; new Figure 3 —figure supplement 1). Moreover, most of the target genes (e.g., Pappa, Sema5a, Glra2) that are downregulated – in vivo – in motor neurons of Hoxc8 MNΔearly and Hoxc8 MNΔ late mice are upregulated upon inducible Hoxc8 expression in vitro generated motor neurons (new data in Figure 5A). Hence, Hoxc8 appears to be both necessary and sufficient for the expression of its target genes.

4) The Irx2 knockout experiments suggest that this downstream target of Hoxc8 may be involved in specification of limb-generating motor neurons, but not in the expression of terminal differentiation markers regulated by Hoxc8. This result seems tangential to the paper as 1) the knockouts are performed very early (prior to cell specification) and therefore does not provide any additional information about how Hoxc8 regulates motor neuron development past specification stage and 2) do not a clear functional link between Hoxc8 and terminal differentiation regulation.

We completely agree and have decided to remove the mouse Irx data from this manuscript. The manuscript is now more focused on Hoxc8 and its conclusions are strengthened by the addition of new molecular and behavioral data, two new main figures [Figure 5 – 6] and 5 new supplementary figures [Figure 1—figure supplement 1; Figure 3—figure supplement 1; Figure 4—figure supplement 1; Figure 5 —figure supplement 1; Figure 6 —figure supplement 1).

5) It is unclear what the C. elegans Irx2 (fosmid) experiments add to this paper. The loss of MNs entirely seems to detract from the overall point of this paper, which is that Hoxc8 helps to establish/maintain brachial motor neuron identity/maturation.

Again, we agree and have removed the C. elegans Irx data from the manuscript.

6) It is unclear what the behavioral experiments add to the paper since would be very difficult to attribute any phenotype to a specific cause. Also, unclear why the experiments were performed only in late Hoxc8 deletion and not the early deletion as well.

Please see ER – Response 1 (page 1 of this document). We conducted new behavioral tests (rotarod, forelimb grip strength, treadmill) on Hoxc8 MNΔearly and Hoxc8 MNΔ late mice. Our new behavioral data (new Figure 6) nicely complement the molecular analysis of brachial motor neurons in Hoxc8 MNΔearly and Hoxc8 MNΔ late mice.

7) The quality of some of the in situs should be improved (e.g. Glra2 in Figure 4E)

We have conducted new RNA FISH experiments to improve the quality of our findings (new Figure 3G; new Figure 3—figure supplement 1). Moreover, we performed double immunofluorescence (instead of RNA ISH) to demonstrate Hoxc8 protein depletion in brachial MNs of Hoxc8 MNΔ late mice (new Figure 4B).

8) It might be of interest to overexpress Hoxc8 in other regions of the spinal cord (e.g. cervical or thoracic) using chick electroporation for example to see if it can lead to overexpression of some of these terminal differentiation genes. This gain-of-function experiment may lend additional support to the proposal that Hoxc8 is required to maintain expression of these genes, although I am not sure that this is a requirement for distinguishing terminal selectors.

This is an excellent idea. In the absence of an established chick electroporation system in our lab, we analyzed recently published RNA-Seq and ChIP-seq datasets from motor neurons derived from mouse ES cells (ESC-MNs), in which Hoxc8 expression is induced with doxycycline (Dox) treatment (Bulajic et al., 2020, PMID: 33028607). We included this analysis in Results as shown below:

“Hoxc8 is sufficient to induce its target genes and acts directly

To gain mechanistic insights, we analyzed recently published RNA-Seq and chromatin immunoprecipitation-sequencing (ChIP-seq) datasets on MNs derived from mouse embryonic stem cells (ESC), in which Hoxc8 expression was induced with doxycycline (Bulajic et al., 2020). Our RNA-Seq analysis showed that induction of Hoxc8 (iHox8) resulted in upregulation of previously known (Ret, Scip/Pouef1) and new (Pappa, Glra2, Sema5a) Hoxc8 target genes (Figure 5A). Moreover, ChIP-seq for Hoxc8 in the context of these iHoxc8 ESC-derived MNs revealed binding in the cis-regulatory region of all these genes (Figure 5B), suggesting Hoxc8 acts directly to activate their expression. This in vitro data together with the in vivo findings in Hoxc8 MNΔ early and Hoxc8 MNΔ late mice (Figure 3F-G, Figure 3 —figure supplement 1, Figure 4C) suggest that Hoxc8 is necessary and sufficient for the expression of several of its target genes in spinal MNs.

Importantly, not all Hoxc8 target genes (e.g., Nrg1, Mcam) we identified in vivo are upregulated in iHoxc8 ESC-derived MNs (Figure 5 —figure supplement 1). This is likely due to the lack of Hoxc8 collaborating factors in these in vitro generated MNs. A putative collaborator is Hoxc6 because (a) Hoxc6 and Hoxc8 are co-expressed in embryonic brachial MNs (Catela et al., 2016), (b) animals lacking either Hoxc6 or Hoxc8 in brachial MNs display similar axon guidance defects (Catela et al., 2016), and (c) Hoxc6 and Hoxc8 control the expression of the same axon guidance molecule (Ret) in brachial MNs (Catela et al., 2016). Supporting the notion of collaboration, our analysis of available ChIP-seq data for Hoxc6 and Hoxc8 from iHoxc6 and iHoxc8 ESC-derived MNs(Bulajic et al., 2020), respectively, showed that these Hox proteins bind directly on the cis-regulatory region of previously known (Ret, Gfra3) and new (Mcam, Pappa, Nrg1, Sema5a) Hoxc8 target genes (Figure 5 —figure supplement 1).”

Altogether, our in vivo data and in vitro analysis suggest that Hoxc8 is necessary and sufficient for the expression of at least some its target genes. Indeed, most terminal selector-type TFs in C. elegans are both necessary and sufficient. Our findings on mouse Hoxc8 support the idea that key features of terminal selector function are conserved across species (please see last paragraph in Discussion).

Reviewer #3 (Recommendations for the authors):

1. The authors used two different genetic systems to label brachial MNs at embryonic day 12 (e12) and postnatal day 8 (p8) as it was not possible for them to label MNs with just a single genetic system. Using these reagents they conclude that Hoxc8 regulates some of the same and some different targets. But can they rule out that some of these results is a consequence of using two different labeling systems? Are they certain that the cells labeled at both time points are the same cells? Perhaps using a lineage tracing tool and/or normalizing with some of the genes they discover in their RNA-seq experiments may be a way add confidence in the similarities and differences that they find in the RNAseq datasets are accurate.

Indeed, this is a very important point which we now address with text changes and new experiments. Please see our detailed responses in ER – Response 4 (page 3 of this document) and R1 – Response 2 (page 6). In brief, Hb9-GFP expression is faint at post-natal stages, which necessitated the use of an additional reporter strategy (ChAT-Cre; Ai9 tdTomato line) for the discovery of genes expressed in brachial MNs via RNA-Sequencing. In Results, we acknowledge the limitations of using two different genetic labeling strategies. We also conducted additional experiments to evaluate the specificity of motor neuron labeling by staining for glia and cholinergic motor neuron markers (new Figure 1 —figure supplement 1).

We note that the two different labeling systems were used in wild-type animals to identify enriched transcripts in embryonic and postnatal MNs (Figure 1). Hence, they do not affect our key conclusions on the function of Hoxc8 in motor neurons for the following reasons:

(a) The new Hoxc8 targets were discovered through RNA-Seq by using a single reporter (Hb9::GFP), not two different labeling systems, in Hoxc8 MNΔearly mice (Figure 3D).

(b) We used additional methods (i.e., RNA ISH) to independently validate our RNA-Seq results and identify new Hoxc8 target genes (Figure 3F, Figure 4C).

(c) We also provide new data to show that Hoxc8 controls terminal identity gene expression specifically in brachial MNs (with FoxP1) (Figure 3G, new Figure 3 —figure supplement 1).

(d) Our new analysis revealed that the same Hoxc8 target genes (e.g., Pappa, Glra2, Sema5a) we found downregulated in brachial motor neurons of Hoxc8 MNΔ early and Hoxc8 MNΔ late mice are upregulated in motor neurons derived from ES cells (ESC-MNs), in which Hoxc8 expression is induced upon doxycycline (Dox) treatment (Bulajic et al., 2020, PMID: 33028607) (new Figure 5, new Figure 5 —figure supplement 1).

2. Along the same lines, the RNA ISH of Hoxc8 at e12 looks dense, suggesting that all MNs in LMC and MMC regions express Hoxc8. On the other hand, expression of Hoxc8 seems sparse at p8, suggesting few Hoxc8+ MNs at p8 compared to e12 stage. Performing dual RNA ISH with Hoxc8 and endogenous genes of interest would provide greater confidence that the same number of Hoxc8+ MNs are present at two different time points.

Yes, the reviewer is correct. Consistent with our findings (Figure 3B), a previous study showed that, at e12, Hoxc8 is expressed both in MMC and LMC motor neurons (Catela et al., 2016, PMID: 26904955). Like most Hox genes, Hoxc8 is also expressed in other neurons (not motor neurons) of the spinal cord (Figure 3B, 4B), which necessitated the need of Cre lines (Olig2::Cre, ChAT-IRES-Cre) to specifically inactivate it in motor neurons at early and late stages of development.

In wild type animals, spinal motor neurons are normally generated in excess and a large fraction of them (~50%) undergoes physiological/developmental cell death after e12, resulting in fewer motor neurons at later developmental stages (PMID: 10928282). Hence, the number of brachial motor neurons expressing Hoxc8 is high at e12 and ~50% lower at p8. To address the reviewer’s point, we conducted double immunofluorescence and RNA ISH. We found that Hoxc8 continues to be expressed in spinal motor neurons at late embryonic (e18.5) and early postnatal (p8) stages (new Figure 4 —figure supplement 1).

3. The authors state that Hoxc8 MN late mutants perform worse in rotarod performance test and forelimb grip strength in 3-month old mice. However, the statistical analysis suggests there is no significant change. It was unclear why the authors chose such a late time point for these assays, when the mice potentially have time to compensate for a compromised motor system. Redoing this experiment at earlier time points, such as with 1 month old mice (there is precedence for this in the literature), might reveal significant differences.

We have now conducted new behavioral tests (rotarod, forelimb grip strength, treadmill) both on Hoxc8 MNΔearly and Hoxc8 MNΔ late mice and significantly increased the number of animals. Please see ER – Response 1 (page 1 of this document) for a detailed discussion of the behavioral data, which nicely complement the molecular analysis of brachial motor neurons in Hoxc8 MNΔearly and Hoxc8 MNΔ late mice.

https://doi.org/10.7554/eLife.70766.sa2

Article and author information

Author details

  1. Catarina Catela

    1. Department of Neurobiology, University of Chicago, Chicago, United States
    2. University of Chicago Neuroscience Institute, Chicago, United States
    Contribution
    Conceptualization, Data curation, Formal analysis, Investigation, Methodology, Visualization, Writing - original draft, Writing - review and editing
    Competing interests
    No competing interests declared
  2. Yihan Chen

    1. Department of Neurobiology, University of Chicago, Chicago, United States
    2. University of Chicago Neuroscience Institute, Chicago, United States
    Contribution
    Formal analysis, Investigation, Validation
    Competing interests
    No competing interests declared
  3. Yifei Weng

    1. Department of Neurobiology, University of Chicago, Chicago, United States
    2. University of Chicago Neuroscience Institute, Chicago, United States
    Contribution
    Formal analysis, Investigation, Validation
    Competing interests
    No competing interests declared
  4. Kailong Wen

    1. Department of Neurobiology, University of Chicago, Chicago, United States
    2. University of Chicago Neuroscience Institute, Chicago, United States
    Contribution
    Formal analysis, Investigation, Validation
    Competing interests
    No competing interests declared
  5. Paschalis Kratsios

    1. Department of Neurobiology, University of Chicago, Chicago, United States
    2. University of Chicago Neuroscience Institute, Chicago, United States
    Contribution
    Conceptualization, Funding acquisition, Investigation, Project administration, Supervision, Visualization, Writing - original draft, Writing - review and editing
    For correspondence
    pkratsios@uchicago.edu
    Competing interests
    No competing interests declared
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1363-9271

Funding

National Institute of Neurological Disorders and Stroke (R01NS116365)

  • Paschalis Kratsios

Robert Packard Center for ALS Research, Johns Hopkins University (Not applicable)

  • Paschalis Kratsios

Lohengrin Foundation (Not applicable)

  • Paschalis Kratsios

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Acknowledgements

We are grateful to members of the Kratsios lab (Yinan Li, Edgar Correa, Nidhi Sharma, Filipe Goncalves Marques) and Drs. Deeptha Vasudevan, Ellie Heckscher, and Oliver Hobert for comments on the manuscript. We thank Dr. Jeremy Dasen (NYU) for providing the following antibodies (rabbit anti-Foxp1, rabbit anti-Lhx3, rabbit anti-Hb9, rabbit anti-Isl1/2), Milica Bulajić for help obtaining the RNA-Seq and ChIP-Seq data on in vitro differentiated iHoxc6 and iHoxc8 motor neurons, and Jihad Aburas for technical assistance. We thank the following Core Facilities at The University of Chicago: (a) Cytometry and Antibody Technology, and (b) Genomics Facility (RRID:SCR019196), especially Dr. Pieter Faber, for his assistance with the RNA-Sequencing. This work was supported by the Lohengrin Foundation and a grant from the National Institute of Neurological Disorders and Stroke (NINDS) of the NIH (Award Number: R01NS116365) to PK. This publication was also supported by a grant from the Robert Packard Center for ALS Research at Johns Hopkins University. Its contents are solely the responsibility of the authors and do not necessarily represent the official views of The Johns Hopkins University or any grantor providing funds to its Robert Packard Center for ALS Research.

Ethics

This study was performed in strict accordance with the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Institutes of Health. All of the animals were handled according to approved institutional animal care and use committee (IACUC) protocol (#72463) of the University of Chicago.

Senior Editor

  1. Piali Sengupta, Brandeis University, United States

Reviewing Editor

  1. Ishmail Abdus-Saboor, Columbia University, United States

Reviewer

  1. Aaron D Gitler, Stanford University School of Medicine, United States

Publication history

  1. Preprint posted: May 27, 2021 (view preprint)
  2. Received: May 28, 2021
  3. Accepted: March 12, 2022
  4. Version of Record published: March 22, 2022 (version 1)

Copyright

© 2022, Catela et al.

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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  1. Catarina Catela
  2. Yihan Chen
  3. Yifei Weng
  4. Kailong Wen
  5. Paschalis Kratsios
(2022)
Control of spinal motor neuron terminal differentiation through sustained Hoxc8 gene activity
eLife 11:e70766.
https://doi.org/10.7554/eLife.70766

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