Integrative and Comparative Biology Integrative and Comparative Biology, volume 54, number 4, pp. 714–722 doi:10.1093/icb/icu027 Society for Integrative and Comparative Biology SYMPOSIUM Old Cell, New Trick? Cnidocytes as a Model for the Evolution of Novelty Leslie S. Babonis1 and Mark Q. Martindale Whitney Laboratory for Marine Bioscience, University of Florida, 9505 N Oceanshore Blvd, St. Augustine, FL 32080, USA From the symposium ‘‘The Cell’s View of Animal Body Plan Evolution’’ presented at the annual meeting of the Society for Integrative and Comparative Biology, January 3–7, 2014 at Austin, Texas. 1 E-mail: [email protected] Synopsis Understanding how new cell types arise is critical for understanding the evolution of organismal complexity. Questions of this nature, however, can be difficult to answer due to the challenge associated with defining the identity of a truly novel cell. Cnidarians (anemones, jellies, and their allies) provide a unique opportunity to investigate the molecular regulation and development of cell-novelty because they possess a cell that is unique to the cnidarian lineage and that also has a very well-characterized phenotype: the cnidocyte (stinging cell). Because cnidocytes are thought to differentiate from the cell lineage that also gives rise to neurons, cnidocytes can be expected to express many of the same genes expressed in their neural ‘‘sister’’ cells. Conversely, only cnidocytes posses a cnidocyst (the explosive organelle that gives cnidocytes their sting); therefore, those genes or gene-regulatory relationships required for the development of the cnidocyst can be expected to be expressed uniquely (or in unique combination) in cnidocytes. This system provides an important opportunity to: (1) construct the gene-regulatory network (GRN) underlying the differentiation of cnidocytes, (2) assess the relative contributions of both conserved and derived genes in the cnidocyte GRN, and (3) test hypotheses about the role of novel regulatory relationships in the generation of novel cell types. In this review, we summarize common challenges to studying the evolution of novelty, introduce the utility of cnidocyte differentiation in the model cnidarian, Nematostella vectensis, as a means of overcoming these challenges, and describe an experimental approach that leverages comparative tissue-specific transcriptomics to generate hypotheses about the GRNs underlying the acquisition of the cnidocyte identity. Why study novelty? The development of novel traits (structures and/or functions) is one critical way in which morphological and functional diversity is generated across taxa; indeed, many of the novel features of greatest interest are complex multicellular traits responsible for major evolutionary transitions (e.g., evolution of the tetrapod limb) (Shubin et al. 1997). Yet a complete understanding of how these complex evolutionary novelties arise (and, ultimately, how animal diversity arises) necessitates an understanding of how new cell types are generated. From a developmental perspective, new cell types are generated when ‘‘error’’ is introduced during the process of differentiation, such that a daughter cell with a new phenotype is produced. From an evolutionary perspective, novel phenotypes of cells may arise either with the advent of novel genes (e.g., by gene duplication followed by neofunctionalization, introduction of transposable elements, and/or lateral gene transfer) (for review, see Hall and Kerney 2012) or as a consequence of novel relationships among deeply homologous genes (resulting in heterochrony, novel regulatory networks, or novel protein–protein interactions) (Hoekstra and Coyne 2007; Wray, 2007; Shubin et al. 2009; Wagner and Lynch 2010). A recent study modeling diversity in types of cells as a function of new regulatory relationships among conserved genes suggests that this latter hypothesis is sufficient to generate extensive novelty and diversity among cell types (Lobo and Vico 2010). Still, many additional examples of novel traits emerging as a consequence of novel genes exist (Khalturin et al. 2009; Milde et al. 2009; Johnson and Tsutsui Advanced Access publication April 25, 2014 ß The Author 2014. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: [email protected]. Cnidocytes model novelty 715 2011), thereby supporting a diverse array of mechanisms responsible for generating diversity at the cellular and tissue level (Oakley 2007). An important future area of study of this topic lies at the intersection of these processes. In particular, how novel genes become incorporated into novel or existing GRNs is a critical next step in revealing the mechanisms that result in the generation of new cell types. Herein, we propose that cnidocytes may be uniquely suited to model the interaction of structural and regulatory novelties and suggest a means by which to capitalize on recent efforts in sequencing across diverse cnidarian taxa to develop hypotheses about the evolution of this important cnidarian-specific cell novelty. Cnidocyte differentiation in Nematostella vectensis: a model for the evolution of novel cells Using the simple terminology of Peterson and Muller (2013), we consider cnidocytes, the stinging cells in cnidarians, a classic example of an evolutionary (phenotypic) novelty. Found in no other organisms, cnidocytes have been studied for decades, in part because of their unique function. Following stimulation of the sensory cilium at the apex of the cnidocyte (Fig. 1), the cnidocyst (the organelle from which the cnidocyte derives its ‘‘sting’’) extrudes from the cell with an acceleration that exceeds that of perhaps any other biological process (Holstein and Tardent 1984). Ultimately, these explosive organelles ensnare, envenomate, or adhere to their target, providing a means by which to capture/subdue prey, defend against predators, or locomote through substrate. While lingering hypotheses have suggested a close evolutionary relationship between cnidocytes and the elaborate extrusive cells of some protists (Shostak 1993; Denker et al. 2008a; Ozbek et al. 2009), the absence of any molecular evidence of lateral gene transfer (Technau et al. 2005) suggests this similarity is little more than impressive homoplasy. The autonomous ability of cnidocytes to sense the environment and respond (by firing) led to early hypotheses that cnidocytes are an unusual type of dual function (sensory/effector) neuron (Pantin 1942), albeit with a highly derived neurosecretory vesicle (the cnidocyst). Expression of many common regulatory genes in the precursors of both neurons and cnidocytes lends support to this idea (e.g., cnox-2, prdl-b, and COUP-TF) (Galliot and Quiquand 2011); however, a recent phylogenetic study suggests that neurons may have evolved long before cnidocytes (Ryan et al. 2013). If cnidocytes Fig. 1 Anatomy of a cnidocyte. (A) Unfired. Stimulation of the cnidocil activates exocytosis of the contents of the cnidocyst. (B) Fired. The tubule is everted from the capsule of the cnidocyst. evolved from within the lineage that gave rise to neurons, it may be reasonable to expect conservation of many of the molecular elements of their differentiation pathways. Understanding the GRNs that underlie the differentiation of both neurons and cnidocytes is a critical first step in evaluating this hypothesis. The concept of cell identity is inherently modular, thus, many components of cell identity may be nested within a single cell. For example, a single cell may at the same time be an epithelial cell, a sensory cell, a secretory cell, and a cnidocyte. Because of this, it may not be surprising to find substantial conservation of GRN modules between cnidocytes and, for example, neurons which may also be epithelial, sensory, and secretory cells. Understanding the evolution of novel cell identity, then, requires first identifying the components of a GRN that underlie a particular module of cell identity and then assessing whether these components are shared across cell types or are unique to the novel cell lineage. Because of their truly unique function, studies of cnidocysts continue to attract attention across fields ranging from venom evolutionary studies to clinical investigations of novel drug delivery techniques (Shaoul et al. 2012; Weston et al. 2013). These and other detailed studies of the cnidocyte proteome (e.g., Hwang et al. 2007) have revealed numerous taxonomically restricted genes in this cell type, providing many possible examples of elements comprising the ‘‘cnidocyte’’ identity module. 716 Importantly, development of the cnidocyst relies both on cnidarian-specific structural proteins (e.g., minicollagens, NOWA, and spinalin) (Kurz et al., 1991; Koch et al., 1998; Engel et al., 2002) and scaffolding by conserved glycosaminoglycans, including chondroitin sulfate (Yamada et al. 2007; Adamczyk et al. 2010; Ozbek 2011). Thus, components comprising the cnidocyte identity module may only need to be regulated together, rather than be uniquely expressed in this cell type to produce a novel phenotype. Although binding sites for conserved transcription factors have yet to be identified in the promoter regions of any cnidocyte-specific genes, functional assays of several conserved transcription factors suggest that the structural elements of the cnidocyst identity module may be regulated (directly or indirectly) by conserved transcription factors (e.g., mef2 and NFkB) (Genikhovich and Technau 2011; Wolenski et al. 2013). In order to elucidate the process by which the cnidocyte identity module became integrated with other GRNs underlying cell-type identity, it is necessary to examine the processes upstream of cnidocyst formation, specifically the differentiation of cnidocytes from a proliferative precursor. Like all other somatic cells, new cnidocytes arise through mitosis of a precursor or ‘‘stem’’ cell, a process that has been well-studied in hydrozoan cnidarians (recently reviewed by David 2012). In hydrozoans, cnidocytes are known to arise from a special progenitor lineage that resides in the interstitium of the body-wall’s epidermis (so-called ‘‘i-cells’’). Following several rounds of mitosis without full cleavage, early-stage cnidocytes are produced in nests and remain attached to each other via cytoplasmic bridges until maturation of the cnidocyst and, finally, migration of the mature cnidocytes to the tentacles, where the majority of cnidocytes are mounted. Studies of the proliferation and differentiation of stem cells in hydrozoans have benefited from both a long history of study (Galliot 2012) and many recent advances in molecular techniques (including the development of i-cell transgenics, which has facilitated the extensive molecular characterization of icells and their descendents) (Wittlieb et al. 2006; Hemmrich et al. 2012). Considering that hydrozoans are a highly derived lineage of cnidarians, the applicability of these studies to a broader understanding of cell biology across cnidarian taxa has been questioned (Extavour et al. 2005; Technau et al. 2005; Steele et al. 2011). In concert with this, i-cells appear to be a type of progenitor cell restricted to the Hydrozoa, yet even among hydrozoans the dynamics of i-cell biology (e.g., their embryonic origins, their contribution to L. S. Babonis and M. Q. Martindale regeneration, and their spatio-temporal progression to cnidocyte development) varies (Denker et al. 2008b; Plickert et al. 2012). These observations make efforts to identify the proliferative cells in other cnidarian lineages, and indeed the mechanism of differentiation from these progenitors, increasingly important (Gold and Jacobs 2013). Comparisons of putative cnidocyte differentiation genes across cnidarian taxa appear to reveal even more substantial diversity; for example, the cnidarian ortholog of the conserved achaete-scute (ash) gene isolated from Hydra (Cnash) is known to regulate the identity of all cells in the cnidocyte lineage (Grens et al. 1995) whereas ash genes in N. vectensis (NvashA-D) appear to be expressed only in neurons or in the endodermal component of the mesenteries, neither of which is consistent with a role in cnidocyte development (despite suggestions to the contrary by Layden et al. 2012). Additionally, a recent study using subtractive library hybridization identified 16 cnidarian-specific genes in the cnidocyte lineage of Hydra, two of which have reasonable homology with sequences in N. vectensis (Milde et al. 2009). One of these (gene 012) is restricted to developing lineages of two types of cnidocytes that are not found in N. vectensis; understanding where this gene is expressed in N. vectensis may provide information about how the diverse repertoire of cnidocytes in Hydra evolved. It is tempting to postulate that the morphological diversity of cnidocytes is mirrored by diversity at the regulatory (differentiation) level; but, before hypotheses like these can be evaluated, it is necessary to characterize the molecular regulation of cnidocyte differentiation in cnidarians outside of the Hydrozoan lineage. Nematostella vectensis, the starlet sea anemone (Fig. 2A), has become an important model for molecular and developmental studies, especially for studies of the molecular regulation of the identity of cells and tissues (Darling et al. 2005; Genikhovich and Technau 2011; Steele et al. 2011; Layden et al. 2012; Nakanishi et al. 2012; Rottinger et al. 2012; Fritz et al. 2013). Several aspects of the biology of N. vectensis also make this animal an attractive model for studies of cellular novelty. First, cnidocytes are found in various tissues in this species but are notably abundant in the epidermis on the tips of tentacles (Fig. 2B) and in the mesenteries (Fig. 2E) where they develop continuously throughout the lifetime of the animal (Fig. 2C and F; Zenkert et al. 2011). Although the identity of the progenitor lineage has yet to be identified in N. vectensis (indeed, in any non-hydrozoan cnidarian) (Gold and Jacobs 2013), the presence of proliferative Cnidocytes model novelty 717 Fig. 2 Cnidocyte development in Nematostella vectensis. (A) An adult polyp showing basic morphology. (B) DIC image of the tip of a tentacle showing the abundance of mature cnidocytes (arrows) in the tentacle’s epidermis (e). (C) Fluorescent in situ hybridization (following the protocol of Layden et al. 2012) for minicollagen 3 shows the distribution of developing cnidocytes (red) in the tentacle in this optical section; nuclei are shown in blue (DAPI). (D) EdU (following the manufacturers’ protocol; Invitrogen USA) reveals the presence of proliferative cells (green) in the tentacle’s epidermis; optical section. (E) DIC image of the ectodermal component of one mesentery showing the abundance of mature cnidocytes (arrows). (F) Confocal projection showing the presence of developing cnidocytes (red) and proliferative cells (green) in the mesentery pictured in E; nuclei as in C. (G) DIC image of an isolated nematosome with abundant mature cnidocytes (arrows). (H) Mature cnidocytes are present in aggregations (arrows) along the mesentery before the nematosomes have fully budded. (I) Fluorescent in situ hybridization for minicollagen 3 (red) overlaid on a DIC image shows developing cnidocytes in the epidermis of the body wall (e) but not in the gastrodermis or nematosome (arrow); optical section. Panel A reprinted with permission: ß SERTC, South Carolina Department of Natural Resources. cells at the site of cnidocyte differentiation (e.g., in the epidermis of the distal tentacle and ectodermal mesenteries) (Fig. 2D and G) suggests that the replacement of cnidocytes occurs locally in this species. This is an important departure from the hydrozoan model as it suggests that progenitor cells comprise a significant component of the epidermal tissue in the adult, rather than being restricted to an atypical lineage of cells found only in the interstitium of the mid-body epidermis (as is the case for Hydrozoans). Another important advantage of using N. vectensis for studies of the differentiation of cnidocytes is the opportunity to compare the molecular regulation of this process both in adults undergoing cnidocyte replacement and during de novo generation of the cnidocytes through embryonic development. Studies comparing eye development and regeneration in planarians suggest these processes may involve different molecular pathways (summarized by Martin-Duran et al. 2012); if this principle holds true in cnidarians, studies aimed only at regenerating cnidocytes in polyps may miss many important elements of the developmental cnidocyte GRN. Comparisons of this type can be made explicitly only after one of these 718 L. S. Babonis and M. Q. Martindale GRNs has been characterized. Below, we discuss a means by which to leverage tissue-specific mRNAseq as a forward approach to characterizing the first cnidocyte GRN in N. vectensis. Tissue-specific transcriptomics: a forward approach to identify cnidocyte GRNs A well-characterized cnidocyte GRN is a critical tool for future testing of hypotheses about conservation of regulatory relationships in different life stages (e.g., adult versus embryos), across different cell types (e.g., cnidocytes versus neurons), and among taxa (e.g., Nematostella versus Hydra). Here, we describe a method that pairs minimal prior knowledge of the molecular differentiation of cnidocytes with mRNAseq technology in an unbiased approach to identifying the elements of the cnidocyte GRN in the adult anemone (outlined in Fig. 3). Because cnidocytes develop both locally and continuously in the tentacles and mesenteries of adult N. vectensis (Fig. 2) (Zenkert et al. 2011), sequencing mRNA from these tissues provides a means by which to sample cells at many stages of differentiation along the cnidocyte pathway. Genes of particular interest for the cnidocyte GRN (target genes) will be expressed in the union of the transcriptomic datasets from these two tissues. However, because developing cnidocytes are not the only cell types shared by these two tissues, many transcripts that are not part of the cnidocyte GRN will also be included in this union (e.g., those expressed in any other cell type undergoing differentiation at the time of collection). Previous studies of transcriptome-level changes in mRNA expression across developmental stages (Helm et al. 2013; Tulin et al. 2013) or treatments (Barshis et al. 2013) have narrowed their list of target genes by examining only those transcripts whose expression changes through time or across treatments using differential expression analysis. When target genes are expressed in the union of two conditions (e.g., in the set of genes shared by tentacles and mesenteries), it is necessary to employ an alternative means to identify transcripts of greatest interest. Nematostella vectensis again provides a unique opportunity for comparative tissue-specific transcriptome analysis in its possession of nematosomes (Fig. 2G). Unique to anemones in the genus Nematostella, nematosomes are small autonomous cell masses that arise from the ectodermal component of the mesenteries (Fig. 2H; Williams 1975) and circulate in the gastrovascular cavity of the adult anemone with an unknown function (Williams Fig. 3 Venn diagram indicating target genes of interest. Targets captured in section A will include those expressed in mature cnidocytes (found in all three tissues) as well as housekeeping genes (found in all cells). Targets in section B will include the genes of the cnidocyte developmental pathway as well as genes from any other cell lineages downstream of the proliferating cells shown in Fig. 2D and F. 1979; Hand and Uhlinger 1992). Although nematosomes are replete with mature cnidocytes (Fig. 2G and H), there is no evidence to suggest that cnidocyte differentiation occurs in this tissue (Fig. 2I), making nematosomes extremely valuable for distinguishing between genes involved in the development of cnidocytes and genes responsible for the maintenance of mature cnidocyte identity. While the latter category of genes (involved in mature cell maintenance) will be expressed in the union of all three tissues (Group A; Fig. 3), those involved largely in the development of cnidocytes will be excluded from the nematosomes (Group B; Fig. 3). Thus, including nematosomes in this analysis provides an important opportunity to focus the suite of genes pursued in downstream studies of cnidocyte development and also provides a reciprocal opportunity for future comparisons of the maintenance of identity in each of the three types of cnidocytes found in the various tissues in N. vectensis. Indeed, future analyses focused on sequences in the union of all three tissues (Group A) will be critical for establishing the molecular identity of mature cnidocytes and will benefit greatly from comparative analyses incorporating recent data on the cnidocyte proteome (Moran et al. 2013). Although simple in design, we suggest that the approach outlined here may be particularly useful for investigations of other emerging model systems wherein some data have already been collected using a candidate-gene strategy but the full Cnidocytes model novelty GRN for the cell, tissue, or process of interest remains to be characterized. Because cnidocytes are easy to identify using only light microscopy (Ostman 2000), this approach may also be particularly useful for future studies aimed at characterizing the tissue-specific generation of cnidocytes across various cnidarian taxa. The dramatic decrease in the cost of sequencing over the past decade has resulted in a dramatic increase in the number of species, tissues, and cells for which transcriptomic (mRNAseq) data have become available. Among cnidarians, mRNAseq datasets are now available for at least 12 different taxa representing both anthozoan and hydrozoan lineages: Acropora millepora, A. palmata, A. hyacinthus, Aiptasia pallida, Craspedacusta sowerbyi, Favia sp., Hydra vulgaris, Hydractinia symbiolongicarpus, Nanomia bijuga, N. vectensis, Pocillopora damicornis, and Porites australiensis (Polato et al. 2011; Siebert et al. 2011; Traylor-Knowles et al. 2011; Hroudova et al. 2012; Lehnert et al. 2012; Moya et al. 2012; Barshis et al. 2013; Mehr et al. 2013; Tulin et al. 2013; Wenger and Galliot 2013; Shinzato et al. 2014; Zárate-Potes and Cadavid 2014). The parallel increase in availability of user-friendly software for de novo transcriptome assembly (Robertson et al. 2010; Grabherr et al. 2011; Schulz et al. 2012; Brown et al. 2013) has greatly facilitated discovery of novel genes (e.g., new taxonomically restricted genes, short-ORF-containing transcripts, and pseudogenes) (Lehnert et al. 2012; Moya et al. 2012; Mehr et al. 2013; Wenger and Galliot 2013) among these non-model taxa. Together with newly developed modeling approaches aimed at inferring cis-regulatory relationships from sequencing data (Dresch et al. 2013), the continued sampling of diverse cnidarian taxa with a particular emphasis on studies of tissue-specific expression will enable future tests of cnidocyte GRN conservation across lineages. As with any transcriptomic study, there are caveats with this approach that must be considered. First, all three target tissues (mesenteries, tentacles, and nematosomes) are comprised of many different cell types; thus, using transcriptomics alone, it will not be possible to discriminate genes expressed in the developing cnidocyte lineage from those expressed in any other cell lineage that might be undergoing proliferation and/or differentiation at the same time. It will still be necessary therefore, to apply downstream processes to determine (1) where/when the target transcripts (e.g., transcription factors and signaling molecules) are expressed relative to the timing of proliferation and of cnidocyst development and (2) the effect of target gene knockdown on the expression of markers of cnidocyst 719 development. Additionally, because cnidocytes develop continuously both in tentacles and inmesenteries and because multiple types of cnidocytes are known to develop in both of these tissues (Zenkert et al. 2011), any single transcriptomic dataset will undoubtedly include expressed genes from multiple types of cnidocytes and from multiple times along the differentiation pathway of these cnidocytes. To construct the relationships among transcripts in the network underlying each type of cnidocyte (e.g., which transcription factors regulate which targets), it will be necessary to pair downstream functional assays (e.g., gene knockdown) with careful analysis of the ultrastructure of cnidocytes (e.g., using electron microscopy). Recent advancements in the number and the nature of molecular tools available for use in N. vectensis (including double fluorescent in situ hybridization, knockdown/ overexpression techniques, and the recent development of transgenic lines) (Renfer et al. 2010; Rottinger et al. 2012; Layden et al. 2013) have made functional assays of this type possible in this system and will facilitate the downstream studies of gene regulation necessary to fully construct the GRNs of each type of cnidocyte. Because little is known about the regulation of cnidocyte development outside of the Hydrozoa, this approach will necessarily require extensive screening of transcription factors expressed in the tissues of interest. Fortunately, the presence/absence of cnidocytes is easy to assay (even when using only light microscopy) thereby providing for a simple and unambiguous means for assessing initial effects of targetgene knockdown. Although it is now technically and financially feasible to collect transcriptome data from numerous samples across several treatments (indeed, even from individual cells) (Hemmrich et al. 2012), many challenges to the analysis of this type of data still exist (for recent reviews, see McGettigan 2013; Sims et al. 2014). Importantly, identifying a reasonable set of target genes to pursue in downstream applications (e.g., knockdown/knockout experiments, directed sequencing, or qPCR) can be a formidable challenge. Many studies seek to identify suites of target genes by identifying transcriptome-level differences in gene expression, but RNAseq datasets are inherently noisy (Marinov et al. 2013; McDavid et al. 2013; Wills et al. 2013) which can result in increased detection of both false-positives and falsenegatives. Fortunately, many analytical approaches have been developed to combat these challenges (Li and Dewey 2011; Tarazona et al. 2011; McDavid et al. 2013; Wagner et al. 2013), thereby facilitating the application of large-scale sequencing data to a 720 diverse array of experimental conditions and across diverse and divergent taxa. Conclusions/Future directions The mechanism underlying the evolution of novel traits continues to garner interest across diverse disciplines, and cnidocytes may make a particularly useful model for studies of this type. Recent studies revealing the diversity of minicollagen genes and their non-overlapping involvement in cnidocyst development undoubtedly will inspire many future studies aimed at understanding how the many unique cnidocyst morphologies arose and we hope these studies will inspire further investigations into cnidocyte differentiation as well. Importantly, the apparent diversity in the regulation of cnidocyte differentiation from a proliferative precursor suggests that while cnidocytes themselves are unique to, and ubiquitous within, the Cnidaria, they may not be patterned the same way across taxa. Considering that cnidocyte diversity in hydrozoan taxa exceeds that of anthozoans, it is tempting to hypothesize that the hydrozoan cnidocyte program evolved from an ancestral GRN that may still be represented in anthozoan taxa. Indeed, the lack of apparent conservation between the cnidocyte GRN in Hydra and the few other cnidarians that are beginning to be examined suggests the process by which cnidocyte differentiation occurs may be just as diverse as the cnidocysts themselves. Evaluating the validity of this hypothesis awaits more extensive studies of cnidocyte differentiation in diverse cnidarian taxa and across multiple life stages and we suggest that studies of this type will be well-served to employ tissue-specific transcriptomic analyses, as discussed. Future studies of cnidocyte development across cnidarian taxa may indeed reveal the ancestral mechanisms by which progenitor cells evolved and will further shed light on the evolution of novel traits. Acknowledgments This manuscript was submitted as part of a symposium at the 2014 meeting of the Society for Integrative and Comparative Biology (SICB). Support for this symposium was provided by the Society for Developmental Biology and SICB (to the organizers). Funding Funding for this manuscript was provided by the National Aeronautics and Space Administration (to M.Q.M.). L. S. Babonis and M. Q. 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