Cultivation and characterization of planarian neuronal cells isolated by fluorescence activated cell sorting (FACS)

Isolation of planarian viable cells using fluorescence-activated cell sorting for advancing single-cell transcriptome analysis

Preparing viable single cells is critical for conducting single-cell RNA sequencing (scRNA-seq) because the presence of ambient RNA from dead or damaged cells can interfere with data analysis. Here, we developed a method for isolating viable single cells from adult planarian bodies using fluorescence-activated cell sorting (FACS). This method was then applied to both adult pluripotent stem cells (aPSCs) and differentiating/differentiated cells. Initially, we employed a violet instead of ultraviolet (UV) laser to excite Hoechst 33342 to reduce cellular damage. After optimization of cell staining conditions and FACS compensation, we generated FACS profiles similar to those created using a previous method that employed a UV laser. Despite successfully obtaining high-quality RNA sequencing data for aPSCs, non-aPSCs produced low-quality RNA reads (i.e., <60% of cells possessing barcoding mRNAs). Subsequently, we identified an effective FACS gating condition that excluded low-quality cells and tissue debris without staining. This non-staining isolation strategy not only reduced post-dissociation time but also enabled high-quality scRNA-seq results for all cell types (i.e., >80%). Taken together, these findings imply that the non-staining FACS strategy may be beneficial for isolating viable cells not only from planarians but also from other organisms and tissues for scRNA-seq studies.

WTAP regulates stem cells via TRAF6 to maintain planarian homeostasis and regeneration

WTAP, a highly conserved Wilms' tumor 1 interacting protein, is involved in a variety of biological processes. However, functional studies of WTAP in planarians have not been reported. In this study, we examined the spatiotemporal expression pattern of planarian DjWTAP and investigated its functions in planarians regeneration and homeostasis. Knocking-down DjWTAP resulted in severe morphological defects leading to lethality within 20 days. Silencing DjWTAP promoted the proliferation of PiwiA⁺ cells but impaired the lineage differentiation of epidermal, neural, digestive, and excretory cell types, suggesting a critical role for DjWTAP in stem cell self-renewal and differentiation in planarian. To further investigate the mechanisms underlying the defective differentiation, RNA-seq was employed to determine the transcriptomic alterations upon DjWTAP RNA interference. Histone 4 (H4), Histone-lysine N-methyltransferase-SETMAR like, and TNF receptor-associated factor 6 (TRAF6), were significantly upregulated in response to DjWTAP RNAi. Knocking-down TRAF6 largely rescued the defective tissue homeostasis and regeneration resulted from DjWTAP knockdown in planarians, suggesting that DjWTAP maintains planarian regeneration and homeostasis via TRAF6.

Pluripotency retention and exogenous mRNA introduction in planarian stem cells in culture

Planarians possess naturally occurring pluripotent adult somatic stem cells (neoblasts) required for homeostasis and whole-body regeneration. However, no reliable neoblast culture methods are currently available, hindering mechanistic studies of pluripotency and the development of transgenic tools. We report robust methods for neoblast culture and delivery of exogenous mRNAs. We identify optimal culture media for the short-term maintenance of neoblasts in vitro and show via transplantation that cultured stem cells retain pluripotency for two days. We developed a procedure that significantly improves neoblast yield and purity by modifying standard flow cytometry methods. These methods enable the introduction and expression of exogenous mRNAs in neoblasts, overcoming a key hurdle impeding the application of transgenics in planarians. The advances in cell culture reported here create new opportunities for mechanistic studies of planarian adult stem cell pluripotency, and provide a systematic framework to develop cell culture techniques in other emerging research organisms.

Live Immunostaining and Flow Cytometry of Schmidtea Mediterranea Cells

The use of flow cytometry and fluorescence-activated cell sorting to roughly separate subpopulations of cells in Schmidtea mediterranea is long established. In this chapter, we describe a method for the immunostaining-either single or double-of live planarian cells, using mouse monoclonal antibodies reactive against S. mediterranea plasma membrane antigens. This protocol allows to sort live cells according to their membrane signature, offering the possibility to further characterize the cell populations in S. mediterranea in a variety of downstream applications, like transcriptomics and cell transplantation, also at the single-cell level.

Convergent evolution of a genotoxic stress response in a parasite-specific p53 homolog

P53 is a widely studied tumor suppressor that plays important roles in cell-cycle regulation, cell death, and DNA damage repair. P53 is found throughout metazoans, even in invertebrates that do not develop malignancies. The prevailing theory for why these invertebrates possess a tumor suppressor is that P53 originally evolved to protect the germline of early metazoans from genotoxic stress such as ultraviolet radiation. This theory is largely based upon functional data from only three invertebrates, omitting important groups of animals including flatworms. Previous studies in the freshwater planarian flatworm Schmidtea mediterranea suggested that flatworm P53 plays an important role in stem cell maintenance and skin production, but these studies did not directly test for any tumor suppressor functions. To better understand the function of P53 homologs across diverse flatworms, we examined the function of two different P53 homologs in the parasitic flatworm Schistosoma mansoni. The first P53 homolog (p53-1) is orthologous to S. mediterranea P53(Smed-p53) and human TP53 and regulates flatworm stem cell maintenance and skin production. The second P53 homolog (p53-2) is a parasite-specific paralog that is conserved across parasitic flatworms and is required for the normal response to genotoxic stress in S. mansoni. We then found that Smed-p53 does not seem to play any role in the planarian response to genotoxic stress. The existence of this parasite-specific paralog that bears a tumor suppressor-like function in parasitic flatworms implies that the ability to respond to genotoxic stress in parasitic flatworms may have arisen from convergent evolution.

A Subtractive FACS Method for Isolation of Planarian Stem Cells and Neural Cells

Planarians are among the metazoan organisms with the greatest regenerative abilities. This ability is based on their pluripotent stem cells, called neoblasts, which constitute 10-20% of the cells in their body. Elucidating the molecular mechanisms of the planarian stem cell system, for example, the maintenance of stem cell homeostasis and orchestration of lineage choices, contributes powerfully to the advancement of regenerative biology. Our group has developed fluorescence activated cell sorting (FACS) methodologies for the reliable isolation of planarian stem cells, which constitutes an important experimental asset in the field. Here, we describe detailed protocols for the isolation of (1) planarian stem cells and (2) neural cells. Planarian stem cells are isolated by subtraction of the FACS profiles of intact and γ-ray-irradiated (= stem cell depleted) animals stained with Hoechst 33342 and Calcein AM. The neural cells are isolated by subtracting the FACS profiles of head and tail fragments stained with Hoechst 33258 and Merocyanine 540.

Draft genome of Dugesia japonica provides insights into conserved regulatory elements of the brain restriction gene nou-darake in planarians

BACKGROUND

Planarians are non-parasitic Platyhelminthes (flatworms) famous for their regeneration ability and for having a well-organized brain. Dugesia japonica is a typical planarian species that is widely distributed in the East Asia. Extensive cellular and molecular experimental methods have been developed to identify the functions of thousands of genes in this species, making this planarian a good experimental model for regeneration biology and neurobiology. However, no genome-level information is available for D. japonica, and few gene regulatory networks have been identified thus far.

RESULTS

To obtain whole-genome information on this species and to study its gene regulatory networks, we extracted genomic DNA from 200 planarians derived from a laboratory-bred asexual clonal strain, and sequenced 476 Gb of data by second-generation sequencing. Kmer frequency graphing and fosmid sequence analysis indicated a complex genome that would be difficult to assemble using second-generation sequencing short reads. To address this challenge, we developed a new assembly strategy and improved the de novo genome assembly, producing a 1.56 Gb genome sequence (DjGenome ver1.0, including 202,925 scaffolds and N50 length 27,741 bp) that covers 99.4% of all 19,543 genes in the assembled transcriptome, although the genome is fragmented as 80% of the genome consists of repeated sequences (genomic frequency ≥ 2). By genome comparison between two planarian genera, we identified conserved non-coding elements (CNEs), which are indicative of gene regulatory elements. Transgenic experiments using Xenopus laevis indicated that one of the CNEs in the Djndk gene may be a regulatory element, suggesting that the regulation of the ndk gene and the brain formation mechanism may be conserved between vertebrates and invertebrates.

CONCLUSION

This draft genome and CNE analysis will contribute to resolving gene regulatory networks in planarians. The genome database is available at: http://www.planarian.jp.

Multiple Neuropeptide-Coding Genes Involved in Planarian Pharynx Extension

Planarian feeding behavior involves three steps: moving toward food, extending the pharynx from their planarian's ventral side after arriving at the food, and ingesting the food through the pharynx. Although pharynx extension is a remarkable behavior, it remains unknown what neuronal cell types are involved in its regulation. To identify neurons involved in regulating pharynx extension, we quantitatively analyzed pharynx extension and sought to identify these neurons by RNA interference (RNAi) and in situ hybridization. This assay, when performed using planarians with amputation of various body parts, clearly showed that the head portion is indispensable for inducing pharynx extension. We thus tested the effects of knockdown of brain neurons such as serotonergic, GABAergic, and dopaminergic neurons by RNAi, but did not observe any effects on pharynx extension behavior. However, animals with RNAi of the Prohormone Convertase 2 (PC2, a neuropeptide processing enzyme) gene did not perform the pharynx extension behavior, suggesting the possible involvement of neuropeptide(s in the regulation of pharynx extension. We screened 24 neuropeptide-coding genes, analyzed their functions by RNAi using the pharynx extension assay system, and identified at least five neuropeptide genes involved in pharynx extension. These was expressed in different cells or neurons, and some of them were expressed in the brain, suggesting complex regulation of planarian feeding behavior by the nervous system.

Alternative flow cytometry strategies to analyze stem cells and cell death in planarians

Planarians possess remarkable stem cell populations that continuously support cellular turnover and are instrumental in the regeneration of tissues upon injury. Cellular turnover and tissue regeneration in planarians rely on the proper integration of local and systemic signals that regulate cell proliferation and cell death. Thus, understanding the signals controlling cellular proliferation and cell death in planarians could provide valuable insights for maintenance of adult body homeostasis and the biology of regeneration. Flow cytometry techniques have been utilized widely to identify, isolate, and characterize planarian stem cell populations. We developed alternative flow cytometry strategies that reduce the number of reagents and the time of sample preparation to analyze stem cells and cell death in planarians. The sensitivity of these methods is validated with functional studies using RNA interference and treatment with  γ irradiation or stressful conditions that are known to trigger cell death. Altogether, we provide a community resource intended to minimize adverse effects during ex vivo studies of stem cells and cell death in planarians.

The history and enduring contributions of planarians to the study of animal regeneration

Having an almost unlimited capacity to regenerate tissues lost to age and injury, planarians have long fascinated naturalists. In the Western hemisphere alone, their documented history spans more than 200 years. Planarians were described in the early 19th century as being 'immortal under the edge of the knife', and initial investigation of these remarkable animals was significantly influenced by studies of regeneration in other organisms and from the flourishing field of experimental embryology in the late 19th and early 20th centuries. This review strives to place the study of planarian regeneration into a broader historical context by focusing on the significance and evolution of knowledge in this field. It also synthesizes our current molecular understanding of the mechanisms of planarian regeneration uncovered since this animal's relatively recent entrance into the molecular-genetic age.

FACS analysis of the planarian stem cell compartment as a tool to understand regenerative mechanisms

Planarians provide a relatively simple model system in which to study stem cell dynamics and regenerative phenomena. As with other systems understanding the dynamics of stem cell and stem cell progeny is crucial in order to get at the molecular mechanisms orchestrating stem cell biology. Planarians have an abundant adult stem cell population that can be observed using Fluorescence-Activated Cell Sorting (FACS). This approach allows different subpopulations of stem cells and their progeny to be monitored and sorted for downstream studies in response to different regenerative scenarios, drug treatments, or RNAi knockdown of genes required for regenerative events.

Study of planarian stem cell proliferation by means of flow cytometry

The stem cells in freshwater flatworms (planarian) are called neoblasts. Neoblasts are capable of proliferation and differentiation into every cell type, including the gametes. For the investigation of the mechanisms of stem cells proliferation and differentiation the proper evaluation of changes in the cell cycle of neoblasts in different physiological conditions of planarian is necessary. In the present study the possibility of qualitative and quantitative characteristics of the neoblasts population were investigated using flow cytometry. In the cell suspension prepared from planarian tissue proliferating neoblasts have been observed in heterogenic cell population. Quantitative estimation of the cell cycle related changes of planarian stem cells system have been performed in various physiological conditions (intact and regenerating animals) and under the influence of physical (ionizing radiation) and chemical (melatonin and colchicine) factors. The modified protocol for planarian stem cells isolation proved to be effective and reproducible and can be recommended for flow cytometry analyses of human and animal proliferating cells.

Brain regeneration from pluripotent stem cells in planarian

How can planarians regenerate their brain? Recently we have identified many genes critical for this process. Brain regeneration can be divided into five steps: (1) anterior blastema formation, (2) brain rudiment formation, (3) pattern formation, (4) neural network formation, and (5) functional recovery. Here we will describe the structure and process of regeneration of the planarian brain in the first part, and then introduce genes involved in brain regeneration in the second part. Especially, we will speculate about molecular events during the early steps of brain regeneration in this review. The finding providing the greatest insight thus far is the discovery of the nou-darake (ndk; 'brains everywhere' in Japanese) gene, since brain neurons are formed throughout the entire body as a result of loss of function of the ndk gene. This finding provides a clue for elucidating the molecular and cellular mechanisms underlying brain regeneration. Here we describe the molecular action of the nou-darake gene and propose a new model to explain brain regeneration and restriction in the head region of the planarians.

Regenerating the central nervous system: how easy for planarians!

The regenerative capabilities of freshwater planarians (Platyhelminthes) are very difficult to match. A fragment as tiny as 1/279th of the planarian body is able to regenerate a whole animal within very few days [Morgan. Arch Entwm 7:364-397 (1898)]. Although the planarian central nervous system (CNS) may appear quite morphologically simple, recent studies have shown it to be more complex at the molecular level, revealing a high degree of molecular compartmentalization in planarian cephalic ganglia. Planarian neural genes include homologues of well-known transcription factors and genes involved in human diseases, neurotransmission, axon guidance, signaling pathways, and RNA metabolism. The availability of hundreds of genes expressed in planarian neurons coupled with the ability to silence them through the use of RNA interference makes it possible to start unraveling the molecular mechanisms underlying CNS regeneration. In this review, I discuss current knowledge on the planarian nervous system and the genes involved in its regeneration, and I discuss some of the important questions that remain to be answered.

Characterization and categorization of fluorescence activated cell sorted planarian stem cells by ultrastructural analysis

Planarians have regenerative ability made possible by pluripotent stem cells referred to as neoblasts. Classical ultrastructural studies have indicated that stem cells can be distinguished by a unique cytoplasmic structure known as the chromatoid body and their undifferentiated features, and they are specifically eliminated by X-ray irradiation. Recently, by using fluorescence activated cell sorting (FACS), planarian cells were separated into two X-ray-sensitive fractions (X1 and X2) and an X-ray-insensitive fraction (XIS) according to DNA content and cytoplasmic size. Here we analyzed the fractionated cells by transmission electron microscopy (TEM). First, we found that both undifferentiated cells (stem cells) and regenerative cells (differentiating cells) were concentrated in the X1 fraction containing the S/G2/M phase cells. The regenerative cells were considered to be committed stem cells or progenitor cells, suggesting that some stem cells may maintain proliferative ability even after cell fate-commitment. Second, we succeeded in identifying a new type of stem cells, which were small in size with few chromatoid bodies and a heterochromatin-rich nucleus. Interestingly, they were concentrated in the X2 fraction, containing G0/G1 phase cells. These results suggest that planarian stem cells are not homogeneous, but may consist of heterogeneous populations, like mammalian stem cells.

Clathrin-mediated endocytic signals are required for the regeneration of,as well as homeostasis in, the planarian CNS

Planarians have a well-organized central nervous system (CNS), including a brain, and can regenerate the CNS from almost any portion of the body using pluripotent stem cells. In this study, to identify genes required for CNS regeneration, genes expressed in the regenerating CNS were systematically cloned and subjected to functional analysis. RNA interference (RNAi) of the planarian clathrin heavy chain (DjCHC) gene prevented CNS regeneration in the intermediate stage of regeneration prior to neural circuit formation. To analyze DjCHC gene function at the cellular level, we developed a functional analysis method using primary cultures of planarian neurons purified by fluorescence-activated cell sorting (FACS) after RNAi treatment. Using this method, we showed that the DjCHC gene was not essential for neural differentiation, but was required for neurite extension and maintenance, and that DjCHC-RNAi-treated neurons entered a TUNEL-positive apoptotic state. DjCHC-RNAi-treated uncut planarians showed brain atrophy, and the DjCHC-RNAi planarian phenotype was mimicked by RNAi-treated planarians of the mu-2 (μ2)gene, which is involved in endocytosis, but not the mu-1(μ1) gene, which is involved in exocytosis. Thus,clathrin-mediated endocytic signals may be required for not only maintenance of neurons after synaptic formation, but also axonal extension at the early stage of neural differentiation.

Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting

The remarkable capability of planarian regeneration is mediated by a group of adult stem cells referred to as neoblasts. Although these cells possess many unique cytological characteristics (e.g. they are X-ray sensitive and contain chromatoid bodies), it has been difficult to isolate them after cell dissociation. This is one of the major reasons why planarian regenerative mechanisms have remained elusive for a long time. Here, we describe a new method to isolate the planarian adult stem cells as X-ray-sensitive cell populations by fluorescence-activated cell sorting (FACS). Dissociated cells from whole planarians were labeled with fluorescent dyes prior to fractionation by FACS. We compared the FACS profiles from X-ray-irradiated and non-irradiated planarians, and thereby found two cell fractions which contained X-ray-sensitive cells. These fractions, designated X1 and X2, were subjected to electron microscopic morphological analysis. We concluded that X-ray-sensitive cells in both fractions possessed typical stem cell morphology: an ovoid shape with a large nucleus and scant cytoplasm, and chromatoid bodies in the cytoplasm. This method of isolating X-ray-sensitive cells using FACS may provide a key tool for advancing our understanding of the stem cell system in planarians.

SMEDWI-2 Is a PIWI-Like Protein That Regulates Planarian Stem Cells

We have identified two genes, smedwi-1 and smedwi-2, expressed in the dividing adult stem cells (neoblasts) of the planarian Schmidtea mediterranea. Both genes encode proteins that belong to the Argonaute/PIWI protein family and that share highest homology with those proteins defined by Drosophila PIWI. RNA interference (RNAi) of smedwi-2 blocks regeneration, even though neoblasts are present, irradiation-sensitive, and capable of proliferating in response to wounding; smedwi-2(RNAi) neoblast progeny migrate to sites of cell turnover but, unlike normal cells, fail at replacing aged tissue. We suggest that SMEDWI-2 functions within dividing neoblasts to support the generation of cells that promote regeneration and homeostasis.

DjPum, a homologue of Drosophila Pumilio, is essential to planarian stem cell maintenance

As stem cells are rare and difficult to study in vivo in adults, the use of classical models of regeneration to address fundamental aspects of the stem cell biology is emerging. Planarian regeneration, which is based upon totipotent stem cells present in the adult--the so-called neoblasts--provides a unique opportunity to study in vivo the molecular program that defines a stem cell. The choice of a stem cell to self-renew or differentiate involves regulatory molecules that also operate as translational repressors, such as members of PUF proteins. In this study, we identified a homologue of the Drosophila PUF gene Pumilio (DjPum) in the planarian Dugesia japonica, with an expression pattern preferentially restricted to neoblasts. Through RNA interference (RNAi), we demonstrate that gene silencing of DjPum dramatically reduces the number of neoblasts, thus supporting the intriguing hypothesis that stem cell maintenance may be an ancestral function of PUF proteins.

Detection of apoptosis during planarian regeneration by the expression of apoptosis-related genes and TUNEL assay

Apoptosis is a tightly organized cell death process that plays a crucial role in metazoan development, but it has not yet been revealed whether apoptotic events are involved in the process of regeneration. Here, we tried to detect apoptotic cells during planarian regeneration using the TdT-mediated dUTP nick-end labeling (TUNEL) assay as well as the expression of apoptosis-related genes. Three novel cDNAs were isolated from a planarian cDNA library and shown to be closely related to other metazoan caspases at the amino acid sequence level. One of these cDNAs, Caspase-like gene 3 (DjClg3), was expressed primarily in apoptotic cells by double detections with the TUNEL assay. Whole mount in situ studies indicated that DjClg3 was expressed in the cells of the mesenchymal space and also around the pharynx of the intact body. Its expression in the regenerating head piece was seen in the blastema and less significantly in the brain, while in the regenerating tail piece, DjClg3 expression was detected uniformly throughout the entire region. In parallel experiments, we performed in situ TUNEL assays to localize the regions where cell death occurred during regeneration and comparable results to the DjClg3 expression patterns were obtained. This is the first report to show that planarians have apoptosis-related genes and the results suggest that the apoptotic mechanism probably takes place to a large extent in normal intact worms as well as during their regeneration. We hypothesize that the presence of apoptosis in planarians may have a role in controlling cell numbers, eliminating unnecessary tissues or cells and remodeling the old tissues of regenerating body parts.

Regeneration and gene regulation in planarians

Planarians can regenerate using a pluripotent stem cell system. This phenomenon provides a unique opportunity to understand gene regulation in the process of differentiation from pluripotent stem cells. Recent studies have made significant advances in our understanding of the pluripotent stem cell system in this model. In particular, a gene knockdown method by RNA interference enabled great progress in identifying genes involved in regeneration and stem cell regulation.