MEETING REVIEW

The stem cell niche finds its true northAgnete Kirkeby1,*, Thomas Perlmann2,* and Carlos-Filipe Pereira3,*

ABSTRACTThe third ‘Stem Cell Niche’ meeting, supported by The Novo NordiskFoundation, was held this year on May 22-26 and brought together185 selected participants from 24 different countries to Hillerød,Denmark. Diverse aspects of embryonic and adult stem cell biologywere discussed, including their respective niches in ageing, diseaseand regeneration. Many presentations focused on emergingtechnologies, including single-cell analysis, in vitro organogenesisand direct reprogramming. Here, we summarize the data presented atthis exciting and highly enjoyable meeting, where speakers as well askitchen chefs were applauded at every session.

KEY WORDS: Stem cell, Niche, Single cell, Organoid,Reprogramming, Pluripotency

IntroductionThis year, on May 22-26, the Novo Nordisk Foundation hosted itsthird Stem Cell Niche meeting at the beautiful Favrholm campus inHillerød (Denmark) as part of the Copenhagen BioscienceConference series. Once again, the organizers succeeded increating a unique experience involving top quality science,gourmet Nordic food, beautiful surroundings and an amazingsightseeing tour of Copenhagen. All of this contributed to creatingan extremely pleasant atmosphere that stimulated constantinteraction, mingling and scientific networking between thespeakers and meeting participants, including via social media (seeBox 1). The scientific content of the meeting was organized byAnne Grapin-Botton, Joshua Brickman, Kristian Helin, Palle Serupand Elisabetta Ferretti from the Danish Stem Cell Centre at theUniversity of Copenhagen, and the programme covered almost allaspects of stem cell biology, from pluripotency, epigenetics andsingle-cell transcriptome analysis to directed differentiation, in vitroorganogenesis and translational research. The thread that tied allthese topics together was the very high quality of the science, and inthis Meeting review, we summarize some of the work presented.The scientific part of the meeting got underway with a captivating

talk by Rudolf Jaenisch (Whitehead Institute, MA, USA), whopresented the work of his lab in generating naïve human pluripotentstem cells (hPSCs), with the aim of using these to generate mouse-human chimeric embryos. The group had previously identifiedchemically defined culture conditions for the induction andmaintenance of naïve hPSCs (Theunissen et al., 2014); however,when injecting these cells into the mouse blastocyst, the efficiencyof chimera formation was <0.01%, and in these embryos, the human

cells accounted for <0.001% of all cells. Jaenisch further presentedhis group’s efforts to create neural crest chimeras through in uteroinjection of hPSC-derived neural crest cells into the amniotic sac ofE8.5 mice. Although the efficiency of chimera formation was 30-40%, the human cell contribution to neural crest lineages was<0.1%. Jaenisch therefore concluded that human-mouse chimeraformation was likely to be hampered by basic biological differencesbetween the species. Finally, Jaenisch presented an intriguingcortical organoid model revealing in vitro induction of neuralconvolution in PTEN mutant hiPSCs. Interestingly, neuralconvolution was not observed in corresponding mouse organoids,indicating that this model can be used to study anatomical speciesdifferences in brain development.

Understanding and mimicking the nicheThe warm pre-summer Danish weather and a beautiful setting atFavrholm campus provided a stimulating ‘niche’ for meetingparticipants. Similarly, the niche where stem cells reside has aprofound influence over cell fate and behaviour. Studying the nicheinvolves careful examination of multiple components, including thedifferent types of neighbouring cells and the signals from them tothe stem cells. Perhaps the best-characterized stem cell niche is thatof the bone marrow. Sean Morrison (University of TexasSouthwestern, USA) discussed niches of the bone marrow, andusing deep imaging and 3D reconstruction showed that bothdividing and non-diving haematopoietic stem cells (HSCs) reside inperivascular niches created by endothelial and perivascular stromalcells (leptin receptor positive, LEPR+), which were associatedmainly with sinusoidal blood vessels (Acar et al., 2015). Morrisonfurther showed that LEPR+ cells are the major source of osteoblastsand fat cells in adult bone marrow, as well as cartilage formed afterfractures. Conditional deletion of Lepr decreased adipogenesis andincreased osteogenesis in limb bones. He suggested that LEPR+

cells act as a diet/adiposity sensor in the bone marrow to promote theformation of fat at the expense of bone. Interestingly, Clec11a, aprotein expressed by a subset of LEPR+ cells, was found to promoteosteogenesis in vitro and in vivo, thereby constituting a promisingnew therapeutic target for osteoporosis treatment.

Simón Méndez-Ferrer (Cambridge Stem Cell Institute, UK)added to discussions of the complexity of the bone marrow niche bypresenting evidence of how autonomic sympathetic nerve fibresactivate and regulate HSCs in the bone marrow to induce circadianrhythms in HSC mobilization. Mendez-Ferrer hypothesized that thesympathetic nerve terminals mediate their effect through directactivation of Nestin+ mesenchymal stem cells (MSCs) in the bonemarrow to regulate the niche environment. This, in turn, mayexplain why some leukaemias cause neuropathy and apoptosis ofMSCs in the bone marrow, and may constitute a mechanism bywhich leukaemia cells can escape the niche. Protecting the HSCniche might therefore represent a novel complementary strategy formyeloproliferative neoplasms. Also in the context of blood cancers,Emanuelle Passegué (University of California, USA) introduced theconcept of ‘emergency myelopoiesis pathways’ in the bone marrow.

1Human Neural Development, Department of Experimental Medical Science, LundUniversity, Lund 22184, Sweden. 2The Ludwig Institute, Department of Cell andMolecular Biology, Karolinska Institutet, Stockholm 17177, Sweden. 3CNC, Centrefor Neuroscience and Cell Biology, University of Coimbra, Coimbra 3004-517,Portugal.

*Authors for correspondence (agnete.kirkeby@med.lu.se;thomas.perlmann@ki.se; filipe.pereira@uc-biotech.pt)

C.-F.P., 0000-0002-9724-1382

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She showed that during blood regeneration, HSCs are induced tooverproduce myeloid-biased multipotent progenitors (Pietras et al.,2015). An important consequence of the activation of this myeloidregeneration axis is the formation of defined granulocyte/macrophage progenitor clusters in the bone marrow cavity, whichdrive the local overproduction of granulocytes. The remodelling ofthe multipotent progenitor compartment and the induction ofclusters represent novel emergency myelopoiesis pathways that aretransiently activated during regeneration and are continuouslytriggered in disease conditions. In leukaemia, the constantproduction of myeloid progenitor clusters directly contributes tomyeloid disease burden and could become a key target for anti-HSCdifferentiation therapies.Beyond the blood, Shosei Yoshida (National Institute for Basic

Biology, Japan) introduced the intriguing concept of an open stemcell niche in the mammalian testis. Taking advantage of intravitallive-imaging, Yoshida showed how spermatogenic stem cells in theseminiferous tubules are not confined to a certain anatomical space.Rather, stem cells are instead highly motile between differentiatingprogenies and somatic supporting cells, and scatter along the tubulesat a constant density. Yoshida presented convincing evidence thatthe mechanism behind this density-dependent open niche liesin competition for a finite supply of mitogens between thespermatogenic stem cells. Moving to the lung, Joo-Hyeon Lee(Cambridge Stem Cell Institute, UK) showed that stromal cells arerequired for the formation of lung organoids that are derived fromadult distal epithelial stem or progenitor cells in vitro. Clonal three-dimensional (3D) co-culture of lung epithelial stem cells withendothelial cells revealed heterotypic organoids that retain multi-lineage differentiated cells. Of note, branching organoids are closelyassociated with endothelial cells that are actively engagedin vascular tube formation. In addition, Lee also showed thatLGR6-expressing peri-airway mesenchymal cells serve as a ‘niche’

for the club cells, which have previously been suggested to have theproperties of lung stem cells. Isolated club cells and LGR6+ cellswere sufficient to form lung organoids in culture, but the precise roleof the LGR6+ cell type within the lung stem cell niche has not yetbeen defined. Extending the theme of 3D tissue reconstructionin vitro, Agnete Kirkeby (Lund University, Sweden) presented analternative approach to the organoid models, namely a microfluidicgradient system for producing controlled rostro-caudal patterning ofneural cells derived from hPSCs. In this system, hPSCs weredifferentiated to produce a single piece of tissue comprisingforebrain, midbrain and hindbrain cells located in a spatially orderedmanner, thereby mimicking the rostro-caudal patterning of the earlyneural tube. Kirkeby further showed how the system could be usedto assess region-specific responses of neural cells to genes andgrowth factors.

The various signals that derive from the niche may be interpreteddifferently by different types of stem cells. This was the take-homemessage of the work presented by Michael Elowitz (Caltech, CA,USA), who discussed the challenge of synthetic circuit design inmulticellular organisms using signalling integration in the bonemorphogenetic protein (BMP) pathway as a model. The BMPpathway has 20 different ligands and numerous receptors that caninteract in a ‘many-to-many’ fashion. Using a BMP reporter cell lineand testing combinations of ligands, Elowitz showed that the effectof each ligand generally depends on the level of other ligands andthat receptor expression can ‘reprogram’ ligand interaction modes.Elowitz presented a mathematical model to enable the analysis ofsuch promiscuous ligand-receptor interactions, which may open upmore sophisticated strategies to understand and re-engineer complexligand-signalling modes in the niche. Continuing the theme of BMPsignalling, a short talk by Alison McGarvey from AlexanderMedvinsky’s group (MRC Centre for Regenerative Medicine, UK)outlined a transcriptomic approach to elucidate niche regulators ofHSC emergence from the embryonic aorta-gonad-mesonephrosregion. By coupling gene expression signatures with an ex-vivo re-aggregate culture followed by transplantation, McGarvey identifieda novel candidate that increases the efficiency of HSC maturationfrom their direct precursors. She proposed that through its action as amodulator of BMP signalling, it supports the maturation of HSCs byfine-tuning the level of BMP signalling in the niche.

Deconstructing the niche at the single-cell levelCopenhagen is a city that maintains its historic charm whilst at thesame time undergoing rapid development. An evening boat tourprovided the opportunity for participants to witness this first hand,cruising the ancient canals whilst surveying the exciting progressbeing made throughout the city. Rapid progress was also evidentfrom talks that utilized research tools for single-cell analysis.Methods for genome-wide RNA sequencing of single cells havebeen well established for several years, but a remaining challengehas been to retrieve spatial information in single-cell RNA-seq datasets. With this in mind, Alexander van Oudenaarden (HubrechtInstitute, The Netherlands) described a strategy whereby bonemarrow cells were incompletely dissociated, allowing cell duplets tobe separately isolated. Single cells were then manually dissociatedand sequenced, allowing information on cell-cell interactions to betraced in the data. This method revealed close interactions betweenneutrophil and megakaryocyte lineages, and this partnership isbelieved to influence cell maturation. Future robust strategies forhigh-throughput isolation of cell duplets followed by single-cellRNA sequencing may therefore serve to retrieve importantinformation of key spatial interactions between cells within a

Box 1. A selection of tweets from the Danish Stem CellNiche (#SCNiche2016)Meral Ilcim Özlü @ilcim_ozlu#SCNiche2016 happening at this beautiful #NovoNordiskFondencampusWalter de Back @wdebackRudolph Jaenisch shows cool use of organoids of human cerebral tissueto study CNS devel. #SCNiche2016Caroline Hendry @CE_HendryShosei Yoshida gives us a cool cow grazing analogy for open v closedstem cell niches - plus a highly entertaining talk too! #SCNiche2016Caroline Hendry @CE_HendrySingle cell tour-de-force in the early mouse embryo from KatHadjantonakis at #SCNiche2016 The regulatory plot thickens…Josh Brickman @josh_brickmanFantastic talk-Allan Spradling: Reversible/functional polyploidy, repair/homeostasis: #SCNiche2016. Diploid parent as #stemcells for polyoidJosh Brickman @josh_brickman#SCNiche2016 - Just finished metabolism/stem cells round table. Agreat innovation, a one hour conversation creating new long term links!Domingos Henrique @domhenri55#SCNiche2016 nice talk from Sally Lowell on the predictive power of Id1expression and cell morphology on the commitment status of ES cellsCaroline Hendry @CE_Hendry@Dev_journal Editor Gordon Keller v epigenetics heavyweight RickYoung at the #SCNiche2016 PI Pub. Fun times!!Harry Leitch @HGLeitchLast man standing at #SCNiche2016 (+@ANTS_ally !). Great job@josh_brickman, brilliant conf

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given niche. Staying in the bone marrow, Franziska Paul(Weizmann Institute, Israel) discussed recent progress in usingsingle-cell RNA-seq to profile myeloid progenitor cells from themurine bone marrow (Paul et al., 2015). Surprisingly, Paul andcolleagues found that there does not seem to be a common myeloidprogenitor population in the bone marrow. Instead, the progenitorpopulation was highly heterogeneous and could be grouped into 19progenitor subgroups that showed unexpected transcriptionalpriming toward seven different cell lineages: erythrocytes,megakaryocytes, monocytes, dendritic cells, neutrophils,basophils and eosinophils.Continuing the theme of single-cell analyses, Thomas Perlmann

(Karolinska Institutet, Sweden) showed how single-cell RNA-seqcan be used to reconstruct lineage development in the centralnervous system at the genome-wide level. The focus was ondeveloping dopamine neurons, which degenerate in Parkinson’sdisease and are therefore of major interest for potential stem cell-based therapies. Perlmann’s results uncover an unexpectedly closelineage relationship between developing dopamine neurons andmore rostral non-dopaminergic neurons. The talk also illustrated theimportance of combining developmental biology and stem cellbiology for clinical translation.Kat Hadjantonakis (Sloan Kettering Institute, NY, USA)

presented her group’s efforts to use quantitative single-cell-resolution imaging of the developing mouse blastocyst in order topinpoint the very first molecular changes that take place in the innercell mass (ICM), which ultimately lead to cell fate segregation intoeither primitive endoderm or the pluripotent epiblast. Combinedwith single-cell transcriptomics, Hadjantonakis showed howlineage segregation is incremental and demonstrated that FGF4 isthe only factor showing differential expression in the ICM cellsprior to lineage segregation. She also showed that the combinatorialactivity of FGFR1 and FGFR2 was essential for these early embryofate decisions. Still in the embryo, Angela Stathopoulos (Caltech,CA, USA) used sophisticated tools to follow the dynamictranscription factor behaviour that governs the patterning of therapidly dividing Drosophila embryo. By following gene expressionof dorsal, a transcription factor expressed in a dorsal-ventral nucleargradient, Stathopoulos described how oscillations drive the step-wise progression of early development. Interestingly, she showedhow the dorso-ventral boundaries of the embryo shift up and downas development progressed. A particularly crucial moment in thedevelopment of the embryo was found to occur at mitotic cycle no.13, where expression of key signalling pathway components isinitiated and required to support proper gene regulatory networkprogression.

The epigenetic ‘niche’ of pluripotency and reprogrammingArchitecture and design play an important role in shaping our world:not just in the biological sense but culturally too. A memorable visitto the Copenhagen Opera House, designed by the renownedarchitect Henning Larsen, solidified this point. Meeting participantslistened with fascination as staff described how both the site of theopera house and the building itself were meticulously designed tomaximize the geographic and artistic impact of this masterpiece ofDanish design, superbly located just opposite Amalienborg castle.The architecture and control of stem cell chromatin was also afascinating subject discussed by several speakers. Rick Young(Whitehead Institute, MA, USA) introduced the concept of‘insulated neighbourhoods’: loop structures in the DNA formedby nested protein complexes of the CCCTC-binding factor CTCF,which forms boundaries around important enhancer-promoter

regions that are necessary for gene control. He showed howCRISPR/Cas9 deletion of CTCF-binding sites altered theexpression of local genes and lead to new topological interactions.Moreover, Young showedmapping data of insulated neighborhoodsin T-cell acute lymphoblastic leukaemia and described how tumourcell genomes contain recurrent microdeletions that eliminate theCTCF boundary sites (Hnisz et al., 2016). Directed perturbation ofsuch boundaries near the TAL1 and LMO2 genes in non-malignantcells was sufficient to activate these proto-oncogenes. Theidentification of these genomic anchors may be important for theinterpretation of genome-wide association studies in cancer.

Ken Zaret (University of Pennsylvania School of Medicine,USA) stressed the importance of understanding how transcriptionfactors access and bind to chromatin. So-called pioneer factors canbind to unprogrammed chromatin – chromatin that is unmarked foractivation or repression – yet there remain heterochromatic regionsnot accessible to pioneer factors. Zaret showed that these regions,which are marked by H3K9me3, represent an impediment totranscription factor-based reprogramming. Mapping of H3K9me3domains throughout development showed unexpectedly highlevels in germ layer cells and a marked diminution duringterminal differentiation. Zaret proposed that the high levels ofheterochromatin in early endoderm and mesoderm germ layerscreate less chromatin that is available to scan, which would allowrelatively fast cell programming in the embryo. Using sucrosegradients coupled with quantitative proteomics, heterochromatinproteins that may impede gene activation were identified. Knockingdown these proteins may represent a way to safely break downheterochromatin to increase reprogramming efficiency.

Achieving reprogramming through the use of small moleculardrugs rather than by conventional reprogramming factors is a majorfocus of Hongkui Deng (Peking University, China), and hepresented an overview of their work to generate iPSCs (Zhaoet al., 2015) and induced neurons via a purely chemical approach.Deng showed how the compound I-BET151, which is used inchemical reprogramming to induce efficient neuronaltransdifferentiation, works by repressing the core fibroblasttranscription programs, potentially through blocking of super-enhancer-driven transcription. Only a few hours of incubation withI-BET151 is required to significantly downregulate the fibroblastcore transcriptional network, which may prove to be a usefulstrategy to enhance all lineage conversions from a fibroblast startingpopulation. In a different direct reprogramming approach, KiranBatta from Georges Lacaud’s group (CRUK Manchester Institute,UK) reported the identification of five transcription factors requiredfor reprogramming of mouse and human dermal fibroblasts tohaematopoietic progenitors. Batta showed that co-culturing thereprogrammed progenitor cells with endothelial cells led tolong-term multilineage potential in vivo, suggesting that theendothelial niche cells protected the progenitors against cell deathand differentiation induced by oxidative stress. Turning thesystem upside down, Carlos-Filipe Pereira (University ofCoimbra, Portugal) showed how information acquired duringhaematopoietic reprogramming informed the complex process ofHSC specification during development. The analysis of inducedhaemogenic cells from fibroblasts revealed a phenotype that couldbe used to isolate precursors of HSCs in vivo from mid-gestationmouse placentas. These early precursor cells of haematopoiesiswere characterized by single-cell RNA-seq and matured in vitro intoHSCs.

Maintaining pluripotency for the correct period of time in vivo isessential for embryonic development, and significant progress has

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been made towards understanding how this is regulated at themolecular and biophysical level. Sally Lowell (University ofEdinburgh, UK) presented convincing evidence that ID1 makesNanoglow cells resistant to differentiation and thereby functions as asafeguard for pluripotency during the transition from naïve toprimed states. Furthermore, Lowell emphasized that tissueorganisation is not just a passive consequence of differentiationbut that it actively feeds back into the decision-making process. Byusing a novel 3D-imaging and data interrogation tool, Lowellshowed how her group is able to track the orientation of celldivisions in the early embryo, and how they use this to study theinterplay between tissue organization and differentiationcompetence. Another safeguard for maintaining pluripotency waspresented by Pablo Navarro (Institute Pasteur, France), whodiscussed the ‘bookmarking’ properties of the transcription factorESRRB, which is an important regulator of pluripotency andreprogramming. Navarro showed that ESRRB binds and coatschromosomes during mitosis – both in PSCs and in the embryo –and that this ESRRB coating might be necessary for themaintenance of epigenetic marks within the daughter cells. Thesedata demonstrated the importance of transcription factorbookmarking to help the transcriptional machinery to perpetuatestem cell fate throughout cell division.

Towards the clinic: stem cells to understand ageing andregenerationOne of the main goals of the stem cell field is to improve healthoutcomes in ageing and disease. Various approaches have beentaken to achieve this, ranging from the use of stem cell-basedmodels of disease to the use of stem cells for cell-based therapies.But in order to accurately model adult diseases or to provide adultcell types, it is absolutely crucial to develop highly specificdifferentiation protocols, not just for one cell type, but potentiallyfor the whole organ. To this end, Gordon Keller (McEwen Centrefor Regenerative Medicine, Canada) presented an impressive tour-de-force in controlling accurate differentiation of hPSCs intopopulations of all the various subtypes of cells in the heart. Heshowed that conventional protocols give rise to mainly ventricularcardiomyocytes intermingled with a smaller population ofpacemaker cells. Addition of retinoic acid shifted cell fate towardsan atrial phenotype. In contrast, activation of the WNT pathway incombination with the BMP pathway was able to shift myocardialcells towards epicardium, while the production of the endocardiumwas still being optimized. Keller and his group were able to purifyand transplant human hPSC-derived pacemaker cells into the ratheart, and upon subsequently lowering the rat heartbeat, theectopically placed human pacemaker cells were able to takecontrol of the heartbeat, thereby demonstrating full in vivofunctionality.Another way to generate mature cell types for translational

research is via direct cell fate reprogramming, also known as lineagereprogramming. To this end, Oliver Brüstle (University of Bonn,Germany) reported on his group’s latest developments using thismethod. They have been able to generate distinct neural stem cellpopulations with defined neuronal and glial differentiationpropensities, and have used this to model late-onsetneurodegenerative disease. Combined with in vitro calibration ofproteostatic pathways, this approach enables highly standardizedphenotypic assays, for example, the assessment of pathologicalprotein aggregation in polyglutamine diseases. Brüstle alsodemonstrated how trans-synaptic rabies virus-based tracingcombined with light sheet microscopy could enable in vivo

connectome studies of grafted hPSC-derived neurons in a whole-brain scenario.

PSC-based approaches are now integral to our understanding ofdisease and represent a theoretically infinite source of cells withwhich to treat it. But not all disease scenarios require PSC-basedtherapies. Adult tissue-residing stem cells – in the skin and eye, forexample, and in various internal organs such as the intestine – arealso critical for homeostasis and for understanding disease. PalomaOrdóñez from Joerg Huelsken’s group (École PolytechniqueFéderale de Lausanne, Switzerland) identified HOXA5 as animportant repressor of intestinal stem cell fate in vivo. HOXA5 isdownregulated by the WNT pathway to maintain stemness andbecomes active only when cells leave the intestinal crypt andundergo differentiation (Ordóñez-Morán et al., 2015). In support ofthis, she showed how HOXA5 expression reduces intestinal LGR5+

stem cells and that intestinal organoids lose the potential to bepassaged. In colon cancer, HOXA5 is downregulated and its re-expression induces the loss of the cancer cell phenotype, preventingtumour progression and metastasis. Ordóñez also showed howretinoids could induce HOXA5 upregulation and block tumourgrowth, opening the way for possible retinoid therapy for coloncancer.

In a different adult stem cell-based system, this time in the eye,Graziella Pellegrini (University of Modena, Italy) presented herdecade-long efforts to produce a treatment for patients withimpaired vision caused by damage to the cornea. Transplantationof autologous, cultured limbal stem cells has been shown to causesignificant and long-term clinical benefits on vision in transplantedpatients (Rama et al., 2010). Now, Pellegrini has embarked on amission to treat not only superficial corneal damage, but alsodeeper lesions of the eye. Pellegrini showed their progress indesigning physiologically relevant extracellular matrix scaffolds oforthogonally located layers of biopolymers. Although they havenow succeeded in producing scaffolds with optimized rigidity and

Theniche

Reconstructingthe niche

Deconstructingthe niche

Understandingthe niche

Using theniche

Epigenetics and chromatin Super-enhancers Insulated neighbourhoods Fate choices

Clinical transplantationCancer therapyOsteoporosis therapy

Organoids

ReprogrammingDirect differentiation

Disease modelling

Single-cell RNA-seqCell-cell interactionsLineage segregation

Fig. 1. Ways around the niche. The topics at the meeting revolved aroundunderstanding the stem cell niche at different levels and with different methods.

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stiffness, some work still remains to render the scaffolds ideal forcell adhesion and differentiation. Finally, in the skin, ValentinaGreco’s talk (Yale University, CT, USA) was a beautiful example ofhow powerful live-imaging techniques can expose well-kept stemcell secrets. In her lab, two-photon microscopy is used in liveimaging of the mouse hair follicle. By combining imaging withtransgenic reporters and functional genetics, she showed how theskin stem cell niche has the potential to eliminate mutant cells withdefects that otherwise would have tumorigenic potential.Understanding the mechanistic basis of this method of diseaseprevention may bring insight into possible targets for skin cancertherapies.Generally speaking, mammalian species do not compare well

with non-mammalian models in terms of their capacity to regenerateand much can be learned from the latter. Brigitte Galliot (Universityof Geneva, Switzerland) introduced the model organism Hydra,which can be used to study regeneration and ageing. It is impressivethat the freshwater Hydra vulgaris polyps can regenerate anymissing body part – even from cellular aggregates. Usingtranscriptomic analysis, she showed that epithelial cells adapt tothe loss of interstitial stem cells and neurogenesis by upregulating alarge subset of neurogenic genes (Wenger et al., 2016). In contrast,epithelial cells in the cold-sensitive strain of Hydra oligactis lackthis adaptive plasticity, as a result of deficient autophagy, therebyproviding a model where epithelial autophagy appears to supportstem cell self-renewal as an anti-ageing mechanism. In a differentmodel organism, this time the fly, Allan Spradling (CarnegieInstitution, MD) described an unexpected, alternative source of cellreplacement by wound-induced polyploidization in Drosophila.Following wounding, the cells that surround the injury site do notdivide, but instead become polyploid, that is, they increase theirchromosomal number. Interestingly, Hippo signalling controlspolyploidization and inversely JNK signalling through AP-1limits it. Spradling showed how the induction of polyploidyoccurs also during wounding of the mouse corneal endothelium andsuggested that the large size and aneuploidy tolerance of polyploidcells represents an evolutionarily conserved mechanism and mayprovide advantages over diploid cells to maintain homeostasis.

ConclusionsJust like the orchestra at the Copenhagen Opera House, the multiplelevels of regulation and components of the stem cell niche is anensemble that needs to be regulated in order to balance stem cellself-renewal and differentiation. It was clear from the 12 sessionsthat unlocking the fundamental mechanisms and therapeuticpotential of stem cells and their particular niches will continue tobe a major focus of stem cell biology. Efforts to deconstruct andreconstruct the niche with emerging technologies are providing newinformation to help understand niche composition and function, andfurther highlight potential pathways for therapeutic manipulation(Fig. 1).In addition to the inspiring talks, the poster sessions were also

remarkable. Of the 134 posters, the two poster prize winners were

Birgit Ritschka (Center for Genomic Regulation, Spain) with herposter entitled ‘Senescence is a regenerative process that instructsstem cell function’ and Jakub Sedzinski (University of Texas, USA)with his poster entitled ‘How to fit in? Emergence of an apicalepithelial surface in vivo’. After four days of lively discussion, themeeting themewas a well-placed reminder that it was indeed time toreturn to our own familiar laboratory ‘niche’, hopefully to generatenew and interesting data in preparation for the next Stem Cell Nichemeeting in two years’ time.

AcknowledgementsWe thank the organizers for a stimulating scientific programme, the speakers forsharing unpublished work, and the Novo Nordisk Foundation staff for their excellentservices. We apologize to the speakers whose work we were unable to discuss dueto space restrictions. We thank Sally Lowell and Guillaume Blin (University ofEdinburgh) for kindly sharing images and Fabio Rosa (University of Coimbra) forassistance with figure preparation.

Competing interestsThe authors declare no competing or financial interests.

FundingC.F.-P. is supported by Fundaça o para a Cie ncia e Tecnologia (FCT, Portugal)[PTDC/BIM-MED/0075/2014]. T.P. is supported by the Knut och Alice WallenbergsStiftelse and the Swedish Strategic Research Foundation. A.K. is supported by theSwedish Research Council [70862601/Bagadilico] and the European Commission(7th Framework Programme/ 602278/NeuroStemcellRepair).

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