Opportunities for organoids as new models of aging.

The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research

Culture and establishment of self-renewing human and mouse adult liver and pancreas 3D organoids and their genetic manipulation.

Adult somatic tissues have proven difficult to expand in vitro, largely because of the complexity of recreating appropriate environmental signals in culture. We have overcome this problem recently and developed culture conditions for adult stem cells that allow the long-term expansion of adult primary tissues from small intestine, stomach, liver and pancreas into self-assembling 3D structures that we have termed 'organoids'. We provide a detailed protocol that describes how to grow adult mouse and human liver and pancreas organoids, from cell isolation and long-term expansion to genetic manipulation in vitro. Liver and pancreas cells grow in a gel-based extracellular matrix (ECM) and a defined medium. The cells can self-organize into organoids that self-renew in vitro while retaining their tissue-of-origin commitment, genetic stability and potential to differentiate into functional cells in vitro (hepatocytes) and in vivo (hepatocytes and endocrine cells). Genetic modification of these organoids opens up avenues for the manipulation of adult stem cells in vitro, which could facilitate the study of human biology and allow gene correction for regenerative medicine purposes. The complete protocol takes 1-4 weeks to generate self-renewing 3D organoids and to perform genetic manipulation experiments. Personnel with basic scientific training can conduct this protocol.LB is supported by an EMBO Postdoctoral fellowship (EMBO ALTF 794-2014). CH is supported by a Cambridge Stem Cell Institute Seed Fund award and the Herchel Smith Fund. BK is supported by a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society. MH is a Wellcome Trust Sir Henry Dale Fellow and is jointly funded by the Wellcome Trust and the Royal Society (104151/Z/14/Z).This is the author accepted manuscript. The final version is available from Nature Publishing Group via http://dx.doi.org/10.1038/nprot.2016.097

Criteria for preclinical models of cholangiocarcinoma:scientific and medical relevance

Cholangiocarcinoma (CCA) is a rare malignancy that develops at any point along the biliary tree. CCA has a poor prognosis, its clinical management remains challenging, and effective treatments are lacking. Therefore, preclinical research is of pivotal importance and necessary to acquire a deeper understanding of CCA and improve therapeutic outcomes. Preclinical research involves developing and managing complementary experimental models, from in vitro assays using primary cells or cell lines cultured in 2D or 3D to in vivo models with engrafted material, chemically induced CCA or genetically engineered models. All are valuable tools with well-defined advantages and limitations. The choice of a preclinical model is guided by the question(s) to be addressed; ideally, results should be recapitulated in independent approaches. In this Consensus Statement, a task force of 45 experts in CCA molecular and cellular biology and clinicians, including pathologists, from ten countries provides recommendations on the minimal criteria for preclinical models to provide a uniform approach. These recommendations are based on two rounds of questionnaires completed by 35 (first round) and 45 (second round) experts to reach a consensus with 13 statements. An agreement was defined when at least 90% of the participants voting anonymously agreed with a statement. The ultimate goal was to transfer basic laboratory research to the clinics through increased disease understanding and to develop clinical biomarkers and innovative therapies for patients with CCA

Epigenetic remodelling licences adult cholangiocytes for organoid formation and liver regeneration.

Following severe or chronic liver injury, adult ductal cells (cholangiocytes) contribute to regeneration by restoring both hepatocytes and cholangiocytes. We recently showed that ductal cells clonally expand as self-renewing liver organoids that retain their differentiation capacity into both hepatocytes and ductal cells. However, the molecular mechanisms by which adult ductal-committed cells acquire cellular plasticity, initiate organoids and regenerate the damaged tissue remain largely unknown. Here, we describe that ductal cells undergo a transient, genome-wide, remodelling of their transcriptome and epigenome during organoid initiation and in vivo following tissue damage. TET1-mediated hydroxymethylation licences differentiated ductal cells to initiate organoids and activate the regenerative programme through the transcriptional regulation of stem-cell genes and regenerative pathways including the YAP-Hippo signalling. Our results argue in favour of the remodelling of genomic methylome/hydroxymethylome landscapes as a general mechanism by which differentiated cells exit a committed state in response to tissue damage.RCUK Cancer Research UK ERC H2020 Wellcome Trus

Human primary liver cancer–derived organoid cultures for disease modeling and drug screening

Human liver cancer research currently lacks in vitro models that can faithfully recapitulate the pathophysiology of the original tumor. We recently described a novel, near-physiological organoid culture system, wherein primary human healthy liver cells form long-term expanding organoids that retain liver tissue function and genetic stability. Here we extend this culture system to the propagation of primary liver cancer (PLC) organoids from three of the most common PLC subtypes: hepatocellular carcinoma (HCC), cholangiocarcinoma (CC) and combined HCC/CC (CHC) tumors. PLC-derived organoid cultures preserve the histological architecture, gene expression and genomic landscape of the original tumor, allowing for discrimination between different tumor tissues and subtypes, even after long-term expansion in culture in the same medium conditions. Xenograft studies demonstrate that the tumorogenic potential, histological features and metastatic properties of PLC-derived organoids are preserved in vivo. PLC-derived organoids are amenable for biomarker identification and drug-screening testing and led to the identification of the ERK inhibitor SCH772984 as a potential therapeutic agent for primary liver cancer. We thus demonstrate the wide-ranging biomedical utilities of PLC-derived organoid models in furthering the understanding of liver cancer biology and in developing personalized-medicine approaches for the disease.M.H. is a Wellcome Trust Sir Henry Dale Fellow and is jointly funded by the Wellcome Trust and the Royal Society (104151/Z/14/Z). L.B. is supported by an EMBO Postdoctoral Fellowship (EMBO ALTF 794-2014) and Marie-Curie Postdoctoral Fellowship (grant no. 656193_H2020-MSCA-IF-2014). G.M. was supported by a Marie Curie Initial Training Network (Marie Curie ITN WntsApp 608180) and a H2020 LSMF4LIFE grant (ECH2020-668350). This work was funded by an NC3Rs International prize, a Beit Prize, a Cambridge Cancer Center-pump priming award (CRUK-RG83267) and, partially, by a NC3Rs project grant (NC/R001162/1), all of them awarded to M.H. Work at the L.J.W.v.d.L lab was funded by the research program InnoSysTox (project number 114027003), by the Netherlands Organisation for Health Research and Development (ZonMw), and part of the research program financed by the Dutch Digestive Foundation (MLDS-Diagnostics project number D16-26). Work in the M.J.G. lab is funded by the Wellcome Trust (102696), Stand Up To Cancer (SU2C-AACRDT1213) and Cancer Research UK (C44943/A22536)

Liver cell therapy: is this the end of the beginning?

The prevalence of liver diseases is increasing globally. Orthotopic liver transplantation is widely used to treat liver disease upon organ failure. The complexity of this procedure and finite numbers of healthy organ donors have prompted research into alternative therapeutic options to treat liver disease. This includes the transplantation of liver cells to promote regeneration. While successful, the routine supply of good quality human liver cells is limited. Therefore, renewable and scalable sources of these cells are sought. Liver progenitor and pluripotent stem cells offer potential cell sources that could be used clinically. This review discusses recent approaches in liver cell transplantation and requirements to improve the process, with the ultimate goal being efficient organ regeneration. We also discuss the potential off-target effects of cell-based therapies, and the advantages and drawbacks of current pre-clinical animal models used to study organ senescence, repopulation and regeneration

Molecular mechanisms of cell death: recommendations of the Nomenclature Committee on Cell Death 2018.

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell death, autophagy-dependent cell death, immunogenic cell death, cellular senescence, and mitotic catastrophe, we discuss the utility of neologisms that refer to highly specialized instances of these processes. The mission of the NCCD is to provide a widely accepted nomenclature on cell death in support of the continued development of the field

L'AFFDU marraine la création de l’Association albanaise des femmes diplômées des universités

Broutier Michelle. L'AFFDU marraine la création de l’Association albanaise des femmes diplômées des universités . In: Diplômées, n°203, 2002. Femmes et sciences biomédicales. pp. 220-223

Involvement of netrin-1/Dependence receptors (DCC and UNC5B) apoptotic control during embryonic development and tumorigenesis : apoptosis induced by dependence receptors : interface between physiology and pathology

Les récepteurs à dépendance présentent la particularité d’induire deux voies de signalisation différentes selon la disponibilité de leur ligand. En présence de leur ligand, ils transduisent une voie de signalisation favorisant notamment la survie cellulaire (signalisation positive), tandis qu’en son absence, ils induisent activement l’apoptose des cellules (signalisation négative). La dualité fonctionnelle de ces récepteurs pourrait leur conférer un rôle central au cours du développement embryonnaire, mais aussi dans le maintien de l’homéostasie cellulaire chez l’adulte. En effet, du fait de leur signalisation pro-apoptotique, les récepteurs à dépendance pourraient limiter le nombre de cellules (en fonction de la disponibilité en ligand), et réguler leur migration (dans des zones dépourvues de ligand), au cours des processus développementaux mais aussi en cas de prolifération tumorale et de dissémination métastatique. Au cours de ma thèse, j’ai donc développé différentes thématiques de recherche visant à préciser le rôle du contrôle apoptotique exercé par les couples nétrine-1/récepteurs à dépendance (DCC et UNC5B) au cours de la tumorigenèse et du développement embryonnaire. Dans ce cadre, nous avons montré que les souris exprimant une forme mutée du récepteur DCC, ayant perdu la capacité d’induire l’apoptose des cellules en absence de son ligand la nétrine-1, étaient prédisposées à la survenue de (1) cancers colorectaux dans un contexte prédisposant, et de (2) lymphomes non hodgkiniens (LNH) dans un modèle de vieillissement. Ces résultats suggèrent que DCC puisse agir comme un suppresseur de tumeur conditionnel, via sa voie de signalisation négative, en absence de son ligand nétrine-1. De plus, nous avons montré qu’il existe un gain de nétrine-1 dans une fraction significative de LNH de type B (LNH-B) chez l’Homme, gain qui leur confère un avantage sélectif en bloquant constitutivement l’apoptose induite par le récepteur DCC. Réciproquement, nous avons montré que l’utilisation d’un anticorps ciblant la nétrine-1 était capable de restaurer l’apoptose induite par le récepteur DCC non lié, dans des lignées tumorales humaines de LNH-B in vitro et ex-vivo dans un modèle de xénogreffe. Ainsi, nos résultats suggèrent que cibler l’interaction nétrine-1/DCC dans les LNH-B pourrait être une stratégie thérapeutique prometteuse. La partie « développement » de mon travail de thèse est encore préliminaire. Elle se focalise sur le rôle du contrôle apoptotique exercé par les couples nétrine-1/récepteurs à dépendance (DCC et UNC5B) au cours de la mise en place des réseaux vasculaire et nerveux chez l’embryon de sourisDependence receptors share the common property of inducing two types of signaling cascades according to the availability of their ligand. In presence of their ligand, they induce a positive signal allowing cell survival whereas in its absence, they induce cell death by apoptosis. Dependence receptors dual functionality could play a major role both during the embryonic development and in the regulation of tissue homeostasis in adult. Indeed, apoptosis induced by dependence receptors would be a safeguard mechanism which regulates the number of cells and their migration during developmental or tumorigenic process. Thus, during my PhD, I have investigated the involvement of netrin- 1/dependence receptors (DCC and UNC5B) apoptotic control during tumorigenesis and embryonic development. We observed that DCC-mutant mice in which DCC pro-apoptotic signaling is genetically silenced show a higher propensity to develop colorectal cancers in a predisposing context and B-cell type non-Hodgkin lymphoma (B-NHL) with age, suggesting than DCC could act as a conditional tumor suppressor gene through its pro-apoptotic signaling, in absence of netrin-1. Moreover, we show that netrin-1 is overexpressed in a significant fraction of Human B-NHL, which confers tumor cells a selective advantage by blocking DCC-induced apoptosis. Reciprocally, we showed that inhibiting the interaction between netrin-1 and its DCC receptor restore apoptosis in lymphoma cells in vitro and in vivo in xenografts experiments, suggesting that targeting netrin-1 and DCC interaction in lymphoma could represent a promising anti-tumor therapeutic strategy. The "developmental" part of my PhD work is in progress and we obtained only few preliminary data. It focuses on the role of apoptotic control mediated by netrin1-/dependence receptor (DCC/UNC5B) during the development of vascular and neural networks in the mouse embry