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Reliable establishment of tumor organoids is paramount to advance applications of organoid technology for personalized medicine. Here, we share our multi-center experience on initiation and tumorigenic confirmation of hepatobiliary cancer organoids. We discuss current concerns, propose potential solutions, and provide future perspectives for improvements in hepatobiliary cancer organoid establishment.

Peer reviewed: True, Funder: King’s College London, Funder: National Institute for Health Research (NIHR), Organoids are 3D cultures that to some extent reproduce the structure, composition and function of the mammalian tissues from which they derive, thereby creating in vitro systems with more in vivo-like characteristics than 2D monocultures. Here, the ability of human organoids derived from normal gastric, pancreas, liver, colon and kidney tissues to metabolise the environmental carcinogen benzo[a]pyrene (BaP) was investigated. While organoids from the different tissues showed varied cytotoxic responses to BaP, with gastric and colon organoids being the most susceptible, the xenobiotic-metabolising enzyme (XME) genes, CYP1A1 and NQO1, were highly upregulated in all organoid types, with kidney organoids having the highest levels. Furthermore, the presence of two key metabolites, BaP-t-7,8-dihydrodiol and BaP-tetrol-l-1, was detected in all organoid types, confirming their ability to metabolise BaP. BaP bioactivation was confirmed both by the activation of the DNA damage response pathway (induction of p-p53, pCHK2, p21 and γ-H2AX) and by DNA adduct formation. Overall, pancreatic and undifferentiated liver organoids formed the highest levels of DNA adducts. Colon organoids had the lowest responses in DNA adduct and metabolite formation, as well as XME expression. Additionally, high-throughput RT-qPCR explored differences in gene expression between organoid types after BaP treatment. The results demonstrate the potential usefulness of organoids for studying environmental carcinogenesis and genetic toxicology.

In June 2022, the second meeting on ‘Engineering Multicellular Systems’, organized by the European Molecular Biology Laboratory and the Institute of Bioengineering of Catalonia, took place in Barcelona. Stem cell and systems biologists, physicists and engineers from all over the world gathered to discuss how recent breakthroughs in organoid technologies, engineering and mechanobiology are boosting our understanding of early morphogenesis, organogenesis and organ function with applications in tissue engineering, disease modeling and drug screening. The meeting was organized with sustainability in mind, and included an ethics session and an outreach public activity.

Complex three-dimensional in vitro organ-like models, or organoids, offer a unique biological tool with distinct advantages over two-dimensional cell culture systems, which can be too simplistic, and animal models, which can be too complex and may fail to recapitulate human physiology and pathology. Significant progress has been made in driving stem cells to differentiate into different organoid types, though several challenges remain. For example, many organoid models suffer from high heterogeneity, and it can be difficult to fully incorporate the complexity of in vivo tissue and organ development to faithfully reproduce human biology. Successfully addressing such limitations would increase the viability of organoids as models for drug development and preclinical testing. On April 3-6, 2022, experts in organoid development and biology convened at the Keystone Symposium "Organoids as Tools for Fundamental Discovery and Translation" to discuss recent advances and insights from this relatively new model system into human development and disease.

Liver regeneration is a complex process involving the crosstalk of multiple cell types, including hepatocytes, hepatic stellate cells, endothelial cells and inflammatory cells. The healthy liver is mitotically quiescent, but following toxic damage or resection the cells can rapidly enter the cell cycle to restore liver mass and function. During this process of regeneration, epithelial and non-parenchymal cells respond in a tightly coordinated fashion. Recent studies have described the interaction between inflammatory cells and a number of other cell types in the liver. In particular, macrophages can support biliary regeneration, contribute to fibrosis remodelling by repressing hepatic stellate cell activation and improve liver regeneration by scavenging dead or dying cells in situ. In this Review, we describe the mechanisms of tissue repair following damage, highlighting the close relationship between inflammation and liver regeneration, and discuss how recent findings can help design novel therapeutic approaches.

Background and aims Cholangiocarcinoma (CCA) is a devastating disease often detected at advanced stages when surgery cannot be performed. Conventional and targeted systemic therapies perform poorly, and therefore effective drugs are urgently needed. Different epigenetic modifications occur in CCA and contribute to malignancy. Targeting epigenetic mechanisms may thus open therapeutic opportunities. However, modifications such as DNA and histone methylation often coexist and cooperate in carcinogenesis. We tested the therapeutic efficacy and mechanism of action of a class of dual G9a histone-methyltransferase and DNA-methyltransferase 1 (DNMT1) inhibitors. Approach and results Expression of G9a, DNMT1, and their molecular adaptor, ubiquitin-like with PHD and RING finger domains-1 (UHRF1), was determined in human CCA. We evaluated the effect of individual and combined pharmacological inhibition of G9a and DNMT1 on CCA cell growth. Our lead G9a/DNMT1 inhibitor, CM272, was tested in human CCA cells, patient-derived tumoroids and xenograft, and a mouse model of cholangiocarcinogenesis with hepatocellular deletion of c-Jun-N-terminal-kinase (Jnk)-1/2 and diethyl-nitrosamine (DEN) plus CCl4 treatment (JnkΔhepa + DEN + CCl4 mice). We found an increased and correlative expression of G9a, DNMT1, and UHRF1 in CCAs. Cotreatment with independent pharmacological inhibitors G9a and DNMT1 synergistically inhibited CCA cell growth. CM272 markedly reduced CCA cell proliferation and synergized with Cisplatin and the ERBB-targeted inhibitor, Lapatinib. CM272 inhibited CCA tumoroids and xenograft growth and significantly antagonized CCA progression in JnkΔhepa + DEN + CCl4 mice without apparent toxicity. Mechanistically, CM272 reprogrammed the tumoral metabolic transcriptome and phenotype toward a differentiated and quiescent status. Conclusions Dual targeting of G9a and DNMT1 with epigenetic small molecule inhibitors such as CM272 is a potential strategy to treat CCA and/or enhance the efficacy of other systemic therapies.

Cell Stem Cell was launched in 2007, and this year marks its 15

Organoids have attracted increasing attention because they are simple tissue-engineered cell-based in vitro models that recapitulate many aspects of the complex structure and function of the corresponding in vivo tissue. They can be dissected and interrogated for fundamental mechanistic studies on development, regeneration, and repair in human tissues. Organoids can also be used in diagnostics, disease modeling, drug discovery, and personalized medicine. Organoids are derived from either pluripotent or tissue-resident stem (embryonic or adult) or progenitor or differentiated cells from healthy or diseased tissues, such as tumors. To date, numerous organoid engineering strategies that support organoid culture and growth, proliferation, differentiation and maturation have been reported. This Primer serves to highlight the rationale underlying the selection and development of these materials and methods to control the cellular/tissue niche; and therefore, structure and function of the engineered organoid. We also discuss key considerations for generating robust organoids, such as those related to cell isolation and seeding, matrix and soluble factor selection, physical cues and integration. The general standards for data quality, reproducibility and deposition within the organoid community is also outlined. Lastly, we conclude by elaborating on the limitations of organoids in different applications, and key priorities in organoid engineering for the coming years.

Background and aims Alpha-1 antitrypsin (AAT) is a product of SERPINA1 gene mainly expressed by hepatocytes. Clinically relevant mutations in the SERPINA1 gene, such as Z (Glu342Lys), results in an expression of misfolded AAT protein having high propensity to polymerize, accumulate in hepatocytes and thus to enhance a risk for hepatocyte damage and subsequent liver disease. So far, the relationship between the Z-AAT accumulation and liver cell damage remains not completely understood. We present three-dimensional organoid culture systems, as a novel tool for modeling Z-AAT-related liver diseases. Methods We have established liver organoids from liver biopsies of patients with homozygous (ZZ) and heterozygous (MZ) deficiency and normal (MM) genotypes of AAT. The features of these organoid models were characterized by analyzing AAT protein secretion and intracellular aggregation in MZ and ZZ genotypes as well as SERPINA1 expression in differentiated cultures. Results Transcriptional analysis of differentiated organoid cultures by RNA-Seq showed hepatocyte-specific gene expression profile. Genes, such as ALB, APOB, CYP3A4 and SERPINA1, were validated and confirmed through quantitative-PCR analysis. The organoids from MZ and ZZ cases showed intracellular aggregation and lower secretion of AAT protein, and lower expression of ALB and APOB, as typically seen in hepatocytes from Z-AAT deficiency patients. Furthermore, organoids responded to external stimulus. Treatment with oncostatin M, a well-known inducer of SERPINA1, increased expression of the full-length transcripts (AAT-1C) as well as the short transcript of AAT (AAT-ST1C4). Conclusions Liver organoid model recapitulates the key features of Z-AAT deficiency and provides a useful tool for disease modeling.

The molecular events that drive hepatitis B virus (HBV)-mediated transformation and tumorigenesis have remained largely unclear, due to the absence of a relevant primary model system. Here we propose the use of human liver organoids as a platform for modeling HBV infection and related tumorigenesis. We first describe a primary ex vivo HBV-infection model derived from healthy donor liver organoids after challenge with recombinant virus or HBV-infected patient serum. HBV-infected organoids produced covalently closed circular DNA (cccDNA) and HBV early antigen (HBeAg), expressed intracellular HBV RNA and proteins, and produced infectious HBV. This ex vivo HBV-infected primary differentiated hepatocyte organoid platform was amenable to drug screening for both anti-HBV activity and drug-induced toxicity. We also studied HBV replication in transgenically modified organoids; liver organoids exogenously overexpressing the HBV receptor sodium taurocholate co-transporting polypeptide (NTCP) after lentiviral transduction were not more susceptible to HBV, suggesting the necessity for additional host factors for efficient infection. We also generated transgenic organoids harboring integrated HBV, representing a long-term culture system also suitable for viral production and the study of HBV transcription. Finally, we generated HBV-infected patient-derived liver organoids from non-tumor cirrhotic tissue of explants from liver transplant patients. Interestingly, transcriptomic analysis of patient-derived liver organoids indicated the presence of an aberrant early cancer gene signature, which clustered with the hepatocellular carcinoma (HCC) cohort on The Cancer Genome Atlas Liver Hepatocellular Carcinoma dataset and away from healthy liver tissue, and may provide invaluable novel biomarkers for the development of HCC and surveillance in HBV-infected patients., eLife, 10, ISSN:2050-084X

Organoid cultures have emerged as an alternative in vitro system to recapitulate tissues in a dish. While mouse models and cell lines have furthered our understanding of liver biology and associated diseases, they suffer in replicating key aspects of human liver tissue, in particular its complex architecture and metabolic functions. Liver organoids have now been established for multiple species from induced pluripotent stem cells, embryonic stem cells, hepatoblasts and adult tissue-derived cells. These represent a promising addition to our toolbox to gain a deeper understanding of this complex organ. In this perspective we will review the advances in the liver organoid field, its limitations and potential for biomedical applications.

Nature Biotechnology asks a selection of faculty about the most exciting frontier in their field and the most needed technologies for advancing knowledge and applications. What will be the most important areas of research in biotech over the coming years? Which technologies will be most important to advance knowledge and applications in these areas? Nature Biotechnology reached out to a set of faculty doing outstanding work in research areas representative of the journal’s remit and asked them to contribute their vision of where their fields are going.

Organoid cultures hold the promise of transforming basic and clinical research. Here, we provide a storyline of the highlights and breakthroughs that have an impact in present clinical research. We also discuss the bottlenecks that delay their full exploitation for the next generation of biomedical research.

Cancer cells voraciously consume nutrients to support their growth, exposing a metabolic vulnerability that can be therapeutically exploited. Here we show in hepatocellular carcinoma (HCC) cells, xenografts, and in patient-derived HCC organoids that fasting can synergistically sensitize resistant HCC to sorafenib. Mechanistically, sorafenib acts non-canonically as an inhibitor of mitochondrial respiration, causing resistant cells to depend on glycolysis for survival. Fasting, through reduction in glucose and impeded AKT/mTOR-signaling, prevents this Warburg shift. Regulating glucose transporter and pro-apoptotic protein expression, p53 is necessary and sufficient for the sorafenib-sensitizing effect of fasting. p53 is also crucial for fasting-mediated improvement of sorafenib efficacy in an orthotopic HCC mouse model. Together, our data suggest intermittent fasting and sorafenib as rational combination therapy for HCC with intact p53 signaling. As HCC therapy is currently severely limited by resistance, these results should instigate clinical studies aimed at improving therapy response in advanced-stage, and possibly even early-stage, HCC.HIGHLIGHTSFasting sensitizes resistant HCC xenografts and patient-derived organoids to sorafenibSorafenib-mediated Warburg shift is prevented by glucose limitation upon fastingFasting synergistically improves sorafenib efficacy in non-resistant modelsp53 is required for synergism by regulating glucose uptake and apoptosisGRAPHICAL ABSTRACT

Hepatic, pancreatic, and biliary (HPB) organoids are powerful tools for studying development, disease, and regeneration. As organoid research expands, the need for clear definitions and nomenclature describing these systems also grows. To facilitate scientific communication and consistent interpretation, we revisit the concept of an organoid and introduce an intuitive classification system and nomenclature for describing these 3D structures through the consensus of experts in the field. To promote the standardization and validation of HPB organoids, we propose guidelines for establishing, characterizing, and benchmarking future systems. Finally, we address some of the major challenges to the clinical application of organoids.

Additional file 7: Fig. S6. Representative overview images of three different mPO cultures grown in Z.1-FEP-cuvettes. (a) mPO grown within the Z.1-FEP-cuvette were kept in an incubator as a control for organoids grown within the Z.1 microscope. Images were taken directly after seeding, after 6 days and 10 days. (b) Two representative mPO cultures expressing the nuclei marker Rosa26-nTnG (grey) were imaged with the Zeiss Z.1 microscope over 6 days. Dependent on the number of views, tiles, z-planes and the temporal resolution, the amount of data which is generated and needs to be processed varies between hundreds of gigabyte and tens of terabyte (cuvette 1: total acquisition time: 6 days, temporal resolution: 30 min, views: 1, tiles: 1, total size: 220 GB; cuvette 2: total acquisition time: 6 days, temporal resolution: 30 min, views: 4 (only one is shown), tiles: 1, total size: 1054 GB). Microscope: (a) Zeiss Axio Imager, (b) Zeiss Lightsheet Z.1; objective lenses: (a) Plan S 1.0x FWD 81 mm, (b) detection: W Plan-Apochromat 20x/1.0, illumination: Zeiss LSFM 10x/0.2; laser lines: 561 nm; filters: laser block filter (LBF) 405/488/561; voxel size: 1.02 × 1.02 × 2.00 μm3, recording interval: 30 min; scale bar: 100 μm.

Additional file 14: Fig. S13. Bright field pipeline allows detailed analysis of polycystic hCCAOs. (a) Polycystic hCCAOs display a dense phenotype. Microscope: Zeiss Axio Observer Z.1; objective lenses: Plan-Apochromat 5x/0.16, avg. z-projection, voxel size: 1.29 × 1.29 × 65 μm3, scale bar overview: 500 μm, close-up: 25 μm. (b) The average circularity is around 0.8 over time. (c) Similarly to monocystic organoid cultures, the detected projected luminal areas and growth behaviours are heterogeneous. Box plot analysis, median in green (n = 87) (d) While the median projected luminal areas of three different wells (technical replicates) vary, the normalised projected area increase is similar (n = 87, 34, 63). (e) The initial projected area correlates with the final projected area (R2 = 0.8744) with a linear regression slope m = 1.5857. (f) The organoids display a similar average expansion factor independent of their initial size with an average of 0.02 and outliers (red) lying above 0.078.

Additional file 3: Fig. S2. Ultra-thin FEP-foil cuvette holders for live recordings with the Zeiss Lightsheet Z.1 microscope system. (a) Illustration of the general setup of the Zeiss Lightsheet Z.1 microscope. (b) Close-up of the microscope chamber with the downwards directed Z1-FEP-cuvette enclosing the sample. (c) Close-up of the sample holder. The shrinking tube that seals the FEP cuvette and connects it with the glass capillary is depicted in black. (d) CAD-derived drawings of positive moulds of the FEP cuvette and the glass capillary needed to produce the Z1-FEP-cuvette. (e) Printed mould with a glass capillary used to form the Z1-FEP-cuvette in the vacuum forming process. (f) Ready-to-use Z1-FEP-cuvette. (g) mPOs grown for 7 days in the Z1-FEP-cuvette.

Additional file 5: Fig. S4. Validation of the pH properties of the Zeiss Lightsheet Z.1 microscope. (a) Illustration of the pH-value distribution inside the chamber of the Zeiss Lightsheet Z.1 microscope and the corresponding measurement landmarks. After filling the chamber with buffered media, the pH-value is evenly distributed at 7.5 throughout the chamber. (b) The constant CO2 fumigation that is directed over the liquid column is not able to recover a lower pH-value over time. The pH-value of the medium changes from 8.5 to 8 but it never reaches the physiologically necessary 7.5 (liquid depth: 3 cm). The same is observed at 1 cm and 2 cm liquid depth. At the bottom of the chamber, the pH-value does not change within 48 h. (c) Once the inserted medium has the right pH-value, the incubation system is able to keep it on the same level for more than 2 days.

Additional file 23: Table S1. Used settings for the segmentation and post-processing of the data obtained with the light-sheet pipeline. Table S2. Evaluation of segmentation performance for different organoids. The performance was measured against a manually determined ground truth for organoid I (red), II (blue) and III (green). The performance metrics recall, precision and F score are determined from the number of true positives, false negatives and false positives. Values range from 0 (worst performance) to 1 (optimal performance). GT: number of cell nuclei in the ground truth; SC: number of cell nuclei determined by segmentation; TP: true positives; FN: false negatives; FP: false negatives.

Additional file 8: Fig. S7. Dynamic processes observed in organoid morphogenesis. hCCAOs expressed the nuclei marker H2B-eGFP (magenta) and the F-actin cytoskeletal marker LifeAct-mCherry (green) and were cultured in Z1-FEP-cuvettes for long-term live observation. The figure shows excerpts of maximum intensity z-projections. Manual tracking of cell nuclei was performed using the Manual Tracking plugin in Fiji. Microscope: Zeiss Lightsheet Z.1; objective lenses: detection: W Plan-Apochromat 20x/1.0, illumination: Zeiss LSFM 10x/0.2; laser lines: 488 nm, 561 nm; filters: laser block filter (LBF) 405/488/561; voxel size: 1.02 × 1.02 × 2.00 μm3; recording interval: 30 min; scale bars: 50 μm, 25 μm (inset).

Additional file 4: Fig. S3. Validation of the temperature properties of the Zeiss Lightsheet Z.1 microscope. (a) Illustration of the temperature distribution inside of the Zeiss Lightsheet Z.1 microscope chamber and the corresponding measurement landmarks. Beside the open, upper part with a slightly lower value, the temperature is equally distributed throughout the chamber. (b) Results of the measurement of the heating-up time. The included heating unit of the microscope needs to heat up the medium starting from room temperature (21 °C). After 12 min the medium reaches the physiological temperature of 37 °C.

Additional file 6: Fig. S5. Overview of entire hCCAO cultures within one Z1-FEP-cuvette and observation of isolated single-cell dynamics. hCCAOs expressed the nuclei marker H2B-eGFP (magenta) and the F-actin cytoskeletal marker LifeAct-mCherry (green). (a) Maximum intensity z-projection of the entire field of view in the Lightsheet Z1 microscope. One cuvette (i) with low organoid density and one cuvette (ii) with high organoid density are displayed. We counted about 120 organoids in the cuvette (ii) with high organoid density. Organoids show different sizes and isolated cell nuclei are visible in the interspaces. Scale bar: 250 μm. (b) Excerpts of the maximum intensity z-projections shown in (a). Isolated single organoid cells show signs of polarisation and undergo cell division. Scale bars: Cell division, Polarisation - 10 μm, Formation – 20 μm. Microscope: Zeiss Lightsheet Z.1; objective lenses: detection: W Plan-Apochromat 20x/1.0, illumination: Zeiss LSFM 10x/0.2; laser lines: 488 nm, 561 nm; filters: laser block filter (LBF) 405/488/561; voxel size: 1.02 × 1.02 × 2.00 μm3; recording interval: 30 min.

Additional file 9: Fig. S8. Time-resolved, representative images of the growth and heterogeneity in mPOs. Illustrated are single organoids extracted from three different cultures showing rotation, size oscillation, luminal dynamics, fusion and different cell nucleus sizes. In addition, cell division events at a late stage (day 4, 5, 6) and the formation of differently sized organoid fragments are shown. Besides the luminal dynamics, which are imaged by the use of a bright field microscope, all behaviour patterns and appearances were observed from organoids expressing the nuclei marker Rosa26-nTnG (grey) and grown within the Z.1-FEP-cuvette inside the Z.1 Lightsheet microscope. The red rectangles indicate the corresponding close-up, the red arrows indicate the position within the organoid where the event occurs, the curved arrow indicate the direction of rotation and the red circle indicates the volume change during a size oscillation event. Microscope fluorescence images: Zeiss Lightsheet Z.1; Plan S 1.0x FWD 81 mm, detection: W Plan-Apochromat 20x/1.0, illumination: Zeiss LSFM 10x/0.2; laser lines: 561 nm; filters: laser block filter (LBF) 405/488/561; voxel size: 1.02 × 1.02 × 2.00 μm3; recording interval: 30 min; Microscope bright field images: Zeiss Axio Observer Z.1; objective lenses: Plan-Apochromat 5x/0.16, voxel size: 1.26 × 1.26 × 4 μm3, avg. z-projection.

The homologous E3 ubiquitin ligases RNF43/ZNRF3 negatively regulate WNT signalling activation. Recently, both genes have been found mutated in several types of cancers. Specifically, loss-of-function mutations result in adenoma formation in mouse small intestine. However, their role in liver cancer has not been explored yet. Here we describe that hepatocyte-specific deletion of both Rnf43/Znrf3 results in altered lipid metabolism and a non-alcoholic steatohepatitis (NASH) phenotype in mouse, in the absence of exogenous fat supplementation. The effect is cell-autonomous, as evidenced by the intracellular lipid accumulation detected in mutant liver organoids. Upon chronic liver damage, Rnf43/Znrf3 deletion results in impaired hepatocyte regeneration, subsequent to an imbalance between hepatocyte differentiation and proliferation, which leads to hepatocellular carcinoma. Remarkably, hepatocellular carcinoma patients with mutations in ZNRF3 also present altered lipid metabolism and poorer survival. Our findings imply that Wnt activation through the RNF43/ZNRF3 module predisposes to liver cancer by altering the liver lipid metabolic ground-state and impairing liver regeneration, which combined, facilitate the progression towards malignancy. Our results highlight the requirement for personalized therapeutic or dietary interventions for those RNF43/ZNRF3 mutated individuals at risk of developing steatosis, NASH and/or liver cancer.

In the homeostatic liver, ductal cells intermingle with a microenvironment of endothelial and mesenchymal cells to form the functional unit of the portal tract. Ductal cells proliferate rarely in homeostasis but do so transiently after tissue injury to replenish any lost epithelium. We have shown that liver ductal cells can be expanded as liver organoids that recapitulate several of the cell-autonomous mechanisms of regeneration, but lack the stromal cell milieu of the biliary tract in vivo. Here, we describe a subpopulation of SCA1+ periportal mesenchymal cells that closely surrounds ductal cells in vivo and exerts a dual control on their proliferative capacity. Mesenchymal-secreted mitogens support liver organoid formation and expansion from differentiated ductal cells. However, direct mesenchymal-to-ductal cell-cell contact, established following a microfluidic co-encapsulation that enables the cells to self-organize into chimeric organoid structures, abolishes ductal cell proliferation in a mesenchyme-dose dependent manner. We found that it is the ratio between mesenchymal and epithelial cell contacts that determines the net outcome of ductal cell proliferation both in vitro, and in vivo, during damage-regeneration. SCA1+ mesenchymal cells control ductal cell proliferation dynamics by a mechanism involving, at least in part, Notch signalling activation. Our findings underscore how the relative abundance of cell-cell contacts between the epithelium and its mesenchymal microenvironment are key regulatory cues involved in the control of tissue regeneration.SummaryIn the homeostatic liver, the ductal epithelium intermingles with a microenvironment of stromal cells to form the functional unit of the portal tract. Ductal cells proliferate rarely in homeostasis but do so transiently after tissue injury. We have shown that these cells can be expanded as liver organoids that recapitulate several of the cell-autonomous mechanisms of regeneration, but lack the stromal cell milieu of the portal tract in vivo. Here, we describe a subpopulation of SCA1+ periportal mesenchymal niche cells that closely surrounds ductal cells in vivo and exerts a dual control on their proliferative capacity. Mesenchymal-secreted mitogens support liver organoid formation and expansion from differentiated ductal cells. However, direct mesenchymal-to-ductal cell-cell contact, established through a microfluidic co-encapsulation method that enables the cells to self-organize into chimeric organoid structures, abolishes ductal cell proliferation in a mesenchyme-dose dependent manner. We found that it is the ratio between mesenchymal and epithelial cell contacts that determines the net outcome of ductal cell proliferation both in vitro, and in vivo, during damage-regeneration. SCA1+ mesenchymal cells control ductal cell proliferation dynamics by a mechanism involving, at least in part, Notch signalling activation. Our findings re-evaluate the concept of the cellular niche, whereby the proportions of cell-cell contacts between the epithelium and its mesenchymal niche, and not the absolute cell numbers, are the key regulatory cues involved in the control of tissue regeneration.

Organoids are morphologically heterogeneous three-dimensional cell culture systems. To understand the cell organisation principles of their morphogenesis, we imaged hundreds of pancreas and liver organoids in parallel using light sheet and bright field microscopy for up to seven days. We quantified organoid behaviour at single-cell (microscale), individual-organoid (mesoscale), and entire-culture (macroscale) levels. At single-cell resolution, we monitored formation, monolayer polarisation and degeneration, and identified diverse behaviours, including lumen expansion and decline (size oscillation), migration, rotation and multi-organoid fusion. Detailed individual organoid quantifications lead to a mechanical 3D agent-based model. A derived scaling law and simulations support the hypotheses that size oscillations depend on organoid properties and cell division dynamics, which is confirmed by bright field macroscale analyses of entire cultures. Our multiscale analysis provides a systematic picture of the diversity of cell organisation in organoids by identifying and quantifying core regulatory principles of organoid morphogenesis.Graphical AbstractCreated with BioRender.com.

Background Pancreatic organoid systems have recently been described for the in vitro culture of pancreatic ductal cells from mouse and human. Mouse pancreatic organoids exhibit unlimited expansion potential, while previously reported human pancreas organoid (hPO) cultures do not expand efficiently long-term in a chemically defined, serum-free medium. We sought to generate a 3D culture system for long-term expansion of human pancreas ductal cells as hPOs to serve as the basis for studies of human pancreas ductal epithelium, exocrine pancreatic diseases and the development of a genomically stable replacement cell therapy for diabetes mellitus. Results Our chemically defined, serum-free, human pancreas organoid culture medium supports the generation and expansion of hPOs with high efficiency from both fresh and cryopreserved primary tissue. hPOs can be expanded from a single cell, enabling their genetic manipulation and generation of clonal cultures. hPOs expanded for months in vitro maintain their ductal morphology, biomarker expression and chromosomal integrity. Xenografts of hPOs survive long-term in vivo when transplanted into the pancreas of immunodeficient mice. Notably, mouse orthotopic transplants show no signs of tumorigenicity. Crucially, our medium also supports the establishment and expansion of hPOs in a chemically defined, modifiable and scalable, biomimetic hydrogel. Conclusions hPOs can be expanded long-term, from both fresh and cryopreserved human pancreas tissue in a chemically defined, serum-free medium with no detectable tumorigenicity. hPOs can be clonally expanded, genetically manipulated and are amenable to culture in a chemically defined hydrogel. hPOs therefore represent an abundant source of pancreas ductal cells that retain the characteristics of the tissue-of-origin, which opens up avenues for modelling diseases of the ductal epithelium and increasing understanding of human pancreas exocrine biology as well as for potentially producing insulin-secreting cells for the treatment of diabetes.

Aerobic glycolysis, characterized by pyruvate reduction to lactate, serves proliferation in cancer cells and stem cells. To clarify whether this metabolic profile is universal to epithelial stem cells, despite vast differences in physiological turnover rates, we characterized the metabolic phenotype of bipotent liver progenitors (low turnover) relative to intestinal progenitors (high turnover). Using human liver and intestinal organoids, we show high glycolytic fluxes which provide substrates for cellular building blocks and reducing equivalents in proliferating progenitors, compared to their quiescent differentiating counterparts. Similar to cancer and pluripotent stem cells, intestinal progenitors display aerobic glycolysis with pyruvate reduction to lactate to serve their high proliferative demands. Strikingly, liver progenitors combine high glycolysis with substantial mitochondrial oxidation of pyruvate, which they require for both proliferation and maintenance of stemness. This concurs with the anabolic and epigenetic effects of mitochondrial pyruvate oxidation and the homeostatic liver function with low physiological turnover rates.

Additional file 1: Figure S1. Optimisation of hPO-Opt.EM culture medium and its expansion potential compared with published pancreatic organoid culture systems. A) To obtain an optimised medium to support hPO isolation and growth, incremental changes were made to previously published protocols. Expansion graphs show the time hPOs survived in vitro for n = 4 donors in mouse pancreatic organoid (mPO) medium [20] supplemented with TGFb inhibitor (top graphs) or in our previously reported medium supplemented with TGFb inhibitor, PGE2 and Wnt-conditioned medium containing 10% serum [23] (middle graphs) or in this new optimised, chemically-defined medium (hPO-Opt.EM) containing TGFb inhibitor, PGE2, FSK and no-FBS (bottom graphs). The ability of the hPOs to expand is indicated by passaging events (cirlces), arrows indicate ongoing cultures, capped lines indicate cultures that deteriorated. While the first two conditions were not able to sustain long-term culture, the hPO-Opt.EM medium demonstrates a much greater expansion potential. B-D) Comparison of the hPO-Opt.EM medium to the chemically-defined hPO medium published by Loomans and colleagues during the course of this project [22]. Although both media enable the initial generation of hPOs, the hPO-Opt.EM medium supports long-term culture to a much greater extent than Medium [22]. B-C) Representative images of hPO cultures derived from fresh pancreas tissue using the the hPO-Opt.EM medium or Medium [22] at B) passage 0 (P0, 8-days post derivation; magnification in lower panels; n = 3), or C) at Passage 3 (top) and Passage 4 (bottom) in two independent donors. D) Graph shows the expansion potential of hPOs cultured with the hPO-Opt.EM medium or the medium published by Loomans and colleagues [22] (arrows indicate ongoing cultures, capped lines indicate cultures that deteriorated). Figure S2. Human pancreas organoids (hPOs) can be derived from fresh and cryopreserved pancreas tissue and are amenable for genetic manipulation. A) Organoid cultures derived from fresh tissue (left) or tissue cryopreserved at the time of collection (right). The organoid formation efficiency from cryopreserved tissue was reduced, yet in all cases, cultures exhibited similar expansion rate to hPOs derived from fresh tissue. Experiments were performed in n = 3 independent donors, with similar outcomes. Representative images are shown. B) Organoid formation from fresh tissue is more efficient than from cryopreserved tissue, the number of organoids formed following the isolation of ductal fragments from either fresh tissue (253 ± 58 organoids; black circles) or cryopreserved tissue (25 ± 3 organoids; blue squares) is shown. Ductal fragments were seeded in a 50 μl BME 2 drop and quantified at P0. Data presented as mean ± SEM. C) hPOs derived from fresh or cryopreserved tissue expand at similar rates (circle = passage). D) Following mechanical dissociation all organoid fragments are capable of forming a new organoid (passage). Representative images of hPO culture during passaging are shown. E) The hPO culture system supports expansion from dissociated single cell suspensions, hPO cultures derived from single cells exhibit similar colony formation efficiency at early as well as late passages (n = 4 independent donors). F-G) Genetic manipulation of hPOs. hPOs were dissociated to single cells at passage 3 and transduced with a lentiviral vector carrying a GFP reporter gene. Following viral transduction the single cells formed hPOs and were expanded for 2 passages. F) hPOs were dispersed into single cells again and FACS sorting was used to select for GFP-positivity. The GFP+ cells were isolated and expanded as genetically modified hPOs for a further 2 passages. G) Representative images of genetically modified organoids at passage 8 are shown (n = 2). Figure S3. hPOs derived from fresh and cryopreserved samples expand as a single cell-layer epithelium of ductal cells and are phenotypically indistinguishable. Comparison of hPOs derived from A) fresh tissue (collected at P3) or B) cryopreserved tissue (collected at P2) from the same donor. Brightfield images (upper panels) indicate that hPO cultures expand efficiently as cystic structures regardless of whether the original tissue is fresh (A) or cryopreserved (B). H&E stainings reveal that hPOs derived from cryopreserved tissue maintain the single cell-layer epithelial architecture seen in the original donor tissue and in hPOs derived from fresh tissue (middle panels). Immunofluorescence stainings demonstrate that hPO cultures maintain ductal identity (KRT19 and SOX9), cellular polarisation (F-Actin) and express PDX1 (lower panels) regardless of the original tissue being fresh (left) or cryopreserved (right). Figure S4. Optimisation of hPO transplantation. A-B) hPOs were transplanted into NSG mice at different sites using a combination of different vehicles and ECMs, tissues were retrieved 1 and 3 months after injections. A) Table outlining engraftment conditions and engrafment success rates of hPO xenografts conducted with a combination of injection medium compositions and injection sites in order to achieve long-term survival of hPOs in vivo (NT – not tested). B) Representative H&E images of engrafted hPO cells at 1 month (upper panels) or 3 months (lower panels) show engrafted cells form ductal-like structures in vivo (G-graft, PN-pancreas). C) Xenografts of hPOs into the pancreas collected after 3 months show the engrafted cells retain SOX9 protein expression. Figure S5 hPOs cultured in optimised hPO-Opt.EM medium grow in a chemically defined hydrogel. A-B) Comparison of hPO cultures in the chemically defined dextran-based hydrogel (DEX-hydrogel) initiated from freshly isolated ducts overlayed with either A) hPO-Opt.EM medium or B) the medium published by Loomans and colleagues [22]. Both media support the formation of cystic structures, however, organoids in Medium [22] quickly deteriorated and could not be passaged. In contrast, organoids formed with the optimised hPO-EM medium could undergo expansion up to P4, after which they deteriorated. C) hPOs generated in hPO-Opt.EM medium expand more slowly in DEX-hydrogel as shown by the longer time taken for the cultures to reach confluency in order to be passaged than hPOs embedded in BME 2 (circles-passage events; arrows indicate ongoing cultures, capped lines indicate cultures that have deteriorated).

Epithelial cell loss alters a tissue's optimal function and awakens evolutionarily adapted healing mechanisms to reestablish homeostasis. Although adult mammalian organs have a limited regeneration potential, the liver stands out as one remarkable exception. Following injury, the liver mounts a dynamic multicellular response wherein stromal cells are activated in situ and/or recruited from the bloodstream, the extracellular matrix (ECM) is remodeled, and epithelial cells expand to replenish their lost numbers. Chronic damage makes this response persistent instead of transient, tipping the system into an abnormal steady state known as fibrosis, in which ECM accumulates excessively and tissue function degenerates. Here we explore the cellular and molecular switches that balance hepatic regeneration and fibrosis, with a focus on uncovering avenues of disease modeling and therapeutic intervention.

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.

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.