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Definitions

• Irreversible epithelial organ remodeling is a major contributing factor to worldwide death and disease, costing healthcare systems billions of dollars every year (Hynds and Giangreco, 2013).
• Diseases of epithelial remodeling include lung and gastrointestinal cancers as well as chronic diseases such as liver cirrhosis, chronic obstructive pulmonary disease (COPD), and inflammatory bowel disease (Hynds and Giangreco, 2013).
• COPD chronic obstructive pulmonary disease
• inflammatory bowel disease Hynds and Giangreco, 2013.
• most epithelial organ research performed primarily on animals fails to produce new therapies for these diseases and mortality rates remain unacceptably high. This is partly due to a lack of predictive human systems to test the efficacy of a vast growing number of compound libraries in pharmaceutical industries, imposing a fundamental challenge to develop a high- fidelity system for modeling inflammation and fibrosis in humans towards clinically relevant therapy development.
• Non-alcoholic Fatty Liver Disease is one of the major challenges to be overcome in developed countries due to the increased chance of developing lethal liver disorders, yet effective treatment is lacking.
• iatrogenic parenteral nutrition associated liver disease is a disorder that arises from parenteral nutrition and which currently has no effective treatment.
• Models having steatohepatitis and/or clinical histopathological features of liver disease such as lipid droplet accumulation and cystoskeleton filament disorganization, steatosis, and hepatocellular ballooning, and which can be used to address these and other liver disorders or disease states, are needed.
• current approaches are limited in their applications to unicellular, monogenic and relatively simple pathologies, failing to capture more prevailing and complex disease pathology such as epithelial organ fibrosis.
• the human liver is a vital organ that provides many essential metabolic functions for life such as lipid metabolism, ammonium and bile production, coagulation, as well as the detoxification of exogenous compounds.
• iPSC induced pluripotent stem cell
• in vitro reconstitution of patients' liver reaction is attractive to the pharmaceutical industry, due to a number of promising applications including regenerative therapy, drug discovery, and drug toxicity studies.
• conventional in vitro approaches study two-dimensional (2-D) and 3-D differentiation platforms to generate liver cells.
• the methods may comprise the steps of contacting a liver organoid with a free fatty acid (FFA) composition.
• FFA free fatty acid
• the FFA composition may comprise oleic acid, linoleic acid, palmitic acid, or combinations thereof.
• FIG. Co-differentiation of pre-fibrotic and inflammatory
• H Single cell RNA sequencing! ! FPKM (log2) values for hepatocyte, stellate cell, Kupffer cell, and endothelial-associated genes expressed by human iPSC, human iPSC derived definitive endoderm, foregut spheroid, HLO, human adult liver tissue and human fetal liver tissue.
• FIG. Generation of steatohepatitis organoids (sHLO) by fatty acid treatment
• A Schematic representing the method for generating steatohepatitis HLO (sHLO)
• B Live-cell imaging of lipid droplets (green), membrane (red), and nuclear (blue). The image was adopted from the overlay of 10-20 Z-stack images. Increase of lipid droplet accumulation and enlargement of lipid droplets and cells were observed in a dose depended manner.
• C Representative total lipid volume normalized by each organoid size. Bar shows the mean of the total lipids volume.
• Lipid droplets were increased in a dose depended manner 0 (black), 200 ⁇ OA (red), 400 ⁇ OA (green), and 800 ⁇ OA (blue).
• D Quantification of triglycerides in HLO.
• HLOs were isolated from one Matrigel drop and divided into HCM media in the presence (blue bar) or absence (black bar) of oleic acid (800 ⁇ ) and cultured for 3 days.
• IL-6 was 2.2-fold released in 800 ⁇ OA treatment (blue bar), when compared with non- treatment (black bar).
• F. Gene expression of pro-inflammatory cytokines TNF-alpha and IL-8. They were normalized by 18S. Both TNF-alpha and IL-8 gene expression were upregulated in 200 ⁇ OA (red bar) and 800 ⁇ OA (blue bar), compared with untreated (black bar).
• G. 10-20 HLO were cultured in HCM media including 0, 400, 800uM OA for 3 days. The cultured supernatants were collected from each well, and THP-1 migration was measured by using transmembrane with those supernatants. Cells that had migrated were counted and normalized by the exact number of organoids in each well.
• H. Trichrome staining of day 25 HLO and percentage of trichrome stained HLO on HLO (black bar), sHLO (red bar) and cHLO (blue bar) populations. Results represent mean +s.d., n 8-20 organoids.
• I. IF staining of day 25 HLO for Epcam and Vimentin and percentages of Epcam and Vimentin positive HLO on HLO (black bar), sHLO (red bar) and cHLO (blue bar) populations. Results represent mean +s.d., n 8-20 organoids.
• J. 20-30 HLO were cultured in the presence or absence of oleic acid (800 ⁇ ) for 5 days. P3NP was measured by ELISA with those supernatants. The final values were normalized by the exact number of organoids in each well. P3NP was 2.8 fold increased in 800 ⁇ OA treatment (blue bar), when compared with non- treatment (black bar).
• FIG. Cirrhotic transition of steatohepatitis HLO measured by
• AFM Schematic representation for measuring the stiffness of HLO by AFM.
• the top region of each single HLO 14x14 matrix in a 25x25 ⁇ square) was scanned with an AFM cantilever, which can provide a spatial mapping of topographical and mechanical information of HLO. Scale bar, 100 ⁇ .
• Young's modulus (stiffness of HLO) was determined from 7-12 organoids and summarized by the dot plot with box-and- whisker plot. Increase of the median value was observed in a dose dependent manner 0 (black), 200 (red), 400 (green) and 800 (blue) ⁇ OA.
• FIG 4. cHLO rigidity recapitulates clinical phenotype of Wolman disease
• A Bright- field image of HLO and cHLO established from several iPSC lines including heathy person (317D6), NAFLD patients (NAFLD150, NAFLD77, and NAFLD27), and the Wolman disease patients (WD90, WD92, and WD91).
• B Young's modulus (stiffness of HLO: Pa) of average of single HLO and cLO derived from several iPSC lines.
• FIG. Modeling human phenotypic variation of steatosis using iPSC-sHLO
• C The table summarizes the donor characteristic including polygenic score assigned in further study.
• D Live-cell imaging of lipid droplets (green) and nuclear (blue) on three group of total polygenic scoring of three allele: 0.6 ⁇ x,
• FIG. Phagocyte activity on THP-1
• FIG 7. Lipids accumulation comparison of 800 ⁇ of OA, PA,
• FIG 8. Actual migration cell number of THP-1 by 400 and 800 ⁇ of OA
• FIG 9. A. Photo of E-cad positive and negative sorted reconstituted spheroids from E-cad-mruby organoids, HepG2, LX-2, and THP-1. B. Gene expression of pro-inflammatory cytokines TNF-alpha and IL-8. C. ELISA measurement of P3NP.
• FIG 10. No effectiveness of resveratrol on ROS production of liver organoids
• FIG. Lipids accumulation in the organoid in the presence and absence of 400 ⁇ Intralipid
• FIG 13 Bright-field image of liver organoids in the culture of non-treatment, 800 ⁇ of OA alone, and 800 ⁇ of OA with 40ng/ml FGF19.
• “about” can mean a range of up to 20%, or up to 10%, or up to 5%, or up to 1% of a given value.
• the term can mean within an order of magnitude, preferably within 5- fold, and more preferably within 2-fold, of a value.
• totipotent stem cells are stem cells that can differentiate into embryonic and extra-embryonic cell types. Such cells can construct a complete, viable organism. These cells are produced from the fusion of an egg and sperm cell. Cells produced by the first few divisions of the fertilized egg are also totipotent.
• PSCs pluripotent stem cells
• PSCs can be the descendants of inner cell mass cells of the preimplantation blastocyst or obtained through induction of a non-pluripotent cell, such as an adult somatic cell, by forcing the expression of certain genes.
• Pluripotent stem cells can be derived from any suitable source.
• sources of pluripotent stem cells include mammalian sources, including human, rodent, porcine, and bovine.
• iPSCs iPSCs
• iPSCs pluripotent stem cells artificially derived from a normally non-pluripotent cell, such as an adult somatic cell, by inducing a "forced” expression of certain genes.
• hiPSC refers to human iPSCs.
• ESCs embryonic stem cells
• ES cells embryonic stem cells
• a precursor cell encompasses any cells that can be used in methods described herein, through which one or more precursor cells acquire the ability to renew itself or differentiate into one or more specialized cell types.
• a precursor cell is pluripotent or has the capacity to becoming pluripotent.
• the precursor cells are subjected to the treatment of external factors (e.g., growth factors) to acquire pluripotency.
• a precursor cell can be a totipotent (or omnipotent) stem cell; a pluripotent stem cell (induced or non-induced); a multipotent stem cell; an oligopotent stem cells and a unipotent stem cell.
• a precursor cell can be from an embryo, an infant, a child, or an adult. In some embodiments, a precursor cell can be a somatic cell subject to treatment such that pluripotency is conferred via genetic manipulation or protein/peptide treatment.
• one step is to obtain stem cells that are pluripotent or can be induced to become pluripotent.
• pluripotent stem cells are derived from embryonic stem cells, which are in turn derived from totipotent cells of the early mammalian embryo and are capable of unlimited, undifferentiated proliferation in vitro.
• Embryonic stem cells are pluripotent stem cells derived from the inner cell mass of the blastocyst, an early-stage embryo. Methods for deriving embryonic stem cells from blastocytes are well known in the art. Human embryonic stem cells H9 (H9-hESCs) are used in the exemplary embodiments described in the present application, but it would be understood by one of skill in the art that the methods and systems described herein are applicable to any stem cells.
• NSCB National Stem Cell Bank
• UCSF Human Embryonic Stem Cell Research Center at the University of California, San Francisco
• WISC cell Bank at the Wi Cell Research Institute
• UW-SCRMC University of Wisconsin Stem Cell and Regenerative Medicine Center
• Novocell, Inc. San Diego, Calif.
• Exemplary embryonic stem cells that can be used in embodiments in accordance with the present invention include but are not limited to SA01 (SA001); SA02 (SA002); ES01 (HES-1); ES02 (HES- 2); ES03 (HES-3); ES04 (HES-4); ES05 (HES-5); ES06 (HES- 6); BG01 (BGN-01); BG02 (BGN-02); BG03 (BGN-03); TE03 (13); TE04 (14); TE06 (16); UCOl (HSF1); UC06 (HSF6); WA01 (HI); WA07 (H7); WA09 (H9); WA13 (H13); WA14 (H14).
• iPSCs Induced Pluripotent Stem Cells
• iPSCs are derived by transfection of certain stem cell-associated genes into non-pluripotent cells, such as adult fibroblasts. Transfection is typically achieved through viral vectors, such as retroviruses. Transfected genes include the master transcriptional regulators Oct- 3/4 (Pouf51) and Sox2, although it is suggested that other genes enhance the efficiency of induction. After 3-4 weeks, small numbers of transfected cells begin to become morphologically and biochemically similar to pluripotent stem cells, and are typically isolated through morphological selection, doubling time, or through a reporter gene and antibiotic selection.
• iPSCs include but are not limited to first generation iPSCs, second generation iPSCs in mice, and human induced pluripotent stem cells.
• a retroviral system is used to transform human fibroblasts intopluripotent stem cells using four pivotal genes: Oct3/4, Sox2, Klf4, and c-Myc.
• a lentiviral system is used to transform somatic cells with OCT4, SOX2, NANOG, and LIN28.
• Genes whose expression are induced in iPSCs include but are not limited to Oct-3/4 (e.g., Pou5fl); certain members of the Sox gene family (e.g., Soxl, Sox2, Sox3, and Soxl5); certain members of the Klf family (e.g., Klfl, Klf2, Klf4, and Klf5), certain members of the Myc family (e.g., C-myc, L-myc, and N-myc), Nanog, and LIN28.
• Oct-3/4 e.g., Pou5fl
• Sox gene family e.g., Soxl, Sox2, Sox3, and Soxl5
• Klf family e.g., Klfl, Klf2, Klf4, and Klf5
• Myc family e.g., C-myc, L-myc, and N-myc
• Nanog LIN28.
• non- viral based technologies are
• an adenovirus can be used to transport the requisite four genes into the DNA of skin and liver cells of mice, resulting in cells identical to embryonic stem cells. Since the adenovirus does not combine any of its own genes with the targeted host, the danger of creating tumors is eliminated.
• reprogramming can be accomplished via plasmid without any virus transfection system at all, although at very low efficiencies.
• direct delivery of proteins is used to generate iPSCs, thus eliminating the need for viruses or genetic modification.
• generation of mouse iPSCs is possible using a similar methodology: a repeated treatment of the cells with certain proteins channeled into the cells via poly- arginine anchors was sufficient to induce pluripotency.
• the expression of pluripotency induction genes can also be increased by treating somatic cellswith FGF2 under low oxygen conditions.
• exemplary iPS cell lines include but not limited to iPS-DF19-9; iPS-DF19-9; iPS-DF4-3; iPS-DF6-9; iPS(Foreskin); iPS(IMR90); and iPS(IMR90).
• Any method for producing definitive endoderm from pluripotent cells are applicable to the methods described herein. Exemplary methods are disclosed in, for example, "Methods and systems for converting precursor cells into intestinal tissues through directed differentiation,"
• pluripotent cells may be derived from a morula.
• pluripotent stem cells may be stem cells.
• Stem cells used in these methods can include, but are not limited to, embryonic stem cells.
• Embryonic stem cells may be derived from the embryonic inner cell mass or from the embryonic gonadal ridges.
• Embryonic stem cells or germ cells can originate from a variety of animal species including, but not limited to, various mammalian species including humans.
• human embryonic stem cells are used to produce definitive endoderm.
• human embryonic germ cells are used to produce definitive endoderm.
• iPSCs are used to produce definitive endoderm. Additional methods for obtaining or creating DE cells that can be used in the present invention include but are not limited to those described in United States Patent No. 7,510,876 to D' Amour et al.; United States Patent No.
• NAFLD Non-alcoholic Fatty Liver Disease
• PNALD parental nutrition associated liver disease
• liver disease such as lipid droplet accumulation and cystoskeleton filament disorganization, steatosis, and hepatocellular ballooning are needed.
• current approaches are limited in their applications to unicellular, monogenic and relatively simple pathologies, failing to capture more prevailing and complex disease pathology such as epithelial organ fibrosis.
• a method of making a lipotoxic organoid model may comprise the steps of contacting a liver organoid made according to the methods described herein, with a free fatty acid (FFA) composition.
• FFA composition may comprise oleic acid, linoleic acid, palmitic acid, or combinations thereof, preferably oleic acid.
• the amount of FFA may be determined by one of ordinary skill in the art.
• the FFA preferably oleic acid
• a liver organoid in an amount of from about 10 ⁇ to about 10,000 ⁇ , or from about 20 ⁇ to about 5,000 ⁇ , or from about 30 ⁇ to about 2500 ⁇ , or from about 40 ⁇ to about 1250 ⁇ or from about 50 ⁇ to about 1000 ⁇ , or from about 75 ⁇ to about 900 ⁇ or from about 80 ⁇ to about 800 ⁇ , or from about 90 ⁇ to about 700 ⁇ , or about 100 ⁇ to about 500 ⁇ , or from about 200 ⁇ to about 400 ⁇ .
• the FFA may be contacted with the liver organoid for a period of time of from about 1 hour to about 10 days, or from about 2 hours to about 9 days, or from about 3 hours to about 8 days, or from about 4 hours to about 7 days, or from about 5 hours to about 6 days, or from about 6 hours to about 5 days, or from about 7 hours to about 4 days, or from about 8 hours to about 3 days, or from about 9 hours to about 2 days, or from about 10 hours to about 1 day.
• the range is about 3 to about 5 days, +/- 24 hours.
• the lipotoxic organoid model is a model of fatty liver disease. [0042] In one aspect, the lipotoxic organoid model is a model of steatohepatitis. [0043] In one aspect, the lipotoxic organoid model is a model of
• the lipotoxic organoid model is a model of
• the lipotoxic organoid model is a model of
• the lipotoxic organoid model may be characterized by cytoskeleton filament disorganization, ROS increase, mitochondrial swelling, trigycleride accumulation, fibrosis, hepatocyte ballooning, IL6 secretion, steatosis, inflammation, ballooning and Mallory's body-like, tissue stiffening, cell-death, and combinations thereof.
• a method of screening for a drug for treatment of a liver disease including NAFLD and/or cholestasis is disclosed.
• the method may comprise the step of contacting a candidate drug with a lipotoxic organoid model as disclosed herein.
• the method may comprise the step of contacting the nutritional supplement/TPN with a lipotoxic organoid model as disclosed herein.
• the three-dimensional (3D) liver organoid model of fatty liver disease is disclosed, wherein the organoid is characterized by steatosis, inflammation, ballooning and
• the three-dimensional (3D) liver organoid model is a model of drug induced hepatotoxicity and
• the three-dimensional (3D) liver organoid model is a model of parenteral nutrition associated liver disease (PNALD)
• the three-dimensional (3D) liver organoid model does not comprise inflammatory cells, for example T-cells or other inflammatory secreted proteins.
• the method may comprise the steps of
• RA retinoic acid
• Fibroblast growth factors are a family of growth factors involved in angiogenesis, wound healing, and embryonic development.
• the FGFs are heparin-binding proteins and interactions with cell-surface associated heparan sulfate proteoglycans have been shown to be essential for FGF signal transduction.
• Suitable FGF pathway activators will be readily understood by one of ordinary skill in the art.
• Exemplary FGF pathway activators include, but are not limited to: one or more molecules selected from the group consisting of FGF1, FGF2, FGF3, FGF4, FGF10, FGF11, FGF12, FGF13, FGF14, FGF15, FGF16, FGF17, FGF18, FGF19, FGF20, FGF21, FGF22, and FGF23.
• FGF1, FGF2, FGF3, FGF4, FGF10, FGF11, FGF12, FGF13, FGF14, FGF15, FGF16, FGF17, FGF18, FGF19, FGF20, FGF21, FGF22, and FGF23 may be used to activate these pathways.
• DE culture is treated with the one or more molecules of a signaling pathway described herein at a concentration of 10 ng/ml or higher; 20 ng/ml or higher; 50 ng/ml or higher; 75 ng/ml or higher; 100 ng/ml or higher; 120 ng/ml or higher; 150 ng/ml or higher; 200 ng/ml or higher; 500 ng/ml or higher; 1,000 ng/ml or higher; 1,200 ng/ml or higher; 1,500 ng/ml or higher; 2,000 ng/ml or higher; 5,000 ng/ml or higher; 7,000 ng/ml or higher; 10,000 ng/ml or higher; or 15,000 ng/ml or higher.
• concentration of signaling molecule is maintained at a constant throughout the treatment. In other embodiments, concentration of the molecules of a signaling pathway is varied during the course of the treatment.
• a signaling molecule in accordance with the present invention is suspended in media comprising DMEM and fetal bovine serine (FBS).
• the FBS can be at a concentration of 2% and more; 5% and more; 10% or more; 15% or more; 20% or more; 30% or more; or 50% or more.
• concentration of signaling molecule in accordance with the present invention is suspended in media comprising DMEM and fetal bovine serine (FBS).
• the FBS can be at a concentration of 2% and more; 5% and more; 10% or more; 15% or more; 20% or more; 30% or more; or 50% or more.
• the regiment described herein is applicable to any known molecules of the signaling pathways described herein, alone or in combination, including but not limited to any molecules in the FGF signaling pathway.
• Suitable GSK3 inhibitors will be readily understood by one of ordinary skill in the art.
• Exemplary GSK3 inhibitors include, but are not limited to: Chiron CHIR99021, for example, which inhibits GSK3 .
• Chiron CHIR99021 for example, which inhibits GSK3 .
• the GSK3 inhibitor may be administered in an amount of from about 1 uM to about 100 uM, or from about 2 uM to about 50 uM, or from about 3 uM to about 25 uM.
• One of ordinary skill in the art will readily appreciate the appropriate amount and duration.
• the stem cells may be mammalian, or human, iPSCs.
• the foregut spheroids may be embedded in a
• basement membrane matrix such as, for example, the commercially available basement membrane matrix sold under the tradename Matrigel.
• the liver organoids may be characterized in that the liver organoids may express alpha-fetoprotein (AFP), albumin (ALB), retinol binding protein (RBP4), cytokeratin 19 (CK19), hepatocyte nuclear factor 6 (HNF6), and cytochrome P450 3A4 (CYP3A4), HNF4a, E-cadherin, DAPI, and Epcam. Such expression may occur, for example, at day 40 to day 50. The expression level may be similar to that observed in human liver cells, for example, that of an adult liver cell.
• AFP alpha-fetoprotein
• ALB albumin
• RBP4 retinol binding protein
• CK19 cytokeratin 19
• HNF6 hepatocyte nuclear factor 6
• CYP3A4 cytochrome P450 3A4
• HNF4a E-cadherin
• Epcam Epcam
• the liver organoid may be characterized in that the liver organoid has bile transport activity.
• the liver organoid may be derived from a stem cell and may comprise a luminal structure further containing internalized microvilli and mesenchymal cells.
• the luminal structure may be surrounded by polarized hepatocytes and a basement membrane.
• the liver organoid may comprise functional stellate cells and functional Kupffer cells.
• the liver organoid may, in certain aspects, be characterized by having one or more of the following: bile production capacity, bile transport activity, Complement factor H expression of at least 50 ng/niL/lxe 6 cells/24hr, Complement factor B of at least 40 ng/mL/l e 6 cells/24hr, C3 expression of at least 1000 ng/mL/lxe 6 cells/24hr; C4 expression of at least 1000 ng/mL/lxe 6 cells/24hr, fibrinogen production of at least 1,000 ng/mL/lxe 6 cells/24hr and albumin production of at least 1,000 ng/mL/lxe 6 cells/24hr.
• the liver organoid may be characterized by having total hepatic protein expression of at least 10,000 ng/mL lxe 6 cells/24 hours.
• the liver organoid may be characterized in that it may express one or more genes selected from PROX1, RBP4, CYP2C9, CYP3A4, ABCC11, CFH, C3, C5, ALB, FBG, MRP2, ALCAM, CD68, CD34, CD31.
• the liver organoid may comprise cells comprising a drug metabolism cytochrome variant, such as, for example, a CY2C9*2 variant.
• the liver organoid may comprise a vasculature, such as that described in US 20160177270.
• the liver organoid may be characterized in that the liver organoid does not comprise inflammatory cells, for example T-cells or other inflammatory secreted proteins.
• HLO human liver organoid
• Atomic force microscopy measurement revealed that overall organoid stiffening correlates the severity of inflammation and fibrosis.
• the measurement fidelity to clinical phenotype was confirmed using three monogenic steatohepatitis-specific iPSC lines.
• Applicant established an iatrogenic parental nutrition associated liver disease (PNALD) model in organoids.
• PNALD parental nutrition associated liver disease
• Retinoic acid (RA) signaling is a well-known important specifier of thyroid, lung, and pancreas from foregut endoderm during the early organ specification phase, whereas it is clearly not essential for specification of the liver in model organisms (Kelly and Drysdale, 2015) with the exception of zebrafish (Negishi et al., 2010). Indeed, xenopus and chick are similar to mammals as liver specification occurs in embryos lacking RA (Chen et al., 2004; Stafford et al., 2004).
• RA promotes hepatic stellate cell differentiation from mesenchyme, which is controlled in part by the zinc finger transcription factor WT1 expressed in the STM and stellate cells (Ijpenberg et al., 2007; Wang et al., 2013). Additionally, several studies suggest that the balanced RA regulation induces monocyte fate specification from human stem cells (Purton et al., 2000; Ronn et al., 2015). Also, later liver bud growth is promoted by RA signaling via unknown mechanisms (Zorn and Wells, 2009).
• liver organoids do not merely generate epithelial cells but also co-develop mesenchymal cell components.
• Applicant tested the hypothesis that the timely RA pulsing into liver organoids preferentially co- differentiates supportive lineages after hepatic specification from human iPSC. By fostering close interactions between epithelial and supportive lineages in a 4-D condition wherein they can co- develop, Applicant demonstrated the applicability of the liver organoid to model inflammation and fibrosis.
• Applicant also established a screen platform to determine the severity of fibrosis by evaluating stiffness at single organoid level in the living state. This method serves as an invaluable application platform for the study of epithelial organ inflammation and fibrosis towards drug development and personalized therapy.
• Applicant established a liver organoid model from human iPSCs by transient induction of RA. Applicant initially differentiated iPSCs to foregut spheroids through definitive endoderm (DE) specification as previously described (Spence et al., 2011). The foregut spheroids were mixed with the attached cells grown in the same well, and the mixture was embedded in Matrigel.
• DE definitive endoderm
• RA is a known specifier for diverse lineages through a context dependent process
• Applicant set the duration of initial RA signaling before the hepatocyte maturation process which is cultured in hepatocyte culture media (HCM) and characterized the established organoids at day 20 as illustrated in FIG 1 , A. Since the highest concentration of albumin in culture media was observed with 4 days of RA exposure among the various duration of RA from 0 to 5 days, the further characterization of the established organoids was compared between two conditions of 0 and 4 days-RA exposure. The number of organoids was increased 1.8-fold in RA treated wells compared to untreated and the size was increased 1.5-fold after RA treatment (FIG 1, B, C, and D).
• HLO human liver organoids
• scRNA-seq single-cell RNA sequencing analysis of RA treated HLO showed the expression signatures specific to stellate cells, liver resident macrophage Kupffer cells, and endothelial cells as evidenced by stellate cell markers (ACTA2, DES, PDGFRB), Kupffer cell markers (CD68, IRF7), and endothelial cell markers (OIT3, DPP4, C1QTNF1; FIG 1, H)
• HLO RA-based liver organoid
• FFA free fatty acids
• Applicant indicated 3 day and 5 days OA treated HLO as steatohepatitis (s)HLO and cirrhosis (c)HLO (FIG. 4, A).
• sHLO is HLO treated with oleic acid for three days and show lipid accumulation and inflammation.
• cHLO is HLO treated with oleic acid for five days and shows fibrosis (HLO is stiffened) in addition to lipid accumulation and inflammation.
• OA oleic acid
• LA linoleic acid
• PA palmitic acid
• SA stearic acid
• Live-cell imaging and subsequent quantitation displayed that lipid accumulation was elevated in sHLO in a dose dependent fashion (up to 18-fold; FIG. 4, B and C).
• the size of lipid droplets was enlarged (FIG. 4, B).
• Hepatocyte ballooning (enlargement) was one of the pathological grading indicators to determine the nonalcoholic steatohepatitis (NASH) activity (NAS scoring), which was confirmed in 800 ⁇ OA treated sHLO by live imaging of cellular membrane (FIG. , 4B).
• NASH nonalcoholic steatohepatitis
• Triglycerides a main constituent of lipids accumulated in the liver, were also detected in 800 ⁇ treated sHLO, but not in untreated sHLO (FIG.4, D).
• ELISA of culture supernatant showed that IL-6 was secreted 2.2-fold in 800 ⁇ OA treated sHLO culture media when compared to the untreated (FIG. 4, E).
• IL-8 and TNF-alpha were also upregulated in a 200 ⁇ or 800 ⁇ OA treated condition (10- and 2-fold increase, respectively; FIG. 4, F).
• the migration of THP1 was assessed in 24hrs after culturing in trans wells, and THP-1 migration cells were elevated in a OA treated sHLO, suggesting FFA treatment naturally evoked an inflammatory response in sHLO presumably by causing stress on hepatocyte like cells (up to 2-fold: FIG.
• E-cad E-cad mRuby embryonic stem (ES) cells derived organoids, reconstructed the spheroids from either E-cad positive or negative cells, and applied for ELISA for IL6 and P3NP and RNA expression for IL8 and TNF-alpha.
• ES E-cad mRuby embryonic stem
• Applicant also tested same experiments using human hepatocyte cell line HepG2, Macrophage cell line THP-1, and hepatic stellate cell LX-2, and had a similar result of E-cad positive and negative cells. The results demonstrated that liver organoids only response to FFA treatment on inflammation and fibrosis response.
• each single HLO 14x14 matrix in a 25x25 ⁇ square
• AFM cantilever which can provide a spatial mapping of topographical and mechanical information of HLO.
• the representative histogram of calculated Young's modulus (E, kPa) of single HLO clearly showed a Gaussian-like distribution and its peak values and width were increased in accordance with the OA concentration (FIG.4, B; 0, 200, 400, 800 ⁇ ). Young's moduli determined from HLOs were summarized by dot plot with box-and-whisker plot (FIG.
• TNF-alpha and IL- 8 were also upregulated by OA addition, known to be correlated with fibrosis severity in NAFLD patients (Ajmera et al., 2017). These results indicate that stiffness of HLO can be a quantifiable measurement for the severity of fibrosis, and thus can be potentially applied for a high-throughput screening of fibrosis.
• Applicant established three Wolman disease patient-specific iPSC lines, which is a mono- genetic disorder with lethal steatohepatitis, and confirmed the significant rigidity increase relative to normal iPSC line-derived organoids, notably with remarkable correlation to enzymatic activity at the time of clinical diagnosis (FIG. 5, B).
• FIG. 6, F but NOT for 'fibrosis' (AFM based stiffness measurements, FIG. 6, G) to polygenic scores.
• Applicant also found that OCA reponse differ among the cell line and response to OCA are depended on SNP number (FIG, 6H)
• stromal populations are fully reactive to known fibrosis inducers including LPS and fatty acids, paving a new way for modeling multicellular and complex pathologies.
• liver measurement is a highly attractive readout due to its robustness, normalization and relative simplicity.
• a functional swelling assay was established for cystic fibrosis patients' gut organoids, demonstrating an effective drug selection (Saini, 2016).
• Live rigidity assessment on a single liver organoid from iPSC is an effective way to predict the severity of fibrosis.
• a significant correlation between liver stiffness measurement and fibrosis stage is clinically reported in fatty liver disease patients by elastography (Yoneda et al., 2008).
• liver stiffness increased in proportion to both LPS and FFAs, accompanied by inflammatory cytokine production and fibroblast expansion.
• an organoid based rigidity detection assay could be used to analyze fibrosis using lung, kidney, cardiac and gut organoids.
• organoid based assay platforms may be used to better understand the human specific mechanisms of fatty liver diseases and establishing high-content screening for drug discovery for these diseases. Combined with compound libraries and nutritional metabolites, organoid based mechanical screening would be highly attractive model system for implicating effective therapy in humans, otherwise not testable preclinically.
• Patient-specific iPSC-derived organoids might be used to predict individualized drug efficacy and epithelial response.
• Human iPSCs can be established from both healthy and diseased individuals.
• the use of patients' iPSCs is expected to model inter- individual differences of lipotoxicity, drug efficacy and safety concerns (Warren et al., 2017a; Warren et al., 2017b).
• phenotypic screening using a liver organoid-based platform will promote personalized selection of highly effective interventions for the disorders.
• the disclosed system may be a highly compatible assay for reflecting nutrition associated conditions before administration.
• patient-specific iPSC-derived organoids can be used to customize PN formulation to each patient with the aim of minimizing the possible progression to hepatic steatosis and fibrosis (PNALD).
• PNALD hepatic steatosis and fibrosis
• PN formulation is often customized (Mercaldi et al., 2012) as commercial solutions do not meet the caloric, amino acid, and electrolyte needs of critically ill patients, who are often obese and require fluid restriction, and display hepatic/renal dysfunction (Boullata et al., 2014). Beyond nutritional needs, there is an urgent need to gain insights for a reduction of possible adverse effects associated with PN products. The liver organoid would thus be useful to evaluate safety concerns especially for PNALD risk assessment, facilitating the customization strategy of PN formulations for each patient.
• hPSCs Maintenance The TkDA3 human iPSC clone used in this study was kindly provided by K. Eto and H. Nakauchi. Human iPSC lines were maintained as described previously (Takebe et al., 2015; Takebe et al., 2014). Undifferentiated hiPSCs were maintained on feeder- free conditions in mTeSRl medium (StemCell technologies, Vancouver, Canada) on plates coated with Matrigel (Corning Inc., NY, USA) at 1/30 dilution at 37°C in 5% C0 2 with 95% air. [0097] Definitive endoderm induction.
• Human iPSCs into definitive endoderm was differentiated using previously described methods with slight modifications (Spence et al., 2011). In brief, colonies of human iPSCs were isolated in Accutase (Thermo Fisher Scientific Inc., MA, USA) and 150,000 cells/mL were plated on Matrigel coated tissue culture plate (VWR Scientific Products, West Chester, PA).
• RPMI 1640 medium (Life Technologies) containing 100 ng/mL Activin A (R&D Systems, MN, USA) and 50 ng/mL bone morphogenetic protein 4 (BMP4; R&D Systems) at day 1, 100 ng/mL Activin A and 0.2 % fetal calf serum (FCS; Thermo Fisher Scientific Inc.) at day 2 and 100 ng/mL Activin A and 2% FCS at day 3.
• Day4-6 cells were cultured in Advanced DMEM/F12 (Thermo Fisher).
• HLO induction At day 7, spheroids and attached cells are gently pipetted to be delaminated from dishes. They were centrifuged at 800 rpm for 3 minutes, embedded in a 100 % Matrigel drop on the dishes in Advanced DMEM/F12 with B27, N2 and 2 uM retinoic acid (RA; Sigma, MO, USA) after removing supernatant, and cultured for 4 days.
• RA retinoic acid
• HCM Hepatocytes Culture Medium
• HGF hepatocyte growth factor
• OSM Oncostatin M
• albumin, IL-6, and P3NP ELISA To measure albumin secretion level of HLO, 200 of culture supernatant was collected from HLO embedded in Matrigel. For IL-6 and P3NP, 20-30 organoids were seeded and cultured on an ultra- low attachment multiwell plates 96 well plate (Corning). To define the exact number of organoids in each well and lastly normalize the secreted level for IL-6 and P3NP by the number, the organoids were captured on The KEYENCE BZ-X710 Fluorescence Microscope.
• the culture supernatants were collected at 24hrs (for albumin), 96 hrs (for IL- 6) and 120 hrs (P3NP) time points after the culture and stored at - 80°C until use.
• the supernatant was centrifuged at 1,500 rpm for 3 min and to pellet debris, and the resulting supernatant was assayed with Human Albumin ELISA Quantitation Set (Bethyl Laboratories, Inc., TX, USA), Human IL-6 ELISA Kit
• Phagocyte, lipids, ROS live-cell imaging After being cultured in an ultra-low attachment 6 multi-well plate, 5-10 HLO were picked up and seeded in a Microslide 8 Well Glass Bottom plate (Ibidi, WI, USA) and subjected to live-cell staining.
• the following antibodies were used: pHrodo® Red S. aureus Bioparticles® Conjugate for Phagocyte activity (Thermo Fisher Scientific Inc.), BODIPY® 493/503 for lipids (Thermo Fisher Scientific Inc.), Di-8-ANEPPS for membrane (Thermo Fisher Scientific Inc.), and CellROX green reagent for ROS detection (Thermo Fisher Scientific Inc.).
• lipid droplet volume was calculated by IMARIS8 and normalized by each organoid size. Significance testing for lipid droplet volume and ROS production (%) was conducted by Student's t-test.
• HLO Flow cytometry. HLO were isolated from 10 Matrigel droplets and washed by 1 x PBS. HLO were dissociated to single cells by the treatment of Trypsin-EDTA (0.05%), phenol red (Gibco) for 10 min. After PBS wash, the single cells were subjected to flow cytometry with BV421 -conjugated Epcam antibody (BioLegend), PE-conjugated CD166 antibody (eBioscience, CA, USA), and PE/Cy7- CD68 (eBioscience). DNA was measured by propidium iodide staining.
• HLO which had been isolated from Matrigel and washed by 1 x PBS, were divided into each condition and cultured on an ultra- low attachment 6 multi-well plates (Corning). HLO were cultured with LPS (Sigma), OA (Sigma), LA (Sigma), SA (Sigma), or PA (Sigma) and collected at day 1 and 3 (for LPS HLO) and at day 3 and 5 (for OA) after the culture.
• HLO human FGF19 recombinant
• 20-30 HLO were cultured in HCM media in the presence or absence of oleic acid (800 ⁇ ), and 1 ⁇ OCA and 40 ng/ ml FGF19 were added into 800 ⁇ OA condition.
• HLO were collected at day 3 for lipids live-cell imaging and at day 5 for stiffness measurement.
• HLO Whole mount immunofluorescence. HLO were fixed for 30 min in 4% paraformaldehyde and permeabilized for 15 min with 0.5% Nonidet P-40. HLO were washed by lx PBS three times and incubated with blocking buffer for 1 h at room temperature. HLO were then incubated with primary antibody; anti- alpha smooth muscle actin antibody (1 :50 dilution; abeam) overnight at 4 °C. HLO were washed by 1 x PBS and incubated in secondary antibody in blocking buffer for 30 min at room temperature. HLO were washed and mounted using Fluoroshield mounting medium with DAPI (abeam). The stained HLO were visualized and scanned on a Nikon Al Inverted Confocal Microscope (Japan) using 60x water immersion objectives.
• RNA isolation RT-qPCR.
• RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany). Reverse transcription was carried out using the SuperScriptlll First-Strand Synthesis System for RT-PCR (Invitrogen, CA, USA) according to manufacturer's protocol. qPCR was carried out using TaqMan gene expression master mix (Applied Biosystems) on a
• QuantStudio 3 Real-Time PCR System (Thermo Fisher Scientific Inc). All primers and probe information for each target gene was obtained from the Universal ProbeLibrary Assay Design Center (https ://qpcr.probefinder.com/organism.j sp) . Significance testing was conducted by Student' s t-test.
• E, Pa Young's moduli
• THP-1 cell migration assay THP-1 cell, which was gifted from
• T. Suzuki was maintained in Advanced DMEM/F12 (Thermo Fisher Scientific Inc.) containing 10% FBS. THP-1 floating cells were collected, and 200,000 cells were added with serum-free Advanced DMEM/F12 to the membrane chamber of the CytoSelectTM 96-Well Cell Migration Assay (5 ⁇ , Fluorometric Format; Cell Biolabs, CA, USA). 10-20 HLO were cultured in HCM media including 0, 400, 800uM OA with an ultra-low attachment 96 multi-well plate (Corning) for three days. To define the exact number of organoids in each well and lastly normalize the final migrated cells by the number, the organoids were captured on The KEYENCE BZ-X710 Fluorescence Microscope.
• HLO hepatic triglycerides
• HCM oleic acid
• oleic acid 800 ⁇
• They were cultured on an ultra-Low attachment 6 multi-well plate for three days. Quantitative estimation of hepatic triglyceride accumulation was performed by an enzymatic assay of triglyceride mass using the EnzyChrom Triglyceride assay kit (Bioassay Systems, CA, USA).
• HLO survival assay HLO were collected from Matrigel and washed by 1 x PBS. 30-40 organoids were cultured on an ultra- low attachment 6 multi-well plate (Corning). HLO were captured on The KEYENCE BZ-X710 Fluorescence Microscope every day. The surviving and dead organoids were counted manually from the photo. HLO with a rounded configuration was counted as the surviving while the organoids with out of shape is counted as dead. To assess the survival rate of OA treated HLO at the same time point, 3D cell titer glo assay was used (Promega, Wi, USA).
• Adiposity amplifies the genetic risk of fatty liver disease conferred by multiple loci. Nat Genet 49, 842-847.
• van de Garde M.D., Movita, D., van der Heide, M., Herschke,
• PNPLA3 patatin-like phospholipase domain containing 3 gene

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