SUPPORTED IN VITRO DEVELOPED TISSUE CULTURE AND CULTURING METHODS

Abstract

An elongated or fiber-supported multicellular aggregation of multipotent cells, wherein multipotent cells are arranged in an oblong or longish arrangement with an aspect ratio of a prolate dimension to a perpendicular dimension of at least 2:1, or supported by a fibrous structure, and wherein the aggregate contains cells at different stages of differentiation, and the aggregate contains polar cells; methods of generating such aggregates; methods of developing the aggregates further into tissue organoids and kits for such methods.

Claims

1-15. (canceled)

16. A method of generating an elongated or fiber-supported multicellular aggregation of neural lineage with neuronal differentiated cells comprising the steps of: a) providing a plurality of pluripotent or non-human totipotent cells (i) that are located in an oblong or longish arrangement adhered to a support, said support has a length of 20 m to 20 mm and a diameter of 1 m to 60 m, wherein said support is a biocompatible polymer that is not a biopolymer or wherein said support is a protein, or (ii) that are arranged on a fibrous structured support, and said support has a length of 20 m to 20 mm and a diameter of 1 m to 60 m, wherein said fibrous structured support is a biocompatible polymer that is not a biopolymer or wherein said fibrous structured support is a protein; and b) letting said cells grow and differentiate in said arrangement, wherein said cells form intercellular bonds and adhere to each other; wherein said cells are stimulated to differentiate by a contacting the cells with a neuronal growth or differentiation factor.

17. The method of claim 16, wherein the arrangement has an aspect ratio of a prolate dimension to a perpendicular dimension of at least 2:1.

18. The method of claim 16, wherein said support is non-porous or has a porosity of less than 5% (v/v) of the supports volume.

19. The method of claim 16, wherein said support is a polymer microfilament and/or is biocompatible but not bioactive.

20. The method of claim 16, wherein said support comprises a polyethylenglycol chain.

21. The method of claim 20, wherein the support comprises or consists of polylactide, polyglycolide or a combination thereof.

22. The method of claim 16, wherein said support is dissolved or bio-resorbed after step b).

23. The method of claim 16, wherein 2 to 500000 cells are located on the oblong or longish arrangement in step a).

24. The method of claim 16, wherein the most apart cells are at least 1 m apart.

25. A multicellular aggregation of neural lineage with neuronal differentiated cells obtainable by a method of claim 16.

26. An elongated or fiber-supported multicellular aggregation of neural lineage with neuronal differentiated cells wherein cells are arranged in an oblong or longish arrangement with an aspect ratio of a prolate dimension to a perpendicular dimension of at least 2:1 on a fibrous structured support, wherein said fibrous structured support is a biocompatible polymer that is not a biopolymer or wherein said fibrous structured support is a protein, and said support has a length of 20 m to 20 mm and a diameter of 1 m to 60 m, and wherein said aggregate contains cells at different stages of differentiation, and said aggregate contains polar cells and said polar cells with a uniform orientation with respect to the center of said aggregate.

27. The aggregation of claim 26, wherein said polar cells constitute at least 50% of the cells of the aggregate.

28. The aggregation of claim 26, comprising between 8000 and 100 Million cells and/or having a size of between 50 m to 40 mm.

29. A method of generating an artificial neuronal tissue culture, comprising: o) providing an elongated or fiber-supported multicellular aggregation of neural lineage as defined in claim 25; p) culturing said elongated or fiber-supported multicellular aggregation in a three dimensional matrix, wherein said cells are allowed to differentiate, thereby expanding said cells; and q) culturing said expanded cells of step p) in a suspension culture.

30. The method of claim 29, further comprising step r) adding dissolved material of a three dimensional matrix to said suspension culture, whereby the dissolved material adheres to the culture and forms a matrix.

31. The method of claim 30, wherein the dissolved material of a three dimensional matrix is dissolved extracellular matrix.

32. A method of generating an artificial neuronal tissue culture, comprising: u) providing multicellular aggregation of neural lineage as defined in claim 25, v) culturing said multicellular aggregation in a three dimensional matrix, wherein said cells are allowed to differentiate, thereby expanding said cells, w) culturing said expanded cells of step v) in a suspension culture; and r) adding dissolved material of a three dimensional matrix to said suspension culture, whereby the dissolved material adheres to the culture and forms a matrix, wherein the dissolved material of a three dimensional matrix is dissolved extracellular matrix.

33. The method of claim 29, wherein the three dimensional matrix is a gel.

34. The method of claim 16, further comprising i) decreasing or increasing the expression in a gene of interest in a cell of the method of claim 16 or ii) administering a candidate drug to the cells of the method of claim 16, at any stage during the method of claim 16, thereby investigating a developmental tissue effect of said gene or candidate drug.

35. The method of claim 34, comprising administering the candidate agent to said cells at all of said stages.

36. An artificial neuronal tissue culture obtainable by a method of claim 29.

37. An artificial neuronal tissue culture comprising a radially organized cortical plate; wherein said tissue culture is in vitro grown from an aggregate of cells and/or is not a culture of an in vivo developed brain or a tissue sample thereof.

38. The tissue culture of claim 37, comprising a basement membrane comprising laminin; a basement membrane covering a basal surface of neuroepithelium; a basement membrane outside of migrating neurons; a radially organized cortical plate comprising the expression markers Ctip2, Map2, DCX, or any combination thereof, especially Ctip2, Map2 and DCX.

39. The tissue culture of claim 37, further comprising Map2 or radial glia.

40. The tissue culture of any one of claim 37, comprising linear units of radial glia and neurons.

41. The method of testing or screening a candidate drug for developmental effects, especially for congenital disorder effects, comprising administering a candidate drug to an artificial culture according to claim 37, or during the method of claim 16, and determining an activity of interest of the cells of said culture and comparing said activity to an activity of cells to the culture without administering said candidate drug, wherein a differential activity indicates a developmental effect.

42. Use of a kit in a method of claim 29, said kit comprises i) a solid support of rod-shaped or lattice-shaped or fibrous structure, and said support has a length of 20 m to 20 mm and a diameter of 1 m to 60 m, and comprises ii) a three-dimensional matrix and/or an extracellular matrix or any component thereof selected from collagen, laminin, entactin, and heparin-sulfated proteoglycan or any combination thereof.

43. The use of claim 42, wherein the kit comprises an extracellular matrix from the Engelbreth-Holm-Swarm tumor or Matrigel.

44. The use of claim 42, wherein the kit further comprises vitamin C; vitamin A, 2-mercaptoethanol; bFGF; ROCK inhibitor; insulin; a GSK3beta inhibitor; a Wnt activator, preferably CHIR 99021; an antibacterial agent; a SMAD inhibitor; a retinoid; or any combination thereof.

45. The use of claim 42, wherein the three dimensional matrix is a gel.

46. Use of a kit in a method of claim 29, said kit comprises a rod-shaped or lattice-shaped or fibrous structured support and said support has a length of 20 m to 20 mm and a diameter of 1 m to 60, and at least a compound selected from vitamin C; vitamin A, 2-mercaptoethanol; bFGF; ROCK inhibitor; insulin; a GSK3beta inhibitor; a Wnt activator; an antibacterial agent; a SMAD inhibitor; a retinoid; or any combination thereof.

47. The use of claim 42, wherein the solid support is non-porous and/or defined in claim 18.

Description

FIGURES

[0095] FIG. 1. a. Schematic of the method for generating microfilament patterned embryoid bodies (EBs) and their subsequent growth as cerebral organoids with cortical plate. b. Bright field image of the intact braided PLGA (poly(lactic-co-glycolic acid)) fiber. c. Bright field image of isolated microfilaments. d. Hydrated microfilaments within a droplet of EB medium. e. Three examples of micropatterned EBs at day 3 of the protocol. Note the elongated and sometimes complex arrangement. f. Micropatterned EBs at later stages, during the neural induction phase, showing clearing along the edges and polarized neural ectoderm (arrows). g, h. Immunohistochemical staining of day 10 micropatterned EBs for the germ layer markers Brachyury for mesoderm (g), N-Cadherin for neural ectoderm (g), Sox17 for endoderm (h) and E-Cadherin for non-neural epithelium (h). Note the prevalence of polarized neural epithelia (arrows) displaying the apical domain on the surface (white asterix) with only occasional mesoderm or endoderm identities (arrowheads). The microfilament can be seen as an autofluorescent rod (yellow asterix).

[0096] FIG. 2. a. Bright field image of micropatterned organoids shortly after matrigel embedding, displaying numerous small buds of neuroepithelium (arrows). b. Embedded micropatterned organoids following three days of treatment with CHIR. Note the larger, more continuous buds of neuroepithelium. c. Histological section stained with haematoxylin and eosin showing pure neural tissue and many large continuous lobes of brain tissue (arrows). d. Immunohistochemical staining shows an absence of nonneural identities (Sox17 and E-Cadherin) and several large lobes of brain tissue (arrows). e. Immunohistochemical staining for the dorsal cortical marker Emx1 (green) and the neural identity marker N-Cadherin (red) reveals much of the tissue is composed of dorsal cortical brain regions. f. Staining for dorsal cortical markers Tbr2 and Tbr1 identifies all large lobes of brain tissue within microfilament patterned organoids treated with CHIR to be dorsal cortex (arrows). Organoids that were not patterned (spheroid) show much fewer dorsal regions and large brain regions that lack this identity. g. Quantification of the ration of lobes of brain tissue that were positive for Tbr1 or Tbr2 in spheroid or microfilament patterned organoids. *P<0.05, Student's t-test.

[0097] FIG. 3. a. Staining for the basement membrane component laminin (green) in spheroid organoids. Note the presence of the basement membrane surrounding the early neuroepithelium before the generation of neurons (first panel, arrow), whereas upon neuron generation only sparse labeling remains (arrowheads) adjacent to the ventricular zone (VZ, brackets) rather than over the surface of the organoid. b. Laminin staining of microfilament patterned organoids following treatment with dissolved extracellular matrix (ECM). Note the presence of a laminin-rich basement membrane covering the surface of the organoid (arrow) and outside both the VZ (bracket) and newly generated neurons. c. Bright field images organoids lacking dissolved ECM and microfilament patterned organoids with dissolved ECM showing a band of density upon addition of ECM (arrow) reminiscent of a dense cortical plate. d. Histological staining by haematoxylin and eosin reveals the presence of a radially oriented dense cortical plate (bracket) upon addition of dissolved ECM. e. Immunohistochemical staining for laminin and the neuronal markers MAP2 and Ctip2. Note the presence of remnant basement membrane without ECM addition (arrowheads), whereas upon addition of ECM a basement membrane (white arrows) forms outside the dense Ctip2+ cortical plate (yellow arrows). f. Higher magnification of immunostaining for Laminin, MAP2 and Ctip2 showing the radial orientation of neurons that have reached the cortical plate (brackets). g. Nuclear staining by DAPI reveals radially organized sections (dashed lines) while sparse staining for radial glial fibers with the marker of mitotic radial glia Phosphorylated vimentin reveals fibers that extend the width of the tissue (arrowheads) reminiscent of radial units.

[0098] FIG. 4. Bright field images of five independent batches of spheroid organoids showing the degree of variability in generation of polarized neuroectoderm and quantification at the right.

[0099] FIG. 5. a. Immunohistochemical staining of day 10 spheroid EBs for the germ layer markers Brachyury for mesoderm, N-Cadherin for neural ectoderm, Sox17 for endoderm and E-Cadherin for non-neural epithelium. Note the polarized neural epithelia (arrows) displaying the apical domain on the surface (white asterix) while some mesoderm or endoderm identities (arrowheads) are visible. b. Haematoxylin and eosin staining of spheroid organoids showing lobes of brain tissue (arrows) but also nonneural regions such as fluid-filled cysts and fibrous regions (arrowheads). Immunohistochemical staining of a spheroid organoid reveals occasional endoderm (Sox17+, inset) and nonneural epithelia (arrow) even at a later time point of 40 days.

[0100] FIG. 6. a. Bright field images showing that treatment of spherical EBs with dual-SMAD inhibition and retinoids improves early (day 3) morphology with a greater extent of surface clearing. b. Bright field imaging following matrigel embedding, however, reveals that treated EBs do not form large buds of neural epithelium instead generating numerous small rosettes and already generating neurons.

[0101] FIG. 7. a. Bright field images of five independent batches of microfilament patterned organoids showing reduced variability in generation of polarized neuroectoderm and quantification at the right. b. Bright field images several days following matrigel embedding showing the prevalence of non-neural cysts in unpatterned organoids compared with microfilament patterned organoids, and quantification at the right.

[0102] FIG. 8. a. RT-PCR for expression of markers of the three germ layers: Neuroectoderm (NE), mesoderm (ME), and endoderm (EN) in 20-day microfilament organoids and organoids lacking a filament (spherical organoids) both made from H9 cells. Neg. is the negative water control. b. Quantification of the mean ratio of individual lobes displaying positive staining for the specified regional markers (see FIG. 15d for representative stained sections). Foxg1 positive regions represent forebrain, regions highly positive for Otx2 represent midbrain, En2 positive regions represent cerebellar or hindbrain identities. *P<0.01, **P<0.0001, Student's t-test, n=8 spheroids (40-day, H9) from three independent batches, n=11 enCOR organoids (40-day, H9) from four independent batches. c. Representative sections of whole 40-day H9 organoids stained for the forebrain marker Foxg1. enCORs display increased numbers of Foxg1+ lobes (arrows) compared with spheroids. d. Heatmap of Spearman correlation coefficients of differentially expressed genes at 60 days in H9 spheroids and enCORs with the Allen BrainSpan transcriptome20. All brain regions are shown for stage I (8-9 post-conception weeks, see FIG. 18c), sorted by anterior-posterior regional identity. Scale bars: 250 m in FIG. 1e., 100 m in FIG. 1g., 500 m in FIG. 5b., FIG. 8c.

[0103] FIG. 9. a. Staining for Reelin in a dorsal cortical region early in CP formation (day-56 H9 enCOR). Several cells, which are strongly reactive for Reelin (arrows), localize outside the newly forming CP (arrowheads, recognizable by the lower intensity Map2 staining), consistent with Cajal-Retzius identity. Staining can also be seen more diffusely, consistent with its secreted role. b. Staining for calretinin, another marker of Cajal-Retzius cells, labels cells outside the newly forming CP (arrows) (day-53, H9 enCOR). Note the gradient of CP formation with more advanced CP to the left (bracket), and the initiation to the right (asterisk). Where the CP is further developed, one can also observe calretinin+ cells internal (arrowheads) to the CP, consistent with preplate splitting, and interneuron identity. c. Staining for chondroitin sulfate proteoglycan (CSPG) in day-68 H9 enCORs further demonstrates preplate splitting. Panels on the left show a less developed CP (yellow brackets) with the initiation of splitting and SP formation (white brackets), while panels on the right show a more developed CP with layers consistent with SP, CP, and MZ. Scale bars: 100 m in all panels. d. Quantification of the mean ratio of individual lobes displaying a CP in H&E stained sections of day-60 H9 organoids. Individual lobes were identified by the presence of a ventricular space and radial VZ. CP was identified by the presence of a condensed band separated from the VZ by a cell-sparse zone. Each point is an independent batch of 2-3 organoids, each with several lobes of brain tissue. n=4 independent batches of 12 spheroids, n=5 independent batches of 12 enCORs. Error bars are standard deviation.

[0104] FIG. 10. enCORs display radial units and radial neuronal migration. a. Nestin staining for radial glia in day-70 H1 enCORs reveals long basal processes (arrowheads) that terminate with end feet at the surface of the organoid (asterisks) outside the CP and MZ. b. Electroporation of the VZ of a 64-day H9 enCOR with a GFP construct and vibratome sectioning the next day reveals individual RG basal processes (arrows) that extend to the outer surface (asterisks). c. Live imaging of an outer/basal RG (arrow marks the cell body) in a H1 enCOR electroporated with GFP on day 63, followed by vibratome sectioning four days later and live imaging 24-hours later. Note the long basal process (arrowheads) and endfoot (asterisk) as well as a division event including mitotic somal translocation beginning at 21:40. The newly generated daughter cell (blue arrow) then extends a process apically (blue arrowheads). Time stamp is hours:minutes. d. Live imaging of migration of several neurons (arrowheads) in the same sample as d., displaying typical radial migration including transient stalling with multipolar morphology (for example white arrowhead 11:40 to 23:00). Time stamp is hours:minutes. e. Individual neurons labeled by electroporation of an H9 enCOR at day 64 with an integrating farnesylated GFP construct to allow for long-term labeling and analysis after 36 days. Note the primary dendrite extending from the cell body (arrows) toward the outer surface (oriented up in all images), as well as many parallel fibers (arrowheads) in the outer cell sparse MZ. Scale bars: 100 m in FIG. 3g., FIG. 10a., b., 50 m in c., d., 20 m in e.

[0105] FIG. 11. Ethanol treatment leads to defects in cortical plate formation which is phenocopied by omitting retinols a. H&E histology of 70-day H1 enCORs treated beginning on day 56 with three doses of ethanol or water as mock control four times over the course of two weeks reveals the loss of the radial cortical plate (arrowheads) in higher ethanol treatments (87 mM and 150 mM) compared with control. These higher concentrations also display smaller ventricular surfaces. b. Quantification of the mean ratio of cortical lobes containing a dense, radial band, recognizable on H&E staining, consistent with cortical plate reveals a reduction in 87 mM and 150 mM ethanol treated tissues. Error bars are SEM. *P<0.05, **P<1.0e-6 Student's t-test, n=13 organoids from five batches (4 H9, 1 H1) for control, 4 organoids from two batches (1 H9, 1 H1) for 87 mM EtOH, and 12 organoids from four batches (3 H9, 1 H1) for 150 mM EtOH. All treatments were performed beginning at day 56 with analysis at day 70. c. H&E stained sections of enCORs treated with 150 mM EtOH or water mock before the onset of CP formation (labeled early, iPSC enCORS treated beginning 11 days after ECM addition before evidence of CP on brightfield, analyzed day 70) reveals a more dramatic effect on VZ morphology and continuity compared with organoids treated after the onset of CP formation (labeled late, H9 enCORs treated beginning 16 days after ECM addition, analyzed day 70). d. Schematic of the metabolic pathways of retinol and ethanol and potential for competitive inhibition. e. H&E histology and immunohistochemical staining for nestin to mark radial processes, and Ctip2 which marks the CP, in mock and treated H9 enCORs at day 70, after 2 weeks treatment. Note the intact CP (arrowheads) in acetaldehyde treated samples, whereas ethanol treated lack a well-developed CP and samples with retinol also display malformed CP. The combination of retinoic acid treatment with ethanol partially rescues the phenotype with the formation of a more discrete condensed CP, but still displaying defects in VZ continuity. Nestin staining reveals bundles of basal processes that extend beyond the main neuronal population and into external heterotopias upon ethanol treatment (arrows). DCX (Doublecortin) marks neurons. This disorganization is also evident in the absence of retinols. Scale bars: 100 m in a., c.bottom panel, e., 500 m in c.top panel.

[0106] FIG. 12. Cellulose fibers with similar dimensions (left panel) fail to form elongated EBs (middle panel) compared with the PLGA based fibers (arrowheads) at day 3 with H9 cells, and instead remain as clumps (arrows) only partially attached to the fibers. Scale bars: 500 m in FIG. 4., FIG. 12., 250 m in FIG. 1c., d., e., 100 m in FIG. 1b.

[0107] FIG. 13. Quantification of the mean ratio of spheroids or enCORs displaying neuroepithelium. *P<0.05, Student's t-test, n=7 independent batches each. Scale bars: 250 m.

[0108] FIG. 14. Decreased formation of non-neural tissue in enCORs a. Immunohistochemical staining of day 10 H9 enCOR EBs for Sox17 for endoderm and E-Cadherin for non-neural epithelium reveals only occasional cells (arrowhead) with these non-neural identities. The microfilament can be seen as an autofluorescent rod (yellow asterisk). b. RT-PCR for markers of pluripotency in 20-day H9 microfilament enCORs or spherical organoids. Embryonic stem cells (H9 cells) are positive control and Neg. is the water control. Scale bars: 100 m in FIG. 14 a., FIG. 5a., 200 m in FIG. 7b, FIG. 5c.

[0109] FIG. 15. Reproducible formation of forebrain tissue in enCORs a. Bright field image of H9 microfilament organoids shortly after Matrigel embedding (day 19), displaying numerous small buds of neuroepithelium (arrows). b. Embedded H9 microfilament organoids at day 19, following three days of treatment with CHIR. Note the larger, more continuous buds of neuroepithelium. c. Staining of day 40 H1 spheroids for neural (N-Cadherin or Nestin) and non-neural identities (Sox17 or Brachyury) revealing similar quantities of these identities with and without a three day pulse of CHIR. d. Representative images of stained sections of day 40 H9 organoids used for quantification shown in FIG. 1f. Individual lobes can be recognized as radially oriented, polarized neuroepithelium surrounding a fluid filled ventricle. Serial sections were stained for the indicated markers. Forebrain tissues (white arrows) are Foxg1+ and exhibit fainter Otx2 signal, midbrain tissue (white arrowhead) exhibits strong immunoreactivity for Otx2 and lack other markers, and cerebellar tissue (yellow arrowhead) exhibits staining for both Otx2 and En2, while En2 single positive regions are hindbrain. Foxg1+ regions showing strong Pax6 staining are dorsal forebrain. However, Pax6 also stains other regions such as that marked by the yellow arrow, which is likely spinal chord, as it does not exhibit staining for the other markers. e. Staining for the ventral forebrain marker Gsh2 and the dorsal marker Tbr2 in H9 enCORs at day 40 reveals the presence of both regions of the forebrain. f. Staining of day 40 H9 enCOR brain organoids and spheroids for the markers of dorsal cortex Tbr1 and Tbr2 reveals large lobes of tissue that are dorsal cortex (arrows) in enCORs. Spheroids show much fewer dorsal regions and some large brain regions that lack this identity. g. Staining for the marker of choroid plexus TTR reveals the presence of this region in H9 40-day enCORs h. Staining for the marker of hippocampus Prox1 reweals the presence of this tissue in H9 40-day enCORs. Scale bars: 500 m in a., b., c., d., f., 100 m in e., g., h.

[0110] FIG. 16. Transcriptome profiling reveals increased neural identity and preferential formation of forebrain a. Fold enrichment and log 10(P-value) of GO Slim Biological Process terms for genes increased or decreased in enCORs at 20 and 60 days. b. Heatmap of hierarchical clustering of genes according to log 2fc values at 20 days and 60 days in enCORs versus spheroids. Clusters are marked and GO biological process term summaries of terms identified (FIG. 17) shown at right.

[0111] FIG. 17. GO terms in identified clusters of gene expression Fold enrichment and log 10(P-value) of GO Biological Process terms for genes in 7 clusters identified by hierarchical clustering according to log 2fc value (FIG. 16b).

[0112] FIG. 18. Individual marker genes of pluripotency, germ layer identity and brain patterning a. Screen shots of the IGV view of single gene tracks of markers of pluripotency, neuroectoderm and mesendoderm in spheroid and enCORs at 20 days. b. Single gene tracks of markers of rostral-caudal and dorsalventral brain patterning in spheroid and enCORs at 60 days. Schematic of marker expression in the developing brain shown below. c. Heatmap of Spearman correlation coefficients between enCOR or spheroid 60 day samples and all brain regions at fetal timepoints from the Allen brainspan transcriptome, sorted by anterior-posterior regional identity and four stages of development.

[0113] FIG. 19. enCORs with ECM addition display organized cortical plate a. H&E staining of 60-day H9 enCORs with dissolved Matrigel show a dense band consistent with CP, whereas enCORs instead treated from day 30 with the matrix metalloprotease inhibitor GM6001 show no signs of CP formation. b. H&E staining of 60-day H9 enCORs with dissolved Matrigel compared with dissolved laminin or dissolved laminin/entactin complex. Note the presence of a dense CP band with Matrigel, while laminin alone displays no evidence of CP formation and laminin/entactin develops only a faint band of cells. c. H&E staining of H9 enCOR, H9 cortical spheroid generated according to Pasca et al.25 and iPSC SFEBq generated according to Kadoshima et al.24, each at 60-days of development. Note the dense CP band (black arrowheads) with the enCOR method and the overall larger size as well as presence of larger lobes surrounding fluid-filled ventricle-like spaces. The SFEBq method gives rise to a marginally condensed band of neurons (white arrowhead). Lower panels are higher magnifications of the boxed regions. d. Staining for neuronal subtypes in developing CP in H9 enCORs at two time points reveals the progressive separation of upper layer (Satb2+ and Cux2+) which labels a broad population, and deep layer (Ctip2+) neurons which label neurons in deeper regions of the CP. Note the progressive thickening of the radially organized CP, and the evident layers exhibiting transitioning organization of neuronal processes (Map2 staining). Scale bars: 200 m in FIG. 3c., 100 um in FIG. 3f., FIGS. 19a., b., and d., and 500 m in FIG. 19 c.

[0114] FIG. 20. Slice culture and live imaging in enCORs enables visualization of neuronal migration and activity. a. Nestin staining reveals basal processes (arrowheads) with end feet that terminate at the laminin positive basement membrane (arrows) in a 60-day H9 enCOR. b. Nestin staining in 60-day H9 spheroid reweals the presence of radial glial processes that show disorganization outside the ventricular zone (arrowheads) and terminal end feet within the tissue (arrows). c. Frames from live imaging of a membrane targeted farnesyl-GFP labeled neuron (arrowhead) showing radial migration into the CP. d. A false color heatmap frame of live imaging with the calcium dye Fluo-4 and single cell tracings of the indicated cells, labeled regions of interest (ROI), as measured by change in relative fluorescence (F/F=(mean grey valueminimum grey value)/minimum grey value) showing spontaneous calcium surges. Scale bars: 100 m in a. and b., 20 m in c., 50 m in d.

[0115] FIG. 21. Ethanol volatility results in a lower than expected concentration and generates specific neuronal migration phenotypes a. Measured concentration in the media at the designated time point for treated H1 enCORs beginning at day 56. Time 0 is immediately after addition of ethanol to the media. BAC eq. refers to the equivalent blood alcohol content % by volume. b. H9 enCORs treated for two weeks beginning at day 46 with a higher dose of 300 mM show completely disorganized cortical lobe with neurons abnormally located in the VZ and the complete absence of recognizable apical surface. 150 mM treated instead show smaller apical surfaces (dashed lines) and no recognizable CP in contrast to water mock (bracket) as well as ectopic neurons (arrow). c. H&E staining of mock water or 150 mM ethanol treated H9 spheroids beginning at day 56 reveals apical surface defects but a failure to detect a CP/neuronal migration defect. d. TUNEL staining in treated and mock water H1 day-70 enCORs after two week treatment, revealing no obvious increase in cell death upon ethanol treatment. Note the presence of the CP (arrowheads) in mock and 47.5 mM ethanol treatments. e. Screen shots of the IGV view of single gene tracks of various alcohol dehydrogenase enzymes in the 60-day enCOR transcriptome. ADH4 and 5 are most highly expressed. Note that ADH4 has previously been described to be involved in metabolism of both ethanol and retinol. Scale bars are 100 m in all panels.

EXAMPLES

Examples Summary

[0116] In order to model more subtle neurological phenotypes, a system was developed that fulfils three important criteria: 1) reliable generation of neural tissues from batch to batch; 2) high purity neural tissues with consistent regional identity;

[0117] and 3) radial cortical plate organization. By making use of fibrous microscaffolds, it was shown that organoids consistently produce neuroepithelium, eliminating batch-to-batch effects. Furthermore, it was shown that tissues are pure neural and reproducibly generate cerebral cortical structures in all organoids. Finally, it was shown show that the addition of dissolved extracellular matrix allows for the formation of a radialized cortical plate and aligned radial units. This combination of micropatterning and organoid culture in the presence of ECM (FIG. 1a) allows for the study of developmental disorders, including those with neuronal migration defects. Developmental disorders can be modelled based on using cells with genetic defects or by investigating the teratogenic properties of chemical substances or other environmental effects.

Example 1: Preparation of Microfilaments

[0118] Poly (lactide-co-glycolide) braided fibers of 10:90 PLGA were obtained commercially as Vicryl sutures (Ethicon). Violet dyed fibers were used to assist in visualization during dispersion and within embryoid bodies. Individual microfilaments were isolated from the braided fiber by mechanical shearing with an angled blade against a stainless steel plate, to obtain filaments of 0.5-1 mm in length, and about 15 m in diameter. Filaments were then hydrated in embryoid body media and transferred to 15 ml conical tube for storage. Comparative filaments of cellulose were obtained by shaving individual fibers from a Whatman paper. Gelatin fibers were produced by wet-spinning as described previously in Han et al., Adv. Funct. Mater. 2012, DOI: 10.1002/adfm.201201212 without cross-linking.

Example 2: General Outline for Preparing Micropatterned Embryoid Bodies and Cerebral Organoids

[0119] Embryoid bodies were prepared from single cell suspension of human ES or iPS cells, following accutase treatment. Cells were counted and resuspended in embryoid body media (EB): DMEM/F12 (Invitrogen, cat. #11330-032) and 20% Knockout Serum replacement (Invitrogen, cat. #10828-028), 3% human ES quality batch-tested fetal bovine serum, 1% Glutamax (Invitrogen, cat. #35050-038), 1% MEM-NEAA (Sigma, cat. #M7145), 0.1 mM 2-mercaptoethanol, 4 ng/ml bFGF (Peprotech, cat. #100-18B), and 50 M Y-27632 ROCK inhibitor (VWR, cat. #688000-5). 18000 cells were added to each well of a 96-well low-attachment U-bottom plate (Sigma, cat. #CLS7007) already containing 5-10 microfilaments in embryoid body media, and media was added to give a final volume of 150 l per well (FIG. 1a, steps 1 and 2). Based on an average hPSC cell size of 15 m (measured from hPSC cell suspensions on EVOS microscope, Invitrogen), we calculated that 18000 cells per 5-10 fibers of maximum length 1 mm would result in, at most, 5-10% of cells having direct contact to the fiber.

[0120] At day 3, half media was changed with EB media without bFGF and Y-27632. On day 5, EBs were moved with an angled cut P200 tip to 24-well low-attachment plates (Sigma, cat. #CLS3473) with neural induction media (NI) as previously described in WO 2014/090993 A1 (incorporated herein by reference) (FIG. 1a, step 3). Media was changed every other day. On day 11, or when polarized neural ectoderm was visible on the surface, organoids were transferred to droplet of Matrigel as previously described in WO 2014/090993 A1 but kept in NI media (FIG. 1a, transition from step 3 to 4). At day 13 (2 days after Matrigel embedding), media was changed to an improved differentiation media-A (IDMA): 1:1 of DMEM/F12 and Neurobasal (Invitrogen, cat. #21103049), 0.5% N2 supplement (Invitrogen, cat. #17502048), 2% B27-vitamin A (Invitrogen, cat. #12587010), 0.25% insulin solution (Sigma, cat. #I9278-5ML), 50 M 2-mercaptoethanol, 1% Glutamax, 0.5% MEM-NEAA, and 1% Penicillin-Streptomycin (Sigma, cat. *P0781). Additionally, CHIR 99021 (Tocris, cat. #4423) at 3 M was added from day 13 to 16. Media was changed every other day and organoids were moved to a spinning bioreactor or orbital shaker as described previously in WO 2014/090993 A1, on day 18 (FIG. 1a, step 5). After moving to the shaker, media was changed every 3-4 days. Shaking speed was calculated based on the throw of the shaker. For a throw of 10 mm, speed was 85 rpm.

Example 3: Addition of Extracellular Matrix (ECM)

[0121] At day 20, media was changed to an improved differentiation+A (IDM+A): 1:1 of DMEM/F12 and Neurobasal, 0.5% N2 supplement, 2% B27+vitamin A, 0.25% insulin solution, 50 M 2-mercaptoethanol, 1% Glutamax, 0.5% MEM-NEAA, 1% Penicillin-Streptomycin, 0.4 mM Vitamin C, and 1.49 g HEPES per 500 ml to control pH levels. Alternatively, media can be pH controlled with further bicarbonate buffering with the addition of 1 mg/ml sodium bicarbonate. At day 40, media was changed to IDM+A with 1 ml dissolved Matrigel per 50 ml media by slowly thawing the Matrigel on ice and addition to cold media to dissolve (FIG. 1a, step 6). A polarized cortical plate was observed.

[0122] Variations and comparative examples For treatment with matrix metalloprotease inhibitor GM6001 (Selleck Chemicals S7157), a final concentration of 3 M was added beginning on day 30. For laminin treatment, 35 g/ml of pure laminin (Corning 354232) was added beginning on day 40, or 45 l of high concentration laminin/entactin gel (Corning 354259) was dissolved per 5 ml media, to obtain a protein concentration comparable to final concentration of Matrigel as obtained above.

[0123] Comparative cortical spheroids were generated as described previously in Pasca et al., Nature Methods 12, 671-678 (2015). Briefly, H9 feeder-free cells were dissociated with EDTA and intact colonies were plated in a low-attachment 6 cm dish in hES media containing drugs as detailed in the published protocol. On day 6, media was changed to Neural Media and addition of growth factors was performed with the timing described in the protocol. Forebrain SFEBq organoids were generated as described previously in Kadoshima et al., Proc. Natl. Acad. Sci. U.S.A. 110, 20284-20289 (2013). Briefly, iPS cells were dissociated to single cells and 9000 cells plated per low attachment u-bottom well in cortex differentiation media containing small molecules as described in the published protocol. Media changes were performed as described and on day 19 the tissues were moved to DMEM/F12+N2 based media with subsequent addition of FBS, heparin and Matrigel on day 35 as described. B27 was included starting at day 70, along with increased Matrigel exactly as described. For ethanol treatments, 100% ethanol was added to achieve the desired final concentration or an equal volume of water to highest volume of ethanol was used as control mock treated. These concentrations are higher than physiological levels but given the volatility of ethanol, this has been shown to be the most effective in eliciting an effect in neurons in vitro. Ethanol concentrations in the media were measured using the colorimetric ethanol concentration assay (Abcam) according to manufacturer's instructions. A base line measurement was taken for media before ethanol addition, which was subtracted from subsequent measurements. Acetaldehyde treatment was performed with 200 M final concentration, a concentration found in serum during ethanol intoxication. Treatment with media lacking retinols was performed with the IDM+A media recipe except that B27-A was used. Rescue with retinoic acid was performed with 1 M final concentration of all-trans retinoic acid. The media was changed with new media containing fresh treatments every 3-4 days.

Example 4: Histological and Immunohistochemical Analysis

[0124] Organoids were fixed in 4% paraformaldehyde for 20 min at room temperature and washed with PBS three times for 10 min each at room temperature before allowing to sink in 30% sucrose at 4 C. The tissues were embedded and sectioned and stained as described in Lancaster et al. Nature Protocols 9, 2329-2340 (2014). Primary antibodies used were: Brachyury (R&D Systems AF2085, 1:200), mouse anti-N-Cadherin (BD 610920, 1:500), mouse anti-E-Cadherin (BD 610182, 1:200), goat anti-Sox17 (R&D systems AF1924, 1:200), rabbit anti-Laminin (Sigma L9393, 1:500), rabbit anti-Tbr1 (Abcam ab31940, 1:300), chicken anti-Tbr2 (Millipore AB15894, 1:100), mouse anti-Map2 (Chemicon MAB3418, 1:300), rat anti-Ctip2 (Abcam, ab18465, 1:300), rabbit anti-Ar113b (Proteintech 17711-1-AP, 1:300), mouse anti-phospho-Vimentin (MBL International D076-35, 1:250), rabbit anti-Emx1 (Sigma HPA006421, 1:200), rabbit anti-FoxG1 (Abcam ab18259, 1:200), mouse anti-Reelin, (Millipore MAB5366, 1:200), mouse antiCalretinin (Swant 6B3, 1:100), rabbit anti-Satb2 (Abcam ab34735, 1:100), rabbit anti-Otx2 (Abcam ab21990, 1:200), goat anti-En2 (Santa Cruz Biotechnology sc-8111, 1:50), goat anti-DCX (Santa Cruz Biotechnology sc-8066, 1:300), mouse anti-CSPG (Abcam ab11570, 1:100), rabbit anti-Cux2 (Abcam ab130395, 1:200), mouse anti-Nestin (BD G11658, 1:500). DAPI was added to secondary antibody to mark nuclei. Secondary antibodies labeled with Alexafluor 488, 568, or 647 (Invitrogen) were used for detection. TUNEL staining was performed using the In Situ Cell Death Detection Kit-Fluorescein (Roche) according to manufacturer's instructions. For histological analysis, sections were stained for hematoxylin/eosin followed by dehydration in ethanol and xylene and mounting in permount mountant media. Images were acquired on a confocal microscope (Zeiss LSM 710 or 780). Statistical analysis of quantifications performed from imaging data was performed using Student's t-test for significance.

Example 5: Electroporation of Organoids and Live Imaging

[0125] Electroporation of pmax-GFP construct (Lonza) or an integrating farnesylated GFP was performed as described previously in Lancaster et al. Nature 501, 373-379 (2013). For pmax-GFP, 4 l of 250 ng/l were injected into several ventricular spaces. The integrating farnesylated GFP was generated by cloning the CAG promoter into the pT2/HB transposon plasmid (a gift from Perry Hackett, Addgene plasmid #26557) followed by inserting a GFP construct with farnesyl sequence (pT2-Cag-fGFP). Sleeping beauty transposase plasmid was generated by cloning the SB100X transposase (pCMV(CAT)T7-SB100, Addgene plasmid #34879) into the pCAGEN plasmid with CAG promoter (Addgene plasmid #11160). Electroporation was performed by injecting 80 ng/l pT2-Cag-fGFP and 240 ng/l pCAGEN-SB100X. For neuronal morphology analysis, samples were fixed 36 days after electroporation of the fGFP and analysed by sectioning and immunohistochemistry as above.

[0126] Slice culture was performed by embedding samples in 3% low-melting point agarose and sectioned on a vibratome to collect 300 m sections on the air side of organotypic culture inserts (Millipore) inside a 3 cm coverglass bottomed dish containing 1 ml serum-supplemented media: DMEM, 10% FBS, 0.5% (w/v) glucose, supplemented with penicillin-streptomycin. Sections were cultured for 1 hour before changing the media to serum-free media: DMEM, 1:50 B27+A, 0.5% (w/v) glucose, glutamine and penicillin-streptomycin. The slices were left to flatten and equilibrate overnight before imaging over several days using a Zeiss 780. For this long-term imaging, addition of HEPES (25 mM final) was performed for added buffering.

[0127] Calcium imaging was performed as previously described in Lancaster et al., Nature 501, 373-379 (2013) using Fluo-4 Direct (Life Technologies) on slice cultures. Frames were analyzed in ImageJ and progressive increasing intensity was corrected by using the Bleach Correction function on frames in reverse order. Individual cell traces were performed by outlining specific cells as regions of interest and mean grey value measured. AF/F was calculated as follows: (mean grey valueminimum grey value)/minimum grey value.

Example 6: RT-PCR Analysis of Gene Expression

[0128] Three organoids for each condition were collected in Trizol reagent (Thermo Fisher) and RNA isolated according to manufacturer. DNA was removed using DNA-Free kit (Ambion) and reverse strand cDNA synthesis was performed using Superscript III (Invitrogen). PCR was performed using primers for a panel of pluripotent and germ layer identities (R&D systems, SC012).

Example 7: RNA-Seq Analysis

[0129] Three individual H9 organoids for each condition were collected at the indicated time points. RNA was isolated using Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific, cat. #KIT0204) (20 days timepoint) or Trizol Reagent (Thermo Fisher Scientific, cat. #15596018) (60 days timepoint) according to the manufacturer's instructions. RNA concentration and integrity was analysed using RNA 6000 Nano Chip (Agilent Technologies, cat. #5067-1511). RNA was enriched for mRNA using Dynabeads mRNA Purification Kit (Thermo Fisher Scientific, cat. #61006). Libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, cat. #E7420L). Barcoded sampies were multiplexed and sequenced 50 bp SE on a HighSeq2500 (Illumina). Sample preparation and sequencing was performed at the VBCF NGS Unit (www.vbcf.ac.at). Data will be submitted to GEO and accession numbers provided.

[0130] The strand specific reads were screened for ribosomal RNA by aligning with BWA (v0.6.1) against known rRNA sequences (RefSeq). The rRNA subtracted reads were aligned with TopHat (v1.4.1) against the Homo sapiens genome (hg38) and a maximum of 6 missmatches. Maximum multihits was set to 1 and InDels as well as Microexon-search was enabled. Additionally, a gene model was provided as GTF (UCSC, 2015 01, hg38). rRNA loci are masked on the genome for downstream analysis. Aligned reads are subjected to FPKM estimation with Cufflinks (v1.3.0). In this step bias detection and correction was performed. Furthermore, only those fragments compatible with UCSC RefSeq annotation (hg38) of genes with at least one protein-coding transcript were allowed and counted towards the number of mapped hits used in the FPKM denominator. Furthermore, the aligned reads were counted with HTSeq (0.6.1p1) and the genes were subjected to differential expression analysis with DESeq2 (v1.6.3).

[0131] GO term enrichment analysis was performed on genes with an adjusted p value <0.1 and absolute log 2fc value >1 in at least one of the conditions (20 day or 60 day, spheroid or enCOR). Each set of differentially expressed genes were analysed using Pantherdb.org for GO Slim biological process enrichment and fold enrichment for terms as well as multi-test corrected P-value (plotted as log 10(Pvalue) were plotted.

[0132] For hierarchical cluster analysis, genes were reorganized based on their similarity of log 2fc values by means of Ward hierarchical clustering using heatmap.2 of the gplots package in R. Cutree function gave the 7 clusters used for subsequent GO term analysis. Gene lists were fed into Pantherdb.org for GO Biological Process Complete, yielding a large list of redundant terms. Therefore, in order to remove redundancy, we narrowed the list using GO Trimming and a cutoff of terms with fold enrichment value >2 yielding the list of GO terms that were plotted by fold enrichment value and log 10(Pvalue). Individual tracks were visualized using Integrative Genomics Viewer IGV 2.3.68 (Broad Institute).

[0133] For comparison to Allen BrainSpan human transcriptome dataset, the RPKM expression values of Brainspan were downloaded (www.brainspan.org/static/download.html). FPKM values were filtered for differential expression in the 60d time-points (padj<0.1) and joined with Brainspan via the gene symbols. The similarity of expression was compared by the rank of the expressed gene via Spearman correlation. The heatmap of Spearman coefficient for each region at fetal time points was generated using heatmap.2 without hierarchical clustering. The list was manually ordered according to anterior-posterior regional position and separated into four developmental stages.

Example 8: Micropatterned Cerebral Organoids Consistently Produce Organized Neuroepithelium

[0134] In order to identify the source of batch-to-batch variability in previous cerebral organoid preparations, five independent comparative batches at various time points were examined. The earliest appearance of batch-to-batch effects could be seen during neural induction. Specifically, there were varying efficiencies of generation of polarized neural ectoderm that ranged from 30% to 100% of organoids per batch (FIG. 4). Notably, batches with low rates of neural ectoderm formation instead contained tissues with other morphologies suggesting the presence of nonneural ectoderm, or other germ layer identities. Therefore immunohistochemical staining of early cerebral organoids was performed for various germ layers. Optimal organoids displayed a well-organized and apicobasally polarized neural epithelium around the surface of the organoid, with only sparse cells staining positive for other germ layers (FIG. 5a). However, suboptimal organoids displayed less well-organized architecture with a greater extent of staining for other cell identities, such as endoderm and mesoderm. Additional histological sectioning and staining at later stages identified a number of tissues with non-neural morphologies in addition to neural regions, such as putative cartilage, mesenchyme and squamous epithelia (FIG. 5b). Furthermore, immunohistochemical staining revealed the existence of occasional definitive endoderm, as well as other nonneural E-cadherin positive regions (FIG. 5c). These findings show variability in the efficiency of neural induction, with some batches giving rise to other germ layers and/or non-neural ectoderm.

[0135] A very high efficiency neural induction and cerebral cortical regionalization can be achieved with dual SMAD inhibition and retinoids. Therefore it was tested whether this approach could improve induction efficiency in the context of organoids, by culturing the organoids at embryoid body (EB) stage in a media composed of retinoids and dual SMAD inhibitors (dorsomorphin and SB-431542). EBs cultured in this combination showed dramatically increased clearing at day 4, indicative of ectoderm formation (FIG. 6a). However, upon embedding in Matrigel, the treated organoids failed to produce buds of neuroepithelium, instead displaying small rosette-like structures with neural processes (FIG. 6b). The finding that dual SMAD inhibition and retinoid signalling could dramatically increase neuroectoderm formation but at the expense of neural tissue morphology suggests that non-neural tissues may be important for the formation of complex morphologies seen in cerebral organoids. Optimal batches of organoids displayed larger quantities of polarized neuroectoderm were observed (FIG. 5a). The ratio of neural to non-neural tissue could still be improved.

[0136] The inventive cerebral organoid protocol begins similar as spheroid EB formation (FIG. 1). It is hypothesized that since neural ectoderm forms on the outside of these tissues during neural induction, a sphere could limit the surface area to volume ratio and potentially allows a greater extent of non-neural tissue formation. In order to increase the surface area of organoids a micropatterning scaffold was used to shape the early

[0137] EB stage organoids and elongate the primitive neuroectoderm. This micropatterning gives rise to microfilament engineered cerebral organoids (also referred to as enCORs herein).

[0138] Fibrous microscaffolds are a widely used system for providing patterned scaffolds in tissue engineering, allowing for diverse shapes that can be seeded with cells and even implanted in vivo. However, because EBs are generated with relatively few cells (thousands rather than the millions typically used in tissue engineering applications), and the goal here was to provide an individual micrometer scale guide, a method was devised for mechanical dispersion of individual filaments from braided fibers (FIG. 1b-d). The effect of addition of 5-10 microfilaments of glycolide/lactide copolymer, a material that can be absorbed by means of hydrolysis over the course of 8-10 weeks when implanted in living tissue, was tested. The microfilaments were collected in a random configuration at the bottom of a low-attachment round-bottom microwell and seeded with 18,000 hPSCs, a ratio that results in only 5-10% of cells in direct contact with the filament. The hPSCs attached evenly along the length of PLGA microfilaments thereby forming a plurality of cells of an oblong or longish arrangement (FIG. 1e). Similar results were observed with gelatin microfilaments. In contrast, microfilaments composed of cellulose instead resulted in round aggregates only partially attached to the fibers (FIG. 12) suggesting filament material is important for adherence of cells along the entire length.

[0139] When microfilaments were added along with hPSCs to low-attachment round-bottom wells, the fibrous scaffolds accumulated at the bottom of the well and were seeded with cells in a random configuration allowing for the successful formation of EBs with elongated morphologies (FIG. 1e). The elongated EBs progressively grew in size and exhibited clearing along the edges with eventual formation of polarized neural ectoderm, much like spheroid EBs; however, the neural ectoderm was dramatically elongated (FIG. 1f) and the efficiency of formation of neuroectoderm was much improved with consistent neural induction in all independent preparations examined (FIG. 7, FIG. 13). These data point to the ability of microfilament scaffolds to more reliably generate radialized neural ectoderm.

[0140] Due to the elongated and, at times, complex configurations of micropatterned EBs, surface area to volume was increased, leading to the hypothesis that resulting early stage organoids would display increased polarized neuroepithelium and decreased quantities of other germ layer identities. In order to test this hypothesis, we performed immunohistochemical staining of early stage micropatterned EBs for various germ layer identities and observed more consistent generation of elongated polarized neuroepithelium with concomitant decreased amounts of endoderm and mesoderm identities (FIG. 1g, h). This was in contrast with spherical organoids, which often displayed non-ectodermal identities, especially in suboptimal organoids (FIG. 5a). Furthermore, expression analysis for pluripotency and germ layer markers by RT-PCR, revealed a decrease in non-neural identities in enCOR organoids (FIG. 8c and FIG. 14b). As organoids developed, enCORs displayed fewer morphological features of other germ layers such as the formation of early fluid-filled cysts (FIG. 7b). Furthermore, enCORs contained large lobes of brain tissue (FIG. 2c) but only few regions expressing markers for endoderm and non-neural epithelia (FIG. 5c), in contrast to spherical organoids. These findings suggest that reproducible generation of elongated neural ectoderm can be accomplished by mechanical means rather than through the addition of patterning growth factors.

Example 9: Consistent Generation of Large Cortical Regions with Dorsal Identity

[0141] Upon Matrigel embedding, micropatterned brain organoids displayed extensive neuroepithelial budding along the length of the previously extended polarized neuroectoderm (FIG. 2a). In contrast to the continuous neuroectoderm that was present prior to embedding which displayed the apical surface directed outwards, neuroepithelial buds were fully enclosed epithelium around a central lumen with the apical surface directed inwards. However, due to the nature of this epithelial reorganization, which in many ways mimics neural tube closure, the resulting neural tube-like epithelia were less continuous.

[0142] Since we were interested in consistently generating large continuous cortical regions, we therefore sought methods to expand these neural tube-like epithelia. Previous in vivo studies have demonstrated the ability of activated Wnt signalling to lead to lateral expansion of cortical neuroepithelium. We therefore tested the effect of adding the GSK3beta inhibitor and Wnt activator CHIR (CHIR99021; stemgent, cat.nr: 04-0004) following neuroepithelial budding. Addition of CHIR led to a dramatic lateral expansion of neuroepithelial tissues and the generation of larger lumens with surrounding continuous neuroepithelium (FIG. 2b). Because Wnt signalling is also an important patterning factor, and we sought to limit the extent of exogenous patterning, we performed also treatment for only a short 3-day pulse. This treatment alone did not influence germ layer induction or overall organoid morphology (FIG. 15c).

[0143] We next examined micropatterned organoids at later stages by histological staining which also revealed more consistent generation of large brain regions (FIG. 2c). Furthermore, consistent with the effect of micropatterning on germ layer identity determination, there were fewer regions with non-neural morphologies. This was confirmed by immunohistochemical staining which revealed a reduction of definitive endoderm and non-neural epithelia in micropatterned brain organoids (FIG. 2d), in contrast to spheroid organoids (FIG. 5c).

[0144] enCORs with the combination of microfilament and CHIR pulse displayed more consistent formation of Foxg1+ forebrain tissues compared with spheroids, as well as decreased frequency of Otx2+ midbrain and En2+ cerebellar/hindbrain regions (FIG. 8b, 8c, 15d), suggesting more reliable formation of forebrain neural tissue. Consistent with this, enCORs displayed both dorsal and ventral forebrain regions (FIG. 15e) with more frequent large regions that stained positive for dorsal cortical markers Tbr1 and Tbr2 (FIG. 15f). Furthermore, enCORs displayed regions with identity consistent with choroid plexus and hippocampus (FIG. 15g, 15h). Thus, together with late GSK3beta inhibition, micropatterning of cerebral organoids results in reproducible formation of forebrain tissue with little contamination from other germ layers and brain regions.

[0145] To further examine the effect of micropatterning and CHIR addition we analyzed gene expression at 20 and 60 days in three enCORs and three spherical organoids. 20 day enCORs were enriched for GO terms neurological system and multicellular organismal processes, while other organ development like digestive tract, muscle, skeletal system and mesoderm were decreased (FIG. 16a). At 60 days, we observed GO term enrichment for nervous system development and transcription while digestive tract, heart, muscle skeletal system, and synaptic transmission were decreased. The decrease in synaptic genes at 60 days suggests a delay in neuronal maturation perhaps due to extended progenitor expansion upon CHIR addition. Hierarchical cluster analysis revealed several gene clusters displaying specific patterns of differential expression (FIG. 16b, 17). Cluster 1 was upregulated in 60 day enCORs and enriched for forebrain and cortical differentiation. Clusters 4 and 5 were increased or unchanged at 20 but decreased at 60 days and were enriched for nervous system development and synaptic transmission. Finally, Clusters 6 and 7 were decreased at 20 days and also decreased or unchanged at 60 days. They were enriched for more caudal expression such as spinal cord and hindbrain, consistent with the effect of micropatterning and CHIR addition on forebrain patterning.

[0146] We next assessed expression of specific germ layer or brain patterning markers (FIG. 18a, b). The pluripotency markers Oct4, Klf4, and Nanog were decreased in enCORs. Neuroectodermal markers appeared unchanged whereas mesendodermal markers such as Sox17, T (Brachyury), Mixl1, and Foxa2 were decreased. Furthermore, the forebrain marker Foxg1 was dramatically increased, whereas caudal markers such as En2, Gbx2 and Hox genes were decreased. Finally, dorsal forebrain markers such as Emx1, Tbr1 and Tbr2 were increased, while ventral forebrain markers were unchanged. These findings suggest a more rostral brain identity in enCORs.

[0147] We compared genes differentially expressed between 60 day spherical organoids and enCORs to gene expression in the human developing brain using Allen BrainSpan Atlas (FIG. 18c). enCORs most closely matched the dorsal forebrain identities of the human brain at early gestation, specifically 8-9 weeks postconception (FIG. 8d). Spherical organoids instead showed the highest correlation with more caudal regions, specifically the thalamus and cerebellum, and showed a broader correlation with later time points. These findings are consistent with the effect of micropatterning and CHIR addition on forebrain regional identity.

[0148] In addition to its proliferative role in neural progenitor expansion, Wnt signalling also plays a regional patterning role. Generally, Wnt is a dorsalizing factor in the CNS, and in the forebrain it is released from the hem, an organizing center that is a stimulator to dorsal cerebral cortex regionalization. Therefore, we tested whether the addition of CHIR during lateral expansion also affected regional identity. We performed staining for dorsal brain region identity, which revealed large Emx1+ regions (FIG. 2e), consistent with dorsal cortex. Furthermore, staining and quantification revealed that virtually all large regions stained positive for dorsal cortical markers Tbr1 and Tbr2 (FIG. 2f, g). This is in contrast to approximately 30% of large regions in spheroid organoids. These findings suggest that not only does the late CHIR treatment expand the neuroepithelium, but it also promotes reliable dorsal forebrain regionalization.

Example 10: Generation of Radial Cortical Plate with Dissolved ECM

[0149] The findings thus far suggest that micropatterning consistently produces cerebral organoids with large dorsal cortical regions, an important step towards modelling more subtle cortical phenotypes. This is improved by a combination with a short pulse of CHIR. However, we next sought to address the issue of neuronal organization and the lack of a cortical plate. We have previously described the generation of neurons of various layer identities, and recently we demonstrated the generation of these identities in a temporally controlled manner that mimics that seen in vivo. However, although excitatory neurons correctly migrate basally outward, once outside the progenitor zones they are randomly oriented and fail to re-establish the radially aligned morphology characteristic of the cortical plate. This reorientation is an important event in neuronal migration and the lack of this feature of cortical development makes it difficult to model neuronal migration defects in cerebral organoids.

[0150] Possibly migrating neurons make use of the basal process of radial glial neural stem cells as a scaffold for orientation and basal migration. Furthermore, because radial glia are epithelial in nature, the basal process contacts the basement membrane covering the surface of the brain. Since the basement membrane is generally thought to be generated by the overlying mesenchyme, a non-neural supportive tissue, we hypothesized that previous cerebral organoids might lack the basement membrane and therefore the contact site of radial glial processes, leading to disruption of the radial glial scaffold.

[0151] In order to test this hypothesis, we performed immunohistochemical staining on cerebral organoids for the basement membrane component laminin. Surprisingly, we found that neuroepithelia that had not yet begun generating neurons displayed a well-formed laminin rich basement membrane covering the surface of the neuroepithelium (FIG. 3a). However, tissues with migrating cells outside the ventricular zone lacked a basement membrane, instead displaying punctate staining at the basal border of the ventricular zone. Interestingly, the staining pattern was consistent with residual basement membrane that had previously covered the basal surface of the neuroepithelium, suggesting breakdown of the membrane upon generation and basal migration of neurons.

[0152] We therefore sought to reconstitute and maintain the overlying basement membrane by providing exogenous extracellular matrix (ECM) components. Initially, brain organoids are embedded in an ECM rich gel (Matrigel) but within 1-2 weeks the organoids grow out of, or fall out of the gel droplets, leaving free floating brain tissue lacking the overlying ECM. We therefore tested the effect of dissolved Matrigel as a means to providing ECM components in the media. Remarkably, the tissues maintained a thick laminin rich basement membrane that was notably outside the migrating neurons (FIG. 3b), suggesting that it was not broken down by their generation and basal migration.

[0153] We allowed the microfilament patterned brain organoids to develop in the presence of dissolved ECM for 20 days and examined their morphology. Bright field imaging revealed a band of density in cortical regions that was absent in organoids lacking dissolved ECM (FIG. 3c). Subsequent sectioning and histological staining revealed a radialized basal layer consistent with cortical plate morphology (FIG. 3d). Indeed, immunohistochemical staining revealed it was positive for the neural markers Ctip2, Map2, and DCX, with a band of lower Map2 staining in cell bodies that is typical of the cortical plate in vivo (FIG. 3e, f). Bright field imaging revealed a band of density in cortical regions that was absent in organoids lacking dissolved ECM (FIG. 3c). Quantification of the presence of a cortical plate revealed reproducible formation in five independent batches of enCORs while a cortical plate was never observed in spheroids (FIG. 9d)

[0154] Since the maintenance of a basement membrane led to establishment of an organized cortical plate, we hypothesized that this may be due to the presence of a radial glial scaffold. We therefore performed staining for individual radial glia and their processes by staining for phosph-vimentin, a cytoplasmic marker of dividing radial glia. We could identify long basal processes that extended the length of the cortical wall (FIG. 3g). Notably, nuclear staining alone revealed linear units of radial glia and neurons aligned in a manner reminiscent of radial units, suggesting an organized radial glial scaffold.

[0155] To further examine the role of Matrigel and its role in formation of a cortical plate (CP), we instead performed treatment with the matrix metalloprotease inhibitor GM6001 to test whether inhibition of ECM breakdown is sufficient for CP formation. Continuous treatment beginning at day 30 did not result in CP formation by 60 days (FIG. 19a), suggesting that it is not simply breakdown of the initial basement membrane that inhibits CP formation in the spherical organoid method, but also a failure to maintain and expand the basement membrane with tissue growth, a hurdle overcome by addition of dissolved Matrigel. We next tested whether laminin alone or in combination with entactin would be sufficient to recapitulate the effect of dissolved Matrigel. These treatments did not recapitulate the extent of CP formation seen with Matrigel (FIG. 19b), suggesting other components of this complex ECM are important for basement membrane maintenance.

Example 11: Comparisons and Further Characteristics of Micropatterned EB Based Organoids (enCORs)

[0156] We compared enCORs with cortical spheroids and SFEBq organoids described by Kadoshima et al., Proc. Natl. Acad. Sci. U.S.A. 110, 20284-20289 (2013). Neither cortical spheroids nor SFEBq organoids displayed a clear, radially organized CP as seen in enCORs (FIG. 19c). These data suggest that in enCORs the events leading to proper neuronal organization may be more similar to in vivo development as compared to cortical spheroids and SFEBq organoids.

[0157] CP establishment in vivo depends upon early pioneer neurons of the preplate, which secrete Reelin to attract subsequent neurons to migrate into and split the preplate into the marginal zone (MZ) and subplate (SP). We therefore tested whether enCORs exhibited Reelin expressing neurons, also called Cajal-Retzius cells, by staining for Reelin and calretinin. Staining for Reelin revealed strongly reactive cells in the most superficial regions, as well as more dispersed signal indicative of the fact that Reelin is a secreted factor (FIG. 9a). Furthermore, calretinin staining revealed neurons in superficial regions as well as just inside the newly forming CP (FIG. 9b), a pattern typical of preplate splitting in vivo. Staining for chondroitin sulfate proteoglycan (CSPG) further revealed splitting and establishment of MZ and SP during early CP condensation (FIG. 9c). This separation was more pronounced with more developed, thicker CP. The CP itself widened over time and even displayed features of early cortical layering (FIG. 19d).

[0158] The basal process of radial glial cells, which contacts the basement membrane covering the surface of the brain, acts as a scaffold for migration and orientation of neurons to allow for formation of the CP and positioning into radial units. Nuclear staining in cortical regions of enCORs which had been sectioned evenly perpendicular to the apicobasal axis revealed linear units of radial glia and neurons aligned in a manner reminiscent of radial units (FIG. 3a), a characteristic architecture not previously recapitulated in vitro. Furthermore, staining for phospho-vimentin, a cytoplasmic marker of dividing radial glia revealed long basal processes extending the length of the cortical wall. These basal processes were also evident upon staining for Nestin, a cytoplasmic marker of radial glia, which revealed processes with end feet that terminated on the outer surface (FIG. 10a, FIG. 20a). In contrast, spherical organoids displayed disorganized radial glial processes with terminating end feet at various locations within the tissue (FIG. 20b).

[0159] In order to label individual cells for live imaging and morphological analyses, we next established combined electroporation and slice culture in organoids, an approach not previously applied to these types of in vitro cultures. We electroporated a GFP construct into the VZ of individual cortical lobes followed by vibratome sectioning and culture at the air-liquid interface. This allowed for marking individual radial glia, further demonstrating the long basal processes terminating superficial to the CP (FIG. 10b).

[0160] Long term live imaging of electroporated slices revealed various cell behaviors including divisions of outer radial glia (oRG), also called basal radial glia (FIG. 10c), which displayed mitotic somal translocation, a feature typical of oRGs in vivo. Furthermore, live imaging of labelled neurons revealed typical radial migration with saltatory movements and transient acquisition of multipolar morphology before reestablishment of radial orientation and migration into the CP (FIG. 10d, FIG. 20c). Establishment of labelling and long term live imaging of slice cultures in this manner thus provides a useful tool for examination of neuronal migration and progenitor division in a human model system.

[0161] Electroporation of a membrane targeted GFP allowed for examination of morphology of single neurons in more developed organoids. This revealed complex dendritic morphologies and neurons with a primary dendrite typical of the pyramidal morphology of cortical neurons (FIG. 10e). Furthermore, these neurons were oriented toward the MZ on the outer surface of the organoid where parallel fibers could frequently be seen. Finally, we performed calcium staining and live imaging on slice cultures, which revealed spontaneous calcium surges suggestive of neuronal activity (FIG. 9d). These data point to proper positioning and maturation of cortical neurons in enCORs.

Example 12: Use of Organoids as Disorder Model and Rescue Screen System

[0162] Because enCORs establish a CP and exhibit characteristic neuronal migration in a manner not previously recapitulated in vivo, this system could provide a useful tool for the investigation of human disorders of neuronal migration or positioning. In order to test this possibility, we sought to model fetal alcohol syndrome (FAS), a leading preventable cause of intellectual disability affecting approximately 0.5-2 in 1000 births in the United States. FAS is characterized by neurodevelopmental abnormalities including microcephaly, thin or absent corpus callosum, and neuronal migration defects such as polymicrogyria, heterotopia, and focal lissencephaly.

[0163] We treated organoids with three concentrations of ethanol to determine the phenotypic range as well as to test the appropriate concentration considering the volatility of ethanol. We performed treatments every 3-4 days for two weeks by adding the appropriate volume at media changes. Measurement of the resultant ethanol concentration in the media revealed that for all doses tested there was a progressive decrease in concentration over time and even the initial concentration was substantially lower due to high volatility (FIG. 21a). Furthermore, while the higher dose of 150 mM ethanol was initially outside the physiological range, it quickly dropped to approximately 60 mM within a day, a concentration equivalent to a blood alcohol content of 0.27% by volume. A similar trend was seen with the lower doses of 87 mM and 43.5 mM. The inconstant nature of the treatment, with transient peak concentration every 3-4 days upon media change, thus reflects a scenario that might be seen with binge drinking.

[0164] We next examined histological preparations of enCORs treated with the three ethanol doses, which revealed a striking effect on CP formation that was dose dependent with the higher dose of 150 mM completely lacking a CP whereas the lowest dose of 43.5 mM was completely normal (FIG. 11a). We quantified the number of tissues displaying a recognizable CP in control and the two higher doses where a phenotype was evident, which further demonstrated the dose responsiveness (FIG. 11b).

[0165] Notably, 150 mM treatment also displayed defects in the VZ with less continuity and smaller ventricular surfaces, a potential feature consistent with microcephaly seen in FAS. To investigate this effect further, we also tested a very high concentration of 300 mM, which resulted in highly disorganized ventricular zones with a large number of abnormally located neurons, having failed to migrate basally outward (FIG. 21b). Furthermore, we tested timing of ethanol challenge by treating enCORs before CP formation when lateral expansion was still occurring (FIG. 11c). These tissues displayed dramatic disruption of the VZ and a lack of large continuous lobes with large ventricles. Importantly, while the effect on CP formation and neuronal migration could not be modelled in spheroids, the effects on VZ continuity were evident (FIG. 21c). Finally, these effects were not simply due to an effect on cell survival as TUNEL staining did not reveal a noticeable increase in apoptotic/necrotic cells in any of the three treatment concentrations (FIG. 21d).

[0166] While the mechanism of action of ethanol teratogenicity in brain development is not yet known, several studies have pointed to the possibility that ethanol may interfere with metabolism of vitamin A to its active form, retinoic acid, through competitive inhibition of alcohol dehydrogenases that act on alcohols including ethanol and retinol (FIG. 11d). Interestingly, there are many members of this class of enzyme, several of which are expressed in enCORs (FIG. 21e). Another possibility, however, is that the acetaldehyde produced from ethanol metabolism acts through its DNA damaging properties to disrupt brain development. We sought to test these two possibilities by performing treatments with metabolites of the retinol and ethanol metabolic pathways.

[0167] We performed a combination of histological and immunohistochemical staining for neurons and nestin in order to examine the effect on the radial scaffold and neuronal positioning. Ethanol treatment resulted in disruption of the CP with overmigration of neurons and abnormal accumulations at the surface of the organoid (FIG. 11e) consistent with the formation of external heterotopias, previously described in models of FAS. This was accompanied by radial processes that extended beyond the main neuronal population and into the ectopic region. In contrast, treatment with acetaldehyde did not result in noticeable defects in either CP formation or VZ morphology (FIG. 11e), suggesting the effects of ethanol are not through its downstream metabolite.

[0168] In order to test for potential competition with vitamin A metabolism and retinoic acid production, we tested whether a complete absence of vitamin A (retinol) could recapitulate the effects, by omitting vitamin A from the media for the same period that we performed ethanol treatment. Similar to ethanol treatment, a lack of retinol resulted in disorganized CP and overmigration with abnormal clusters of nestin positive basal processes (FIG. 11e). Furthermore, treatment with the downstream active product, retinoic acid, along with ethanol, led to a partial rescue with a notably intact CP. However, there were still defects in the VZ suggesting this aspect of the phenotype is not through competitive inhibition of retinol metabolism. These data support that retinoids are required for proper neuronal migration and formation of a CP, and further suggest the teratogenic effects of ethanol may be through interference with this pathway.

[0169] The remarkable self-organization and ability to generate the full repertoire of organ cell types have made organoids an important new model system. However, the high variability and difficulties modelling later tissue architecture has meant that subtle defects are difficult to discern. To overcome this, we have combined organoids with bioengineering using a novel microscale internal scaffold. This method enables the study of neuronal migration disorders, and we examine such defects associated with FAS as a proof of principle. Finally, we demonstrate interaction with retinol metabolism as a mechanism of ethanol induced CP defects and heterotopias.