Deep-learning analysis of micropattern-based organoids enables high-throughput drug screening of Huntington's disease models

Organoids are carrying the promise of modeling complex disease phenotypes and serving as a powerful basis for unbiased drug screens, potentially offering a more efficient drug-discovery route. However, unsolved technical bottlenecks of reproducibility and scalability have prevented the use of current organoids for high-throughput screening. Here, we present a method that overcomes these limitations by using deep-learning-driven analysis for phenotypic drug screens based on highly standardized micropattern-based neural organoids. This allows us to distinguish between disease and wild-type phenotypes in complex tissues with extremely high accuracy as well as quantify two predictors of drug success: efficacy and adverse effects. We applied our approach to Huntington's disease (HD) and discovered that bromodomain inhibitors revert complex phenotypes induced by the HD mutation. This work demonstrates the power of combining machine learning with phenotypic drug screening and its successful application to reveal a potentially new druggable target for HD.

Huntingtin CAG expansion impairs germ layer patterning in synthetic human 2D gastruloids through polarity defects

Huntington's disease (HD) is a fatal neurodegenerative disorder caused by an expansion of the CAG repeats in the huntingtin gene (HTT). Although HD has been shown to have a developmental component, how early during human embryogenesis the HTT-CAG expansion can cause embryonic defects remains unknown. Here, we demonstrate a specific and highly reproducible CAG length-dependent phenotypic signature in a synthetic model for human gastrulation derived from human embryonic stem cells (hESCs). Specifically, we observed a reduction in the extension of the ectodermal compartment that is associated with enhanced activin signaling. Surprisingly, rather than a cell-autonomous effect, tracking the dynamics of TGFβ signaling demonstrated that HTT-CAG expansion perturbs the spatial restriction of activin response. This is due to defects in the apicobasal polarization in the context of the polarized epithelium of the 2D gastruloid, leading to ectopic subcellular localization of TGFβ receptors. This work refines the earliest developmental window for the prodromal phase of HD to the first 2 weeks of human development, as modeled by our 2D gastruloids.

Summary: 2D gastruloids of isogenic human embryonic stem cells modeling Huntington's Disease reveal that huntingtin CAG expansion perturbs the spatial restriction of the activin response in the context of the polarized epithelium.

WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids

Self-organization of discrete fates in human gastruloids is mediated by a hierarchy of signaling pathways. How these pathways are integrated in time, and whether cells maintain a memory of their signaling history remains obscure. Here, we dissect the temporal integration of two key pathways, WNT and ACTIVIN, which along with BMP control gastrulation. CRISPR/Cas9-engineered live reporters of SMAD1, 2 and 4 demonstrate that in contrast to the stable signaling by SMAD1, signaling and transcriptional response by SMAD2 is transient, and while necessary for pluripotency, it is insufficient for differentiation. Pre-exposure to WNT, however, endows cells with the competence to respond to graded levels of ACTIVIN, which induces differentiation without changing SMAD2 dynamics. This cellular memory of WNT signaling is necessary for ACTIVIN morphogen activity. A re-evaluation of the evidence gathered over decades in model systems, re-enforces our conclusions and points to an evolutionarily conserved mechanism.

Synthetic embryology: controlling geometry to model early mammalian development

Differentiation of embryonic stem cells in vitro is an important tool in dissecting and understanding the mechanisms that govern early embryologic development. In recent years, there has been considerable progress in creating organoids that model gastrulation, neurulation or organogenesis. However, one of the key challenges is reproducibility. Geometrically confining stem cell colonies considerably improves reproducibility and provides quantitative control over differentiation and tissue shape. Here, we review recent advances in controlling the two-dimensional or three-dimensional organization of cells and the effect on differentiation phenotypes. Improved methods of geometrical control will allow for an even more detailed understanding of the mechanisms underlying embryologic development and will eventually pave the way for the highly reproducible generation of specific tissue types.

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

During gastrulation epiblast cells exit pluripotency as they specify and spatially arrange the three germ layers of the embryo. Similarly, human pluripotent stem cells (PSCs) undergo spatially organized fate specification on micropatterned surfaces. Since in vivo validation is not possible for the human, we developed a mouse PSC micropattern system and, with direct comparisons to mouse embryos, reveal the robust specification of distinct regional identities. BMP, WNT, ACTIVIN and FGF directed mouse epiblast-like cells to undergo an epithelial-to-mesenchymal transition and radially pattern posterior mesoderm fates. Conversely, WNT, ACTIVIN and FGF patterned anterior identities, including definitive endoderm. By contrast, epiblast stem cells, a developmentally advanced state, only specified anterior identities, but without patterning. The mouse micropattern system offers a robust scalable method to generate regionalized cell types present in vivo, resolve how signals promote distinct identities and generate patterns, and compare mechanisms operating in vivo and in vitro and across species.

Chromosomal instability during neurogenesis in Huntington's disease

Huntington's disease (HD) is a fatal neurodegenerative disease caused by expansion of CAG repeats in the Huntingtin gene (HTT). Neither its pathogenic mechanisms nor the normal functions of HTT are well understood. To model HD in humans, we engineered a genetic allelic series of isogenic human embryonic stem cell (hESC) lines with graded increases in CAG repeat length. Neural differentiation of these lines unveiled a novel developmental HD phenotype: the appearance of giant multinucleated telencephalic neurons at an abundance directly proportional to CAG repeat length, generated by a chromosomal instability and failed cytokinesis over multiple rounds of DNA replication. We conclude that disrupted neurogenesis during development is an important, unrecognized aspect of HD pathogenesis. To address the function of normal HTT protein we generated HTT^+/- and HTT^-/- lines. Surprisingly, the same phenotype emerged in HTT^-/- but not HTT^+/- lines. We conclude that HD is a developmental disorder characterized by chromosomal instability that impairs neurogenesis, and that HD represents a genetic dominant-negative loss of function, contrary to the prevalent gain-of-toxic-function hypothesis. The consequences of developmental alterations should be considered as a new target for HD therapies.

Channeling of Branched Flow in Weakly Scattering Anisotropic Media

When waves propagate through weakly scattering but correlated, disordered environments they are randomly focused into pronounced branchlike structures, a phenomenon referred to as branched flow, which has been studied in a wide range of isotropic random media. In many natural environments, however, the fluctuations of the random medium typically show pronounced anisotropies. A prominent example is the focusing of tsunami waves by the anisotropic structure of the ocean floor topography. We study the influence of anisotropy on such natural focusing events and find a strong and nonintuitive dependence on the propagation angle which we explain by semiclassical theory.

Distribution of the fittest individuals and the rate of Muller's ratchet in a model with overlapping generations

Muller's ratchet is a paradigmatic model for the accumulation of deleterious mutations in a population of finite size. A click of the ratchet occurs when all individuals with the least number of deleterious mutations are lost irreversibly due to a stochastic fluctuation. In spite of the simplicity of the model, a quantitative understanding of the process remains an open challenge. In contrast to previous works, we here study a Moran model of the ratchet with overlapping generations. Employing an approximation which describes the fittest individuals as one class and the rest as a second class, we obtain closed analytical expressions of the ratchet rate in the rare clicking regime. As a click in this regime is caused by a rare, large fluctuation from a metastable state, we do not resort to a diffusion approximation but apply an approximation scheme which is especially well suited to describe extinction events from metastable states. This method also allows for a derivation of expressions for the quasi-stationary distribution of the fittest class. Additionally, we confirm numerically that the formulation with overlapping generations leads to the same results as the diffusion approximation and the corresponding Wright-Fisher model with non-overlapping generations.

Muller's ratchet is a paradigmatic model in population genetics which describes the fixation of a deleterious mutation in a population of finite size due to an unfortunate stochastic fluctuation. Obtaining quantitative predictions of the ratchet rate, i.e. the frequency with which such a mutation fixes, is believed to be important for understanding a broad range of effects ranging from the degeneration of the Y-chromosome to the evolution of sex as a means of avoiding the fixation of deleterious mutations. To obtain a better understanding of how Muller's ratchet operates, we have considered a model with overlapping generations, which allows for the application of methods specifically tailored for the analysis of rare stochastic fluctuations which drive the ratchet. We obtain concise and accurate results for the rate of Muller's ratchet. Additionally, we are able to predict the full distribution of the frequency of the fittest individuals, a quantity of central interest in understanding the ratchet rate and possibly experimentally much more accessible than the rate, in particular when the ratchet rate is very large.

Experimental observation of a fundamental length scale of waves in random media

Waves propagating through a weakly scattering random medium show a pronounced branching of the flow accompanied by the formation of freak waves, i.e., extremely intense waves. Theory predicts that this strong fluctuation regime is accompanied by its own fundamental length scale of transport in random media, parametrically different from the mean free path or the localization length. We show numerically how the scintillation index can be used to assess the scaling behavior of the branching length. We report the experimental observation of this scaling using microwave transport experiments in quasi-two-dimensional resonators with randomly distributed weak scatterers. Remarkably, the scaling range extends much further than expected from random caustics statistics.

Intensity fluctuations of waves in random media: what is the semiclassical limit?

Waves traveling through weakly random media are known to be strongly affected by their corresponding ray dynamics, in particular in forming linear freak waves. The ray intensity distribution, which, e.g., quantifies the probability of freak waves is unknown, however, and a theory of how it is approached in an appropriate semiclassical limit of wave mechanics is lacking. We show that this limit is not the usual limit of small wavelengths, but that of decoherence. Our theory, which can describe the intensity distribution for an arbitrary degree of coherence is relevant to a wide range of physical systems, as decoherence is omnipresent in real systems.

Universal statistics of branched flows

Even very weak correlated disorder potentials can cause extreme fluctuations in Hamiltonian flows. In two dimensions this leads to a pronounced branching of the flow. Although present in a great variety of physical systems, a quantitative theory of the branching statistics is lacking. Here, we derive an analytical expression for the number of branches valid for all distances from a source. We also derive the scaling relations that make this expression universal for a wide range of random potentials. Our theory has possible applications in many fields ranging from semiconductor to geophysics.

Recognition of HLA class I molecules by antisera directed to synthetic peptides corresponding to different regions of the HLA-B7 heavy chain

Antisera have been prepared in rabbits and in mice against different peptides corresponding to four hydrophilic and variable regions of HLA-B7 heavy chain (65-82, 99-118, 138-157, and 164-187). Specific antipeptide sera have been obtained with all synthetic peptides; for three of them which were more than 20 amino acids long, highly potent sera were elicited by injection of the free peptide. Three overlapping peptides included in region 138-157 have been used, and two different antigenic sites were detected in this region. HLA molecules solubilized in nonionic detergent were precipitated by antipeptide sera directed against regions 65-82, 138-157, and 164-187, but not by antipeptide serum directed against the less hydrophilic region 99-118. Analysis by two-dimensional electrophoresis of the isolated molecules confirmed the anti-HLA specificity of the antipeptide 65-82 and 138-157 sera. Variable numbers of HLA-related spots were found according to the antisera used. Antipeptide 138-157 serum precipitated numerous HLA molecules and therefore probably reacted with monomorphic determinants whereas antipeptide 65-82 appeared specific for a more limited number of HLA antigens. Such reagents directed against well-defined regions of the HLA class I heavy chain are of considerable interest, notably for the mapping of antigenic epitopes on the molecule and for the study of relationships between structure and function.

Recognition of HLA class I molecules by antisera directed to synthetic peptides corresponding to different regions of the HLA-B7 heavy chain

Antisera have been prepared in rabbits and in mice against different peptides corresponding to four hydrophilic and variable regions of HLA-B7 heavy chain (65-82, 99-118, 138-157, and 164-187). Specific antipeptide sera have been obtained with all synthetic peptides; for three of them which were more than 20 amino acids long, highly potent sera were elicited by injection of the free peptide. Three overlapping peptides included in region 138-157 have been used, and two different antigenic sites were detected in this region. HLA molecules solubilized in nonionic detergent were precipitated by antipeptide sera directed against regions 65-82, 138-157, and 164-187, but not by antipeptide serum directed against the less hydrophilic region 99-118. Analysis by two-dimensional electrophoresis of the isolated molecules confirmed the anti-HLA specificity of the antipeptide 65-82 and 138-157 sera. Variable numbers of HLA-related spots were found according to the antisera used. Antipeptide 138-157 serum precipitated numerous HLA molecules and therefore probably reacted with monomorphic determinants whereas antipeptide 65-82 appeared specific for a more limited number of HLA antigens. Such reagents directed against well-defined regions of the HLA class I heavy chain are of considerable interest, notably for the mapping of antigenic epitopes on the molecule and for the study of relationships between structure and function.

Serological expression after sequential double transfection with purified HLA-A11 gene of mouse fibroblasts carrying human beta-2 microglobulin

A genomic cosmid library constructed from DNA from a genotyped individual (JF = HLA-A11, Cw-, B38/A26, Cw7, B51) was screened for clones containing class I histocompatibility genes. Among these clones, one was found to carry a 4.8 kb Hind III fragment which is highly correlated with HLA-A11. This clone was used to transfect LMTK+ cultured mouse fibroblast transformants expressing human beta-2 microglobulin. The human beta-2 microglobulin heavy chain-associated determinant was positively detected by the M18 monoclonal antibody. HLA-A11 expression on these doubly transformed cells was specifically demonstrated by complement-dependent cytotoxicity with HLA-A11 + A3-specific but not with HLA-A3-specific monoclonal antibodies. Absorption studies with human alloantisera confirmed the presence on these cells of HLA-A11 determinants and of cross-reacting determinants which absorbed anti-HLA-A1 and -A3 alloantisera. The JF5-J27 transfected cell expressed both heavy and light chains of human class I histocompatibility genes.

Transplantation in miniature swine. XII. N-terminal sequences of class I histocompatibility antigens (SLA) and beta 2-microglobulin

Purified class I histocompatibility antigens (SLA) from three haplotypes were prepared by papain treatment of lymphoid cell membranes obtained from spleens and lymph nodes of miniature swine homozygous at their major histocompatibility complex. Antigens were purified by ion-exchange chromatography followed by gel filtration. Purity was analyzed by SDS-PAGE, and antigenic specificity by inhibition of complement-dependent, alloantiserum-mediated cytotoxicity. The SLA antigens were reduced and alkylated, and the component heavy and light chains were isolated by gel filtration under dissociating conditions. N-terminal amino acid sequences were obtained for SLAaa, SLAcc, and SLAdd heavy chains, as well as for the light chain, beta 2-microglobulin. The swine antigens showed high levels of homology with class I antigens from other animal species. Heterogeneity was observed among the swine haplotypes, and several of the positions at which substitutions were found are apparently invariant in other animal species. In contrast, only minimal sequence heterogeneity was detected within haplotypes, the basis of which may be of relevance to understanding the evolutionary development of these molecules.

Transplantation in miniature swine. XII. N-terminal sequences of class I histocompatibility antigens (SLA) and beta 2-microglobulin

Purified class I histocompatibility antigens (SLA) from three haplotypes were prepared by papain treatment of lymphoid cell membranes obtained from spleens and lymph nodes of miniature swine homozygous at their major histocompatibility complex. Antigens were purified by ion-exchange chromatography followed by gel filtration. Purity was analyzed by SDS-PAGE, and antigenic specificity by inhibition of complement-dependent, alloantiserum-mediated cytotoxicity. The SLA antigens were reduced and alkylated, and the component heavy and light chains were isolated by gel filtration under dissociating conditions. N-terminal amino acid sequences were obtained for SLAaa, SLAcc, and SLAdd heavy chains, as well as for the light chain, beta 2-microglobulin. The swine antigens showed high levels of homology with class I antigens from other animal species. Heterogeneity was observed among the swine haplotypes, and several of the positions at which substitutions were found are apparently invariant in other animal species. In contrast, only minimal sequence heterogeneity was detected within haplotypes, the basis of which may be of relevance to understanding the evolutionary development of these molecules.

Transplantation in miniature swine. IX. Swine histocompatibility antigens: isolation and purification of papain-solubilized SLA antigens

Histocompatibility antigens have been purified by papain treatment of crude cellular membranes obtained from spleen and mesenteric lymph nodes of individual miniature swine that are homozygous at the major histocompatibility complex. The purification protocol included ultracentrifugation, gel filtration, ion-exchange chromatography, and in some instances preparative isoelectric focusing. This procedure was applied to the preparation of sLA antigens from the 3 haplotypes available in our partially inbred miniature swine herd. The purity of the SLAdd molecules was evidenced by: 1) a single activity peak of approximately 50,000 daltons on gel-permeation chromatography; 2) the antigen elution as a symmetrical peak from ion-exchange resins and from isoelectric focusing columns; 3) the presence of 2 predominant polypeptide chains on SDS-PAGE at apparent m.w. 43,000 and 13,000 daltons; and 4) specific immunoprecipitations by alloantisera and by anti-beta 1 microglobulin antisera. The antigenic activity of SLA products was analyzed by inhibition of complement-mediated cytotoxicity and by removal on anti-beta 2-microglobulin affinity columns. Heavy and light chains were separated by gel-filtration on Sephacryl S-200 in 6 molar guanidine. These SLA products, which have thus been shown to be pure by a variety of criteria, are now readily available for structural analysis and for analysis of biologic activity.

Transplantation in miniature swine. IX. Swine histocompatibility antigens: isolation and purification of papain-solubilized SLA antigens

Histocompatibility antigens have been purified by papain treatment of crude cellular membranes obtained from spleen and mesenteric lymph nodes of individual miniature swine that are homozygous at the major histocompatibility complex. The purification protocol included ultracentrifugation, gel filtration, ion-exchange chromatography, and in some instances preparative isoelectric focusing. This procedure was applied to the preparation of sLA antigens from the 3 haplotypes available in our partially inbred miniature swine herd. The purity of the SLAdd molecules was evidenced by: 1) a single activity peak of approximately 50,000 daltons on gel-permeation chromatography; 2) the antigen elution as a symmetrical peak from ion-exchange resins and from isoelectric focusing columns; 3) the presence of 2 predominant polypeptide chains on SDS-PAGE at apparent m.w. 43,000 and 13,000 daltons; and 4) specific immunoprecipitations by alloantisera and by anti-beta 1 microglobulin antisera. The antigenic activity of SLA products was analyzed by inhibition of complement-mediated cytotoxicity and by removal on anti-beta 2-microglobulin affinity columns. Heavy and light chains were separated by gel-filtration on Sephacryl S-200 in 6 molar guanidine. These SLA products, which have thus been shown to be pure by a variety of criteria, are now readily available for structural analysis and for analysis of biologic activity.

Use of fluorescein conjugated staphylococcal protein-A as a labeling agent for porcine lymphocytes

Staphylococcal Protein-A conjugated to fluorescein (FPA) was compared to a fluorescein conjugated sheep immunoglobulin anti-pig IgG (FSAPG) as a labeling agent for surface IgG positive (sIg+) porcine lymphoid cells. At plateau concentration of the reagents, more lymphoid cells were labeled with FPA than with FSAPG. However, on a protein concentration basis, FPA was less sensitive than FSAPG. As a control, FPA proved to be a poor labeling agent for sIg+ bovine lymphoid cells when compared to FITC conjugated rabbit IgG anti-bovine IgG (FRABG). Adsorptions of porcine lymphoid cells onto Protein-A Sepharose were performed in order to study the differential specificity of the Protein-A for sIg and for free immunoglobulins. The results of such absorptions showed that Protein-A Sepharose, whatever its affinity for Fab fragments from porcine immunoglobulins, could be used to enrich the sIg negative lymphoid cell populations in the pig.

Rapid method for screening of immunoglobulins in porcine fetuses, using rocket immunoelectrophoresis. Application of an interspecies reaction between human and porcine mu-chain

A method for screening of immunoglobulin levels in porcine fetuses is presented. The method is based on rocket electrophoresis. This method is sensitive, but when used for assaying immunoglobulins it is only semiquantitative. It was shown that sera from 11 hysterectomy-derived colostrum-deprived neonatal pigs from a normal gilt contained no IgM or IgA, but small amounts of IgG. Sera from 9 piglets isolated in the same way from a gilt infected with porcine parvovirus contained all 3 antibody classes. IgM was detected by an interspecies reaction using anti human μ-chain immunoglobulin.

Partial inhibition of the humoral immune response of pigs after early postnatal immunization

The ability of young pigs to be immunized during the postnatal period was studied. Eight groups of pigs born on the same day from 3 sows were injected with hen egg-white lysozyme in Freund's incomplete adjuvant at days 0, 1, 2, 3, 4, 5, 7, and 10 after birth. The serum antibody titers were determined each week. Results indicated that pigs injected within the first 3 days of life exhibited a delay of 10 days in the appearance of the humoral antibodies, compared with the antibody response observed in pigs injected later. Serum antibody titers were markedly lower in the early immunized pigs. The secondary immune response was similar in all pigs. This partial inhibition is not directly linked to the corticoids present in the serum at the immunization day. Possible reasons for this impairment of the humoral immune response were reviewed.

[Adjuvant effect of Quil-A on the porcine humoral immune response (author's transl)]

Quil-A, a purified extract of saponin, was analyzed for its adjuvant properties in the porcine humoral immune response against lysozyme. The adjuvant properties of Quil-A are comparable to the oil adjuvant properties in the pig. The optimal dose was found to be 1 mg per pig. Quil-A enhanced also slightly the homocytotropic antibodies.

Heat sensitivity of porcine IgG

The sensitivity to heat of porcine IgG was studied. The serum from immunized pigs was heated at 56 degrees C for 30 min as for decomplementation. The elution pattern of the serum proteins on an agarose gel column showed a dramatic change with the appearance of a large peak of the gel-excluded material. This peak contained mainly IgG molecules which still retained its antibody activity. This fact points to misinterpretations which can easily occur in 7S and 19S antibody recognition during the porcine immune response. Correlation is suggested of this property with the large number of interheavy chain disulfide bridges present in porcine IgG.