Retinoblastoma protein controls growth, survival and neuronal migration in human cerebral organoids

Pax6 mutant cerebral organoids partially recapitulate phenotypes of Pax6 mutant mouse strains

Cerebral organoids show great promise as tools to unravel the complex mechanisms by which the mammalian brain develops during embryogenesis. We generated mouse cerebral organoids harbouring constitutive or conditional mutations in Pax6, which encodes a transcription factor with multiple important roles in brain development. By comparing the phenotypes of mutant organoids with the well-described phenotypes of Pax6 mutant mouse embryos, we evaluated the extent to which cerebral organoids reproduce phenotypes previously described in vivo. Organoids lacking Pax6 showed multiple phenotypes associated with its activity in mice, including precocious neural differentiation, altered cell cycle and an increase in abventricular mitoses. Neural progenitors in both Pax6 mutant and wild type control organoids cycled more slowly than their in vivo counterparts, but nonetheless we were able to identify clear changes to cell cycle attributable to the absence of Pax6. Our findings support the value of cerebral organoids as tools to explore mechanisms of brain development, complementing the use of mouse models.

RB1-Negative Retinal Organoids Display Proliferation of Cone Photoreceptors and Loss of Retinal Differentiation

Simple Summary

Retinoblastoma is a tumor of the eye’s retina, which is the very specialized tissue responsible for vision. In 98% of cases, the tumor is caused by inactivation of the RB1 gene. Due to lack of material and models, the understanding of RB1 mutations in tumor development is still unsatisfactory. We aimed to establish a human laboratory model for retinoblastoma. While differentiating stem cells with a mutation in RB1 into retina, we observed reduced differentiation potential but enhanced proliferation—general hallmarks of tumor development. The gene expression signature in the model resembled that of tumor material. This approach now enables research on retinoblastoma and probably therapy in the correct tissue, the human retina.

Abstract

Retinoblastoma is a tumor of the eye in children under the age of five caused by biallelic inactivation of the RB1 tumor suppressor gene in maturing retinal cells. Cancer models are essential for understanding tumor development and in preclinical research. Because of the complex organization of the human retina, such models were challenging to develop for retinoblastoma. Here, we present an organoid model based on differentiation of human embryonic stem cells into neural retina after inactivation of RB1 by CRISPR/Cas9 mutagenesis. Wildtype and RB1 heterozygous mutant retinal organoids were indistinguishable with respect to morphology, temporal development of retinal cell types and global mRNA expression. However, loss of pRB resulted in spatially disorganized organoids and aberrant differentiation, indicated by disintegration of organoids beyond day 130 of differentiation and depletion of most retinal cell types. Only cone photoreceptors were abundant and continued to proliferate, supporting these as candidate cells-of-origin for retinoblastoma. Transcriptome analysis of RB1 knockout organoids and primary retinoblastoma revealed gain of a retinoblastoma expression signature in the organoids, characterized by upregulation of RBL1 (p107), MDM2, DEK, SYK and HELLS. In addition, genes related to immune response and extracellular matrix were specifically upregulated in RB1-negative organoids. In vitro retinal organoids therefore display some features associated with retinoblastoma and, so far, represent the only valid human cancer model for the development of this disease.

Advancing Drug Discovery for Neurological Disorders Using iPSC-Derived Neural Organoids

In the last decade, different research groups in the academic setting have developed induced pluripotent stem cell-based protocols to generate three-dimensional, multicellular, neural organoids. Their use to model brain biology, early neural development, and human diseases has provided new insights into the pathophysiology of neuropsychiatric and neurological disorders, including microcephaly, autism, Parkinson’s disease, and Alzheimer’s disease. However, the adoption of organoid technology for large-scale drug screening in the industry has been hampered by challenges with reproducibility, scalability, and translatability to human disease. Potential technical solutions to expand their use in drug discovery pipelines include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) to create isogenic models, single-cell RNA sequencing to characterize the model at a cellular level, and machine learning to analyze complex data sets. In addition, high-content imaging, automated liquid handling, and standardized assays represent other valuable tools toward this goal. Though several open issues still hamper the full implementation of the organoid technology outside academia, rapid progress in this field will help to prompt its translation toward large-scale drug screening for neurological disorders.

Challenges in Modeling Human Neural Circuit Formation via Brain Organoid Technology

Human brain organoids are three-dimensional self-organizing tissues induced from pluripotent cells that recapitulate some aspects of early development and some of the early structure of the human brain in vitro. Brain organoids consist of neural lineage cells, such as neural stem/precursor cells, neurons, astrocytes and oligodendrocytes. Additionally, brain organoids contain fluid-filled ventricle-like structures surrounded by a ventricular/subventricular (VZ/SVZ) zone-like layer of neural stem cells (NSCs). These NSCs give rise to neurons, which form multiple outer layers. Since these structures resemble some aspects of structural arrangements in the developing human brain, organoid technology has attracted great interest in the research fields of human brain development and disease modeling. Developmental brain disorders have been intensely studied through the use of human brain organoids. Relatively early steps in human brain development, such as differentiation and migration, have also been studied. However, research on neural circuit formation with brain organoids has just recently began. In this review, we summarize the current challenges in studying neural circuit formation with organoids and discuss future perspectives.

Innovations in 3-Dimensional Tissue Models of Human Brain Physiology and Diseases

3-dimensional (3D) laboratory tissue cultures have emerged as an alternative to traditional 2-dimensional (2D) culture systems that do not recapitulate native cell behavior. The discrepancy between in vivo and in vitro tissue-cell-molecular responses impedes understanding of human physiology in general and creates roadblocks for the discovery of therapeutic solutions. Two parallel approaches have emerged for the design of 3D culture systems. The first is biomedical engineering methodology, including bioengineered materials, bioprinting, microfluidics and bioreactors, used alone or in combination, to mimic the microenvironments of native tissues. The second approach is organoid technology, in which stem cells are exposed to chemical and/or biological cues to activate differentiation programs that are reminiscent of human (prenatal) development. This review article describes recent technological advances in engineering 3D cultures that more closely resemble the human brain. The contributions of in vitro 3D tissue culture systems to new insights in neurophysiology, neurological diseases and regenerative medicine are highlighted. Perspectives on designing improved tissue models of the human brain are offered, focusing on an integrative approach merging biomedical engineering tools with organoid biology.

In vitro models for ASD-patient-derived iPSCs and cerebral organoids

Autism spectrum disorder (ASD) is a set of pervasive neurodevelopmental disorders. The causation is multigenic in most cases, which makes it difficult to model the condition in vitro. Advances in pluripotent stem cell technology has made it possible to generate in vitro models of human brain development. Induced pluripotent stem cells (iPSCs) can be generated from somatic cells and have the ability to differentiate to all of the body's cells. This chapter aims to give an overview of the iPSC technology for generating neural cells and cerebral organoids as models for neurodevelopment and how these models are utilized in the study of ASD. The combination of iPSC technology and the genetic modification tool CRISPR/Cas9 is described, and current limitations and future perspectives of iPSC technology is discussed.

Role of RB1 in human embryonic stem cell-derived retinal organoids

Three-dimensional (3D) organoid models derived from human pluripotent stem cells provide a platform for studying human development and understanding disease mechanisms. Most studies that examine biallelic inactivation of the cell cycle regulator Retinoblastoma 1 (RB1) and the link to retinoblastoma is in mice, however, less is known regarding the pathophysiological role of RB1 during human retinal development. To study the role of RB1 in early human retinal development and tumor formation, we generated retinal organoids from CRISPR/Cas9-derived RB1-null human embryonic stem cells (hESCs). We showed that RB is abundantly expressed in retinal progenitor cells in retinal organoids and loss of RB1 promotes S-phase entry. Furthermore, loss of RB1 resulted in widespread apoptosis and reduced the number of photoreceptor, ganglion, and bipolar cells. Interestingly, RB1 mutation in retinal organoids did not result in retinoblastoma formation in vitro or in the vitreous body of NOD/SCID immunodeficient mice. Together, our work identifies a crucial function for RB1 in human retinal development and suggests that RB1 deletion alone is not sufficient for tumor development, at least in human retinal organoids.

Genetic Modification of Brain Organoids

Brain organoids have become increasingly used systems allowing 3D-modeling of human brain development, evolution, and disease. To be able to make full use of these modeling systems, researchers have developed a growing toolkit of genetic modification techniques. These techniques can be applied to mature brain organoids or to the preceding embryoid bodies (EBs) and founding cells. This review will describe techniques used for transient and stable genetic modification of brain organoids and discuss their current use and respective advantages and disadvantages. Transient approaches include adeno-associated virus (AAV) and electroporation-based techniques, whereas stable genetic modification approaches make use of lentivirus (including viral stamping), transposon and CRISPR/Cas9 systems. Finally, an outlook as to likely future developments and applications regarding genetic modifications of brain organoids will be presented.

Organotypic Neurovascular Models: Past Results and Future Directions

The high failure rates of clinical trials in neurodegeneration, perhaps most apparent in recent high-profile failures of potential Alzheimer's disease therapies, have partially motivated the development of improved human cell-based models to bridge the gap between well-plate assays and preclinical efficacy studies in mice. Recently, cerebral organoids derived from stem cells have gained significant traction as 3D models of central nervous system (CNS) regions. Although this technology is promising, several limitations still exist; most notably, improper structural organization of neural cells and a lack of functional glia and vasculature. Here, we provide an overview of the cerebral organoid field and speculate how engineering strategies, including biomaterial fabrication and templating, might be used to overcome existing challenges.

CDK14 involvement in proliferation migration and invasion of esophageal cancer

Background

CDK14 has significant involvement in tumorigenesis of cancers including hepatocellular carcinoma, gastric carcinoma and breast cancer. In esophageal cancer, CDK14 is useful as a prognostic marker and as a predictor of response to chemotherapy. However, the exact mechanism of CDK14 n chemotherapy for esophageal squamous cell carcinoma (ESCC) has not been explored.

Methods

Western blots and immunohistochemistry (IHC) analysis were performed to analyse the expression of CDK14 in ESCC. Co-immunoprecipitation and immunofluorescence assays were used to explore the mechanism of CDK14 involvement in ESCC. Colony formation assays and proliferation assays were used to investigate the function of CDK14 in ESCC. At last, we constructed two truncated mutants of CDK14 by the PCR technology to research the functional structural domain.

Results

Western blots and IHC analysis showed that CDK14 expression was higher n tumor tissues and cell lines than that in normal tissues. IHC staining revealed that CDK14 positively correlated with clinical pathological variables of tumor size (P=0.001), tumor grade (P=0.004), Ki-67 (P=0.012) and survival (P=0.000). Immunoprecipitation and immunofluorescence assays revealed that CDK-activating kinase (CAK), namely CDK7/CCNH complex physically interacted and was collocated with CDK14 in the cell nucleus. This direct interaction increased CDK14 phosphorylation and inhibited Rb function through phosphorylation. In vitro starvation and refeeding assays demonstrated that CDK14 expression was related to proliferation of ESCC cells. Overexpression of CDK14 in Eca109 cells increased colony formation and reduced sensitivity to cisplatin. Overexpressing CDK7 with CDK14 strengthened these effects, demonstrating that CDK7 was a major component in CDK14 activation.

Conclusions

Expression of CDK14 worsened the effects of cisplatin chemotherapy by promoting ESCC proliferation.

Genome Editing in Human Neural Stem and Progenitor Cells

Experimental tools for precise manipulation of mammalian genomes enable reverse genetic approaches to explore biology and disease. Powerful genome editing technologies built upon designer nucleases, such as CRISPR/Cas9, have recently emerged. Parallel progress has been made in methodologies for the expansion and differentiation of human pluripotent and tissue stem cells. Together these innovations provide a remarkable new toolbox for human cellular genetics and are opening up vast opportunities for discoveries and applications across the breadth of life sciences research. In this chapter, we review the emergence of genome editing technologies and how these are being deployed in studies of human neurobiology, neurological disease, and neuro-oncology. We focus our discussion on CRISPR/Cas9 and its application in studies of human neural stem and progenitor cells.

Applications of Human Brain Organoids to Clinical Problems

Brain organoids are an exciting new technology with the potential to significantly change how diseases of the brain are understood and treated. These three-dimensional neural tissues are derived from the self-organization of pluripotent stem cells, and they recapitulate the developmental process of the human brain, including progenitor zones and rudimentary cortical layers. Brain organoids have been valuable in investigating different aspects of developmental neurobiology and comparative biology. Several characteristics of organoids also make them attractive as models of brain disorders. Data generated from human organoids are more generalizable to patients because of the match in species background. Personalized organoids also can be generated from patient-derived induced pluripotent stem cells. Furthermore, the three-dimensionality of brain organoids supports cellular, mechanical, and topographical cues that are lacking in planar systems. In this review, we discuss the translational potential of brain organoids, using the examples of Zika virus, autism-spectrum disorder, and glioblastoma multiforme to consider how they could contribute to disease modeling, personalized medicine, and testing of therapeutics. We then discuss areas of improvement in organoid technology that will enhance the translational potential of brain organoids, as well as the possibility of their use as substrates for repairing cerebral circuitry after injury. Developmental Dynamics 248:53-64, 2019. © 2018 Wiley Periodicals, Inc.

Microglia support neural stem cell maintenance and growth

Increasing evidence suggests that disease-associated microglia play a protective role in neurodegenerative diseases. Microglia are known to polarize into two reciprocate forms in response to external cues - inflammatory M1 state and anti-inflammatory M2 state. These cells perform key functions in the development of the brain, such as circuit refinement, neurogenesis, and neuronal growth. In this study, we analyzed the secretion effect of microglia on neural stem/progenitor cell (NSPC) proliferation and differentiation. We cultured adult mouse-derived NSPCs in a conditioned medium from BV2 immortalized microglia without growth factors and evaluated their differentiation. When cultivated with BV2-derived soluble factors in the presence of basic fibroblast growth factor (bFGF) and epidermal growth factor (EGF), NSPCs were able to maintain Nestin expression and showed increased proliferation compared with those cells cultivated with bFGF and EGF only. Moreover, conditioned media from M2-polarized primary microglia, stimulated by IL-10/IL-13, showed supportive effect on NSPC proliferation. These data suggest that microglia support neural stem cell proliferation through secreting neuro-nutritious soluble factors.

Brain organoids as models to study human neocortex development and evolution

Since their recent development, organoids that emulate human brain tissue have allowed in vitro neural development studies to go beyond the limits of monolayer culture systems, such as neural rosettes. We present here a review of organoid studies that focuses on cortical wall development, starting with a technical comparison between pre-patterning and self-patterning brain organoid protocols. We then follow neocortex development in space and time and list those aspects where organoids have succeeded in emulating in vivo development, as well as those aspects that continue to be pending tasks. Finally, we present a summary of medical and evolutionary insight made possible by organoid technology.

Studying the Brain in a Dish: 3D Cell Culture Models of Human Brain Development and Disease

The study of the cellular and molecular processes of the developing human brain has been hindered by access to suitable models of living human brain tissue. Recently developed 3D cell culture models offer the promise of studying fundamental brain processes in the context of human genetic background and species-specific developmental mechanisms. Here, we review the current state of 3D human brain organoid models and consider their potential to enable investigation of complex aspects of human brain development and the underpinning of human neurological disease.

Organoids: An intermediate modeling platform in precision oncology

Cancer harbors variable heterogeneity and plasticity. Thus far, our comprehension is greatly based on cell lines, organoids, and patient-derived tumor xenografts (PDTXs). Organoids are a three-dimensional in vitro culture platform constructed from self-organizing stem cells. They can almost accurately recapitulate tumor heterogeneity and microenvironment "in a dish," which surpass established cell lines and are not as expensive and time-consuming as PDTXs. As an intermediate model, tumor organoids are also used to study the fundamental issues of tumorigenesis and metastasis. They are specifically applied for drug testing and stored as "living biobanks." In this review, we highlight the translational applications of organoid technologies in tumor research and precision medicine, discuss the advantages and limitations compared with other mentioned methods, and provide our outlook on its future.

Opportunities for organoids as new models of aging

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

Organoids: a Special Issue

Summary: This Editorial provides an overview of the entire contents of the Special Issue, highlighting some of the important findings and major themes therein.

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

The cell cycle coordinates core functions such as replication and cell division. However, cell-cycle-regulated transcription in the control of non-core functions, such as cell identity maintenance through specific transcription factors (TFs) and signalling pathways remains unclear. Here, we provide a resource consisting of mapped transcriptomes in unsynchronized HeLa and U2OS cancer cells sorted for cell cycle phase by Fucci reporter expression. We developed a novel algorithm for data analysis that enables efficient visualization and data comparisons and identified cell cycle synchronization of Notch signalling and TFs associated with development. Furthermore, the cell cycle synchronizes with the circadian clock, providing a possible link between developmental transcriptional networks and the cell cycle. In conclusion we find that cell cycle synchronized transcriptional patterns are temporally compartmentalized and more complex than previously anticipated, involving genes, which control cell identity and development.

Neural stem cells and epilepsy: functional roles and disease-in-a-dish models

Epilepsy is a disorder of the central nervous system characterized by spontaneous recurrent seizures. Although current therapies exist to control the number and severity of clinical seizures, there are no pharmacological cures or disease-modifying treatments available. Use of transgenic mouse models has allowed an understanding of neural stem cells in their relation to epileptogenesis in mesial temporal lobe epilepsy. Further, with the significant discovery of factors necessary to reprogram adult somatic cell types into pluripotent stem cells, it has become possible to study monogenic epilepsy-in-a-dish using patient-derived neurons. This discovery along with some of the newest technological advances in recapitulating brain development in a dish has brought us closer than ever to a platform in which to study and understand the mechanisms of this disease. These technologies will be critical in understanding the mechanism of epileptogenesis and ultimately lead to improved therapies and precision medicine for patients with epilepsy.

Genetic and Molecular Approaches to Study Neuronal Migration in the Developing Cerebral Cortex

The migration of neuronal cells in the developing cerebral cortex is essential for proper development of the brain and brain networks. Disturbances in this process, due to genetic abnormalities or exogenous factors, leads to aberrant brain formation, brain network formation, and brain function. In the last decade, there has been extensive research in the field of neuronal migration. In this review, we describe different methods and approaches to assess and study neuronal migration in the developing cerebral cortex. First, we discuss several genetic methods, techniques and genetic models that have been used to study neuronal migration in the developing cortex. Second, we describe several molecular approaches to study aberrant neuronal migration in the cortex which can be used to elucidate the underlying mechanisms of neuronal migration. Finally, we describe model systems to investigate and assess the potential toxicity effect of prenatal exposure to environmental chemicals on proper brain formation and neuronal migration.