Three-dimensional brain organoids have emerged as a valuable model system for studies of human brain development and pathology. Here we establish a midbrain organoid culture system to study the developmental trajectory from pluripotent stem cells to mature dopamine neurons. Using single cell RNA sequencing, we identify the presence of three molecularly distinct subtypes of human dopamine neurons with high similarity to those in developing and adult human midbrain. However, despite significant advancements in the field, the use of brain organoids can be limited by issues of reproducibility and incomplete maturation which was also observed in this study. We therefore designed bioengineered ventral midbrain organoids supported by recombinant spider-silk microfibers functionalized with full-length human laminin. We show that silk organoids reproduce key molecular aspects of dopamine neurogenesis and reduce inter-organoid variability in terms of cell type composition and dopamine neuron formation.

The human forebrain has expanded in size and complexity compared to chimpanzees despite limited changes in protein-coding genes, suggesting that gene expression regulation is an important driver of brain evolution. Here, we identify a KRAB-ZFP transcription factor, ZNF558, that is expressed in human but not chimpanzee forebrain neural progenitor cells. ZNF558 evolved as a suppressor of LINE-1 transposons but has been co-opted to regulate a single target, the mitophagy gene SPATA18. ZNF558 plays a role in mitochondrial homeostasis, and loss-of-function experiments in cerebral organoids suggests that ZNF558 influences developmental timing during early human brain development. Expression of ZNF558 is controlled by the size of a variable number tandem repeat that is longer in chimpanzees compared to humans, and variable in the human population. Thus, this work provides mechanistic insight into how a cis-acting structural variation establishes a regulatory network that affects human brain evolution.

Human midbrain dopamine (DA) neurons are a heterogeneous group of cells that share a common neurotransmitter phenotype and are in close anatomical proximity but display different functions, sensitivity to degeneration, and axonal innervation targets. The A9 DA neuron subtype controls motor function and is primarily degenerated in Parkinson’s disease (PD), whereas A10 neurons are largely unaffected by the condition, and their dysfunction is associated with neuropsychiatric disorders. Currently, DA neurons can only be reliably classified on the basis of topographical features, including anatomical location in the midbrain and projection targets in the forebrain. No systematic molecular classification at the genome-wide level has been proposed to date. Although many years of scientific efforts in embryonic and adult mouse brain have positioned us to better understand the complexity of DA neuron biology, many biological phenomena specific to humans are not amenable to being reproduced in animal models. The establishment of human cell-based systems combined with advanced computational single-cell transcriptomics holds great promise for decoding the mechanisms underlying maturation and diversification of human DA neurons, and linking their molecular heterogeneity to functions in the midbrain. Human pluripotent stem cells have emerged as a useful tool to recapitulate key molecular features of mature DA neuron subtypes. Here, we review some of the most recent advances and discuss the current challenges in using stem cells, to model human DA biology. We also describe how single cell RNA sequencing may provide key insights into the molecular programs driving DA progenitor specification into mature DA neuron subtypes. Exploiting the state-of-the-art approaches will lead to a better understanding of stem cell-derived DA neurons and their use in disease modeling and regenerative medicine.

Dopaminergic (DA) neurons derived from human pluripotent stem cells (hPSCs) represent a renewable and available source of cells useful for understanding development, developing disease models, and stem-cell therapies for Parkinson’s disease (PD). To assess the utility of stem cell cultures as an in vitro model system of human DA neurogenesis, we performed high-throughput transcriptional profiling of ~20,000 ventral midbrain (VM)-patterned stem cells at different stages of maturation using droplet-based single-cell RNA sequencing (scRNAseq). Using this dataset, we defined the cellular composition of human VM cultures at different timepoints and found high purity DA progenitor formation at an early stage of differentiation. DA neurons sharing similar molecular identities to those found in authentic DA neurons derived from human fetal VM were the major cell type after two months in culture. We also developed a bioinformatic pipeline that provided a comprehensive long noncoding RNA landscape based on temporal and cell-type specificity, which may contribute to unraveling the intricate regulatory network of coding and noncoding genes in DA neuron differentiation. Our findings serve as a valuable resource to elucidate the molecular steps of development, maturation, and function of human DA neurons, and to identify novel candidate coding and noncoding genes driving specification of progenitors into functionally mature DA neurons.

Dopaminergic neurons in the ventral midbrain are critical for regulating movement, cognition, and emotion. Ventral midbrain organoids can be used to model both development and diseases of the dopaminergic system, especially Parkinson’s disease. Here, we summarize recent advances and remaining challenges in developing such three-dimensional organoids from human pluripotent stem cells. We outline how ventral midbrain organoid systems have progressed from early three-dimensional culture models to sophisticated, engineered, multiregional systems that more accurately replicate the complex network of dopaminergic neurons. Furthermore, we examine how the development of organoid models from other brain regions, particularly the forebrain, provides complementary insights that can accelerate progress also in the field of midbrain organoids, towards the generation of more advanced in vitro systems for midbrain dopaminergic neurons and their circuitry. Such cutting-edge human stem cell-based models offer powerful platforms for investigating dopaminergic neuron generation, function, and connectivity, thereby enhancing disease modelling, drug discovery, and the development of targeted cell-based therapies.

The role of long non-coding RNAs (lncRNAs) in early mammalian embryogenesis remains unclear due to the complexity of the regulatory mechanisms involving lncRNAs and the limited availability of embryo samples. Stem cell-based models, such as mouse gastruloids, provide new ways to address these challenges. Here, we investigate the function of ultra-conserved lncRNA T-UCstem1 in mammalian body plan formation. Combining morphological and immunofluorescence imaging analyses with bulk and single-cell transcriptomics, we provide evidence indicating that T-UCstem1 is important for mouse gastruloid development and anteroposterior axis extension. T-UCstem1 depletion in gastruloids results in their aberrant development, with defects in the expression of differentiation markers and persistence of pluripotency gene expression. Our single-cell analyses reveal higher levels of cellular heterogeneity in T-UCstem1 -knockdown gastruloids. The presence of cell populations co-expressing pluripotency and differentiation markers points to an important role of T-UCstem1 in the establishment and maintenance of cell identity. Mechanistically, we show that T-UCstem1 acts in a non-cell-autonomous manner through regulation of the Dickkopf-related protein 1 (DKK1)-dependent WNT pathway. Our study identifies a new role for an ultra-conserved lncRNA in gastruloid development and highlights gastruloids as a model system for studying lncRNAs in early development.