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Human TKTL1 implies greater neurogenesis in frontal neocortex of modern humans than Neanderthals.
Neanderthal brains were similar in size to those of modern humans. We sought to investigate potential differences in neurogenesis during neocortex development. Modern human transketolase-like 1 (TKTL1) differs from Neanderthal TKTL1 by a lysine-to-arginine amino acid substitution. Using overexpression in developing mouse and ferret neocortex, knockout in fetal human neocortical tissue, and genome-edited cerebral organoids, we found that the modern human variant, hTKTL1, but not the Neanderthal variant, increases the abundance of basal radial glia (bRG) but not that of intermediate progenitors (bIPs). bRG generate more neocortical neurons than bIPs. The hTKTL1 effect requires the pentose phosphate pathway and fatty acid synthesis. Inhibition of these metabolic pathways reduces bRG abundance in fetal human neocortical tissue. Our data suggest that neocortical neurogenesis in modern humans differs from that in Neanderthals.
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Modeling neuro-immune interactions using human pluripotent stem cells.
Human pluripotent stem cells can be differentiated into cell types that are representative of the central nervous system. Under specific culture conditions, these cells can be induced to self-organize into 3D organoids that are reminiscent of the developing brain. Microglia are the resident immune cells of the brain but are derived from a different lineage than neural cells, which presents a challenge to modeling neuroimmune interactions. Although human microglia-like cells can be differentiated from pluripotent stem cells, important considerations include ensuring the identity of microglia, which can be influenced by both the lineage and the local environment, and developing culture methods that promote the integration and survival of diverse cell types in a physiologically relevant model. Recently, several strategies to generate neural organoids with integrated microglia have been demonstrated and provide new opportunities to interrogate interactions among microglia and neurons during development and in response to injury and disease.
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Human Stem Cell Resources Are an Inroad to Neandertal DNA Functions.
Induced pluripotent stem cells (iPSCs) from diverse humans offer the potential to study human functional variation in controlled culture environments. A portion of this variation originates from an ancient admixture between modern humans and Neandertals, which introduced alleles that left a phenotypic legacy on individual humans today. Here, we show that a large iPSC repository harbors extensive Neandertal DNA, including alleles that contribute to human phenotypes and diseases, encode hundreds of amino acid changes, and alter gene expression in specific tissues. We provide a database of the inferred introgressed Neandertal alleles for each individual iPSC line, together with the annotation of the predicted functional variants. We also show that transcriptomic data from organoids generated from iPSCs can be used to track Neandertal-derived RNA over developmental processes. Human iPSC resources provide an opportunity to experimentally explore Neandertal DNA function and its contribution to present-day phenotypes, and potentially study Neandertal traits.
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Noncoding RNA of Zika Virus Affects Interplay between Wnt-Signaling and Pro-Apoptotic Pathways in the Developing Brain Tissue.
Zika virus (ZIKV) has a unique ability among flaviviruses to cross the placental barrier and infect the fetal brain causing severe abnormalities of neurodevelopment known collectively as congenital Zika syndrome. In our recent study, we demonstrated that the viral noncoding RNA (subgenomic flaviviral RNA, sfRNA) of the Zika virus induces apoptosis of neural progenitors and is required for ZIKV pathogenesis in the developing brain. Herein, we expanded on our initial findings and identified biological processes and signaling pathways affected by the production of ZIKV sfRNA in the developing brain tissue. We employed 3D brain organoids generated from induced human pluripotent stem cells (ihPSC) as an ex vivo model of viral infection in the developing brain and utilized wild type (WT) ZIKV (producing sfRNA) and mutant ZIKV (deficient in the production of sfRNA). Global transcriptome profiling by RNA-Seq revealed that the production of sfRNA affects the expression of >1000 genes. We uncovered that in addition to the activation of pro-apoptotic pathways, organoids infected with sfRNA-producing WT, but not sfRNA-deficient mutant ZIKV, which exhibited a strong down-regulation of genes involved in signaling pathways that control neuron differentiation and brain development, indicating the requirement of sfRNA for the suppression of neurodevelopment associated with the ZIKV infection. Using gene set enrichment analysis and gene network reconstruction, we demonstrated that the effect of sfRNA on pathways that control brain development occurs via crosstalk between Wnt-signaling and proapoptotic pathways.
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Visualization of migration of human cortical neurons generated from induced pluripotent stem cells.
BACKGROUND: Neuronal migration is considered a key process in human brain development. However, direct observation of migrating human cortical neurons in the fetal brain is accompanied by ethical concerns and is a major obstacle in investigating human cortical neuronal migration. NEW METHOD: We established a novel system that enables direct visualization of migrating cortical neurons generated from human induced pluripotent stem cells (hiPSCs). RESULTS: We observed the migration of cortical neurons generated from hiPSCs derived from a control and from a patient with lissencephaly. METHODS: Our system needs no viable brain tissue, which is usually used in slice culture. Migratory behavior of human cortical neuron can be observed more easily and more vividly by its fluorescence and glial scaffold than that by earlier methods. CONCLUSIONS: Our in vitro experimental system provides a new platform for investigating development of the human central nervous system and brain malformation.
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Cleavage site-directed antibodies reveal the prion protein in humans is shed by ADAM10 at Y226 and associates with misfolded protein deposits in neurodegenerative diseases.
Proteolytic cell surface release ('shedding') of the prion protein (PrP), a broadly expressed GPI-anchored glycoprotein, by the metalloprotease ADAM10 impacts on neurodegenerative and other diseases in animal and in vitro models. Recent studies employing the latter also suggest shed PrP (sPrP) to be a ligand in intercellular communication and critically involved in PrP-associated physiological tasks. Although expectedly an evolutionary conserved event, and while soluble forms of PrP are present in human tissues and body fluids, for the human body neither proteolytic PrP shedding and its cleavage site nor involvement of ADAM10 or the biological relevance of this process have been demonstrated thus far. In this study, cleavage site prediction and generation (plus detailed characterization) of sPrP-specific antibodies enabled us to identify PrP cleaved at tyrosin 226 as the physiological and apparently strictly ADAM10-dependent shed form in humans. Using cell lines, neural stem cells and brain organoids, we show that shedding of human PrP can be stimulated by PrP-binding ligands without targeting the protease, which may open novel therapeutic perspectives. Site-specific antibodies directed against human sPrP also detect the shed form in brains of cattle, sheep and deer, hence in all most relevant species naturally affected by fatal and transmissible prion diseases. In human and animal prion diseases, but also in patients with Alzheimer`s disease, sPrP relocalizes from a physiological diffuse tissue pattern to intimately associate with extracellular aggregated deposits of misfolded proteins characteristic for the respective pathological condition. Findings and research tools presented here will accelerate novel insight into the roles of PrP shedding (as a process) and sPrP (as a released factor) in neurodegeneration and beyond.
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FABP7 controls radial glial scaffold stability during human cortical development.
Radial glial (RG) cells serve as both neural progenitors and structural scaffolds for neuronal migration during cortical development. Although FABP7 has long been recognized as a marker of RG cells, its regulatory function has remained poorly defined. Using human fetal brain slices, embryonic mouse model, cerebral organoids, and assembloids, we demonstrate that FABP7 is essential for maintaining RG scaffold architecture and coordinating neuronal positioning. Single-cell analysis revealed that FABP7 deficiency induces transcriptional dysregulation, particularly affecting cytoskeletal organization, neural fate specification, and stress responses. Furthermore, transcriptomic features in FABP7 knockdown organoids exhibit convergence with neurodevelopmental disorders such as autism, alongside recapitulation of scaffold defects observed in idiopathic autism organoids. Mechanistically, FABP7 loss suppresses the mevalonate (MVA) pathway, resulting in impaired GTPase-mediated cytoskeletal organization and disruption of radial scaffold integrity. These findings identify FABP7 as a key regulator of cortical development and disease-relevant molecular programs, linking metabolic signaling to neurodevelopmental vulnerability.
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Methotrexate-induced disruption of the serum-glucocorticoid inducible protein kinase 3 signaling pathway and its effects on brain development.
Methotrexate (MTX) is a widely used chemotherapeutic and immunosuppressive agent. It is frequently detected in the environment due to its low biodegradability and toxic properties, which may pose risk to humans via contaminated drinking water. MTX impacts brain development; however, the underlying mechanisms remain poorly understood. In this study, we aimed to investigate the potential of brain cortical organoids (COs) to exhibit developmental neurotoxicity upon exposure to MTX and elucidated the underlying mechanisms. We showed that MTX affected brain development by increasing reactive oxygen species production, endoplasmic reticulum stress, and apoptosis in COs, affecting immature neurons, gamma-aminobutyric acid (GABA)ergic neurons, and astrocytes. Treatment with folic acid ameliorated the MTX-induced cellular damage. Furthermore, RNA-seq analysis revealed the significant downregulation of serum/glucocorticoid-regulated kinase family member 3 (SGK3) by MTX treatment. Further investigation using RNA interference with an siRNA targeting SGK3 confirmed that the SGK3 signaling pathway plays an essential role in regulating brain development. Finally, we demonstrated calcium homeostasis disruption in MTX-treated COs (MTX-COs). Our findings suggest that MTX affects cortical development in the brain by increasing intracellular ROS and ER stress, ultimately inducing apoptosis through the inhibition of the SGK3 signaling pathway in MTX-COs. Furthermore, abnormal brain development can be caused by an imbalance in intracellular calcium homeostasis and alterations in the neuronal cell expression in MTX-COs. These results indicate that MTX causes developmental neurotoxicity and underscore the importance of informed decision making regarding the clinical use of MTX, particularly during pregnancy.
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Novel fragile X syndrome 2D and 3D brain models based on human isogenic FMRP-KO iPSCs.
Fragile X syndrome (FXS) is a neurodevelopmental disorder, characterized by intellectual disability and sensory deficits, caused by epigenetic silencing of the FMR1 gene and subsequent loss of its protein product, fragile X mental retardation protein (FMRP). Delays in synaptic and neuronal development in the cortex have been reported in FXS mouse models; however, the main goal of translating lab research into pharmacological treatments in clinical trials has been so far largely unsuccessful, leaving FXS a still incurable disease. Here, we generated 2D and 3D in vitro human FXS model systems based on isogenic FMR1 knock-out mutant and wild-type human induced pluripotent stem cell (hiPSC) lines. Phenotypical and functional characterization of cortical neurons derived from FMRP-deficient hiPSCs display altered gene expression and impaired differentiation when compared with the healthy counterpart. FXS cortical cultures show an increased number of GFAP positive cells, likely astrocytes, increased spontaneous network activity, and depolarizing GABAergic transmission. Cortical brain organoid models show an increased number of glial cells, and bigger organoid size. Our findings demonstrate that FMRP is required to correctly support neuronal and glial cell proliferation, and to set the correct excitation/inhibition ratio in human brain development.
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Longer metaphase and fewer chromosome segregation errors in modern human than Neanderthal brain development.
Since the ancestors of modern humans separated from those of Neanderthals, around 100 amino acid substitutions spread to essentially all modern humans. The biological significance of these changes is largely unknown. Here, we examine all six such amino acid substitutions in three proteins known to have key roles in kinetochore function and chromosome segregation and to be highly expressed in the stem cells of the developing neocortex. When we introduce these modern human-specific substitutions in mice, three substitutions in two of these proteins, KIF18a and KNL1, cause metaphase prolongation and fewer chromosome segregation errors in apical progenitors of the developing neocortex. Conversely, the ancestral substitutions cause shorter metaphase length and more chromosome segregation errors in human brain organoids, similar to what we find in chimpanzee organoids. These results imply that the fidelity of chromosome segregation during neocortex development improved in modern humans after their divergence from Neanderthals.