The cerebral cortex-the brain's covering and largest region-has increased in size and complexity in humans and supports higher cognitive functions such as language and abstract thinking. There is a ...growing understanding of the human cerebral cortex, including the diversity and number of cell types that it contains, as well as of the developmental mechanisms that shape cortical structure and organization. In this review, we discuss recent progress in our understanding of molecular and cellular processes, as well as mechanical forces, that regulate the folding of the cerebral cortex. Advances in human genetics, coupled with experimental modeling in gyrencephalic species, have provided insights into the central role of cortical progenitors in the gyrification and evolutionary expansion of the cerebral cortex. These studies are essential for understanding the emergence of structural and functional organization during cortical development and the pathogenesis of neurodevelopmental disorders associated with cortical malformations.
Primates and rodents, which descended from a common ancestor around 90 million years ago
, exhibit profound differences in behaviour and cognitive capacity; the cellular basis for these differences ...is unknown. Here we use single-nucleus RNA sequencing to profile RNA expression in 188,776 individual interneurons across homologous brain regions from three primates (human, macaque and marmoset), a rodent (mouse) and a weasel (ferret). Homologous interneuron types-which were readily identified by their RNA-expression patterns-varied in abundance and RNA expression among ferrets, mice and primates, but varied less among primates. Only a modest fraction of the genes identified as 'markers' of specific interneuron subtypes in any one species had this property in another species. In the primate neocortex, dozens of genes showed spatial expression gradients among interneurons of the same type, which suggests that regional variation in cortical contexts shapes the RNA expression patterns of adult neocortical interneurons. We found that an interneuron type that was previously associated with the mouse hippocampus-the 'ivy cell', which has neurogliaform characteristics-has become abundant across the neocortex of humans, macaques and marmosets but not mice or ferrets. We also found a notable subcortical innovation: an abundant striatal interneuron type in primates that had no molecularly homologous counterpart in mice or ferrets. These interneurons expressed a unique combination of genes that encode transcription factors, receptors and neuropeptides and constituted around 30% of striatal interneurons in marmosets and humans.
Highlights • Single-cell RNA sequencing revolutionizes systematic classification of neurons. • Classification by scRNA-seq reveals new neuronal subtypes. • Matching transcriptionally and classically ...defined subtypes is challenging. • Developmental classifications need larger sample sizes across many time-points.
Although cell lineage information is fundamental to understanding organismal development, very little direct information is available for humans. We performed high-depth (250×) whole-genome ...sequencing of multiple tissues from three individuals to identify hundreds of somatic single-nucleotide variants (sSNVs). Using these variants as "endogenous barcodes" in single cells, we reconstructed early embryonic cell divisions. Targeted sequencing of clonal sSNVs in different organs (about 25,000×) and in more than 1000 cortical single cells, as well as single-nucleus RNA sequencing and single-nucleus assay for transposase-accessible chromatin sequencing of ~100,000 cortical single cells, demonstrated asymmetric contributions of early progenitors to extraembryonic tissues, distinct germ layers, and organs. Our data suggest onset of gastrulation at an effective progenitor pool of about 170 cells and about 50 to 100 founders for the forebrain. Thus, mosaic mutations provide a permanent record of human embryonic development at very high resolution.
Whether somatic mutations contribute functional diversity to brain cells is a long-standing question. Single-neuron genomics enables direct measurement of somatic mutation rates in human brain and ...promises to answer this question. A recent study (Upton et al., 2015) reported high rates of somatic LINE-1 element (L1) retrotransposition in the hippocampus and cerebral cortex that would have major implications for normal brain function, and suggested that these events preferentially impact genes important for neuronal function. We identify aspects of the single-cell sequencing approach, bioinformatic analysis, and validation methods that led to thousands of artifacts being interpreted as somatic mutation events. Our reanalysis supports a mutation frequency of approximately 0.2 events per cell, which is about fifty-fold lower than reported, confirming that L1 elements mobilize in some human neurons but indicating that L1 mosaicism is not ubiquitous. Through consideration of the challenges identified, we provide a foundation and framework for designing single-cell genomics studies.
The integration of core sedimentology, seismic stratigraphy and seismic geomorphology has enabled interpretation of delta‐scale (i.e. tens of metres high) subaqueous clinoforms in the upper Jurassic ...Sognefjord Formation of the Troll Field. Mud‐prone subaqueous deltas characterized by a compound clinoform morphology and sandy delta‐scale subaqueous clinoforms are common in recent tide‐influenced, wave‐influenced and current‐influenced settings, but ancient examples are virtually unknown. The data presented help to fully comprehend the criteria for the recognition of other ancient delta‐scale subaqueous clinoforms, as well as refining the depositional model of the reservoir in the super‐giant Troll hydrocarbon field. Two 10 to 60 m thick, overall coarsening‐upward packages are distinguished in the lower Sognefjord Formation. Progressively higher energy, wave‐dominated or current‐dominated facies occur from the base to the top of each package. Each package corresponds to a set of seismically resolved, westerly dipping clinoforms, the bounding surfaces of which form the seismic ‘envelope’ of a clinoform set and the major marine flooding surfaces recognized in cores. The packages thicken westwards, until they reach a maximum where the clinoform ‘envelope’ rolls over to define a topset–foreset–toeset geometry. All clinoforms are consistently oriented sub‐parallel to the edge of the Horda Platform (N005–N030). In the eastern half of the field, individual foresets are relatively gently dipping (1° to 6°) and bound thin (10 to 30 m) clinothems. Core data indicate that these proximal clinothems are dominated by fine‐grained, hummocky cross‐stratified sandstones. Towards the west, clinoforms gradually become steeper (5° to 14°) and bound thicker (15 to 60 m) clinothems that comprise medium‐grained, cross‐bedded sandstones. Topsets are consistently well‐developed, except in the westernmost area. No seismic or sedimentological evidence of subaerial exposure is observed. Deposition created fully subaqueous, near‐linear clinoforms that prograded westwards across the Horda Platform. Subaqueous clinoforms were probably fed by a river outlet in the north‐east and sculpted by the action of currents sub‐parallel to the clinoform strike.
In the human brain, distinct functions tend to be localized in the left or right hemispheres, with language ability usually localized predominantly in the left and spatial recognition in the right. ...Furthermore, humans are perhaps the only mammals who have preferential handedness, with more than 90% of the population more skillful at using the right hand, which is controlled by the left hemisphere. How is a distinct function consistently localized in one side of the human brain? Because of the convergence of molecular and neurological analysis, we are beginning to consider the puzzle of brain asymmetry and handedness at a molecular level.
To investigate the mechanism that drives dramatic mistargeting of active chromatin in NUT midline carcinoma (NMC), we have identified protein interactions unique to the BRD4–NUT fusion oncoprotein ...compared with wild-type BRD4. Using cross-linking, affinity purification, and mass spectrometry, we identified the EP300 acetyltransferase as uniquely associated with BRD4 through the NUT fusion in both NMC and non-NMC cell types. We also discovered ZNF532 associated with BRD4–NUT in NMC patient cells but not detectable in 293T cells. EP300 and ZNF532 are both implicated in feed-forward regulatory loops leading to propagation of the oncogenic chromatin complex in BRD4–NUT patient cells. Adding key functional significance to our biochemical findings, we independently discovered a ZNF532–NUT translocation fusion in a newly diagnosed NMC patient. ChIP sequencing of the major players NUT, ZNF532, BRD4, EP300, and H3K27ac revealed the formation of ZNF532–NUT–associated hyperacetylated megadomains, distinctly localized but otherwise analogous to those found in BRD4–NUT patient cells. Our results support a model in which NMC is dependent on ectopic NUT-mediated interactions between EP300 and components of BRD4 regulatory complexes, leading to a cascade of misregulation.
Detection of mosaic mutations that arise in normal development is challenging, as such mutations are typically present in only a minute fraction of cells and there is no clear matched control for ...removing germline variants and systematic artifacts. We present MosaicForecast, a machine-learning method that leverages read-based phasing and read-level features to accurately detect mosaic single-nucleotide variants and indels, achieving a multifold increase in specificity compared with existing algorithms. Using single-cell sequencing and targeted sequencing, we validated 80-90% of the mosaic single-nucleotide variants and 60-80% of indels detected in human brain whole-genome sequencing data. Our method should help elucidate the contribution of mosaic somatic mutations to the origin and development of disease.
Mutations in several genes encoding centrosomal proteins dramatically decrease the size of the human brain. We show that Aspm (abnormal spindle-like, microcephaly-associated) and Wdr62 (WD ...repeat-containing protein 62) interact genetically to control brain size, with mice lacking Wdr62, Aspm, or both showing gene dose-related centriole duplication defects that parallel the severity of the microcephaly and increased ectopic basal progenitors, suggesting premature delamination from the ventricular zone. Wdr62 and Aspm localize to the proximal end of the mother centriole and interact physically, with Wdr62 required for Aspm localization, and both proteins, as well as microcephaly protein Cep63, required to localize CENPJ/CPAP/Sas-4, a final common target. Unexpectedly, Aspm and Wdr62 are required for normal apical complex localization and apical epithelial structure, providing a plausible unifying mechanism for the premature delamination and precocious differentiation of progenitors. Together, our results reveal links among centrioles, apical proteins, and cell fate, and illuminate how alterations in these interactions can dynamically regulate brain size.
•Wdr62 and Aspm interact genetically to control brain size in mice•Loss of Wdr62 or Aspm causes centriole duplication defects proportional to microcephaly•WDR62 and ASPM are maternal centriolar proteins that recruit CPAP to the centrosome•Loss of Wdr62 and Aspm causes gene dose-dependent disruption of the apical complex
Jayaraman et al. show that microcephaly proteins Wdr62 and Aspm localize to the maternal centriole and physically interact. Mice lacking Wdr62, Aspm, or both show gene dose-dependent defects in brain size, centriole duplication, centrosomal localization of CPAP, and the apical complex, which plays a critical role in cell fate.
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