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1.
Nature ; 597(7875): 250-255, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34497389

RESUMEN

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.


Asunto(s)
Envejecimiento , Sistema Nervioso Entérico/citología , Feto/citología , Salud , Intestinos/citología , Intestinos/crecimiento & desarrollo , Ganglios Linfáticos/citología , Ganglios Linfáticos/crecimiento & desarrollo , Adulto , Animales , Niño , Enfermedad de Crohn/patología , Conjuntos de Datos como Asunto , Sistema Nervioso Entérico/anatomía & histología , Sistema Nervioso Entérico/embriología , Sistema Nervioso Entérico/crecimiento & desarrollo , Células Epiteliales/citología , Femenino , Feto/anatomía & histología , Feto/embriología , Humanos , Intestinos/embriología , Intestinos/inervación , Ganglios Linfáticos/embriología , Ganglios Linfáticos/patología , Ratones , Ratones Endogámicos C57BL , Organogénesis , Receptores de IgG/metabolismo , Transducción de Señal , Análisis Espacio-Temporal , Factores de Tiempo
2.
Am J Hum Genet ; 105(3): 606-615, 2019 09 05.
Artículo en Inglés | MEDLINE | ID: mdl-31474318

RESUMEN

Cerebellar malformations are diverse congenital anomalies frequently associated with developmental disability. Although genetic and prenatal non-genetic causes have been described, no systematic analysis has been performed. Here, we present a large-exome sequencing study of Dandy-Walker malformation (DWM) and cerebellar hypoplasia (CBLH). We performed exome sequencing in 282 individuals from 100 families with DWM or CBLH, and we established a molecular diagnosis in 36 of 100 families, with a significantly higher yield for CBLH (51%) than for DWM (16%). The 41 variants impact 27 neurodevelopmental-disorder-associated genes, thus demonstrating that CBLH and DWM are often features of monogenic neurodevelopmental disorders. Though only seven monogenic causes (19%) were identified in more than one individual, neuroimaging review of 131 additional individuals confirmed cerebellar abnormalities in 23 of 27 genetic disorders (85%). Prenatal risk factors were frequently found among individuals without a genetic diagnosis (30 of 64 individuals [47%]). Single-cell RNA sequencing of prenatal human cerebellar tissue revealed gene enrichment in neuronal and vascular cell types; this suggests that defective vasculogenesis may disrupt cerebellar development. Further, de novo gain-of-function variants in PDGFRB, a tyrosine kinase receptor essential for vascular progenitor signaling, were associated with CBLH, and this discovery links genetic and non-genetic etiologies. Our results suggest that genetic defects impact specific cerebellar cell types and implicate abnormal vascular development as a mechanism for cerebellar malformations. We also confirmed a major contribution for non-genetic prenatal factors in individuals with cerebellar abnormalities, substantially influencing diagnostic evaluation and counseling regarding recurrence risk and prognosis.


Asunto(s)
Cerebelo/anomalías , Cerebelo/diagnóstico por imagen , Estudios de Cohortes , Femenino , Humanos , Masculino , Embarazo
3.
Cereb Cortex ; 27(10): 4971-4987, 2017 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-28922831

RESUMEN

In human telencephalon at 8-12 postconceptional weeks, ribonucleic acid quantitative sequencing and immunohistochemistry revealed cortical chicken ovalbumin upstream promotor-transcription factor 1 (COUP-TFI) expression in a high ventro-posterior to low anterior gradient except for raised immunoreactivity in the anterior ventral pallium. Unlike in mouse, COUP-TFI and SP8 were extensively co-expressed in dorsal sensory neocortex and dorsal hippocampus whereas COUPTFI/COUPTFII co-expression defined ventral temporal cortex and ventral hippocampus. In the ganglionic eminences (GEs) COUP-TFI immunoreactivity demarcated the proliferative zones of caudal GE (CGE), dorsal medial GE (MGE), MGE/lateral GE (LGE) boundary, and ventral LGE whereas COUP-TFII was limited to ventral CGE and the MGE/LGE boundary. Co-labeling with gamma amino butyric acidergic interneuron markers revealed that COUP-TFI was expressed in subpopulations of either MGE-derived (SOX6+) or CGE-derived (calretinin+/SP8+) interneurons. COUP-TFII was mainly confined to CGE-derived interneurons. Twice as many GAD67+ cortical cells co-labeled for COUP-TFI than for COUP-TFII. A fifth of COUP-TFI cells also co-expressed COUP-TFII, and cells expressing either transcription factor followed posterior or anterio-lateral pathways into the cortex, therefore, a segregation of migration pathways according to COUP-TF expression as proposed in mouse was not observed. In cultures differentiated from isolated human cortical progenitors, many cells expressed either COUP-TF and 30% also co-expressed GABA, however no cells expressed NKX2.1. This suggests interneurons could be generated intracortically from progenitors expressing either COUP-TF.


Asunto(s)
Factor de Transcripción COUP II/metabolismo , Factor de Transcripción COUP I/metabolismo , Neuronas GABAérgicas/metabolismo , Interneuronas/metabolismo , Telencéfalo/crecimiento & desarrollo , Diferenciación Celular/fisiología , Movimiento Celular/fisiología , Regulación del Desarrollo de la Expresión Génica/fisiología , Hipocampo/metabolismo , Humanos , Inmunohistoquímica/métodos , Neocórtex/crecimiento & desarrollo , Neocórtex/metabolismo
4.
Nature ; 478(7370): 483-9, 2011 Oct 26.
Artículo en Inglés | MEDLINE | ID: mdl-22031440

RESUMEN

Brain development and function depend on the precise regulation of gene expression. However, our understanding of the complexity and dynamics of the transcriptome of the human brain is incomplete. Here we report the generation and analysis of exon-level transcriptome and associated genotyping data, representing males and females of different ethnicities, from multiple brain regions and neocortical areas of developing and adult post-mortem human brains. We found that 86 per cent of the genes analysed were expressed, and that 90 per cent of these were differentially regulated at the whole-transcript or exon level across brain regions and/or time. The majority of these spatio-temporal differences were detected before birth, with subsequent increases in the similarity among regional transcriptomes. The transcriptome is organized into distinct co-expression networks, and shows sex-biased gene expression and exon usage. We also profiled trajectories of genes associated with neurobiological categories and diseases, and identified associations between single nucleotide polymorphisms and gene expression. This study provides a comprehensive data set on the human brain transcriptome and insights into the transcriptional foundations of human neurodevelopment.


Asunto(s)
Envejecimiento/genética , Encéfalo/crecimiento & desarrollo , Encéfalo/metabolismo , Perfilación de la Expresión Génica , Regulación del Desarrollo de la Expresión Génica/genética , Transcriptoma/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Encéfalo/embriología , Niño , Preescolar , Exones/genética , Femenino , Feto/metabolismo , Redes Reguladoras de Genes/genética , Humanos , Lactante , Masculino , Persona de Mediana Edad , Control de Calidad , Sitios de Carácter Cuantitativo/genética , Caracteres Sexuales , Factores de Tiempo , Adulto Joven
5.
Nat Neurosci ; 24(8): 1163-1175, 2021 08.
Artículo en Inglés | MEDLINE | ID: mdl-34140698

RESUMEN

The human neonatal cerebellum is one-fourth of its adult size yet contains the blueprint required to integrate environmental cues with developing motor, cognitive and emotional skills into adulthood. Although mature cerebellar neuroanatomy is well studied, understanding of its developmental origins is limited. In this study, we systematically mapped the molecular, cellular and spatial composition of human fetal cerebellum by combining laser capture microscopy and SPLiT-seq single-nucleus transcriptomics. We profiled functionally distinct regions and gene expression dynamics within cell types and across development. The resulting cell atlas demonstrates that the molecular organization of the cerebellar anlage recapitulates cytoarchitecturally distinct regions and developmentally transient cell types that are distinct from the mouse cerebellum. By mapping genes dominant for pediatric and adult neurological disorders onto our dataset, we identify relevant cell types underlying disease mechanisms. These data provide a resource for probing the cellular basis of human cerebellar development and disease.


Asunto(s)
Cerebelo/embriología , Neurogénesis , Feto , Humanos , Captura por Microdisección con Láser , Análisis de la Célula Individual , Transcriptoma
6.
Science ; 366(6464): 454-460, 2019 10 25.
Artículo en Inglés | MEDLINE | ID: mdl-31624095

RESUMEN

We present histological and molecular analyses of the developing human cerebellum from 30 days after conception to 9 months after birth. Differences in developmental patterns between humans and mice include spatiotemporal expansion of both ventricular and rhombic lip primary progenitor zones to include subventricular zones containing basal progenitors. The human rhombic lip persists longer through cerebellar development than in the mouse and undergoes morphological changes to form a progenitor pool in the posterior lobule, which is not seen in other organisms, not even in the nonhuman primate the macaque. Disruptions in human rhombic lip development are associated with posterior cerebellar vermis hypoplasia and Dandy-Walker malformation. The presence of these species-specific neural progenitor populations refines our insight into human cerebellar developmental disorders.


Asunto(s)
Cerebelo/embriología , Cerebelo/crecimiento & desarrollo , Células Madre/citología , Animales , Síndrome de Dandy-Walker , Humanos , Ratones , Malformaciones del Sistema Nervioso , Análisis Espacio-Temporal , Especificidad de la Especie , Transcriptoma
7.
Sci Data ; 5: 180164, 2018 09 04.
Artículo en Inglés | MEDLINE | ID: mdl-30179233

RESUMEN

Left-right asymmetry is subtle but pervasive in the human central nervous system. This asymmetry is initiated early during development, but its mechanisms are poorly known. Forebrains and midbrains were dissected from six human embryos at Carnegie stages 15 or 16, one of which was female. The structures were divided into left and right sides, and RNA was isolated. RNA was sequenced with 100 base-pair paired ends using Illumina Hiseq 4000. After quality control, five paired brain sides were available for midbrain and forebrain. A paired analysis between left- and right sides of a given brain structure across the embryos identified left-right differences. The dataset, consisting of Fastq files and a read count table, can be further used to study early development of the human brain.


Asunto(s)
Mesencéfalo/fisiología , Prosencéfalo/fisiología , Transcriptoma , Tipificación del Cuerpo , Femenino , Perfilación de la Expresión Génica , Humanos , Masculino , Mesencéfalo/embriología , Prosencéfalo/embriología , Análisis de Secuencia de ARN
8.
Sci Rep ; 8(1): 12606, 2018 09 04.
Artículo en Inglés | MEDLINE | ID: mdl-30181561

RESUMEN

Left-right laterality is an important aspect of human -and in fact all vertebrate- brain organization for which the genetic basis is poorly understood. Using RNA sequencing data we contrasted gene expression in left- and right-sided samples from several structures of the anterior central nervous systems of post mortem human embryos and foetuses. While few individual genes stood out as significantly lateralized, most structures showed evidence of laterality of their overall transcriptomic profiles. These left-right differences showed overlap with age-dependent changes in expression, indicating lateralized maturation rates, but not consistently in left-right orientation over all structures. Brain asymmetry may therefore originate in multiple locations, or if there is a single origin, it is earlier than 5 weeks post conception, with structure-specific lateralized processes already underway by this age. This pattern is broadly consistent with the weak correlations reported between various aspects of adult brain laterality, such as language dominance and handedness.


Asunto(s)
Encéfalo/embriología , Feto/fisiología , Lateralidad Funcional , Transcriptoma , Animales , Tipificación del Cuerpo , Encéfalo/fisiología , Feto/embriología , Regulación del Desarrollo de la Expresión Génica , Humanos , Pez Cebra
9.
Eur J Hum Genet ; 23(5): 621-7, 2015 May.
Artículo en Inglés | MEDLINE | ID: mdl-25138100

RESUMEN

Joubert syndrome (JS) is a genetically heterogeneous autosomal recessive ciliopathy with 22 genes implicated to date, including a small, ciliary GTPase, ARL13B. ARL13B is required for cilia formation in vertebrates. JS patients display multiple symptoms characterized by ataxia due to the cerebellar vermis hypoplasia, and that can also include ocular abnormalities, renal cysts, liver fibrosis or polydactyly. These symptoms are shared with other ciliopathies, some of which display additional phenotypes, such as obesity. Here we identified a novel homozygous missense variant in ARL13B/JBTS8 in a JS patient who displayed retinal defects and obesity. We demonstrate the variant disrupts ARL13B function, as its expression did not rescue the mutant phenotype either in Arl13b(scorpion) zebrafish or in Arl13b(hennin) mouse embryonic fibroblasts, while the wild-type ARL13B did. Finally, we show that ARL13B is localized within the primary cilia of neonatal mouse hypothalamic neurons consistent with the known link between hypothalamic ciliary function and obesity. Thus our data identify a novel ARL13B variant that causes JS and retinopathy and suggest an extension of the phenotypic spectrum of ARL13B mutations to obesity.


Asunto(s)
Factores de Ribosilacion-ADP/genética , Enfermedades Cerebelosas/diagnóstico , Enfermedades Cerebelosas/genética , Enfermedades Hereditarias del Ojo/diagnóstico , Enfermedades Hereditarias del Ojo/genética , Mutación , Obesidad/genética , Fenotipo , Enfermedades de la Retina/genética , Factores de Ribosilacion-ADP/química , Factores de Ribosilacion-ADP/metabolismo , Secuencia de Aminoácidos , Animales , Encéfalo/patología , Biología Computacional , Consanguinidad , Modelos Animales de Enfermedad , Ligamiento Genético , Homocigoto , Humanos , Inmunohistoquímica , Lactante , Imagen por Resonancia Magnética , Masculino , Ratones , Modelos Moleculares , Datos de Secuencia Molecular , Obesidad/diagnóstico , Linaje , Conformación Proteica , Enfermedades de la Retina/diagnóstico , Alineación de Secuencia , Análisis de Secuencia de ADN , Pez Cebra
10.
PLoS One ; 9(2): e88810, 2014.
Artículo en Inglés | MEDLINE | ID: mdl-24533152

RESUMEN

During brain development, neural stem cells (NSCs) receive on-or-off signals important for regulating their amplification and reaching adequate neuron density. However, how a coordinated regulation of intracellular pathways and genetic programs is achieved has remained elusive. Here, we found that the embryonic (e) CSF contains 10¹² nanoparticles/ml (77 nm diameter), some of which were identified as exosome nanovesicles that contain evolutionarily conserved molecules important for coordinating intracellular pathways. eCSF nanovesicles collected from rodent and human embryos encapsulate protein and microRNA components of the insulin-like growth factor (IGF) signaling pathway. Supplementation of eCSF nanovesicles to a mixed culture containing eNSCs activated the IGF-mammalian target of rapamycin complex 1 (mTORC1) pathway in eNSCs and expanded the pool of proliferative eNSCs. These data show that the eCSF serves as a medium for the distribution of nanovesicles, including exosomes, and the coordinated transfer of evolutionary conserved molecules that regulate eNSC amplification during corticogenesis.


Asunto(s)
Líquido Cefalorraquídeo/citología , Embrión de Mamíferos/citología , Evolución Molecular , Nanopartículas , Células-Madre Neurales/citología , Animales , Proliferación Celular , Exosomas/metabolismo , Femenino , Humanos , Diana Mecanicista del Complejo 1 de la Rapamicina , Ratones , MicroARNs/genética , MicroARNs/metabolismo , Complejos Multiproteicos/metabolismo , Embarazo , Ratas , Transducción de Señal , Somatomedinas/metabolismo , Serina-Treonina Quinasas TOR/metabolismo
11.
Science ; 343(6172): 764-8, 2014 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-24531968

RESUMEN

The human neocortex has numerous specialized functional areas whose formation is poorly understood. Here, we describe a 15-base pair deletion mutation in a regulatory element of GPR56 that selectively disrupts human cortex surrounding the Sylvian fissure bilaterally including "Broca's area," the primary language area, by disrupting regional GPR56 expression and blocking RFX transcription factor binding. GPR56 encodes a heterotrimeric guanine nucleotide-binding protein (G protein)-coupled receptor required for normal cortical development and is expressed in cortical progenitor cells. GPR56 expression levels regulate progenitor proliferation. GPR56 splice forms are highly variable between mice and humans, and the regulatory element of gyrencephalic mammals directs restricted lateral cortical expression. Our data reveal a mechanism by which control of GPR56 expression pattern by multiple alternative promoters can influence stem cell proliferation, gyral patterning, and, potentially, neocortex evolution.


Asunto(s)
Empalme Alternativo , Tipificación del Cuerpo/genética , Corteza Cerebral/embriología , Células-Madre Neurales/fisiología , Receptores Acoplados a Proteínas G/genética , Animales , Secuencia de Bases , Evolución Biológica , Gatos , Proliferación Celular , Corteza Cerebral/anatomía & histología , Corteza Cerebral/citología , Codón sin Sentido , Lóbulo Frontal/anatomía & histología , Lóbulo Frontal/citología , Lóbulo Frontal/embriología , Variación Genética , Haplotipos , Humanos , Ratones , Datos de Secuencia Molecular , Células-Madre Neurales/citología , Linaje , Regiones Promotoras Genéticas/genética , Eliminación de Secuencia
13.
J Proteome Res ; 6(9): 3537-48, 2007 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-17696520

RESUMEN

During vertebrate central nervous system development, the apical neuroepithelium is bathed with embryonic Cerebrospinal Fluid (e-CSF) which plays regulatory roles in cortical cell proliferation and maintenance. Here, we report the first proteomic analysis of human e-CSF and compare it to an extensive proteomic analysis of rat e-CSF. As expected, we identified a large collection of protease inhibitors, extracellular matrix proteins, and transport proteins in CSF. However, we also found a surprising suite of signaling and intracellular proteins not predicted by previous proteomic analysis. Some of the intracellular proteins are likely to represent the contents of microvesicles recently described within the CSF (Marzesco, A. M., et al. J. Cell Sci. 2005, 118 (Pt. 13), 2849-2858). Defining the rich composition of e-CSF will enable a greater understanding of its concerted actions during critical stages of brain development.


Asunto(s)
Líquido Cefalorraquídeo/metabolismo , Proteómica/métodos , Animales , Encéfalo/metabolismo , Electroforesis en Gel de Poliacrilamida , Embrión de Mamíferos/citología , Matriz Extracelular/metabolismo , Humanos , Espectrometría de Masas/métodos , Ratones , Microcirculación , Inhibidores de Proteasas/farmacología , Proteínas/química , Proteoma , Ratas
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