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1.
Cell ; 184(12): 3281-3298.e22, 2021 06 10.
Artigo em Inglês | MEDLINE | ID: mdl-34019796

RESUMO

Organs are composed of diverse cell types that traverse transient states during organogenesis. To interrogate this diversity during human development, we generate a single-cell transcriptome atlas from multiple developing endodermal organs of the respiratory and gastrointestinal tract. We illuminate cell states, transcription factors, and organ-specific epithelial stem cell and mesenchyme interactions across lineages. We implement the atlas as a high-dimensional search space to benchmark human pluripotent stem cell (hPSC)-derived intestinal organoids (HIOs) under multiple culture conditions. We show that HIOs recapitulate reference cell states and use HIOs to reconstruct the molecular dynamics of intestinal epithelium and mesenchyme emergence. We show that the mesenchyme-derived niche cue NRG1 enhances intestinal stem cell maturation in vitro and that the homeobox transcription factor CDX2 is required for regionalization of intestinal epithelium and mesenchyme in humans. This work combines cell atlases and organoid technologies to understand how human organ development is orchestrated.


Assuntos
Anatomia Artística , Atlas como Assunto , Desenvolvimento Embrionário , Endoderma/embriologia , Modelos Biológicos , Organoides/embriologia , Fator de Transcrição CDX2/metabolismo , Linhagem Celular , Fator de Crescimento Epidérmico/farmacologia , Células Epiteliais/citologia , Feminino , Gastrulação , Deleção de Genes , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Humanos , Intestinos/embriologia , Masculino , Mesoderma/embriologia , Pessoa de Meia-Idade , Neuregulina-1/metabolismo , Especificidade de Órgãos , Células-Tronco Pluripotentes/citologia
2.
Development ; 149(20)2022 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-36278875

RESUMO

Many esophageal diseases can arise during development or throughout life. Therefore, well-characterized in vitro models and detailed methods are essential for studying human esophageal development, homeostasis and disease. Here, we (1) create an atlas of the cell types observed in the normal adult human esophagus; (2) establish an ancestrally diverse biobank of in vitro esophagus tissue to interrogate homeostasis and injury; and (3) benchmark in vitro models using the adult human esophagus atlas. We created a single-cell RNA sequencing reference atlas using fresh adult esophagus biopsies and a continuously expanding biobank of patient-derived in vitro cultures (n=55 lines). We identify and validate several transcriptionally distinct cell classes in the native human adult esophagus, with four populations belonging to the epithelial layer, including basal, epibasal, early differentiating and terminally differentiated luminal cells. Benchmarking in vitro esophagus cultures to the in vivo reference using single-cell RNA sequencing shows that the basal stem cells are robustly maintained in vitro, and the diversity of epithelial cell types in culture is dependent on cell density. We also demonstrate that cultures can be grown in 2D or as 3D organoids, and these methods can be employed for modeling the complete epithelial layers, thereby enabling in vitro modeling of the human adult esophagus.


Assuntos
Esôfago , Organoides , Adulto , Humanos , Células-Tronco , Células Epiteliais/metabolismo , Diferenciação Celular
3.
Cerebellum ; 23(2): 620-677, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-36781689

RESUMO

The cerebellum is a key player in many brain functions and a major topic of neuroscience research. However, the cerebellar nuclei (CN), the main output structures of the cerebellum, are often overlooked. This neglect is because research on the cerebellum typically focuses on the cortex and tends to treat the CN as relatively simple output nuclei conveying an inverted signal from the cerebellar cortex to the rest of the brain. In this review, by adopting a nucleocentric perspective we aim to rectify this impression. First, we describe CN anatomy and modularity and comprehensively integrate CN architecture with its highly organized but complex afferent and efferent connectivity. This is followed by a novel classification of the specific neuronal classes the CN comprise and speculate on the implications of CN structure and physiology for our understanding of adult cerebellar function. Based on this thorough review of the adult literature we provide a comprehensive overview of CN embryonic development and, by comparing cerebellar structures in various chordate clades, propose an interpretation of CN evolution. Despite their critical importance in cerebellar function, from a clinical perspective intriguingly few, if any, neurological disorders appear to primarily affect the CN. To highlight this curious anomaly, and encourage future nucleocentric interpretations, we build on our review to provide a brief overview of the various syndromes in which the CN are currently implicated. Finally, we summarize the specific perspectives that a nucleocentric view of the cerebellum brings, move major outstanding issues in CN biology to the limelight, and provide a roadmap to the key questions that need to be answered in order to create a comprehensive integrated model of CN structure, function, development, and evolution.


Assuntos
Núcleos Cerebelares , Cerebelo , Núcleos Cerebelares/diagnóstico por imagem , Núcleos Cerebelares/fisiologia , Cerebelo/fisiologia , Neurônios/fisiologia
4.
BMC Genomics ; 24(1): 351, 2023 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-37365500

RESUMO

BACKGROUND: The development of the brain requires precise coordination of molecular processes across many cell-types. Underpinning these events are gene expression programs which require intricate regulation by non-coding regulatory sequences known as enhancers. In the context of the developing brain, transcribed enhancers (TEs) regulate temporally-specific expression of genes critical for cell identity and differentiation. Transcription of non-coding RNAs at active enhancer sequences, known as enhancer RNAs (eRNAs), is tightly associated with enhancer activity and has been correlated with target gene expression. TEs have been characterized in a multitude of developing tissues, however their regulatory role has yet to be described in the context of embryonic and early postnatal brain development. In this study, eRNA transcription was analyzed to identify TEs active during cerebellar development, as a proxy for the developing brain. Cap Analysis of Gene Expression followed by sequencing (CAGE-seq) was conducted at 12 stages throughout embryonic and early postnatal cerebellar development. RESULTS: Temporal analysis of eRNA transcription identified clusters of TEs that peak in activity during either embryonic or postnatal times, highlighting their importance for temporally specific developmental events. Functional analysis of putative target genes identified molecular mechanisms under TE regulation revealing that TEs regulate genes involved in biological processes specific to neurons. We validate enhancer activity using in situ hybridization of eRNA expression from TEs predicted to regulate Nfib, a gene critical for cerebellar granule cell differentiation. CONCLUSIONS: The results of this analysis provide a valuable dataset for the identification of cerebellar enhancers and provide insight into the molecular mechanisms critical for brain development under TE regulation. This dataset is shared with the community through an online resource ( https://goldowitzlab.shinyapps.io/trans-enh-app/ ).


Assuntos
Encéfalo , Regulação da Expressão Gênica no Desenvolvimento , Transcrição Gênica , Análise de Sequência de RNA , Encéfalo/embriologia , Encéfalo/metabolismo , Animais , Camundongos , Elementos Facilitadores Genéticos , RNA/genética
5.
Cerebellum ; 21(4): 606-614, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35857265

RESUMO

This report presents the first comprehensive database that specifically compiles genes critical for cerebellar development and function. The Cerebellar Gene Database details genes that, when perturbed in mouse models, result in a cerebellar phenotype according to available data from both Mouse Genome Informatics and PubMed, as well as references to the corresponding studies for further examination. This database also offers a compilation of human genetic disorders with a cerebellar phenotype and their associated gene information from the Online Mendelian Inheritance in Man (OMIM) database. By comparing and contrasting the mouse and human datasets, we observe that only a small proportion of human mutant genes with a cerebellar phenotype have been studied in mouse knockout models. Given the highly conserved nature between mouse and human genomes, this surprising finding highlights how mouse genetic models can be more frequently employed to elucidate human disease etiology. On the other hand, many mouse genes identified in the present study that are known to lead to a cerebellar phenotype when perturbed have not yet been found to be pathogenic in the cerebellum of humans. This database furthers our understanding of human cerebellar disorders with yet-to-be-identified genetic causes. It is our hope that this gene database will serve as an invaluable tool for gathering background information, generating hypotheses, and facilitating translational research endeavors. Moreover, we encourage continual inputs from the research community in making this compilation a living database, one that remains up-to-date with the advances in cerebellar research.


Assuntos
Cerebelo , Bases de Dados Genéticas , Animais , Modelos Animais de Doenças , Humanos , Camundongos , Fenótipo
6.
Am J Public Health ; 109(10): 1462-1464, 2019 10.
Artigo em Inglês | MEDLINE | ID: mdl-31415191

RESUMO

Objectives. To conduct a content analysis of news articles to investigate the relationship between language used to describe e-cigarettes, how the news articles framed (conveyed information to influence a certain perception of the news read by its audience) e-cigarettes, and the Food and Drug Administration's (FDA's) oversight of e-cigarettes.Methods. We searched a database of articles published across the United States from February 1, 2016, to February 28, 2017, using the headline terms "e-cigarette," "e-cig," and "vape." We then dichotomized terms into 2 categories: technical ("e-cigarette" or "e-cig") and nontechnical ("vape"). We coded the frame of each article body as positive, negative, or neutral or mixed.Results. Articles containing the term "vape" in the headline were more likely to positively frame e-cigarettes (P ≤ .001) and negatively frame FDA oversight (P ≤ .001) in the body than were those with "e-cigarette" or "e-cig" in the headline.Conclusions. Omitting the word "cigarette" when describing tobacco products may reduce the negative perception associated with tobacco use, making it more appealing. It is important to know which terms are used to describe e-cigarettes and how these terms can make those products appear less harmful.


Assuntos
Sistemas Eletrônicos de Liberação de Nicotina , Jornais como Assunto/estatística & dados numéricos , Terminologia como Assunto , Vaping , Humanos , Estados Unidos
7.
Sensors (Basel) ; 19(3)2019 Feb 08.
Artigo em Inglês | MEDLINE | ID: mdl-30743986

RESUMO

Wearable technology-based measurement systems hold potential for the therapeutic and rehabilitation management of patients with various chronic diseases. The purpose of this study was to assess the accuracy and test⁻retest reliability of a new-generation wearable sensor-based system, dubbed Ambulosono, for bio-feedback training. The Ambulosono sensor system was cross-validated by comparing its functionality with the iPod touch (4th generation) sensor system. Fifteen participants underwent a gait test to measure various gait parameters while wearing both the iPod-based and Ambulosono sensors simultaneously. The physically measured values (i.e., the true values) of step length, distance traveled, velocity, and cadence were then compared to those obtained via the two-sensor systems using the same calculation algorithms. While the mean percentage error was <10% for all measured parameters, and the intra-class correlation coefficient revealed a high level of agreement between trials for both sensor systems, it was found that the Ambulosono sensor system outperformed the iPod-based system in some respects. The Ambulosono sensor system possessed both reliability and accuracy in obtaining gait parameter measurements, which suggests it can serve as an economical alternative to the iPod-based system that is currently used in various clinical rehabilitation programs.


Assuntos
Biorretroalimentação Psicológica/instrumentação , Reabilitação/instrumentação , Dispositivos Eletrônicos Vestíveis , Acelerometria/instrumentação , Desenho de Equipamento , Marcha/fisiologia , Humanos , Masculino , Reabilitação/métodos
8.
Am J Ophthalmol Case Rep ; 36: 102135, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-39188855

RESUMO

Purpose: To describe an alternate surgical technique for fluocinolone acetonide (Retisert) implantation in patients with extensive pars plana and pars plicata fibrosis secondary to chronic non-infectious uveitis. Methods: This retrospective, interventional case series included five eyes of four patients who had poorly controlled chronic non-infectious uveitis. Retisert was implanted successfully using a novel approach. The device was introduced into the posterior segment through the anterior chamber and posterior capsulotomy, forgoing the need for full-thickness scleral incision and minimizing the risk of retinal detachment and associated complications. Results: Five eyes underwent passage of Retisert implant through the anterior segment via a limbal incision and a posterior capsulotomy. Retisert was successfully implanted in all patients in the posterior chamber. No intraoperative or postoperative complications were encountered. Up until the last follow-up, all eyes demonstrated the stability of the implant. Visual acuity improved in four out of five eyes. Conclusions: Retisert can be implanted via the anterior chamber in patients with extensive fibrosis in the pars plana and pars plicata regions. This approach may minimize the risk of retinal traction and damage to the implant when compared to the traditional full-thickness sclerotomy method in these high-risk cases.

9.
bioRxiv ; 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-38463979

RESUMO

Pathophysiology of many neuropsychiatric disorders, including schizophrenia (SCZD), is linked to habenula (Hb) function. While pharmacotherapies and deep brain stimulation targeting the Hb are emerging as promising therapeutic treatments, little is known about the cell type-specific transcriptomic organization of the human Hb or how it is altered in SCZD. Here we define the molecular neuroanatomy of the human Hb and identify transcriptomic changes in individuals with SCZD compared to neurotypical controls. Utilizing Hb-enriched postmortem human brain tissue, we performed single nucleus RNA-sequencing (snRNA-seq; n=7 neurotypical donors) and identified 17 molecularly defined Hb cell types across 16,437 nuclei, including 3 medial and 7 lateral Hb populations, several of which were conserved between rodents and humans. Single molecule fluorescent in situ hybridization (smFISH; n=3 neurotypical donors) validated snRNA-seq Hb cell types and mapped their spatial locations. Bulk RNA-sequencing and cell type deconvolution in Hb-enriched tissue from 35 individuals with SCZD and 33 neurotypical controls yielded 45 SCZD-associated differentially expressed genes (DEGs, FDR < 0.05), with 32 (71%) unique to Hb-enriched tissue. eQTL analysis identified 717 independent SNP-gene pairs (FDR < 0.05), where either the SNP is a SCZD risk variant (16 pairs) or the gene is a SCZD DEG (7 pairs). eQTL and SCZD risk colocalization analysis identified 16 colocalized genes. These results identify topographically organized cell types with distinct molecular signatures in the human Hb and demonstrate unique genetic changes associated with SCZD, thereby providing novel molecular insights into the role of Hb in neuropsychiatric disorders. One Sentence Summary: Transcriptomic analysis of the human habenula and identification of molecular changes associated with schizophrenia risk and illness state.

10.
Invest Ophthalmol Vis Sci ; 64(10): 26, 2023 07 03.
Artigo em Inglês | MEDLINE | ID: mdl-37471072

RESUMO

Purpose: Early and intermediate non-neovascular AMD (NN-AMD) has the potential to progress to either advanced NN-AMD with geographic atrophy, or to neovascular AMD (N-AMD) with CNV. This exploratory study performed an unbiased analysis of aqueous humor transcriptome in patients with early or intermediate NN-AMD vs. treatment-naïve N-AMD to determine the feasibility of using this method in future studies investigating pathways and triggers for conversion from one form to another. Methods: Aqueous humor samples were obtained from 20 patients with early or intermediate NN-AMD and 20 patients with untreated N-AMD, graded on clinical examination and optical coherence tomography. Transcriptome profiles were generated using next-generation sequencing methods optimized for ocular samples. Top-ranked transcripts were compared between groups, and pathway enrichment analysis was performed. Results: Seventy-eight differentially expressed transcripts were identified. Unsupervised clustering of differentially expressed transcripts was able to successfully differentiate between the two groups based on aqueous transcriptome alone. Pathway analysis highlighted changes in expression of genes associated with mitochondrial respiration, oxidative stress, ubiquitination, and neurogenesis between the two groups. Conclusions: This pilot study compared the aqueous fluid transcriptome of patients with early or intermediate NN-AMD and untreated N-AMD. Differences in transcripts and transcriptome pathways identified in the aqueous of patients with early or intermediate NN-AMD compared with patients with N-AMD are consistent with those previously implicated in the pathogenesis of these distinct AMD subtypes. The findings from this exploratory study warrant further investigation using a larger, prospective study design, with the inclusion of a control group of eyes without AMD.


Assuntos
Neovascularização de Coroide , Atrofia Geográfica , Degeneração Macular Exsudativa , Humanos , Estudos Prospectivos , Projetos Piloto , Atrofia Geográfica/diagnóstico , Perfilação da Expressão Gênica , Tomografia de Coerência Óptica/métodos , Neovascularização de Coroide/tratamento farmacológico , Degeneração Macular Exsudativa/diagnóstico , Degeneração Macular Exsudativa/genética , Degeneração Macular Exsudativa/complicações
11.
Transl Vis Sci Technol ; 12(11): 30, 2023 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-38010281

RESUMO

Purpose: Epidemiologically, men have a higher incidence, severity, and progression of diabetic retinopathy (DR) than women. We investigated microvascular differences between men and women with diabetes on optical coherence tomography angiography (OCTA). Methods: Three × 3 mm OCTA macula scans of non-diabetic and patients with diabetes were obtained. Vascular parameters included parafoveal vessel density (VD), vessel length density (VLD), and flow index (FI) of the superficial capillary plexus (SCP) and deep capillary plexus (DCP) as well as foveal avascular zone (FAZ) area and perimeter. Multivariable linear regression was used for statistical analysis. Results: There were 1809 patients with diabetes and 217 non-diabetic participants that were included in this study. Diabetic individuals included those with no DR (n = 1356), mild non-proliferative DR (NPDR; n = 286), moderate NPDR (n = 126), and severe NPDR/proliferative DR (PDR; n = 41). Male sex was significantly associated with smaller FAZ area/perimeter and lower DCP VLD in both non-diabetic subjects and patients with diabetes. Male sex in the diabetic group was additionally associated with lower SCP VD/VLD and DCP VD. Addition of an interaction between male sex and diabetes status in the interaction analysis showed that being male and diabetic conferred increased reduction in DCP VD and VLD compared to sex-based changes in non-diabetics. Larger FAZ perimeter, lower SCP VD/VLD, and lower DCP VLD were associated with poorer visual acuity in diabetics. Conclusions: On OCTA, male patients with diabetes may have more severe microvascular disease especially in the DCP compared to women. Translational Evidence: Sex-based alterations in diabetic microvascular disease has the potential to influence future basic and clinical studies as well as the implementation of OCTA disease markers.


Assuntos
Diabetes Mellitus , Retinopatia Diabética , Macula Lutea , Humanos , Masculino , Feminino , Angiofluoresceinografia/métodos , Tomografia de Coerência Óptica/métodos , Vasos Retinianos/diagnóstico por imagem , Retinopatia Diabética/diagnóstico por imagem , Retinopatia Diabética/epidemiologia , Diabetes Mellitus/epidemiologia
12.
JCI Insight ; 8(6)2023 03 22.
Artigo em Inglês | MEDLINE | ID: mdl-36821371

RESUMO

Epithelial organoids derived from intestinal tissue, called enteroids, recapitulate many aspects of the organ in vitro and can be used for biological discovery, personalized medicine, and drug development. Here, we interrogated the cell signaling environment within the developing human intestine to identify niche cues that may be important for epithelial development and homeostasis. We identified an EGF family member, EPIREGULIN (EREG), which is robustly expressed in the developing human crypt. Enteroids generated from the developing human intestine grown in standard culture conditions, which contain EGF, are dominated by stem and progenitor cells and feature little differentiation and no spatial organization. Our results demonstrate that EREG can replace EGF in vitro, and EREG leads to spatially resolved enteroids that feature budded and proliferative crypt domains and a differentiated villus-like central lumen. Multiomic (transcriptome plus epigenome) profiling of native crypts, EGF-grown enteroids, and EREG-grown enteroids showed that EGF enteroids have an altered chromatin landscape that is dependent on EGF concentration, downregulate the master intestinal transcription factor CDX2, and ectopically express stomach genes, a phenomenon that is reversible. This is in contrast to EREG-grown enteroids, which remain intestine like in culture. Thus, EREG creates a homeostatic intestinal niche in vitro, enabling interrogation of stem cell function, cellular differentiation, and disease modeling.


Assuntos
Fator de Crescimento Epidérmico , Intestinos , Humanos , Epirregulina , Mucosa Intestinal , Diferenciação Celular
13.
Curr Opin Neurobiol ; 73: 102522, 2022 04.
Artigo em Inglês | MEDLINE | ID: mdl-35453000

RESUMO

Animals move in three dimensions (3D). Thus, 3D measurement is necessary to report the true kinematics of animal movement. Existing 3D measurement techniques draw on specialized hardware, such as motion capture or depth cameras, as well as deep multi-view and monocular computer vision. Continued advances at the intersection of deep learning and computer vision will facilitate 3D tracking across more anatomical features, with less training data, in additional species, and within more natural, occlusive environments. 3D behavioral measurement enables unique applications in phenotyping, investigating the neural basis of behavior, and designing artificial agents capable of imitating animal behavior.


Assuntos
Comportamento Animal , Movimento , Animais , Fenômenos Biomecânicos , Computadores , Movimento (Física)
14.
Front Mol Neurosci ; 15: 921901, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35935334

RESUMO

The cerebellar nuclear (CN) neurons are a molecularly heterogeneous population whose specification into the different cerebellar nuclei is defined by the expression of varying sets of transcription factors. Here, we present a novel molecular marker, Pou3f1, that delineates specific sets of glutamatergic CN neurons. The glutamatergic identity of Pou3f1+ cells was confirmed by: (1) the co-expression of vGluT2, a cell marker of glutamatergic neurons; (2) the lack of co-expression between Pou3f1 and GAD67, a marker of GABAergic neurons; (3) the co-expression of Atoh1, the master regulator required for the production of all cerebellar glutamatergic lineages; and (4) the absence of Pou3f1-expressing cells in the Atoh1-null cerebellum. Furthermore, the lack of Pax6 and Tbr1 expression in Pou3f1+ cells reveals that Pou3f1-expressing CN neurons specifically settle in the interposed and dentate nuclei. In addition, the Pou3f1-labeled glutamatergic CN neurons can be further classified by the expression of Brn2 and Irx3. The results of the present study align with previous findings highlighting that the survival of the interposed and dentate CN neurons is largely independent of Pax6. More importantly, the present study extends the field's collective knowledge of the molecular diversity of cerebellar nuclei.

15.
Neurosurgery ; 91(5): 808-820, 2022 11 01.
Artigo em Inglês | MEDLINE | ID: mdl-36069524

RESUMO

BACKGROUND: Frailty, a decline in physiological reserve, prognosticates poorer outcomes for several neurosurgical conditions. However, the impact of frailty on traumatic brain injury outcomes is not well characterized. OBJECTIVE: To analyze the association between frailty and traumatic intracranial hemorrhage (tICH) outcomes in a nationwide cohort. METHODS: We identified all adult admissions for tICH in the National Trauma Data Bank from 2007 to 2017. Frailty was quantified using the validated modified 5-item Frailty Index (mFI-5) metric (range = 0-5), with mFI-5 ≥2 denoting frailty. Analyzed outcomes included in-hospital mortality, favorable discharge disposition, complications, ventilator days, and intensive care unit (ICU) and total length of stay (LOS). Multivariable regression assessed the association between mFI-5 and outcomes, adjusting for patient demographics, hospital characteristics, injury severity, and neurosurgical intervention. RESULTS: A total of 691 821 tICH admissions were analyzed. The average age was 57.6 years. 18.0% of patients were frail (mFI-5 ≥ 2). Between 2007 and 2017, the prevalence of frailty grew from 7.9% to 21.7%. Frailty was associated with increased odds of mortality (odds ratio [OR] = 1.36, P < .001) and decreased odds of favorable discharge disposition (OR = 0.72, P < .001). Frail patients exhibited an elevated rate of complications (OR = 1.06, P < .001), including unplanned return to the ICU (OR = 1.55, P < .001) and operating room (OR = 1.17, P = .003). Finally, frail patients experienced increased ventilator days (+12%, P < .001), ICU LOS (+11%, P < .001), and total LOS (+13%, P < .001). All associations with death and disposition remained significant after stratification for age, trauma severity, and neurosurgical intervention. CONCLUSION: For patients with tICH, frailty predicted higher mortality and morbidity, independent of age or injury severity.


Assuntos
Lesões Encefálicas Traumáticas , Fragilidade , Adulto , Lesões Encefálicas Traumáticas/complicações , Lesões Encefálicas Traumáticas/epidemiologia , Lesões Encefálicas Traumáticas/cirurgia , Fragilidade/complicações , Fragilidade/epidemiologia , Hospitalização , Humanos , Tempo de Internação , Pessoa de Meia-Idade , Procedimentos Neurocirúrgicos
16.
Elife ; 112022 08 09.
Artigo em Inglês | MEDLINE | ID: mdl-35942939

RESUMO

We have identified active enhancers in the mouse cerebellum at embryonic and postnatal stages which provides a view of novel enhancers active during cerebellar development. The majority of cerebellar enhancers have dynamic activity between embryonic and postnatal development. Cerebellar enhancers were enriched for neural transcription factor binding sites with temporally specific expression. Putative gene targets displayed spatially restricted expression patterns, indicating cell-type specific expression regulation. Functional analysis of target genes indicated that enhancers regulate processes spanning several developmental epochs such as specification, differentiation and maturation. We use these analyses to discover one novel regulator and one novel marker of cerebellar development: Bhlhe22 and Pax3, respectively. We identified an enrichment of de novo mutations and variants associated with autism spectrum disorder in cerebellar enhancers. Furthermore, by comparing our data with relevant brain development ENCODE histone profiles and cerebellar single-cell datasets we have been able to generalize and expand on the presented analyses, respectively. We have made the results of our analyses available online in the Developing Mouse Cerebellum Enhancer Atlas, where our dataset can be efficiently queried, curated and exported by the scientific community to facilitate future research efforts. Our study provides a valuable resource for studying the dynamics of gene expression regulation by enhancers in the developing cerebellum and delivers a rich dataset of novel gene-enhancer associations providing a basis for future in-depth studies in the cerebellum.


Assuntos
Transtorno do Espectro Autista , Elementos Facilitadores Genéticos , Animais , Transtorno do Espectro Autista/genética , Regulação da Expressão Gênica no Desenvolvimento , Camundongos , Neurogênese/genética , Fatores de Transcrição/metabolismo
17.
Front Oncol ; 12: 910199, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36686824

RESUMO

Meningiomas are the most common primary intracranial neoplasm. While traditionally viewed as benign, meningiomas are associated with significant patient morbidity, and certain meningioma subgroups display more aggressive and malignant behavior with higher rates of recurrence. Historically, the risk stratification of meningioma recurrence has been primarily associated with the World Health Organization histopathological grade and surgical extent of resection. However, a growing body of literature has highlighted the value of utilizing molecular characteristics to assess meningioma aggressiveness and recurrence risk. In this review, we discuss preclinical and clinical evidence surrounding the use of molecular classification schemes for meningioma prognostication. We also highlight how molecular data may inform meningioma treatment strategies and future directions.

18.
Stem Cell Reports ; 17(5): 1138-1153, 2022 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-35395175

RESUMO

NOTCH signaling is a key regulator involved in maintaining intestinal stem cell (ISC) homeostasis and for balancing differentiation. Using single-cell transcriptomics, we observed that OLFM4, a NOTCH target gene present in ISCs, is first expressed at 13 weeks post-conception in the developing human intestine and increases over time. This led us to hypothesize that the requirement for NOTCH signaling is acquired across human development. To test this, we established a series of epithelium-only organoids (enteroids) from different developmental stages and used γ-secretase inhibitors (dibenzazepine [DBZ] or DAPT) to functionally block NOTCH signaling. Using quantitative enteroid-forming assays, we observed a decrease in enteroid forming efficiency in response to γ-secretase inhibition as development progress. When DBZ was added to cultures and maintained during routine passaging, enteroids isolated from tissue before 20 weeks had higher recovery rates following single-cell serial passaging. Finally, bulk RNA sequencing (RNA-seq) analysis 1 day and 3 days after DBZ treatment showed major differences in the transcriptional changes between developing or adult enteroids. Collectively, these data suggest that ISC dependence on NOTCH signaling increases as the human intestine matures.


Assuntos
Secretases da Proteína Precursora do Amiloide , Receptores Notch , Células-Tronco , Secretases da Proteína Precursora do Amiloide/genética , Diferenciação Celular , Humanos , Mucosa Intestinal , Intestinos , Organoides , Receptores Notch/genética
19.
Cell Rep ; 38(7): 110379, 2022 02 15.
Artigo em Inglês | MEDLINE | ID: mdl-35172130

RESUMO

Pluripotent-stem-cell-derived human intestinal organoids (HIOs) model some aspects of intestinal development and disease, but current culture methods do not fully recapitulate the diverse cell types and complex organization of the human intestine and are reliant on 3D extracellular matrix or hydrogel systems, which limit experimental control and translational potential for regenerative medicine. We describe suspension culture as a simple, low-maintenance method for culturing HIOs and for promoting in vitro differentiation of an organized serosal mesothelial layer that is similar to primary human intestinal serosal mesothelium based on single-cell RNA sequencing and histological analysis. Functionally, HIO serosal mesothelium has the capacity to differentiate into smooth-muscle-like cells and exhibits fibrinolytic activity. An inhibitor screen identifies Hedgehog and WNT signaling as regulators of human serosal mesothelial differentiation. Collectively, suspension HIOs represent a three-dimensional model to study the human serosal mesothelium.


Assuntos
Epitélio/crescimento & desenvolvimento , Intestinos/crescimento & desenvolvimento , Organoides/crescimento & desenvolvimento , Membrana Serosa/crescimento & desenvolvimento , Técnicas de Cultura de Tecidos , Alginatos/farmacologia , Adesão Celular/efeitos dos fármacos , Diferenciação Celular/efeitos dos fármacos , Linhagem Celular , Colágeno/farmacologia , Combinação de Medicamentos , Epitélio/efeitos dos fármacos , Proteínas Hedgehog/metabolismo , Humanos , Intestinos/ultraestrutura , Laminina/farmacologia , Músculo Liso/citologia , Organoides/efeitos dos fármacos , Organoides/ultraestrutura , Proteoglicanas/farmacologia , Membrana Serosa/efeitos dos fármacos , Membrana Serosa/ultraestrutura , Transdução de Sinais/efeitos dos fármacos , Suspensões , Proteínas Wnt/metabolismo
20.
Dev Cell ; 57(13): 1598-1614.e8, 2022 07 11.
Artigo em Inglês | MEDLINE | ID: mdl-35679862

RESUMO

The human respiratory epithelium is derived from a progenitor cell in the distal buds of the developing lung. These "bud tip progenitors" are regulated by reciprocal signaling with surrounding mesenchyme; however, mesenchymal heterogeneity and function in the developing human lung are poorly understood. We interrogated single-cell RNA sequencing data from multiple human lung specimens and identified a mesenchymal cell population present during development that is highly enriched for expression of the WNT agonist RSPO2, and we found that the adjacent bud tip progenitors are enriched for the RSPO2 receptor LGR5. Functional experiments using organoid models, explant cultures, and FACS-isolated RSPO2+ mesenchyme show that RSPO2 is a critical niche cue that potentiates WNT signaling in bud tip progenitors to support their maintenance and multipotency.


Assuntos
Células-Tronco Mesenquimais , Organogênese , Humanos , Pulmão , Organoides , Via de Sinalização Wnt
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