scholarly journals The gastrointestinal development ‘parts list’: transcript profiling of embryonic gut development in wildtype and Ret-deficient mice

2019 ◽  
Author(s):  
Sumantra Chatterjee ◽  
Priyanka Nandakumar ◽  
Dallas R. Auer ◽  
Stacey B. Gabriel ◽  
Aravinda Chakravarti
Keyword(s):  
Hirschsprung Disease ◽  
Major Effect ◽  
Enteric Neurons ◽  
Null Mouse ◽  
Wildtype Mouse ◽  
Rna Seq ◽  
Gut Development ◽  
Molecular Processes ◽  
The Universe ◽  
Deficient Mice

AbstractThe development of the gut from endodermal tissue to an organ with multiple distinct structures and functions occurs over a prolonged time during embryonic days E10.5-E14.5 in the mouse. During this process, one major event is innervation of the gut by enteric neural crest cells (ENCC) to establish the enteric nervous system (ENS). To understand the molecular processes underpinning gut and ENS development, we generated RNA-seq profiles from wildtype mouse guts at E10.5, E12.5 and E14.5 from both sexes. We also generated these profiles from homozygous Ret null embryos, a model for Hirschsprung disease (HSCR), in whom the ENS is absent. These data reveal four major features: (1) between E10.5 to E14.5 the developmental genetic programs change from expression of major transcription factors (TF) and its modifiers to genes controlling tissue (epithelium, muscle, endothelium) specialization; (2) the major effect of Ret is not only on ENCC differentiation to enteric neurons but also on the enteric mesenchyme and epithelium; (3) a muscle genetic program exerts significant effects on ENS development, and (4) sex differences in gut development profiles are minor. The genetic programs identified, and their changes across development, suggests that both cell autonomous and non-autonomous factors, and interactions between the different developing gut tissues, are important for normal ENS development and its disorders.Significance statementThe mammalian gut is a complex set of tissues formed during development by orchestrating the timing of expression of many genes. Here we uncover the identity of these genes, their pathways and how they change during gut organogenesis. We used RNA-seq profiling in the wildtype mouse gut in both sexes during development (E10.5 - E14.5), as well as in a Ret null mouse, a model of Hirschsprung disease (HSCR). These studies have allowed us to expand the universe of genes and developmental processes that contribute to enteric neuronal innervation and to its dysregulation in disease.

scholarly journals Gene- and tissue-level interactions in normal gastrointestinal development and Hirschsprung disease

2019 ◽  
Vol 116 (52) ◽  
pp. 26697-26708 ◽  
Author(s):  
Sumantra Chatterjee ◽  
Priyanka Nandakumar ◽  
Dallas R. Auer ◽  
Stacey B. Gabriel ◽  
Aravinda Chakravarti
Keyword(s):  
Wild Type Mouse ◽  
Hirschsprung Disease ◽  
Tissue Level ◽  
Major Effect ◽  
Enteric Neurons ◽  
Gut Development ◽  
Major Event ◽  
Molecular Processes ◽  
Wild Type ◽  
Developmental Genetic

The development of the gut from endodermal tissue to an organ with multiple distinct structures and functions occurs over a prolonged time during embryonic days E10.5–E14.5 in the mouse. During this process, one major event is innervation of the gut by enteric neural crest cells (ENCCs) to establish the enteric nervous system (ENS). To understand the molecular processes underpinning gut and ENS development, we generated RNA-sequencing profiles from wild-type mouse guts at E10.5, E12.5, and E14.5 from both sexes. We also generated these profiles from homozygousRetnull embryos, a model for Hirschsprung disease (HSCR), in which the ENS is absent. These data reveal 4 major features: 1) between E10.5 and E14.5 the developmental genetic programs change from expression of major transcription factors and its modifiers to genes controlling tissue (epithelium, muscle, endothelium) specialization; 2) the major effect ofRetis not only on ENCC differentiation to enteric neurons but also on the enteric mesenchyme and epithelium; 3) a muscle genetic program exerts significant effects on ENS development; and 4) sex differences in gut development profiles are minor. The genetic programs identified, and their changes across development, suggest that both cell autonomous and nonautonomous factors, and interactions between the different developing gut tissues, are important for normal ENS development and its disorders.

scholarly journals Genetic background-dependent abnormalities of the enteric nervous system and intestinal function in Kif26a-deficient mice

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yukiko Ohara ◽  
Lisa Fujimura ◽  
Akemi Sakamoto ◽  
Youichi Teratake ◽  
Shuichi Hiraoka ◽  
...  
Keyword(s):  
Genetic Background ◽  
Survival Rates ◽  
Gastrointestinal Diseases ◽  
Negative Regulator ◽  
Enteric Neurons ◽  
Enteric Neuron ◽  
Protein Coding ◽  
Underlying Mechanisms ◽  
Functional Gastrointestinal Diseases ◽  
Deficient Mice

AbstractThe Kif26a protein-coding gene has been identified as a negative regulator of the GDNF-Ret signaling pathway in enteric neurons. The aim of this study was to investigate the influence of genetic background on the phenotype of Kif26a-deficient (KO, −/−) mice. KO mice with both C57BL/6 and BALB/c genetic backgrounds were established. Survival rates and megacolon development were compared between these two strains of KO mice. Functional bowel assessments and enteric neuron histopathology were performed in the deficient mice. KO mice with the BALB/c genetic background survived more than 400 days without evidence of megacolon, while all C57BL/6 KO mice developed megacolon and died within 30 days. Local enteric neuron hyperplasia in the colon and functional bowel abnormalities were observed in BALB/c KO mice. These results indicated that megacolon and enteric neuron hyperplasia in KO mice are influenced by the genetic background. BALB/c KO mice may represent a viable model for functional gastrointestinal diseases such as chronic constipation, facilitating studies on the underlying mechanisms and providing a foundation for the development of treatments.

scholarly journals “Too much guts and not enough brains”: (epi)genetic mechanisms and future therapies of Hirschsprung disease — a review

2019 ◽  
Vol 11 (1) ◽  
Author(s):  
Emilie G. Jaroy ◽  
Lourdes Acosta-Jimenez ◽  
Ryo Hotta ◽  
Allan M. Goldstein ◽  
Ragnhild Emblem ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
Enteric Nervous System ◽  
Hirschsprung's Disease ◽  
Hirschsprung’S Disease ◽  
Current Knowledge ◽  
Hirschsprung Disease ◽  
Gut Development ◽  
Dna And Rna ◽  
Expression Of Genes

Abstract Hirschsprung disease is a neurocristopathy, characterized by aganglionosis in the distal bowel. It is caused by failure of the enteric nervous system progenitors to migrate, proliferate, and differentiate in the gut. Development of an enteric nervous system is a tightly regulated process. Both the neural crest cells and the surrounding environment are regulated by different genes, signaling pathways, and morphogens. For this process to be successful, the timing of gene expression is crucial. Hence, alterations in expression of genes specific for the enteric nervous system may contribute to the pathogenesis of Hirschsprung’s disease. Several epigenetic mechanisms contribute to regulate gene expression, such as modifications of DNA and RNA, histone modifications, and microRNAs. Here, we review the current knowledge of epigenetic and epitranscriptomic regulation in the development of the enteric nervous system and its potential significance for the pathogenesis of Hirschsprung’s disease. We also discuss possible future therapies and how targeting epigenetic and epitranscriptomic mechanisms may open new avenues for novel treatment.

scholarly journals Semaphorin 3A controls enteric neuron connectivity and is inversely associated with synapsin 1 expression in Hirschsprung disease

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Jacques Gonzales ◽  
Catherine Le Berre-Scoul ◽  
Anne Dariel ◽  
Paul Bréhéret ◽  
Michel Neunlist ◽  
...  
Keyword(s):  
Synapse Formation ◽  
Colonic Motility ◽  
Hirschsprung Disease ◽  
Perinatal Period ◽  
Cellular Level ◽  
Postnatal Period ◽  
Enteric Neurons ◽  
Semaphorin 3A ◽  
Potential Implication ◽  
Synapsin 1

Abstract Most of the gut functions are controlled by the enteric nervous system (ENS), a complex network of enteric neurons located throughout the wall of the gastrointestinal tract. The formation of ENS connectivity during the perinatal period critically underlies the establishment of gastrointestinal motility, but the factors involved in this maturation process remain poorly characterized. Here, we examined the role of Semaphorin 3A (Sema3A) on ENS maturation and its potential implication in Hirschsprung disease (HSCR), a developmental disorder of the ENS with impaired colonic motility. We found that Sema3A and its receptor Neuropilin 1 (NRP1) are expressed in the rat gut during the early postnatal period. At the cellular level, NRP1 is expressed by enteric neurons, where it is particularly enriched at growth areas of developing axons. Treatment of primary ENS cultures and gut explants with Sema3A restricts axon elongation and synapse formation. Comparison of the ganglionic colon of HSCR patients to the colon of patients with anorectal malformation shows reduced expression of the synaptic molecule synapsin 1 in HSCR, which is inversely correlated with Sema3A expression. Our study identifies Sema3A as a critical regulator of ENS connectivity and provides a link between altered ENS connectivity and HSCR.

scholarly journals A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Abbas Jariani ◽  
Lieselotte Vermeersch ◽  
Bram Cerulus ◽  
Gemma Perez-Samper ◽  
Karin Voordeckers ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Mammalian Cells ◽  
Yeast Cells ◽  
Lag Phase ◽  
Rna Seq ◽  
Molecular Processes ◽  
Sequencing Technology ◽  
Single Cell Rna Sequencing ◽  
Order Of Magnitude

Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics’ droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.

scholarly journals lncRNA-RMST functioned as a SOX2 transcription co-regulator to regulate miR-1251 in the progression of Hirschsprung’s disease

2020 ◽  
Author(s):  
Lingling Zhou ◽  
Zhengke Zhi ◽  
Pingfa Chen ◽  
Zhonghong Wei ◽  
Chunxia Du ◽  
...  
Keyword(s):  
Hirschsprung's Disease ◽  
Hirschsprung’S Disease ◽  
Hirschsprung Disease ◽  
Underlying Mechanism ◽  
Bioinformatic Analysis ◽  
Enteric Neurons ◽  
Intron Region ◽  
Non Coding Rnas ◽  
And Migration

ABSTRACTHirschsprung’s disease (HSCR) is a congenital disorder characterized by the absence of enteric neural crest cells (ENCCs). Non-coding RNAs including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been authenticated as important regulators of biological functions. We conducted a microarray analysis and found lncRNA Rhabdomyosarcoma 2-associated transcript (RMST) was down-regulated in the stenotic segment of HSCR patients. MiR-1251 is transcribed from the intron region of RMST and was also low-expressed. When the expression of RMST or miR-1251 was reduced, the cell proliferation and migration were attenuated. However, RMST didn’t affect the expression of miR-1251 directly found in this study. Through bioinformatic analysis, transcription factor SOX2 was predicted to bind to the promoter region of miR-1251 which was confirmed by CHIP assay. Herein, we demonstrated that RMST exerted as a co-regulator of SOX2 to regulate the expression of miR-1251. Furtherly, AHNAK was proved to be the target gene of miR-1251 in this study. Taken together, we revealed the role of RMST/SOX2/miR-1251/AHNAK pathway in the occurrence of Hirschsprung’s disease and provided a potential therapeutic target for this disease.SUMMARY STATEMENTHirschsprung disease (HSCR) is characterized by a deficit in enteric neurons, however, the underlying mechanism remains unclear. This study revealed the role of lnc-RMST during the occurrence of HSCR.

scholarly journals Cx3cr1-deficient microglia exhibit a premature aging transcriptome

2019 ◽  
Vol 2 (6) ◽  
pp. e201900453 ◽  
Author(s):  
Stefka Gyoneva ◽  
Raghavendra Hosur ◽  
David Gosselin ◽  
Baohong Zhang ◽  
Zhengyu Ouyang ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Immunohistochemical Analysis ◽  
Premature Aging ◽  
Rna Seq ◽  
Active Chromatin ◽  
Chronological Aging ◽  
Transcriptomic Signature ◽  
Immune Related Genes ◽  
Old Mice ◽  
Deficient Mice

CX3CR1, one of the highest expressed genes in microglia in mice and humans, is implicated in numerous microglial functions. However, the molecular mechanisms underlying Cx3cr1 signaling are not well understood. Here, we analyzed transcriptomes of Cx3cr1-deficient microglia under varying conditions by RNA-sequencing (RNA-seq). In 2-mo-old mice, Cx3cr1 deletion resulted in the down-regulation of a subset of immune-related genes, without substantial epigenetic changes in markers of active chromatin. Surprisingly, Cx3cr1-deficient microglia from young mice exhibited a transcriptome consistent with that of aged Cx3cr1-sufficient animals, suggesting a premature aging transcriptomic signature. Immunohistochemical analysis of microglia in young and aged mice revealed that loss of Cx3cr1 modulates microglial morphology in a comparable fashion. Our results suggest that CX3CR1 may regulate microglial function in part by modulating the expression levels of a subset of inflammatory genes during chronological aging, making Cx3cr1-deficient mice useful for studying aged microglia.

scholarly journals Muscularis macrophage development in the absence of an enteric nervous system

2018 ◽  
Vol 115 (18) ◽  
pp. 4696-4701 ◽  
Author(s):  
Marina Avetisyan ◽  
Julia E. Rood ◽  
Silvia Huerta Lopez ◽  
Rajarshi Sengupta ◽  
Elizabeth Wright-Jin ◽  
...  
Keyword(s):  
Nervous System ◽  
Enteric Nervous System ◽  
Hirschsprung Disease ◽  
Human Colon ◽  
Enteric Neurons ◽  
Local Source ◽  
Normal Numbers ◽  
Adult Mice ◽  
Inflammatory Phenotype ◽  
Cells Of Cajal

The nervous system of the bowel regulates the inflammatory phenotype of tissue resident muscularis macrophages (MM), and in adult mice, enteric neurons are the main local source of colony stimulating factor 1 (CSF1), a protein required for MM survival. Surprisingly, we find that during development MM colonize the bowel before enteric neurons. This calls into question the requirement for neuron-derived CSF1 for MM colonization of the bowel. To determine if intestinal innervation is required for MM development, we analyzed MM of neonatal Ret−/− (Ret KO) mice that have no enteric nervous system in small bowel or colon. We found normal numbers of well-patterned MM in Ret KO bowel. Similarly, the abundance and distribution of MM in aganglionic human colon obtained from Hirschsprung disease patients was normal. We also identify endothelial cells and interstitial cells of Cajal as the main sources of CSF1 in the developing bowel. Additionally, MM from neonatal Ret KOs do not differ from controls in baseline activation status or cytokine-production in response to lipopolysaccharide. Unexpectedly, these data demonstrate that the enteric nervous system is dispensable for MM colonization and patterning in the bowel, and suggest that modulatory interactions between MM and the bowel nervous system are established postnatally.

scholarly journals RNA-Seq analysis of isolated satellite cells in Prmt5 deficient mice

Genomics Data ◽  
2015 ◽  
Vol 5 ◽  
pp. 122-125 ◽  
Author(s):  
Carsten Kuenne ◽  
Stefan Guenther ◽  
Mario Looso ◽  
Ting Zhang ◽  
Marcus Krueger ◽  
...  
Keyword(s):  
Satellite Cells ◽  
Rna Seq ◽  
Deficient Mice
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