Analysis of Xenopus tropicalis stage NF33 regional gene expression in micro-dissected domains along anterior-posterior axis and Hedgehog, Retinoic Acid, and Rfx6 dependent gene expression in micro-dissected NF33 foregut tissue (mesoderm + endoderm)
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ABSTRACT:
ORGANISM(S): Xenopus tropicalis
PROVIDER: GSE310727 | GEO | 2025/11/24
REPOSITORIES: GEO
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Project description:Analysis of Xenopus tropicalis stage NF33 regional gene expression in micro-dissected domains along anterior-posterior axis and Hedgehog, Retinoic Acid, and Rfx6 dependent gene expression in micro-dissected NF33 foregut tissue (mesoderm + endoderm)
| PRJNA1366989 | ENA
Project description:Recently a new neonatal diabetes syndrome, Mitchell-Riley syndrome, was discovered. To identify the genetic cause of the syndrome homozygosity mapping was used, several chromosomal regions were linked to Mitchell-Riley syndrome. In situ hybridization of genes from one such region using model organism Xenopus laevis identified RFX6 as a potential candidate gene; mutant forms of RFX6 were subsequently found in Mitchell-Riley patients. Analysis of the expression pattern of RFX6 in Xenopus development shows it is expressed broadly in the endoderm early in development, and later RFX6 becomes restricted to the endocrine cells of the gut and pancreas. Morpholino knockdown of RFX6 in Xenopus caused a loss of pancreas marker gene expression. Injection of exogenous wild type RFX6 rescued the morpholino phenotype in Xenopus tadpoles. Attempts to rescue the loss-of-function phenotype using mutant forms of RFX6 found in Mitchell-Riley patients were unsuccessful suggesting the changes lead to loss-of-function and could be the cause of Mitchell-Riley syndrome. Microarray analysis of gene expression in knockdown tissue suggested a downregulation in marker genes for lung, stomach and heart, ambiguous results for the liver, and an upregulation in kidney marker gene expression. RT-PCR and in situ hybridization confirms a loss of lung, stomach and heart gene expression, no change in liver marker hex and an upregulation in kidney marker KcnJ1. The fact that the morpholino phenotype affects multiple organs suggests that RFX6 has a broad role early in endoderm development. Xenopus laevis embryos were injected with morpholinos, either mismatch control (MM) or RFX6 start site (MO1), at the 8-cell stage. The foreguts of the resulting tadpoles were dissected at 3 different stages of development, NF30, NF40 and NF44.
2011-01-24 | E-GEOD-23642 | biostudies-arrayexpress
Project description:Recently a new neonatal diabetes syndrome, Mitchell-Riley syndrome, was discovered. To identify the genetic cause of the syndrome homozygosity mapping was used, several chromosomal regions were linked to Mitchell-Riley syndrome. In situ hybridization of genes from one such region using model organism Xenopus laevis identified RFX6 as a potential candidate gene; mutant forms of RFX6 were subsequently found in Mitchell-Riley patients. Analysis of the expression pattern of RFX6 in Xenopus development shows it is expressed broadly in the endoderm early in development, and later RFX6 becomes restricted to the endocrine cells of the gut and pancreas. Morpholino knockdown of RFX6 in Xenopus caused a loss of pancreas marker gene expression. Injection of exogenous wild type RFX6 rescued the morpholino phenotype in Xenopus tadpoles. Attempts to rescue the loss-of-function phenotype using mutant forms of RFX6 found in Mitchell-Riley patients were unsuccessful suggesting the changes lead to loss-of-function and could be the cause of Mitchell-Riley syndrome. Microarray analysis of gene expression in knockdown tissue suggested a downregulation in marker genes for lung, stomach and heart, ambiguous results for the liver, and an upregulation in kidney marker gene expression. RT-PCR and in situ hybridization confirms a loss of lung, stomach and heart gene expression, no change in liver marker hex and an upregulation in kidney marker KcnJ1. The fact that the morpholino phenotype affects multiple organs suggests that RFX6 has a broad role early in endoderm development.
2011-01-24 | GSE23642 | GEO
Project description:We performed bulk RNA-seq analysis for CRISPR-Cpf1 mutated H1 cells that were differentiated into pancreatic cells. Homozygous mutant was compared to control cells (RFX6-/- vs RFX6+/+) at stage 3 (PF) and stage 5 (EP), and heterozygous mutant was compared to control cells (RFX6-/+ vs RFX6+/+) at stage 7 (SC-islets).
2024-04-11 | GSE234289 | GEO
Project description:To define Retinoic Acid and Rfx6 regulated genes in Xenopus laevis foregut tissue, during developmental window of NF15 to NF38, we micro-dissected foregut explants containing both mesoderm and endoderm at stage NF15 from embryos injected with a translation blocking Rfx6 Morpholino Oligo or a control 5bp mismatch oligo, cultured explants, and harvested at NF25, NF33, or NF38 for bulk RNA-seq analysis. For RA loss of function, foregut explants containing both mesoderm and endoderm were treated with pan RAR antagonist BMS493 from NF15 to NF33, harvested either at NF25 or NF33 for bulk RNA-seq analysis.
2025-11-24 | GSE310726 | GEO
Project description:Background: Hepatocellular carcinoma (HCC) cells undergo reprogramming of glucose metabolism to support uncontrolled proliferation, of which the intrinsic mechanism still merits further investigation. Although regulatory factor X6 (RFX6) is aberrantly expressed in different cancers, its precise role in cancer development remains ambiguous. Methods: Microarrays of HCC tissues were employed to investigate the expression of RFX6 in tumor and adjacent non-neoplastic tissues. Functional assays were employed to explore the role of RFX6 in HCC development. Chromatin immunoprecipitation (ChIP), untargeted metabolome profiling, and sequencing were performed to identify potential downstream genes and pathways regulated by RFX6. Metabolic assays were employed to investigate the effect of RFX6 on glycolysis in HCC cells. Bioinformatics databases were used to validate the above findings. Results: HCC tissues exhibited elevated expression of RFX6. High RFX6 expression represented as an independent hazard factor correlated to poor prognosis in patients with HCC. RFX6 deficiency inhibited HCC development in vitro and in vivo, while its overexpression exerted opposite functions. Mechanistically, RFX6 bound to the promoter area of PGAM1 and upregulated its expression. The increased PGAM1 protein levels enhanced glycolysis and further promoted the development of HCC. Conclusions: RFX6 acted as a novel driver for HCC development by promoting aerobic glycolysis, disclosing the potential of the RFX6-PGAM1 axis for therapeutic targeting.
2023-12-20 | GSE248063 | GEO
Project description:Background: Hepatocellular carcinoma (HCC) cells undergo reprogramming of glucose metabolism to support uncontrolled proliferation, of which the intrinsic mechanism still merits further investigation. Although regulatory factor X6 (RFX6) is aberrantly expressed in different cancers, its precise role in cancer development remains ambiguous. Methods: Microarrays of HCC tissues were employed to investigate the expression of RFX6 in tumor and adjacent non-neoplastic tissues. Functional assays were employed to explore the role of RFX6 in HCC development. Chromatin immunoprecipitation (ChIP), untargeted metabolome profiling, and sequencing were performed to identify potential downstream genes and pathways regulated by RFX6. Metabolic assays were employed to investigate the effect of RFX6 on glycolysis in HCC cells. Bioinformatics databases were used to validate the above findings. Results: HCC tissues exhibited elevated expression of RFX6. High RFX6 expression represented as an independent hazard factor correlated to poor prognosis in patients with HCC. RFX6 deficiency inhibited HCC development in vitro and in vivo, while its overexpression exerted opposite functions. Mechanistically, RFX6 bound to the promoter area of PGAM1 and upregulated its expression. The increased PGAM1 protein levels enhanced glycolysis and further promoted the development of HCC. Conclusions: RFX6 acted as a novel driver for HCC development by promoting aerobic glycolysis, disclosing the potential of the RFX6-PGAM1 axis for therapeutic targeting.
2023-12-20 | GSE248062 | GEO
Project description:The goal of this experiment was to identify Rfx6-regulated genes in the ileum of adult mice by comparative transcriptome studies, 8 days and 3 months after Rfx6 removal .
2019-08-15 | GSE132997 | GEO
Project description:RFX6 is a key transcription factor for the development of mouse pancreas, however the functional roles of RFX6 in human beta cells are poorly explored. Thus transcriptome analysis was perfomed to determine the functional targets of RFX6 in human beta cells using the recently developed human beta cell-line EndoC-βH2.
2014-12-22 | GSE59049 | GEO
Project description:The gastrointestinal (GI) tract consists of highly specialized organs from the proximal esophagus to the distal colon, each with unique functions. Rare congenital malformations of the GI tract, including organ atresia, agenesis or mispatterning are linked to gene mutations although the molecular basis of these malformations has been poorly studied due to lack of model systems to study human development. We identified a patient with compound heterozygous mutations in the transcription factor RFX6 with pancreatic agenesis as previously described. In addition, the patient had duodenal mal-rotation and atresia suggesting that establishment of the proximal small intestine was impaired in these patients. To identify the molecular basis of the intestinal malformation we generated induced pluripotent stem cell lines from this patient, and derived human intestinal organoid (HIOs) to identify how mutations in RFX6 impact intestinal patterning and function. We identified that the duodenal identity of HIOs and patient tissues had adopted a more distal small intestinal signature, including expression of SATB2, normally expressed in the ileum and colon. CRISPR-mediated correction of RFX6 restored duodenal identity, including expression of PDX1, which is required for duodenal development. Using transcriptomic approaches in HIOs and Xenopus embryos we identified that PDX1 is a downstream transcriptional target of RFX6 and that PDX1 expression in a RFX6 mutant background was sufficient to rescue duodenal identity. However, RFX6 had additional transcriptional activities that were separate from PDX1, in particular to regulate multiple components of signaling pathways that are critical for establishing early regional identity in the GI tract including WNT, HH, and BMP pathways. In summary, we have identified that RFX6 is one of the most upstream regulators early intestinal patterning in vertebrates and that it acts by regulating key transcriptional and signaling pathways.
2024-03-19 | GSE245474 | GEO