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Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation

ABSTRACT: Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation

PROVIDER: PRJEB21589 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR2020658_1.fastq.gz	Fastqsanger.gz
	ERR2020658_2.fastq.gz	Fastqsanger.gz

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Potential damaging mutation in LRP5 from genome sequencing of the first reported chimpanzee with the Chiari malformation.

Project description:The genus Pan is the closest related to humans (Homo sapiens) and it includes two species: Pan troglodytes (chimpanzees) and Pan paniscus (bonobos). Different characteristics, some of biomedical aspect, separate them from us. For instance, some common human medical conditions are rare in chimpanzees (menopause, Alzheimer disease) although it is unclear to which extent longevity plays an active role in these differences. However, both humans and chimpanzees present similar pathologies, thus, understanding traits in chimpanzees can help unravel the molecular basis of human conditions. Here, we sequenced the genome of Nico, a central chimpanzee diagnosed with a particular biomedical condition, the Chiari malformation. We performed a variant calling analysis comparing his genome to 25 whole genomes from healthy individuals (bonobos and chimpanzees), and after predicting the effects of the genetic variants, we looked for genes within the OMIM database. We found a novel, private, predicted as damaging mutation in Nico in LRP5, a gene related to bone density alteration pathologies, and we suggest a link between this mutation and his Chiari malformation as previously shown in humans. Our results reinforce the idea that a comparison between humans and chimpanzees can be established in this genetic frame of common diseases.

| S-EPMC5680330 | biostudies-literature

Genetic Analysis of the Chiari I Malformation

Project description:Genetic Analysis of the Chiari I Malformation

| PRJNA526760 | ENA

Genetic Analysis of the Chiari I Malformation

Project description:Genetic Analysis of the Chiari I Malformation

| PRJNA526759 | ENA

Quantitative trait loci (QTL) study identifies novel genomic regions associated to Chiari-Like Malformation in Griffon Bruxellois dogs

Project description:Chiari-like malformation (CM) is a developmental abnormality of the craniocervical junction that is common in the Griffon Bruxellois (GB) breed with an estimated prevalence of 65%. This disease is characterized by overcrowding of the neural parenchyma at the craniocervical junction and disturbance of cerebrospinal fluid (CSF) flow. The most common clinical sign is pain either as a direct consequence of CM or neuropathic pain as a consequence of secondary syringomyelia. The etiology of CM remains unknown but genetic factors play an important role. To investigate the genetic complexity of the disease, a quantitative trait locus (QTL) approach was adopted. A total of 14 quantitative skull and atlas measurements were taken and were tested for association to CM. Six traits were found to be associated to CM and were subjected to a whole-genome association study using the Illumina canine high density bead chip in 74 GB dogs (50 affected and 24 controls). Linear and mixed regression analyses were used to identify quantitative trait loci. To identify the presence of causative haplotype for Chiari-Like Malformation 80 Griffon Bruxellois dogs were genotyped using Illumina CanineHD Beadchip. This cohort consisted of 53 cases and 27 controls. Ten samples were whole genome amplified using the Qiagen Repli-g kit following the protocol. Linear and mixed regression model were used to define association between morphologic traits and genetic data. The sample traits (provided in the sample characteristics field) are described in the 'README_Traits_description.pdf' Processed data were obtained in 3 different normalization batches. The normalization batch/raw data file information is provided in the sample description field.

2014-05-19 | E-GEOD-52221 | biostudies-arrayexpress

Expression Analysis of Mammary Epithelial Cells Isolated from 12-16 Week Old Virgin C57Bl6 Lrp5+/+ and Lrp5-/- Mice

Project description:Investigation of whole-genome gene expression level changes in C57Bl6 Lrp5-/- mammary epithelial cells, compared to the wild-type strain. The mammary epithelial cells were isolated from numbers 4 and 5 mammary glands. The Lrp5-/- mouse strain described in this study has been further described in Lindvall C, Evans NC, Zylstra CR, Li Y, Alexander CM, Williams BO. 2006. The Wnt signaling receptor Lrp5 is required for mammary ductal stem cell activity and Wnt1-induced tumorigenesis. J Biol Chem. 2006 Nov 17;281(46):35081-7. Epub 2006 Sep 13. PMID: 16973609. Mammary epithelial cells were isolated from 6 groups of Lrp5+/+ and 3 groups of Lrp5-/- mice. The isolated RNA was submitted to the Gene Expression Center, University of Wisconsin-Madison where it was labelled with Cy3. Labelled samples were submitted to Roche Nimblegen and were hybridized to Mus musculus 1-Plex arrays that represent 42,586 mouse genes.

2010-05-19 | E-GEOD-19228 | biostudies-arrayexpress

Expression Analysis of Mammary Epithelial Cells Isolated from 12-16 Week Old Virgin C57Bl6 Lrp5+/+ and Lrp5-/- Mice

2009-12-01 | GSE19228 | GEO

Effect of endovascular treatment on gene expression in patients with Budd-Chiari syndrome

Project description:Budd-Chiari syndrome (BCS) results in sinusoidal congestion and hepatocyte apoptosis, which can further progress to liver fibrosis, cirrhosis, and hepatocellular carcinoma. Endovascular (EV) treatment has been the primary therapeutic method and achieved excellent outcomes. However, whether EV treatment could reverse liver cirrhosis in patients with BCS is still unclear. To investigate the effect of endovascular treatment on liver cirrhosis in patients with Budd-Chiari syndrome, we performed gene expression profiling analysis of the liver from patients with or without EV treatment.

2023-03-26 | GSE228205 | GEO

Differential gene expression analysis of eys+/-; lrp5+/- zebrafish eye by microarray

Project description:Vision is essential for vertebrates including humans. Sustained vision is accomplished by retinoid metabolism, the ‘visual cycle’, where all-trans retinol (atROL) is incorporated into the retinal pigment epithelium (RPE) from photoreceptors presumably through decade-long missing receptor(s). Here, we show that the LDL-related receptor-5 (Lrp5) protein is linked to the retinol binding protein 1a (Rbp1a), the transporter of atROL in the visual cycle, by generating and analyzing the digenic eyes shut homolog+/-; lrp5+/- zebrafish, the same form of gene defect detected in a human case of inherited retinal degeneration. Global gene expression analysis followed by genetic study clarified that rbp1a played a role downstream of lrp5. Rbp1a protein was colocalized with Lrp5 protein at microvilli of RPE cells. Furthermore, Rbp1a directly bound to the C-terminal intracellular region of Lrp5 in vitro. Collectively, these results strongly suggest that Lrp5 is a potent candidate of the receptor of atROL in the visual cycle.

2020-12-01 | GSE160663 | GEO

Transcriptome analysis of LRP5- and LRP6-depleted HCC38 cells.

Project description:In order to characterize the differences between the co-receptors LRP5 and LRP6, we have analyzed the transcriptome of HCC38 cells - a triple negative breast cancer cell line - 24, 48 and 72 hours following the depletion of LRP5 or LRP6 using siRNAs.

2018-06-06 | GSE109004 | GEO

Transcriptome analysis of Wnt3a-treated Wild Type, Lrp5KO , Lrp6KO and Lrp5/6KO osteoblasts

Project description:Wnt signaling is a major regulator of osteoblast differentiation and function. To investigate how Wnt3a signaling regulates osteoblastic gene expression and to identify the role of Lrp5 and Lrp6 in mediating Wnt3a signaling in osteoblasts, neonatal calvarial osteoblasts isolated from C57Bl6 (WT) and osteoblasts lacking Lrp5 (Lrp5KO), Lrp6 (Lrp6KO) and, both Lrp5 and 6 (Lrp5/6KO) were treated with Wnt3a for 24 hours and gene expression changes were quantified by RNA-seq.

2017-11-07 | GSE103492 | GEO

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