MiRNA seq of kidney tissues from amyloidosis affected and healthy Abyssinian cats
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ABSTRACT:
PROVIDER: PRJEB37989 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Five kidney sections of 10 μm of thickness were sliced from each FFPE block of three amyloidosis affected and three healthy cats. The total miRNAome was isolated using the miRNeasy FFPE kit by Qiagen. A total amount of 200ng of extracted miRNA/sample was sequenced using the smallRNA-seq kit by Illumina and the Illumina NextSeq500 platform. The read length obtained was 1x75bp for a total of 30 million reads. The quality control of the reads was assessed with FastQC and the adapter sequences were removed using Cutadapt.
2020-12-31 | E-MTAB-8556 | biostudies-arrayexpress
Project description:The amyloidoses constitute a group of diseases occurring in humans and animals that are characterized by abnormal deposits of aggregated proteins in organs, affecting their structure and function. In the Abyssinian cat breed, a familial form of renal amyloidosis has been described. In this study, multi-omics analyses were applied and integrated to explore some aspects of the unknown pathogenetic processes in cats. Whole-genome sequences of two affected Abyssinians and 195 controls of other breeds (part of the 99 Lives initiative) were screened to prioritize potential disease-associated variants. Proteome and miRNAome from formalin-fixed paraffin-embedded kidney specimens of fully necropsied Abyssinian cats, three affected and three non-amyloidosis affected were characterized. While the trigger of the disorder remains unclear, overall, i) 35,960 genomic variants were detected; ii) 215 and 56 proteins were identified as exclusive or overexpressed in the affected and control kidneys, respectively; iii) 60 miRNAs were differentially expressed, 20 of which are newly described. With omics data integration, the general conclusions are:i) the familial amyloid renal form in Abyssinians is not a simple monogenic trait ii) amyloid deposition is not triggered by mutated amyloidogenic proteins but is a mix of proteins codified by wild-type genes iii) the form is biochemically classifiable as AA amyloidosis.
2021-09-10 | PXD024140 | Pride
Project description:MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease Blood was drawn from two groups of cats: 12 healthy cats and 11 cats suffering from hypertrophic cardiomyopathy. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 23 serum samples were analyzed and the groups were compared
2015-07-22 | E-GEOD-49427 | biostudies-arrayexpress
Project description:MicroRNAs negatively regulate gene expression and may serve as biomarkers for human cardiomyopathy. In the domestic cat, hypertrophic cardiomyopathy (HCM) represents the most common primary cardiomyopathy. In humans, the etiology of HCM is linked to mutations in genes of contractile muscle proteins, while in cats a clear proof for causal mutations is missing. The etiology of feline HCM is uncertain. Diagnosis is made by heart ultrasound examination and measuring the serum level of N-terminal pro B-type natriuretic peptide. The purpose of this study was to investigate whether microRNA profiles in the serum of cats with HCM are different from the profiles of healthy cats and whether specific miRNAs can be detected to serve as potential biomarkers for feline HCM or may help in understanding the etiology of this disease
2015-07-22 | GSE49427 | GEO
Project description:BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats. METHODS: Total RNA was extracted from 400 M-BM-5l serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats. RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL cats. CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM. Blood was drawn from two groups of cats: 8 healthy cats and 8 cats suffering from diabetes. After clotting, samples were centrifuged and total mRNA was extracted from serum. These 16 serum samples were analyzed and the groups were compared. Due to technical problems during hybridization (leaking chamber), sample 1_4_B (Serum_diabetic_8) was not included into analysis.
2013-04-11 | E-GEOD-37177 | biostudies-arrayexpress
Project description:BACKGROUND: MicroRNAs negatively regulate gene expression and play a pivotal role in the pathogenesis of human type 2 diabetes mellitus (T2DM). As the domestic cat presents a spontaneous animal model for human T2DM, the purpose of this study was to investigate whether microRNAs are detectable in feline serum and whether microRNA expression profiles differ between healthy and diabetic cats. METHODS: Total RNA was extracted from 400 µl serum of healthy lean (HL) and newly diagnosed diabetic (D) cats. MicroRNA microarrays representing 1079 distinct mouse miRNA targets were used to measure miRNA expression in samples from eight HL and eight D cats. RESULTS: By microarray, 227 distinct microRNAs were identified. Nineteen miRNAs were differentially expressed in diabetic cats, but only two reached statistical significance after correction for multiple comparisons. In qRT-PCR, miR-122* was found to be upregulated in diabetic cats more than 40-fold compared to HL cats, while miR-193b was upregulated about 10-fold. MiR-483* showed a 6- fold increase in diabetic cats compared to HL cats. CONCLUSIONS: Small volumes of serum samples yield sufficient material to detect altered microRNA expression profiles in diabetic cats. The domestic cat may be considered a useful animal model for studying miRNAs involved in human T2DM.
2013-04-11 | GSE37177 | GEO
Project description:The glaucomas are a group of diseases characterized by optic nerve damage that together represent a leading cause of blindness in the human population and in domestic animals. Here we report a mutation in LTBP2 that causes primary congenital glaucoma (PCG) in domestic cats. We identified a spontaneous form of PCG in cats and established a breeding colony segregating for PCG consistent with fully penetrant, autosomal recessive inheritance of the trait. Elevated intraocular pressure, globe enlargement and elongated ciliary processes were consistently observed in all affected cats by 8 weeks of age. Varying degrees of optic nerve damage resulted by 6 months of age. Although subtle lens zonular instability was a common feature in this cohort, pronounced ectopia lentis was identified in less than 10% of cats examined. Thus, glaucoma in this pedigree is attributed to histologically confirmed arrest in the early post-natal development of the aqueous humor outflow pathways in the anterior segment of the eyes of affected animals. Using a candidate gene approach, significant linage was established on cat chromosome B3 (LOD 18.38, q = 0.00) using tightly linked short tandem repeat (STR) loci to the candidate gene, LTBP2. A 4 base-pair insertion was identified in exon 8 of LTBP2 in affected individuals that generates a frame shift that completely alters the downstream open reading frame and eliminates functional domains. Thus, we describe the first spontaneous and highly penetrant non-rodent model of PCG, identifying a valuable animal model for primary glaucoma that closely resembles the human disease providing valuable insights into mechanisms underlying the disease and a valuable animal model for testing therapies.
2016-05-01 | GSE73263 | GEO
Project description:Abdominal subcutaneous adipose tissue protein profiles from control subjects, and ALK (Kappa) and ALL (Lambda) amyloidosis patients. Raw data were acquired by
LTQ, Orbitrap and QExactive instruments. For major chromatographic details refers to doi:10.1182/blood-2011-07-365510, doi:10.3109/13506129.2012.674989, doi:10.3390/molecules26071913.
2022-12-09 | MSV000090875 | MassIVE
Project description:The purpose of this study was the identification of RNAs contained in the urinary exosome (UExo) from dogs and cats. The quality of total RNA in isolated urinary exosome (UExo)-derived total RNAs obtained from the column-based method (urine 1 mL) was checked by using a Bioanalyzer, and samples from normal renal function (NR) group and kidney disease (KD) group were pooled as one sample for each group. We collected NR dogs (n = 37), KD dogs (n = 47), NR cats (n=43), and KD cats (n = 45). For the next generation sequencing, libraries were prepared according to the manufacturer’s protocols and sequenced using 50-base reads acquired by using a HiSeq 2000 platform. The December 2011 (GRCm38/mm10) mouse (Mus musculus) genome data were used as reference. As a result, we could identify the miRNA from these samples.
2018-12-10 | GSE121156 | GEO
Project description:Immunoglobulin light chain (AL) amyloidosis is characterized by deposition of abnormal amyloid fibrils in multiple organs impairing their function. CD138-purified plasma cells producing these fibrils are investigated regarding chromosomal alterations by interphase fluorescence in situ hybridization (iFISH) using a multiple myeloma specific probe set for the IgH translocations as well as recurrent numerical aberrations. Aberrations genuine to AL amyloidosis cannot be detected due to the inherent limitation of this probe panel to known loci. We analyzed 118 AL amyloidosis patients by high-density copy number array to quantitatively detect genome-wide chromosomal imbalances. Most prevalent gains affected chromosomes 1q (37%), 9 (24%), 11q (24%), and 19 (16%). The most frequent deletion was monosomy 13 (28%) followed by partial deletions on 14q (21%), 16q (14%), and 13q (12%). The results were analyzed with respect to cytogenetic subgroups. In 88% of patients with translocation t(11;14) and concomitant gain of 11q22.3/11q23 detected by iFISH, the latter aberration was not due to trisomy of chromosome 11 but part of the unbalanced translocation der(14)t(11;14)(q13;q32) with breakpoint in the CCND1/MYEOV gene region. Partial loss of chromosomes 14q and 16q were significantly associated to patients with gain 1q. Our iFISH probe set is highly concordant with copy number results as it detects the most common cytogenetic aberrations present in AL amyloidosis. Beyond that, the probe panel is also the method of choice to detect translocations involving the IgH locus. In contrast to the results of our iFISH panel the frequency of hyperdiploidy detected by copy number array analysis is higher.
2017-03-29 | GSE89616 | GEO