Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA428434 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6448768_1.fastq.gz | Fastqsanger.gz | |||
| SRR6448768_2.fastq.gz | Fastqsanger.gz |
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Project description:In this work we employed the comprehensive evaluation of clinical data of the cohort of CD patients along with the sequencing of 14 exon of USP8 to estimate the prevalence of USP8 mutations in our cohort and transcriptome analysis of tumor tissue to search for the associations between USP8 mutation status, molecular markers of pituitary adenomas, and clinical and diagnostic parameters of Cushing’s syndrome including hormonal secretion, tumor size, aggressiveness, and SSRT2/SSRT5 expression.
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Project description:Pituitary adenomas are benign tumors originating from the endocrine cells of the pituitary gland, but some pathological subtypes are highly invasive, known as invasive pituitary adenomas. Invasive pituitary adenomas are relatively rare, progress rapidly, easily invade surrounding tissues, have a high risk of recurrence, and have poor response to standard treatments. This study collected tumor specimens from 17 patients with non-invasive pituitary adenomas (FSH type) and 15 patients with invasive pituitary adenomas (ACTH-silent type), and performed transcriptome sequencing, aiming to explore the genetic differences between invasive and non-invasive pituitary adenomas.
2024-03-04 | GSE260487 | GEO
Project description:The clinical characteristics of growth hormone (GH)-producing pituitary adenomas vary across patients. In this study, we aimed to integrate the genetic alterations, protein expression profiles, transcriptomes, and clinical characteristics of GH-producing pituitary adenomas to detect molecules associated with acromegaly characteristics. Targeted capture sequencing and copy number analysis of 36 genes and non-targeted proteomics analysis were performed on fresh-frozen samples from 121 sporadic GH-producing pituitary adenomas. Targeted capture sequencing revealed GNAS as the only driver gene, as previously reported. Classification by consensus clustering using both RNA sequencing and proteomics revealed many similarities between the proteome and the transcriptome. Gene ontology analysis was performed for differentially expressed proteins between wild-type and mutant GNAS samples identified by non-targeted proteomics analysis and involved in G protein–coupled receptor (GPCR) pathways. The results suggested that GNAS mutations impact endocrinological features in acromegaly through GPCR pathway induction. ATP2A2 and ARID5B correlated with the GH change rate in the octreotide loading test, and WWC3, SERINC1, and ZFAND3 correlated with the tumor volume change rate after somatostatin analog treatment. These results identified a biological connection between GNAS mutations and the clinical and biochemical characteristics of acromegaly, revealing novel molecules associated with acromegaly that may affect medical treatment efficacy.
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Project description:Gene alteration analysis on 121 GH-producing pituitary adenomas and non-target proteomics analysis with RNA sequencing analysis on 45 non-functioning pituitary adenomas (NFPAs) and 60 growth hormone (GH)-producing pituitary adenomas were performed, and integrated these results with the clinical characteristics of acromegaly. We attempted to identify key players involved in shaping the clinical features of acromegaly, especially those related to treatment efficacy. This project revealed the importance of GNAS mutations in terms of clinical and biochemical characteristics and identified novel molecules that may be involved in the responsiveness to medical treatment.
2022-11-24 | PXD036604 | JPOST Repository
Project description:Background: USP8 mutations are the most common driver changes in corticotroph pituitary tumors. They have direct effect on cells’ proteome through disturbance of ubiquitination process and also influence gene expression. The aim of this study was to compare microRNA profiles in USP8- mutated and wild-type tumors and determine the probable role of differential microRNA expression by integrative microRNA and mRNA analysis. Methods: Patients with Cushing’s disease (n = 28) and silent corticotroph tumors (n = 20) were included. USP8 mutations were identified with Sanger sequencing. MicroRNA and gene expression was determined with next-generation sequencing. Results: USP8-mutated patients with Cushing’s disease showed higher rate of clinical remission and trend towards lower tumor volume than wild-type patients. Comparison of microRNA profiles of USP8-mutated and wild-type tumors revealed 68 differentially expressed microRNAs. Their target genes were determined by in silico prediction and microRNA/mRNA correlation analysis. GeneSet Enrichment analysis of putative targets showed that the most significantly overrepresented genes are involved in protein ubiquitination-related processes. Only few microRNAs influence the expression of genes differentially expressed between USP8-mutated and wild-type tumors. Conclusions: Differences in microRNA expression in corticotropinomas stratified according to USP8 status reflect disturbed ubiquitination processes, but do not correspond to differences in gene expression between these tumors.
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Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.
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Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO
Project description:Gene expression analysis of growth hormone producing somatotroph pituitary adenomas
| PRJNA198731 | ENA
Project description:Differential gene expression in pituitary adenomas by oligonucleotide array analysis
| PRJNA91221 | ENA
Project description:As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.
| S-EPMC4686780 | biostudies-literature