Papillary Tumor of the Pineal Region: analysis of DNA methylation profiles and clinical outcomes in 76 cases
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE254031 | GEO | 2024/07/19
REPOSITORIES: GEO
Similar Datasets
Project description:Papillary Tumor of the Pineal Region: analysis of DNA methylation profiles and clinical outcomes in 76 cases
| PRJNA1068152 | ENA
Project description:Pineal gland is a neuroendocrine gland located at the center of the brain. It protects the body from the effect of toxic compounds and regulates sleep-wake cycle, body temperature and sexual maturity through the secretion of melatonin. Abnormal functioning of pineal glands is known to be associated with Smith-Magenis syndrome, autism spectrum disorder, sleep disorders and Alzheimer’s disease. Characterization of pineal gland proteome will facilitate molecular level investigations on pathophysiological conditions underlying these diseases. We aimed to characterize the proteome of human pineal glands using a high resolution mass spectrometry- based approach. A total of 5,752 proteins were identified from human pineal glands in this study. Of these, 1,108 proteins contained signal peptide domain. We identified 2 novel proteins in this study, which are predicted by computational methods. In addition, a large number of proteins were uniquely identified in this study. A comprehensive list of proteins identified from human pineal glands will aid in unraveling the role of pineal glands in sleep disorders, neuropsychiatric and neurodegenerative diseases.
2017-02-02 | PXD004332 | Pride
Project description:Genomewide DNA methylation array profiling of 37 BCOR altered tumors and 37 non-BCOR altered tumors to study the rare tumor entity of EP300::BCOR fusion in central nervous system. The raw methylation idat files and processed beta values were provided here.
2022-10-09 | GSE211156 | GEO
Project description:Between 80% and 90% of renal carcinomas are either clear cell renal cell carcinoma or papillary RCC although there are at least 20 other distinct forms of RCC recognised by the World Health Organization (WHO). Emerging or provisional entities have been considered as variants of PRCC, including papillary renal neoplasm with reversed polarity (PRNRP). However, the molecular basis of PRNRP is unknown. We used microarray analysis to elucidate the gene profile of 10 PRNRP cases and an additional 7 PRCC cases. Cases were only considered for this study after fulfilment of strict inclusive histological and immunohistochemical criteria. We used Affymetrix Clariom D human arrays to elucidate the expression of these samples.
2024-02-18 | GSE255706 | GEO
Project description:Epigenetic regulation of gene transcription may play a critical role in the onset of puberty. Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. This study aims to screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, to clarify the initiation mechanism of goat puberty and lay the foundation for improving goat reproductive performance. Pineal gland was collected from three female Anhui white goats during prepuberty (2.5 to 3.0 mo) and three during puberty (4.0 to 4.5 mo). Genome-wide hydrogen sulfite sequencing determined the DNA methylation profile, while RNA sequencing determined the transcriptome. The relationship between gene transcription and DNA methylation was determined by joint analysis. We found that there was no significant change in the whole genome methylation level of goat pineal gland before and after puberty, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland may be involved in regulating goat puberty initiation. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes was not affected by DNA methylation differences. Genes regulated by DNA methylation were mainly involved in metabolic processes, oxidative phosphorylation (OXPHOS), and signaling pathways related to thermogenesis. The differential genes ATP5F1D, CACNB2, and PTEN were significantly regulated by methylation, and the difference multiples of LIN28B, GIP, OPN1SW, and DCC were the most significant, possibly involved in puberty initiation.
2024-11-14 | GSE234298 | GEO
Project description:Epigenetic regulation of gene transcription may play a critical role in the onset of puberty. Previous studies have confirmed that methylation regulates gene transcription in the hypothalamus-pituitary-gonadal axis during puberty initiation, but little is known about the regulation of DNA methylation on gene expression in the pineal gland. This study aims to screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, to clarify the initiation mechanism of goat puberty and lay the foundation for improving goat reproductive performance. Pineal gland was collected from three female Anhui white goats during prepuberty (2.5 to 3.0 mo) and three during puberty (4.0 to 4.5 mo). Genome-wide hydrogen sulfite sequencing determined the DNA methylation profile, while RNA sequencing determined the transcriptome. The relationship between gene transcription and DNA methylation was determined by joint analysis. We found that there was no significant change in the whole genome methylation level of goat pineal gland before and after puberty, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland may be involved in regulating goat puberty initiation. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes was not affected by DNA methylation differences. Genes regulated by DNA methylation were mainly involved in metabolic processes, oxidative phosphorylation (OXPHOS), and signaling pathways related to thermogenesis. The differential genes ATP5F1D, CACNB2, and PTEN were significantly regulated by methylation, and the difference multiples of LIN28B, GIP, OPN1SW, and DCC were the most significant, possibly involved in puberty initiation.
2024-11-14 | GSE234928 | GEO
Project description:Genomewide DNA methylation array profiling of 244 gliobastoma and ganglioglioma samples to study FGFR3-TACC3 gene fusions and resolved into a new entity, glioblastoma IDH-wildtype, FGFR3-TACC3 fusion postive methylation outlier group (GBM-F3T3-O). GBM-F3T3-O showed a unique methylation profile and better survival than other glioblastoma patients. The methylation idat profiles were provided here.
2022-05-16 | GSE200647 | GEO
Project description:This study determines pineal gland gene expression levels in the NeuroD1 knockout mouse at postnatal day zero. Comparison was performed against pineal gland gene expression levels in 129 wildtype mice also disected at P0. Keywords: Comparison of wildtype versus transgenic pineal gland gene expression
2007-10-13 | GSE6030 | GEO
Project description:Between 80% and 90% of renal carcinomas are either clear cell renal cell carcinoma or papillary RCC although there are at least 20 other distinct forms of RCC recognised by the World Health Organization (WHO). Emerging or provisional entities have been considered as variants of PRCC, including papillary renal neoplasm with reversed polarity (PRNRP). However, the molecular basis of PRNRP, and miRNA expression profile, is unknown. We used microarray analysis to elucidate the non-coding RNA (ncRNA) profiles of 10 PRNRP cases and compared them with other renal neoplasms. Cases were only considered for this study after fulfilment of strict inclusive histological and immunohistochemical criteria. We used Affymetrix miRNA v.4.0 arrays to elucidate the expression of these samples.
2024-02-18 | GSE255707 | GEO
Project description:We identify and correlate chromosomal alterations, methylation patterns and gene expression in pediatric pineal germinomas. Due the low incidence of pineal germinoma, there is insufficient molecular data related to chromosomal alterations, methylation patterns and genetic expression that may help understand the changes that influence tumor development. In addition, at present, the diagnosis of this tumor in childhood is challenging because of its location and cellular origin, which is why our aim was to understand and to identify possible molecular biomarkers to provide information on the diagnosis and tumor development. Tumor biopsies were obtained from pediatric patients of 0 to 16 years of age, they were subsequently evaluated by histopathological analysis. Sample selection was based on the percentage of tumor cells present in the tumor samples, processing the samples containing the lowest 70% and 80% tumor cells, respectively.
2016-11-26 | E-MTAB-5107 | biostudies-arrayexpress