Papillary tumor of the pineal region: analysis of DNA methylation profiles and clinical outcomes in 76 cases
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ABSTRACT:
SUBMITTER: Wu Z
PROVIDER: S-EPMC11251120 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:Genomewide DNA methylation array profiling and analysis of 76 new and public published Papillary Tumor of the Pineal Region (PTPR). The methylation idat profiles of 39 newly profiled tumors were provided here.
2024-07-19 | GSE254031 | GEO
Project description:Papillary Tumor of the Pineal Region: analysis of DNA methylation profiles and clinical outcomes in 76 cases
| PRJNA1068152 | ENA
Project description:Papillary tumor of the pineal region (PTPR) is a neuroepithelial brain tumor, which might pose diagnostic difficulties and recurs often. Little is known about underlying molecular alterations. We therefore investigated chromosomal copy number alterations, DNA methylation patterns and mRNA expression profiles in a series of 24 PTPRs. Losses of chromosome 10 were identified in all 13 PTPRs examined. Losses of chromosomes 3 and 22q (54%) as well as gains of chromosomes 8p (62%) and 12 (46%) were also common. DNA methylation profiling using Illumina 450k arrays reliably distinguished PTPR from ependymomas and pineal parenchymal tumors of intermediate differentiation. PTPR could be divided into two subgroups based on methylation pattern, PTPR group 2 showing higher global methylation and a tendency toward shorter progression-free survival (P = 0.06). Genes overexpressed in PTPR as compared with ependymal tumors included SPDEF, known to be expressed in the rodent subcommissural organ. Notable SPDEF protein expression was encountered in 15/19 PTPRs as compared with only 2/36 ependymal tumors, 2/19 choroid plexus tumors and 0/23 samples of other central nervous system (CNS) tumor entities. In conclusion, PTPRs show typical chromosomal alterations as well as distinct DNA methylation and expression profiles, which might serve as useful diagnostic tools.
| S-EPMC8029206 | biostudies-literature
Project description:Papillary tumor of the pineal region (PTPR) is a rare entity. Its clinical presentation is diverse, and establishing an accurate and timely diagnosis may be challenging. Treatment recommendations are based on the evidence level of case series. Recently, several key advances have been made for immunohistochemical characterization, molecular diagnostics, and neurosurgical treatment of PTPR. Here, we describe our single-center experience.
| S-EPMC7571506 | biostudies-literature
Project description:PurposeSurgical series of pineal region gliomas are rarely available. Whereas it is a general assumption that the extent of surgical resection correlates with survival outcomes of intracranial gliomas; the impact of the microsurgical resection on the long-term outcomes of pineal gliomas has been questioned. We present a surgical series of pineal region gliomas with focus on the survival outcome analysis.Methods17 histologically confirmed pineal region glioma patients classified as diffuse and non-diffuse gliomas were retrospectively analyzed. A detailed description of the series was followed by regression models to identify predictors of clinical outcomes. Uni- a multivariate survival analysis was performed to determine independent predictors of mortality.ResultsAlthough the number of treated patients was small, only WHO grade histopathology remained significant (p = 0.02) after multivariate survival analysis with extent of resection, age, tumor volume, and preoperative functional status. The extent of the surgical resection did not correlate with the disease survival rates of non-diffuse (p = 1), diffuse (p = 0.2), nor all gliomas (p = 0.6). 15 of 17 patients underwent gross total (nine patients) or subtotal resection. The preoperative functional status of the patients showed overall improvement on the immediate (p < 0.001) and long-term (p = 0.03) follow-up after 106 (3 - 324) months.ConclusionThe extent of the surgical resection does not seem to significantly impact on the survival outcomes of pineal region gliomas. Thus, genotype and molecular features may essentially affect the outcome. Further research on the field is required.
| S-EPMC7438290 | biostudies-literature
Project description:MNTI is a rare tumor of indeterminate histogenesis and molecular signature. We performed methylation and copy number variation (CNV) profiles in patients with MNTI (n = 7) and PAT (n = 1) compared to the methylation brain tumor classifier v11b4 (BT-C) and the medulloblastoma (MB) classifier group 3/4 v1.0 (MB3/4-C). The patients' mean age was 8 months (range: 4-48). The BT-C classified five MNTIs and one PAT (relapse) as class family MB-G3/G4, subclass group 3 (score: >0.9). The remaining two MNTIs and PAT (primary) were classified as class family plexus tumor, subclass pediatric (scores: >0.45). The MB3/4-C classified all MNTIs as high-risk MB-G3, Subtype II (score: >0.45). The primary PAT was classified as subtype III (score: 0.99) and its relapse as subtype II/III. MNTI and PAT clustered close to MB-G3. CNV analysis showed multiple rearrangements in one PAT and two MNTIs. The median follow-up was 54 months (four MNTIs in remission, one PAT died). In conclusion, we demonstrated that MNTI shares a homogenous methylation profile with MB-G3, and possibly with PAT. The role of a multipotent progenitor cell (i.e., early cranial neural crest cell) in their histogenesis and the influence of the anatomical site, tumor microenvironment, and other cytogenetic events in their divergent biologic behavior deserve further investigation.
| S-EPMC7916108 | biostudies-literature
Project description:Deficiency in DNA MMR activity results in tumors with a hypermutator phenotype, termed microsatellite instability (MSI). Beyond its utility in Lynch syndrome screening algorithms, today MSI has gained importance as predictive biomarker for various anti-PD-1 therapies across many different tumor types. Over the past years, many computational methods have emerged to infer MSI using either DNA- or RNA-based approaches. Considering this together with the fact that MSI-high tumors frequently exhibit a hypermethylated phenotype, herein we developed and validated MSIMEP, a computational tool for predicting MSI status from microarray DNA methylation tumor profiles of colorectal cancer samples. We demonstrated that MSIMEP optimized and reduced models have high performance in predicting MSI in different colorectal cancer cohorts. Moreover, we tested its consistency in other tumor types with high prevalence of MSI such as gastric and endometrial cancers. Finally, we demonstrated better performance of both MSIMEP models vis-à-vis a MLH1 promoter methylation-based one in colorectal cancer.
| S-EPMC9984554 | biostudies-literature
Project description:We present a young adult woman who developed a myxoid tumor of the pineal region having a SMARCB1 mutation, which was phenotypically similar to the recently described desmoplastic myxoid, SMARCB1-mutant tumor of the pineal region (DMT-SMARCB1). The 24-year-old woman presented with headaches, nausea, and emesis. Neuroimaging identified a hypodense lesion in CT scans that was T1-hypointense, hyperintense in both T2-weighted and FLAIR MRI scans, and displayed gadolinium enhancement. The resected tumor had an abundant, Alcian-blue positive myxoid matrix with interspersed, non-neoplastic neuropil-glial-vascular elements. It immunoreacted with CD34 and individual cells for EMA. Immunohistochemistry revealed loss of nuclear INI1 expression by the myxoid component but its retention in the vascular elements. Molecular analyses identified a SMARCB1 deletion and DNA methylation studies showed that this tumor grouped together with the recently described DMT-SMARCB1. A cerebrospinal fluid cytologic preparation had several cells morphologically similar to those in routine and electron microscopy. We briefly discuss the correlation of the pathology with the radiology and how this tumor compares with other SMARCB1-mutant tumors of the nervous system.
| S-EPMC10240954 | biostudies-literature
Project description:BackgroundPineal region tumors often present with hydrocephalus. Endoscopic third ventriculostomy (ETV) and simultaneous tumor biopsy remain a minimally invasive procedure offering both diagnostic and therapeutic advantages in the management of these tumors. However, different operative techniques have been described in the literature.AimThe aim is to study the ETV success rate, diagnostic rate of simultaneous tumor biopsy, complications, and follow-up of patients of pineal region tumors managed with ETV and simultaneous tumor biopsy using the single burr hole technique.MethodsThe study was performed by retrospectively reviewing the records of patients of pineal region tumors managed by simultaneous ETV and tumor biopsy using a "single burr hole" technique from January 2012 to December 2019.ResultsThirty-four patients (22 males and 12 females) with a mean age of 28.7 years were analyzed. ETV was successful in relieving hydrocephalus in 29 (87.8%) patients. Three patients needed a ventriculoperitoneal shunt, and one required Ommaya reservoir placement for persistent hydrocephalus. Histological diagnosis was successfully established in 26 (78.8%) patients. There were two procedure-related mortalities. Two patients underwent craniotomy and tumor excision subsequently. Radiotherapy was given to 11 patients, and 9 patients were managed by observation alone. The mean follow-up of our study was 15.8 months.ConclusionsSimultaneous ETV and tumor biopsy using a single burr hole technique is a safe, minimally invasive procedure for the management of pineal region tumors.
| S-EPMC7869259 | biostudies-literature
Project description: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. To screen pineal gland candidate genes related to the onset of goat puberty and regulated by genome methylation, we collected pineal glands from prepubertal and pubertal female goats, then, determined the DNA methylation profile by whole genome bisulfite sequencing and the transcriptome by RNA sequencing on Illumina HiSeqTM2500. We analyzed differentially expressed genes between the Pre group and Pub group using the DESeq2 software (version 1.20.0), and applied the Benjamini and Hochberg method for adjusting P-values. Genes with a P-value less than 0.05 and an absolute log2 fold change greater than 0 were considered differentially expressed genes. Results showed that there was no significant difference in the whole-genome methylation level of the pineal gland between prepubertal and pubertal goats, but the methylation pattern changed significantly, indicating that genomic DNA methylation of the pineal gland might play a role in regulating the initiation of goat puberty. Changes in DNA methylation patterns affected some pineal gland transcriptomes, while the transcriptional level of most genes remained unaffected by DNA methylation differences. Genes regulated by DNA methylation regulates genes primarily involved in metabolic processes, oxidative phosphorylation, and signaling pathways related to thermogenesis. Methylation significantly regulated the expression of genes such as ATP5F1D, CACNB2, and PTEN, while genes like LIN28B, GIP, OPN1SW, and DCC showed the most notable fold changes, which may indicate their involvement in the onset of puberty.
| S-EPMC11742059 | biostudies-literature