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Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE199748 | GEO | 2022/09/06

REPOSITORIES: GEO

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Potential methylation-regulated genes and pathways in hepatocellular neoplasm, not otherwise specified.

Project description:Background and aimsThe molecular basis of hepatocellular neoplasm, not otherwise specified (HCN-NOS) is unknown. We aimed to identify gene expression patterns, potential methylation-regulated genes and pathways that characterize the tumor, and its possible relationship to hepatoblastoma and hepatocellular carcinoma (HCC).Approach & resultsParallel genome-wide profiling of gene expression (RNAseq) and DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls. 2530 significantly differentially expressed genes (DEGs) were identified between tumors and controls. Many of these DEGs were associated with hepatoblastoma and/or HCC. Analysis Match in Ingenuity Pathway Analysis determined that the gene expression profile of HCN-NOS was unique but significantly similar to that of both hepatoblastoma and HCC. A total of 27,195 CpG sites (CpGs) were significantly differentially methylated (DM) between tumors and controls, with a global hypomethylation pattern and predominant CpG island hypermethylation in promotor regions. Aberrant DNA methylation predominated in Developmental Process and Molecular Function Regulator pathways. Embryonic stem cell pathways were significantly enriched. In total, 1055 aberrantly methylated (at CpGs) and differentially expressed genes were identified, including 25 upstream regulators and sixty-one potential CpG island methylation-regulated genes. Eight methylation-regulated genes (TCF3, MYBL2, SRC, HMGA2, PPARGC1A, SLC22A1, COL2A1 and MYCN) had highly consistent gene expression patterns and prognostic value in patients with HCC, based on comparison to publicly available datasets.ConclusionsHCN-NOS has a unique, stem-cell like gene expression and DNA methylation profile related to both hepatoblastoma and HCC but distinct therefrom. Further, 8 methylation-regulated genes associated with prognosis in HCC were identified.

| S-EPMC9532972 | biostudies-literature

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (EPIC850)

Project description:genome-wide profiling of DNA methylation (EPIC850) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls.

2022-09-02 | GSE199747 | GEO

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

Project description:genome-wide profiling of gene expression (RNAseq) was performed on 4 pairs of pre-treatment HCN-NOS tumors and adjacent non-tumor controls.

2022-09-02 | GSE195664 | GEO

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

Project description:Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified

| PRJNA821432 | ENA

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (EPIC850)

Project description:Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (EPIC850)

| PRJNA821441 | ENA

Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

Project description:Potential Methylation-regulated Genes and Pathways in Hepatocellular Malignant Neoplasm, Not Otherwise Specified (RNA-seq)

| PRJNA801686 | ENA

Hepatic small vessel neoplasm, a rare infiltrative vascular neoplasm of uncertain malignant potential.

Project description:Characteristic but rare vascular neoplasms in the adult liver composed of small vessels with an infiltrative border were collected from an international group of collaborators over a 5-year period (N=17). These tumors were termed hepatic small vessel neoplasm (HSVN), and the histologic differential diagnosis was angiosarcoma (AS). The average age of patients was 54years (range, 24-83years). HSVN was more common in men. The average size was 2.1cm (range, 0.2-5.5cm). Diagnosis was aided by immunohistochemical stains for vascular lineage (CD31, CD34, FLI-1), which were uniformly positive in HSVN. Immunohistochemical stains (p53, c-Myc, GLUT-1, and Ki-67) for possible malignant potential are suggestive of a benign/low-grade tumor. Capture-based next-generation sequencing (using an assay that targets the coding regions of more than 500 cancer genes) identified an activating hotspot GNAQ mutation in 2 of 3 (67%) tested samples, and one of these cases also had a hotspot mutation in PIK3CA. When compared with hepatic AS (n=10) and cavernous hemangioma (n=6), the Ki-67 proliferative index is the most helpful tool in excluding AS, which demonstrated a tumor cell proliferative index greater than 10% in all cases. Strong p53 and diffuse c-Myc staining was also significantly associated with AS but not with HSVN or cavernous hemangioma. There have been no cases with rupture/hemorrhage, disseminated intravascular coagulation, or Kasabach-Merritt syndrome. Thus far, there has been no metastasis or recurrence of HSVN, but complete resection and close clinical follow-up are recommended because the outcome remains unknown.

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Peripheral T-cell lymphoma, not otherwise specified- Case report.

Project description:T-cell lymphomas are rare malignancies that are often found in older individuals. Here we present the case of a 63 year old female that presented with diffuse cervical, inguinal, and axillary lymphadenopathy with associated weight loss and night sweats. The patient underwent excisional lymph node biopsy which revealed a T-cell lymphoma with findings characteristic of peripheral T-cell lymphoma, not otherwise specified.

| S-EPMC7296317 | biostudies-literature

BCL6 mRNA Expression Level in Invasive Duct Carcinoma not otherwise Specified.

Project description:IntroductionB-Cell Lymphoma 6 (BCL6) has an oncogenic role in tumourigenesis of various malignancies. It represses genes involved in terminal differentiation and plays complementary role with Signal Transducer and Activator of Transcription 3 (STAT3) in triple-negative breast cancer cellular function.AimTo evaluate the expression of BCL6 in cancer breast and determine its correlation with the clinico-pathological features including the molecular subtype of breast carcinoma.Materials and methodsThis prospective case control study was carried out on 150 patients, divided into 100 cases of invasive duct carcinoma not otherwise specified and 50 benign breast lesions including fibroadenoma and fibrocystic disease. Fresh tissues were excised, which were then subjected to RNA extraction. The BCL6 mRNA level was assessed using real-time reverse transcription Polymerase Chain Reaction (PCR).ResultsThere was a significant higher levels of BCL6 mRNA in malignant cases compared to benign ones (p<0.001). The level of BCL6 mRNA was higher in cases showing advanced tumor stage (p<0.04), triple negative subtype and associated in situ component (p<0.001) compared to cases with an early stage, luminal or Her 2-neu positive subtypes and those lacking in situ component.ConclusionBCL6 is up-regulated in breast cancer and is associated with poor prognostic features such as advanced stage and triple negative molecular subtype. BCL6 inhibitors might be considered as targeted therapy for breast cancer.

| S-EPMC5296560 | biostudies-literature

Detecting subgroups in children diagnosed with pervasive developmental disorder - not otherwise specified.

Project description:Hierarchical cluster analyses were used to detect three subgroups in a sample of children with pervasive developmental disorder--not otherwise specified (PDD-NOS) evaluated at ages 2 and 4. At age 2, Cluster 1 demonstrated few autism symptoms and high cognitive scores; 60% no longer met criteria for PDD at 4. Cluster 2 exhibited more autism symptoms and lower cognitive scores at 2; 89.5% met criteria for ASD at 4. Cluster 3 had the lowest cognitive scores and most impaired social/communication skills at 2, but no repetitive behaviors; 60% diagnosed with Autistic Disorder at 4. Results shed light on outcomes for different PDD-NOS types and raise questions regarding the increased importance of repetitive behaviors in DSM-5.

| S-EPMC5391033 | biostudies-literature

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