Molecular Portraits of Social Adversity in Breast Cancer [RNA-Seq]
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PROVIDER: PRJNA1229680 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Molecular Portraits of Social Adversity in Breast Cancer
| PRJNA1229676 | ENA
Project description:Molecular Portraits of Social Adversity in Breast Cancer [RRBS]
| PRJNA1229682 | ENA
Project description:Molecular Portraits of Social Adversity in Breast Cancer [smallRNA-Seq]
| PRJNA1229681 | ENA
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290736 | GEO
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290735 | GEO
Project description:Neighborhood disadvantage (ND) is associated with shorter breast cancer (BCa) survival. Although studies have identified that ND is associated with alterations in DNA methylation (DNAme) or gene expression, a comprehensive study integrating DNAme with coding (mRNA) and non-coding (miRNA, tRNA) transcriptomic data to understand how the epigenome regulates key biological pathways is lacking. DNAme, mRNA, miRNA, and tRNA-derived fragment data were analyzed from 80 ER+/HER2- BCa samples from Hispanic White women with no significant differences in genetic ancestry, BMI, smoking, alcohol, Oncotype DX scores, and stage. We analyzed the association between objective ND [Area Deprivation Index (ADI)], subjective ND [Neighborhood Social Environment Adversity Survey (NSEAS)], DNAme, coding, and non-coding data to understand how the epigenome regulates key biological pathways among women living in ND. The cohort was divided into neighborhood advantage (NA, ADI<5; n=55, 69%) and ND (ADI≥5; n=25, 31%). In tumors from ND, calcium signaling and cell adhesion pathways were hypermethylated, immune-related pathways hypomethylated, immune response genes upregulated, and estrogen response genes downregulated. Small RNA analysis showed differential expression of miRNA isoforms and tRNA-derived fragments related to ND. Subjective ND correlated with epigenetic changes in calcium signaling, cell adhesion, and metabolic pathways, along with upregulation of proliferative and stemness pathways. We discovered novel associations between ND and epigenomic regulation of key clinically relevant oncogenesis pathways associated with aggressive biology, such as estrogen response pathways. These findings lay the foundation for multi-institutional studies to validate our findings and guide future treatment and cancer control interventions.
2025-08-15 | GSE290733 | GEO
Project description:This SuperSeries is composed of the SubSeries listed below.
2025-08-15 | GSE290738 | GEO
Project description:Social anxiety disorder (SAD) is a psychiatric disorder characterized by extensive fear in social situations. Multiple genetic and environmental factors are known to contribute to its pathogenesis. One of the main environmental risk factors is early life adversity (ELA). Evidence is emerging that epigenetic mechanisms such as DNA methylation might play an important role in the biological mechanisms underlying SAD and ELA. To investigate the relationship between ELA, DNA methylation, and SAD, we performed an epigenome-wide association study for SAD and ELA examining DNA from whole blood of a cohort of 143 individuals using DNA methylation arrays. We identified two differentially methylated regions (DMRs) associated with SAD located within the genes SLC43A2 and TNXB. As this was the first epigenome-wide association study for SAD, it is worth noting that both genes have previously been associated with panic disorder. Further, we identified two DMRs associated with ELA within the SLC17A3 promoter region and the SIAH3 gene and several DMRs that were associated with the interaction of SAD and ELA. Of these, the regions within C2CD2L and MRPL28 showed the largest difference in DNA methylation. Lastly, we found that two DMRs were associated with both the severity of social anxiety and ELA, however, neither of them was found to mediate the contribution of ELA to SAD later in life. Future studies are needed to replicate our findings in independent cohorts and to investigate the biological pathways underlying these effects.
2021-01-31 | GSE164056 | GEO
Project description:DNA Methylation Differences Associated with Social Anxiety Disorder and Early Life Adversity
| PRJNA688716 | ENA
Project description:Molecular Determinants of Post-Mastectomy Breast Cancer Recurrence
2018-09-20 | PRJEB28702 | EVA