Methylomic and transcriptomic differences in treatment-naïve profiles among black and non-Hispanic white (NHW) women [RNA-Seq]
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1005901 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25654723.fastq.gz | Fastqsanger.gz | |||
| SRR25654724.fastq.gz | Fastqsanger.gz | |||
| SRR25654725.fastq.gz | Fastqsanger.gz | |||
| SRR25654726.fastq.gz | Fastqsanger.gz | |||
| SRR25654727.fastq.gz | Fastqsanger.gz |
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Project description:Epithelial ovarian cancer (EOC) is a highly lethal gynecological malignancy, with the high-grade serous ovarian cancer subtype (HGSOC) accounting for a significant proportion of cases. Despite platinum-based chemotherapies being the primary treatment for EOC, HGSOC displays high resistance to these therapies. Black women have the highest mortality/incidence ratio of all ethnic groups, and recent studies suggest significant genetic and epigenetic differences between black and non-Hispanic white women who are treatment naïve. This study aims to explore immunogenic differences and hypermethylation phenotype in black women that may contribute to poorer outcomes within this patient group. We collected primary tumor samples from 36 black and 31 non-Hispanic white (NHW) treatment-naïve patients via biopsy and performed methylomic and transcriptomic analyses. Our analysis revealed significant differences in gene expression and methylation between black and NHW patients. Among the differentially expressed genes, we found significant pathway enrichment within p53/apoptosis signaling pathway and cholesterol/lipid modulation. Additionally, we observed mild hypermethylation in black patients vs. the NHW cohort. Furthermore, we discovered differences in the proportion of important immune cell types between the two groups, with CD8+ T-cells and CD4+ memory-resting T-cells being significantly higher proportionally in black patients. In conclusion, our study identified significant differential expression between black and NHW patient groups, as well as mild hypermethylation and differences in the proportion of important immune cell types. These findings provide further insights into the biological mechanisms underlying the disparities in outcomes between black and NHW patients with EOC. Further exploration of the contribution of these differences to clinical outcomes and treatment response in black women is warranted.
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Project description:Methylomic and transcriptomic differences in treatment-naïve profiles among black and non-Hispanic white (NHW) women
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Project description:Methylomic and transcriptomic differences in treatment-naïve profiles among black and non-Hispanic white (NHW) women [Methylation]
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Project description:BackgroundTo understand potential racial differences in disease susceptibility and develop targeted prevention strategies, it is essential to establish biological differences between racial groups in healthy individuals. However, knowledge about how race impacts metabolites is limited. We therefore performed a cross-sectional study using comprehensive metabolomics analysis to investigate racial differences in metabolites among 506 non-Hispanic White (NHW) women and 163 non-Hispanic Black (NHB) women.MethodsWe performed untargeted plasma metabolomic profiling using Metabolon's platform (Durham, NC®) and identified 1074 metabolites in 9 super-pathways. We used multivariable linear regression models, adjusted for confounders, to identify associations between race and metabolites. We applied a Bonferroni correction (p-value < 10-5) to account for multiple testing.ResultsWe identified 26 metabolites that differed significantly between NHW and NHB women. Seven, 10, 17, and 23 metabolites showed absolute percentage differences ≥ 50, ≥ 40%, ≥ 30%, and ≥ 20%, respectively. Xenobiotics (n = 5) and amino acids (n = 2) exhibited the largest absolute percentage differences (≥ 50%) between NHB and NHW women. In the xenobiotics super-pathway, NHB women had higher thymol sulfate, 2-naphthol sulfate, and 2-hydroxyfluorene sulfate, derived from the exposure to polycyclic aromatic hydrocarbons, while NHW women had higher xanthine metabolites. In the amino acid super-pathway, lysine and tryptophan metabolites were lower in NHB women.ConclusionsWe report differences in several metabolites between NHW and NHB women. These findings require validation in a different study and could provide insight into investigating how racial differences in metabolites may impact disease burden across diverse populations.
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Project description:The Subgingival Microbiome in Non-Hispanic Black Women: Relationship to Periodontal Inflammation, Systemic Inflammation, and Preterm Birth
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Project description:BackgroundPreterm birth (PTB) disproportionately affects African American compared with Caucasian women, although reasons for this disparity remain unclear. Some suggest that a differential effect of maternal age by race/ethnicity, especially at older maternal ages, may explain disparities.ObjectiveTo determine whether the relationship between maternal age and preterm birth varies by race/ethnicity among primiparae non-Hispanic blacks (NHB) and non-Hispanic whites (NHW).MethodsA cross-sectional study of 367 081 singleton liveborn first births to NHB and NHW women in California from 2008 to 2012 was conducted. Rate ratios (RR) were estimated for PTB and its subtypes-spontaneous and clinician-initiated-after adjusting for confounders through Poisson regression. Universal age/race reference groups (NHW, 25-29 years) and race-specific reference groups (NHW or NHB, 25-29 years) were used for comparisons.ResultsAmong all women, RR of PTB was highest at the extremes of age (<15 and ≥40 years). Among NHBs, the risk of PTB was higher than among NHWs at all maternal ages (adjusted RR of PTB 1.38-2.93 vs 0.98-2.38). However, using race-specific reference groups, the risk of PTB for NHB women (RR 0.91-1.88) vs NHW women (RR 0.98-2.39) was nearly identical at all maternal ages, with overlapping confidence intervals. Analyses did not demonstrate substantial divergence of risk with advancing maternal age. PTB, spontaneous PTB, and clinician-initiated PTB demonstrated similar risk patterns at younger but not older maternal ages, where risk of clinician-initiated PTB increased sharply for all women.ConclusionsPrimiparae NHBs demonstrated increased risk of PTB, spontaneous PTB, and clinician-initiated PTB compared with NHWs at all maternal ages. However, RRs using race-specific reference groups converged across maternal ages, indicating a similar independent effect of maternal age on PTB by race/ethnicity. A differential effect of maternal age does not appear to explain disparities in preterm birth by race/ethnicity.
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