Publications by authors named "Dereje D Jima"
Exposure to prenatal social stressors during pregnancy is associated with adverse birth outcomes and has been linked to epigenetic changes in DNA methylation (DNAm); however, less understood is the effect of neighborhood-level stressors like crime during pregnancy on offspring DNAm. Using data from the Newborn Epigenetic Study, we conducted epigenome-wide and regional analyses of the association between exposure to neighborhood crime and DNAm in offspring cord blood using Illumina's HumanMethylation450k BeadChip among 185 mother-offspring pairs. Prenatal exposure to neighborhood crime at the census block group level was mapped to participants' residential addresses during the gestational window from the date of last menstrual period to delivery.
View Article and Find Full Text PDFPrenatal Smoking Exposures and Epigenome-wide Methylation in Newborn Blood.
Environ Health Perspect
June 2025
Background: Maternal sustained smoking during pregnancy is associated with thousands of differentially methylated CpGs in newborns, but impacts of other prenatal tobacco smoking exposures remain unclear.
Objective: To identify differential DNA methylation in newborns from maternal sustained smoking and less studied prenatal smoking exposures (i.e.
Micro- and nanoplastics (MNPs) are widespread environmental pollutants that pose significant health risks. They originate from industrial processes, consumer products, and environmental degradation, inducing oxidative stress through cellular dysfunctions such as membrane interaction, internalization, mitochondrial damage, inflammation, metal ion leaching, and impaired antioxidant defense. Despite increasing evidence of their toxicity-particularly developmental neurotoxicity (DNT) and mitochondrial impairment-our understanding remains limited due to the high costs of animal studies, which reduce the overall size of experimental data.
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- Microenvironmental factors play a key yet unclear role in the progression of soft tissue sarcomas, especially during their onset.
- A novel zebrafish model was developed to differentiate among microenvironmental, precancerous, and cancer cells, focusing on malignant peripheral nerve sheath tumors (MPNST), which grow aggressively.
- The study reveals that specific inflammatory signaling pathways are activated during the transition from precancerous to cancerous states, highlighting the role of macrophages and identifying periostin as a significant protein in MPNST progression.
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- Alzheimer's disease is more prevalent in non-Hispanic Blacks compared to non-Hispanic Whites, prompting a study on the role of methylation in this disparity.
- Researchers analyzed brain tissue DNA to identify differentially methylated regions (DMRs) related to imprint control regions (ICRs) in both AD patients and controls, revealing significant differences in methylation patterns.
- The study found 81 DMRs in non-Hispanic Black AD patients and 27 in non-Hispanic White AD patients, suggesting that changes in DNA methylation related to genomic imprinting may influence the risk of Alzheimer's and vary between these populations.
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- Malrotation of the intestine is a common birth defect, and research indicates that exposure to the herbicide atrazine during late-stage development in Xenopus embryos significantly increases the occurrence of this defect.
- Atrazine disrupts key processes needed for gut tube growth, such as cell arrangement and proliferation, leading to insufficient gut lengthening and altered rotation direction.
- The study highlights the connection between metabolic disruptions caused by atrazine exposure (such as reduced important metabolites and increased oxidative stress) and intestinal malrotation, suggesting that these metabolic issues play a role in this developmental anomaly.
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- Differentially methylated imprint control regions (ICRs) play a crucial role in regulating gene expression, and their dysregulation can lead to chronic diseases, but current methods for profiling them are limited.
- A custom methylation array with 22,819 probes was developed to better assess ICRs, showing promise in comparison to traditional methods like WGBS and the Human Imprintome array.
- This new tool aims to enhance the accuracy of ICR assessments and facilitate research on their links to diseases and genetic imprinting throughout an individual’s life.
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- * A meta-analysis of 37 studies revealed that higher MEA is linked to different DNA methylation patterns in offspring at birth, childhood, and adolescence, with significant findings at 473 specific sites associated with maternal factors like smoking and nutrition.
- * The research underscores the connection between socio-economic status and biological processes, enhancing our understanding of how maternal education impacts health through genetic mechanisms and emphasizing the role of social determinants in health disparities.
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- Seasonal variations at birth can influence DNA methylation, which may affect health outcomes over a person’s lifetime.
- A study involving multiple cohorts discovered specific DNA methylation patterns linked to different birth seasons, revealing 26 differentially methylated regions (DMRs) at birth and 32 in childhood.
- Results suggested that geographic latitude plays a role in these associations, linking certain genes to conditions like schizophrenia and asthma, particularly in infants born in higher latitudes (≥50°N).
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- Cadmium (Cd) is a toxic heavy metal linked to severe fetal health issues, including growth restriction and malformations, with unclear mechanisms behind these effects.
- Researchers used a mouse model to investigate how Cd impacts gene expression in the placenta, revealing a significant increase in a specific long non-coding RNA after Cd exposure.
- The study suggests that this lncRNA may influence gene expression related to oxidative stress responses, highlighting a potential pathway through which Cd causes negative outcomes in fetal development.
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- The skin serves as a crucial defense against infections, with keratinocytes activating the type I interferon (IFN) response to combat pathogens.
- A study involving the deletion of the C/EBPβ transcription factor in mouse epidermis showed increased levels of IFNβ and other interferon-stimulated genes (ISGs) in keratinocytes.
- The absence of C/EBPβ enhanced the keratinocytes' response to viral and pathogen mimics, leading to greater activation of immune responses and increased cell death through apoptosis, highlighting C/EBPβ's role as a repressor in this protective mechanism.
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- Ecologists have noted a decline in freshwater biodiversity due to increased salinization, particularly affecting organisms like mayflies, but the physiological impacts of salinity changes on these species remain largely unexplored.
- The study focuses on N. triangulifer mayflies to investigate how chronic exposure to different salinity levels affects protein expression in the gills, using shotgun proteomics to identify key proteins involved in ion transport.
- Findings reveal significant changes in protein expression linked to salinity exposure, identifying 710 unique peptide sequences and highlighting critical transporters, while also addressing broader physiological functions related to ATP synthesis and stress response.
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- Cadmium exposure in adulthood is linked to nonalcoholic fatty liver disease (NAFLD), and rising NAFLD cases in children indicate the importance of early life environmental factors.
- Research suggests that imprinted genes, especially Zac1, may connect early exposure to disease susceptibility later in life.
- Experiments in mice revealed that developmental cadmium chloride exposure led to NAFLD characteristics and showed that Zac1 is a significant factor in this programming process, influencing lipid accumulation through its interaction with the Pparγ promoter.
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- HIF-PHIs are being developed to treat anemia in CKD, but it's crucial to ensure they are safe for the heart.
- Genetic variants can potentially predict the risk of adverse cardiovascular effects from these treatments.
- A specific genetic variant related to EPO levels was identified and tested, showing no increased risk of coronary artery disease, heart attack, or stroke with higher EPO levels, indicating a safer profile for these therapies.
Imprinted genes - critical for growth, metabolism, and neuronal function - are expressed from one parental allele. Parent-of-origin-dependent CpG methylation regulates this expression at imprint control regions (ICRs). Since ICRs are established before tissue specification, these methylation marks are similar across cell types.
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- Research shows that children exhibit sex-specific differences in disease prevalence, onset age, and susceptibility, potentially linked to DNA methylation variations.
- A meta-analysis of 8438 newborns and 4268 older children found significant differences in DNA methylation at nearly 47,000 CpG sites, with males generally showing lower methylation than females.
- The study identified additional methylation sites related to conditions like cancer and psychiatric disorders, emphasizing the role of DNA methylation in understanding health disparities between sexes.
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- NAFLD is projected to become the leading cause of childhood liver failure in developed countries, with maternal metabolic syndrome (MetS) potentially influencing its development in offspring.
- Research using a mouse model revealed that exposure to MetS after birth (postnatal) leads to significant liver issues such as steatosis (fatty liver) and fibrosis, while prenatal exposure does not.
- Key findings highlighted the role of imprinted genes, especially the Zac1 gene, in linking maternal MetS to juvenile NAFLD, suggesting that these genes may be critical in understanding and potentially preventing metabolic diseases.
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- Cadmium (Cd) is a harmful heavy metal that can hinder fetal growth and neurodevelopment despite limited transfer through the placenta.
- Research using mouse models reveals that maternal Cd exposure leads to significant brain enlargement and behavioral changes in offspring, indicating serious developmental impacts.
- Molecular analysis shows that Cd exposure alters gene expression related to brain development, affects energy pathways, and disrupts retinoic acid signaling, pointing to potential mechanisms behind these developmental issues.
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- DNA methylation in childhood and adolescence shows significant correlations with body mass index (BMI), suggesting potential early indicators of obesity.
- Analysis involved cord blood and whole blood measurements from up to 4,133 children in various studies, indicating the importance of age-specific patterns in dietary and physical health.
- Findings reveal that as children age, the strength of the associations between DNA methylation and BMI increases, emphasizing the potential for using methylation patterns in obesity prevention strategies.
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- ADHD is a childhood disorder with a genetic basis, and this study investigates the role of epigenetic mechanisms, specifically DNA methylation, in its development.
- The research involved epigenome-wide association studies to find methylation sites linked to ADHD symptoms at two key times: at birth and school age, analyzing data from thousands of children across multiple cohorts.
- Results indicated that certain DNA methylation markers at birth were strongly associated with later ADHD symptoms, while no significant associations were found for school-age methylation, highlighting the need for further research in this area.
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- The study examined how transient thermal stress affects aquatic insect larvae by identifying temperature thresholds linked to fitness issues and rearing them under varying temperatures.
- RNA sequencing showed minimal changes in gene expression under stable temperatures, but significant changes occurred with daily temperature fluctuations, impacting genes related to energy and metabolism.
- Even when larvae were later exposed to optimal temperatures, lingering effects of thermal stress were noted, indicating that brief exposure to stress couldn’t be completely mitigated by time in ideal conditions.
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- Birthweight is linked to health outcomes throughout life, and DNA methylation may play a significant role, as shown in a meta-analysis involving 8,825 neonates.
- The study identified 914 DNA methylation sites in neonatal blood associated with birthweight, revealing a weight difference from -183 to 178 grams per 10% increase in methylation.
- Although some of the methylation changes related to birthweight were also seen in childhood, they did not persist into adulthood, suggesting the need for further research to clarify the causal relationships involved.
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- p53 is activated by DNA damage and helps regulate key processes like cell cycle arrest and apoptosis to prevent cancer, while C/EBPβ acts as a survival factor by negatively regulating p53's apoptotic functions.
- UVB radiation increases p53 levels and enhances apoptosis, but in mice lacking C/EBPβ, this p53 activity is significantly boosted, suggesting a feedback loop between p53 and C/EBPβ.
- The deletion of C/EBPβ in the epidermis makes mice more resistant to UVB-induced skin cancer by promoting pro-apoptotic responses and enhancing the type 1 interferon pathway alongside p53.
Epigenome-wide meta-analysis of DNA methylation and childhood asthma.
Sarah E Reese
,
Cheng-Jian Xu
,
Herman T den Dekker
,
Mi Kyeong Lee
,
Sinjini Sikdar
,
Dereje D Jima
J Allergy Clin Immunol
June 2019
Background: Epigenetic mechanisms, including methylation, can contribute to childhood asthma. Identifying DNA methylation profiles in asthmatic patients can inform disease pathogenesis.
Objective: We sought to identify differential DNA methylation in newborns and children related to childhood asthma.
C/EBPβ deletion in oncogenic Ras skin tumors is a synthetic lethal event.
Cell Death Dis
October 2018
Article Synopsis
- The study explores how deleting a protein called C/EBPβ in skin tumors driven by the oncogene Ha-Ras leads to rapid tumor shrinkage, highlighting its role in tumor survival.
- It was found that removing C/EBPβ increases the activity of the protein p53, which helps trigger cell death (apoptosis) specifically in the cancerous cells.
- The research suggests that targeting C/EBPβ may be an effective therapeutic strategy for treating Ras-driven tumors by exploiting their dependency on this protein for survival.