Publications by authors named "Karen N Conneely"

Article Synopsis
  • * A study analyzed DNA methylation patterns in buccal cells from VPT infants to see how their gestational age (GA) and age since conception (post-menstrual age, PMA) affect their development.
  • * Researchers found thousands of DNA sites linked to GA and PMA, with pathways related to brain development and growth significantly affected, indicating that early life epigenetic changes are vital for neurodevelopment in preterm infants.
View Article and Find Full Text PDF

Cancer patients are commonly affected by fatigue. Herein, we sought to examine epigenetic modifications (i.e.

View Article and Find Full Text PDF

Prior studies showed increased age acceleration (AgeAccel) is associated with worse cognitive function among old adults. We examine the associations of childhood, adolescence and midlife cognition with AgeAccel based on DNA methylation (DNAm) in midlife. Data are from 359 participants who had cognition measured in childhood and adolescence in the Child Health and Development study, and had cognition, blood based DNAm measured during midlife in the Disparities study.

View Article and Find Full Text PDF

Allele-specific methylation (ASM) is an epigenetic modification whereby one parental allele becomes methylated and the other unmethylated at a specific locus. ASM is most often driven by the presence of nearby heterozygous variants that influence methylation, but also occurs somatically in the context of genomic imprinting. In this study, we investigate ASM using publicly available single-cell reduced representation bisulfite sequencing (scRRBS) data on 608 B cells sampled from six healthy B cell samples and 1,230 cells from 11 chronic lymphocytic leukemia (CLL) samples.

View Article and Find Full Text PDF

Background: In peripheral blood, DNA methylation (DNAm) patterns in inflammatory bowel disease patients reflect inflammatory status rather than disease status. Here, we examined DNAm in diseased rectal mucosa from ulcerative colitis (UC) patients, focusing on constituent cell types with the goal of identifying therapeutic targets for UC other than the immune system. We profiled DNAm of rectal mucosal biopsies of pediatric UC at diagnosis (n = 211) and non-IBD control (n = 85) patients and performed epigenome-wide association studies (EWAS) of specific cell types to understand DNAm changes in epithelial, immune and fibroblast cells across disease states, course, and clinical outcomes.

View Article and Find Full Text PDF

Recent efforts have focused on developing methylation risk scores (MRS), a weighted sum of the individual's DNA methylation (DNAm) values of pre-selected CpG sites. Most of the current MRS approaches that utilize Epigenome-wide association studies (EWAS) summary statistics only include genome-wide significant CpG sites and do not consider co-methylation. New methods that relax the p-value threshold to include more CpG sites and account for the inter-correlation of DNAm might improve the predictive performance of MRS.

View Article and Find Full Text PDF

This study sought to examine the association between DNA methylation and body mass index (BMI) and the potential of BMI-associated cytosine-phosphate-guanine (CpG) sites to provide information about metabolic health. We pooled summary statistics from six trans-ethnic epigenome-wide association studies (EWASs) of BMI representing nine cohorts (n = 17,034), replicated these findings in the Women's Health Initiative (WHI, n = 4,822), and developed an epigenetic prediction score of BMI. In the pooled EWASs, 1,265 CpG sites were associated with BMI (p < 1E-7) and 1,238 replicated in the WHI (FDR < 0.

View Article and Find Full Text PDF

Purpose: Established prognostic factors for head and neck squamous cell carcinoma (HNSCC) mostly consist of clinical and tumor features assessed before treatment. We report a novel application of DNA methylation in peripheral blood before and after radiation therapy to further improve outcomes stratification.

Methods And Materials: Peripheral blood samples from patients with nonmetastatic HNSCC were obtained for methylation analysis 1 week before and 1 month after radiation therapy.

View Article and Find Full Text PDF
Article Synopsis
  • Age-related changes in DNA methylation patterns in blood are linked to health issues like blood cancer and coronary artery disease (CAD), particularly through a condition called clonal hematopoiesis of indeterminate potential (CHIP).
  • The study focused on two frequently mutated genes associated with CHIP, DNMT3A and TET2, which exhibit opposite patterns of DNA methylation despite both supporting the self-renewal of hematopoietic stem cells.
  • Findings suggest that certain methylation changes connected to DNMT3A and TET2 could increase the risk for coronary artery disease, as verified by analyses in two different participant groups.
View Article and Find Full Text PDF

We performed a multi-ethnic Epigenome Wide Association study on 22,774 individuals to describe the DNA methylation signature of chronic low-grade inflammation as measured by C-Reactive protein (CRP). We find 1,511 independent differentially methylated loci associated with CRP. These CpG sites show correlation structures across chromosomes, and are primarily situated in euchromatin, depleted in CpG islands.

View Article and Find Full Text PDF
Article Synopsis
  • Scientists are studying how air pollution might change DNA and affect health.
  • They looked at data from over 8,000 women to see how pollutants like carbon monoxide and ozone impact DNA changes in different groups of people.
  • They found some specific spots in DNA that change when air pollution levels go up, but not all results could be repeated in other studies. *
View Article and Find Full Text PDF

Recently, we identified 1,189 CpG sites whose DNA methylation level in blood associated with Crohn's disease. Here, we examined associations between DNA methylation and genetic variants to identify methylation quantitative trait loci across disease states in (1) 402 blood samples from 164 newly diagnosed pediatric Crohn's disease patients taken at 2 time points (diagnosis and follow-up), and 74 non-inflammatory bowel disease controls, (2) 780 blood samples from a non-Crohn's disease adult population, and (3) 40 ileal biopsies (17 Crohn's disease cases and 23 non-inflammatory bowel disease controls) from group (1). Genome-wide DNAm profiling and genotyping were performed using the Illumina MethylationEPIC and Illumina Multi-Ethnic arrays.

View Article and Find Full Text PDF

Background: Non-alcoholic fatty liver disease (NAFLD) is characterized by changes in cell composition that occur throughout disease pathogenesis, which includes the development of fibrosis in a subset of patients. DNA methylation (DNAm) is a plausible mechanism underlying these shifts, considering that DNAm profiles differ across tissues and cell types, and DNAm may play a role in cell-type differentiation. Previous work investigating the relationship between DNAm and fibrosis in NAFLD has been limited by sample size and the number of CpG sites interrogated.

View Article and Find Full Text PDF

Obesity is associated with widespread differential DNA methylation (DNAm) patterns, though there have been limited overlap in the obesity-associated cytosine-guanine nucleotide pair (CpG) sites that have been identified in the literature. We systematically searched four databases for studies published until January 2020. Eligible studies included cross-sectional, longitudinal, or intervention studies examining adiposity and genome-wide DNAm in non-pregnant adults aged 18-75 in all tissue types.

View Article and Find Full Text PDF
Article Synopsis
  • The study investigates genetic and environmental factors influencing biological aging, using DNA methylation data from over 40,000 individuals to identify genetic loci associated with epigenetic aging markers.
  • It identified 137 significant genetic loci, including 113 that were previously unknown, linked to various epigenetic clocks and related biological measurements.
  • The findings suggest a connection between genetic factors, lifestyle choices, and longevity, shedding light on the complex genetics of aging.
View Article and Find Full Text PDF
Article Synopsis
  • The study examined epigenetic age acceleration (EAA) in head and neck cancer patients during and after treatment, focusing on its relationship with inflammation and fatigue.
  • Results showed a significant increase in EAA of about 4.9 years right after radiotherapy, with higher fatigue levels linked to greater EAA, particularly in patients with severe fatigue.
  • Inflammation markers, like C-reactive protein and interleukin-6, were also associated with increased EAA, suggesting they play a role in the relationship between EAA and patient fatigue.
View Article and Find Full Text PDF

Background: Medulloblastoma (MB) is the most common malignant pediatric brain tumor that originates in the cerebellum and brainstem. Frequent somatic mutations and deregulated expression of epigenetic regulators in MB highlight the substantial role of epigenetic alterations. 5-hydroxymethylcytosine (5hmC) is a highly abundant cytosine modification in the developing cerebellum and is regulated by ten-eleven translocation (TET) enzymes.

View Article and Find Full Text PDF

Background: Short-duration exposure to ambient particulate matter (PM) air pollution is associated with cardiac autonomic dysfunction and prolonged ventricular repolarization. However, associations with sub-chronic exposures to coarser particulates are relatively poorly characterized as are molecular mechanisms underlying their potential relationships with cardiovascular disease.

Materials And Methods: We estimated associations between monthly mean concentrations of PM < 10 μm and 2.

View Article and Find Full Text PDF

Purpose: Epigenetic age acceleration (EAA) is robustly linked with mortality and morbidity. This study examined risk factors of EAA and its association with overall survival (OS), progression-free survival (PFS), and quality of life (QOL) in patients with head and neck cancer (HNC) receiving radiation therapy.

Methods And Materials: Patients without distant metastasis were enrolled and followed before and at the end of radiation therapy and at 6 and 12 months after radiation therapy.

View Article and Find Full Text PDF

Background: Cognitive trajectory varies widely and can distinguish people who develop dementia from people who remain cognitively normal. Variation in cognitive trajectory is only partially explained by traditional neuropathologies. We sought to identify novel genes associated with cognitive trajectory using DNA methylation profiles from human postmortem brain.

View Article and Find Full Text PDF

Purpose: Multiple myeloma is a malignancy of plasma cells. Extensive genetic and transcriptional characterization of myeloma has identified subtypes with prognostic and therapeutic implications. In contrast, relatively little is known about the myeloma epigenome.

View Article and Find Full Text PDF

Background: Diet quality is a risk factor for chronic disease and mortality. Differential DNA methylation across the epigenome has been associated with chronic disease risk. Whether diet quality is associated with differential methylation is unknown.

View Article and Find Full Text PDF

Purpose: Recent evidence supports a key role of gut microbiome in brain health. We conducted a pilot study to assess associations of gut microbiome with cancer-related fatigue and explore the associations with DNA methylation changes.

Methods: Self-reported Multidimensional Fatigue Inventory and stool samples were collected at pre-radiotherapy and one-month post-radiotherapy in patients with head and neck cancer.

View Article and Find Full Text PDF

Objective: Major depressive disorder (MDD) arises from a combination of genetic and environmental risk factors and DNA methylation is one of the molecular mechanisms through which these factors can manifest. However, little is known about the epigenetic signature of MDD in brain tissue. This study aimed to investigate associations between brain tissue-based DNA methylation and late-life MDD.

View Article and Find Full Text PDF
Article Synopsis
  • PCBs, banned for decades, continue to pose health risks such as type 2 diabetes and cancer due to widespread exposure, which affects gene expression and epigenetic modifications.
  • A study measured DNA methylation in blood samples, identifying 1,345 CpG sites linked to higher PCB levels, particularly in regions important for gene activity and immune function.
  • Findings suggest that PCB exposure alters epigenetic marks correlated with immune responses, highlighting the need for further research to understand how these changes may impact health outcomes.
View Article and Find Full Text PDF