Browsing by Author "Sun, Jie"
Now showing 1 - 16 of 16
- Results Per Page
- Sort Options
Item Absolute Quantification of Mitochondrial DNA in Peripheral Blood from Women with Preeclampsia(2020) Silzer, Talisa; Phillips, Nicole; Goulopoulou, Styliani; Reid, Danielle; Sun, Jie; Scroggins, Sabrina; Santillan, Mark; Santillan, Donna; Cushen, SpencerIntroduction Mitochondrial DNA (mtDNA) in maternal blood has been proposed as a potential predictor of preeclampsia (PE). The objective of this study was to use an absolute PCR (abPCR) quantification protocol to determine concentrations of mtDNA in maternal plasma and peripheral blood mononuclear cells (PBMC) from normal and PE pregnancies. Methods Blood samples were collected from pregnant women with uncomplicated pregnancies and pregnancies with PE (University of Iowa IRB#200910784). abPCR quantification of mtDNA and nDNA was performed on DNA extracts from plasma (in the presence or absence of lysis buffer) and PBMCs using TaqMan(TM) probes and chemistry. Results When plasma DNA was extracted using lysis buffer, mtDNA concentrations were lower in women with PE than in controls (Control: 4.83 ± 1.09 vs. PE: 1.72 ± 0.38 pg/uL, n=19, P=0.017), while concentrations of nDNA did not differ (P=0.39). Without lysis buffer, plasma mtDNA remained lower in women with PE compared to controls (Control: 0.0106 ± 0.0019 vs PE: 0.0019 ± 0.0003 pg/uL, n=16-20, P< 0.0001). There were no group differences in PBMC mtDNA (P=0.66) and nDNA (P=0.13) concentrations. Conclusion mtDNA concentrations were lower in plasma of pregnant women with PE compared to controls. A significant amount of mtDNA was membrane bound as indicated by a 480-fold greater concentration in DNA isolated from plasma with lysis buffer vs. without. Use of this improved method of quantification of mtDNA in multiple blood fractions may allow for its development as a biomarker to detect PE prior to the onset of organ damage.Item Assessment of Mitochondrial DNA Damage in Cognitive Impairment via NGS: Health Disparities in Mexican Americans(2022) Reid, Danielle; Barber, Robert C.; Sun, Jie; Thorpe, Roland; Zhou, Zhengyang; Phillips, NicoleMexican Americans (MAs) are the fastest growing subpopulation in the US, and as age increases, this population will be disproportionately affected by age-related diseases such as Alzheimer's disease (AD). Diabetes, stroke, depression, and obesity are common risk factors for developing cognitive impairment (CI) and may be of particular relevance to MAs due to their increased prevalence. MtDNA damage has been implicated in AD, and since metabolic comorbidities are more common in MAs, mtDNA damage and mitochondrial dysfunction may be related to the increased burden and earlier age-of-onset among MAs. Mitochondrial dysfunction can induce oxidative damage to guanosine (8oxoG) and cause DNA deletions, both of which have been well-documented in AD. The mitochondrial genome is particularly vulnerable to DNA damage, and age-associated decline in mitochondrial function results in accumulating reactive oxygen species capable of damaging essential biomolecules. We hypothesize that MAs incur mtDNA damage at an elevated rate due to increased comorbidity burden altering mitochondrial function. MtDNA from buffy coat and plasma samples of participants enrolled in the Texas Alzheimer's Research Care and Consortium were amplified using the RepliG mtDNA Amplification kit and were sequenced via NexteraXT on Illumina NextSeq. Somatic variants indicative of oxidative DNA damage and the commonly observed 5kb deletion were quantified in both the buffy coat mtDNA and ccf-mtDNA. These data were analyzed for association with CI and T2D in both the NHW and MA populations. Further, haplogroup-associated risk for mtDNA damage and ccf-mtDNA status was assessed. Our preliminary findings suggest clinical implications of oxidative mtDNA damage as a risk factor for CI specifically in MA females. These data highlight ethnic/racial differences in oxidative burden which may elucidate sex-specific mechanisms contributing to the manifestation of age-related disease etiology as AD, and the results may ultimately inform precision-based approaches to design therapeutics for mitigating AD disparities in the MA population.Item CELL-FREE MEMBRANE-BOUND AND MEMBRANE-UNBOUND MITOCHONDRIAL DNA IN MATERNAL CIRCULATION IN PREECLAMPSIA(2021) Cushen, Spencer; Ricci, Contessa; Bradshaw, Jessica L.; Silzer, Talisa; Blessing, Alexandra M.; Sun, Jie; Scroggins, Sabrina; Santillan, Mark; Santillan, Donna; Phillips, Nicole; Goulopoulou, StylianiPURPOSE: Cell-free circulating mitochondrial DNA (CFCmtDNA) is a damage-associated molecular pattern (DAMP) that activates Toll-like receptor-9 (TLR-9). Previous studies suggested that CFCmtDNA may be a potential pathogenic trigger or a contributor to the maintenance of preeclampsia. The main objectives of this study were 1) to determine absolute concentrations of CFCmtDNA, in membrane-bound and -unbound states, independent of nuclear DNA (nDNA) changes, in cases with preeclampsia and healthy controls and 2) to implement a penalized regression analysis to establish the contribution of CFCmtDNA to preeclampsia diagnosis and its interaction with commonly collected patient characteristics. METHODS: Plasma CFCmtDNA (MT-ND5 gene) concentrations were quantified using an absolute quantification protocol. DNase I concentrations in maternal plasma were measured using an enzyme-linked immunosorbent assay and TLR-9 activity was monitored using SEAP reporter 293 cells expressing the human TLR-9 gene. RESULTS: Concentrations of CFCmtDNA were reduced in preeclampsia compared to healthy controls both in lysis buffer-treated samples (P=0.02) and in samples not treated with lysis buffer (P< 0.0001). Even though CFCmtDNA concentrations were reduced, plasma from women with preeclampsia induced greater TLR-9 activation than plasma from gestational age matched controls (P< 0.01). Multivariate analysis showed that high concentrations of nDNA and DNase I, a prior history of preeclampsia, and a lower concentration of CFCmtDNA are predictors of preeclampsia diagnosis. CONCLUSIONS: In conclusion, our data demonstrate an increased immunostimulatory potential of CFCmtDNA and upregulation of DNA degradation mechanisms in women with preeclampsia at the third trimester.Item Circulating mitochondrial DNA: New indices of type 2 diabetes-related cognitive impairment in Mexican Americans(PLoS, 2019-03-12) Silzer, Talisa K.; Barber, Robert C.; Sun, Jie; Pathak, Gita A.; Johnson, Leigh A.; O'Bryant, Sid E.; Phillips, NicoleMitochondrial function has been implicated and studied in numerous complex age-related diseases. Understanding the potential role of mitochondria in disease pathophysiology is of importance due to the rise in prevalence of complex age-related diseases, such as type 2 diabetes (T2D) and Alzheimer's disease (AD). These two diseases specifically share common pathophysiological characteristics which potentially point to a common root cause or factors for disease exacerbation. Studying the shared phenomena in Mexican Americans is of particular importance due to the disproportionate prevalence of both T2D and AD in this population. Here, we assessed the potential role of mitochondria in T2D and cognitive impairment (CI) in a Mexican American cohort by analyzing blood-based indices of mitochondrial DNA copy number (mtDNACN) and cell-free mitochondrial DNA (CFmtDNA). These mitochondrial metrics were also analyzed for correlation with relevant neuropsychological variables and physiological data collected as indicators of disease and/or disease progression. We found mtDNACN to be significantly decreased in individuals with CI, while CFmtDNA was significantly elevated in T2D; further, CFmtDNA elevation was significantly exacerbated in individuals with both diseases. MtDNACN was found to negatively correlate with age and fatty acid binding protein concentration, while positively correlating with CFmtDNA as well as CERAD total recall score. Candidate gene SNP-set analysis was performed on genes previously implicated in maintenance and control of mitochondrial dynamics to determine if nuclear variants may account for variability in mtDNACN. The results point to a single significant locus, in the LRRK2/MUC19 region, encoding leucine rich repeat kinase 2 and mucin 19. This locus has been previously implicated in Parkinson's disease, among others; rs7302859 was the driver SNP. These combined findings further indicate that mitochondrial dysfunction (as assessed by proxy via mtDNACN) is intimately linked to both T2D and CI phenotypes as well as aging.Item Comparison of Four Differential DNA Extraction Methods for Casework Analysis of Sexual Assualt Kit Swabs(2016-03-23) Warren, Joseph; Capt, Christina; Sun, Jie; Proctor, F. B.S.; Brignac, Francine J.Sexual assault kits comprise 40-50% of a typical Forensic Laboratory caseload. The traditional method to process these samples is time-consuming, and requires the use a dangerous chemical known as Phenol:Chloroform:Isoamyl Alcohol (PCIA). The purpose of this study is to assess the relative efficacy of the PCIA method when compared to three other currently available differential extraction methods. A single male volunteer and a single female volunteer donated semen and saliva, respectively. Aliquots of semen were serially diluted such that three decreasing concentrations of semen could be assessed alongside a consistent concentration of saliva. From these three different mixtures, swabs were made and allowed to dry in a 37 °C drying oven for two weeks, then at room temperature for an additional four weeks in order to simulate aged samples. Three days prior to DNA extraction and purification, another set of swabs were created to simulate fresh samples. The aged and unaged samples were tested in triplicate for each of the four extraction methods. The methods to be compared include two manual and two automated methods. The manual methods include the standard differential (SD) and the Lounsbury Method, which is a modified version of the SD. The two automated methods include the AutoMate ExpressTM DNA Extraction System (ThermoFisher Scientific, Carlsbad, CA), and a method employing the use of two of Qiagen’s DNA platforms: the QIAcube and the Qiagen EZ1® Advanced XL (Qiagen®, Hilden, Germany). Results indicate that as sperm sample concentration decreases, automated methods produce superior results both in DNA quantity obtained and in quality of STR profiles produced. Automated methods reduce hands-on time, facilitate higher through-put of samples, and reduce analyst contact with hazardous chemicals such as PCIA, making it an all around great choice for labs. All Real-Time PCR and electropherogram data were analyzed using Microsoft® Excel (Microsoft® Corp., Redmond, WA), and RStudio® (RStudio® Inc., Boston, MA).Item Epigenetic Changes of Nuclear-Encoded Oxidative Phosphorylation Genes and Cognitive Function: A Study of Mexican Americans and Non-Hispanic Whites(2024-03-21) Swami, Anjana; Daniel, Ann Abraham; Silzer, Talisa; Sun, Jie; Barber, Robert; Phillips, NicolePurpose: There is a higher prevalence of metabolic disease and Alzheimer’s Disease (AD) in Mexican Americans (MA). Despite this data, there has been minimal research done on the methylation status of genes involved in mitochondrial oxidative phosphorylation (OXPHOS)/cellular metabolism and how this influences the risk for developing cognitive impairment (CI). Methods: Results were derived from 299 MAs and 252 non-Hispanic Whites (NHW), all of whom were participants of the Texas Alzheimer’s Research and Care Consortium (TARCC). Themethylation status of CpG sites was assessed by running peripheral blood samples on the InfiniumMethylationEPIC BeadChip array. Results: Based on a Bonferroni adjusted alpha of7.36485 x 10⁶, six differentially methylated sites were significant in MAs: cg07470503, cg10057295, cg13823120, cg26891598, cg21490662, and cg17904988. All the sites were hypomethylated in CI/AD cohorts compared to NC except for cg26891598. There were no sites of significance in NHWs. Conclusions: The strongest association with CI/AD within the MA cohort was at cg07470503, with a p-value of 1.00 x 10⁶ in MAs. This CpG site is found within the DGUOK gene. The DGUOK gene is responsible for making the enzyme deoxyguanosine kinase, which is needed to properly create mitochondrial DNA; a dysfunctional gene leads to impaired mitochondrial function that could decrease the efficiency of OXPHOS. The abnormal cellular metabolism that ensues could set up the foundation for neurodegeneration to occur. Moving forward, the cg07470503 site could serve as a marker to identify the risk of metabolic disease and consequent CI/AD in MA patients.Item Epigenetic Risk Factors for Mild Cognitive Impairment, Alzheimer’s Disease and Metabolic Dysfunction in Mexican Americans(2018-03-14) Silzer, Talisa; Sun, Jie; Phillips, Nicole; Johnson, Leigh; O'Bryant, Sid; Barber, Robert C.; Abraham Daniel, AnnPurpose: Alzheimer’s is the most common form of dementia and the 5th leading cause of death for those over 651. The population of Mexican American elders will grow seven-fold by 20502 with rates of mild cognitive decline (MCI) and Alzheimer’s disease (AD) increasing exponentially1. Mexican Americans are diagnosed with MCI and AD at younger ages than non-Hispanic whites3; 4. In addition, Mexican Americans who are diagnosed with AD are 1) less likely to carry the ApoEε4 genotype3-5., 2) suffer a greater burden of type 2 diabetes3; 6, 3) experience greater metabolic-related cognitive decline7; 8 and 4) display a proteomic signature of AD that is heavily metabolic in nature4; 9, compared to non-Hispanic whites, whose proteomic signature for AD is dominated by inflammatory proteins. We hypothesized that differentially methylated regions of DNA (DMRs) are associated with age at onset of cognitive decline (MCI/AD) and metabolic dysfunction (metabolic syndrome/type 2 diabetes) in Mexican Americans. Methods: To test this hypothesis, we assayed genomic DNA methylation in samples from 14 female Mexican American participants enrolled in the Health and Aging Brain study in Latino Elders (HABLE). Participants were diagnosed with cognitive decline (n=4), metabolic dysfunction (n=3), both (n=4), or as a control (n=3). We isolated DNA from leukocytes and bisulfite treated the samples before running them on an Illumina MethylationEPIC chip in accordance with manufacturer’s recommendations to assay genomic DNA methylation. Results: Several interesting biological pathways showed significantly different methylation status between groups. When the participants were split on cognitive decline, DNA in the amyloid secretase, EGF receptor signaling, PDGF signaling, gonadotropin-releasing hormone receptor and Wnt signaling pathways were significantly hypermethylated in cases. In comparison, analyses based on metabolic dysfunction showed significant DNA hypomethylation in the beta1 and beta2 adrenergic receptor signaling pathways and hypomethylation of the gonadotropin releasing hormone receptor pathway in cases. Conclusions: The etiology of cognitive decline appears to differ between Mexican Americans and non-Hispanic whites. Future work will resolve how dementia risk differs between these and other ethnic groups. The knowledge gained from these studies will be critical to a better understanding of AD pathophysiology and the development of ethnicity-focused AD treatment options. Acknowledgements: Research reported here was supported by the National Institute On Aging of the National Institutes of Health under Award Number R01AG054073. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The research team also thanks the local Fort Worth community and participants of the Health & Aging Brain Study.Item Hypermethylation at CREBBP Is Associated with Cognitive Impairment in a Mexican American Cohort(IOS Press, 2023-03-07) Abraham Daniel, Ann; Silzer, Talisa; Sun, Jie; Zhou, Zhengyang; Hall, Courtney; Phillips, Nicole; Barber, Robert C.BACKGROUND: The aging Mexican American (MA) population is the fastest growing ethnic minority group in the US. MAs have a unique metabolic-related risk for Alzheimer's disease (AD) and mild cognitive impairment (MCI), compared to non-Hispanic whites (NHW). This risk for cognitive impairment (CI) is multifactorial involving genetics, environmental, and lifestyle factors. Changes in environment and lifestyle can alter patterns and even possibly reverse derangement of DNA methylation (a form of epigenetic regulation). OBJECTIVE: We sought to identify ethnicity-specific DNA methylation profiles that may be associated with CI in MAs and NHWs. METHODS: DNA obtained from peripheral blood of 551 participants from the Texas Alzheimer's Research and Care Consortium was typed on the Illumina Infinium® MethylationEPIC chip array, which assesses over 850K CpG genomic sites. Within each ethnic group (N = 299 MAs, N = 252 NHWs), participants were stratified by cognitive status (control versus CI). Beta values, representing relative degree of methylation, were normalized using the Beta MIxture Quantile dilation method and assessed for differential methylation using the Chip Analysis Methylation Pipeline (ChAMP), limma and cate packages in R. RESULTS: Two differentially methylated sites were significant: cg13135255 (MAs) and cg27002303 (NHWs) based on an FDR p < 0.05. Three suggestive sites obtained were cg01887506 (MAs) and cg10607142 and cg13529380 (NHWs). Most methylation sites were hypermethylated in CI compared to controls, except cg13529380 which was hypomethylated. CONCLUSION: The strongest association with CI was at cg13135255 (FDR-adjusted p = 0.029 in MAs), within the CREBBP gene. Moving forward, identifying additional ethnicity-specific methylation sites may be useful to discern CI risk in MAs.Item Maternal and fetal mitochondrial gene dysregulation in hypertensive disorders of pregnancy(American Physiological Society, 2023-05-15) Ricci, Contessa A.; Reid, Danielle M.; Sun, Jie; Santillan, Donna A.; Santillan, Mark K.; Phillips, Nicole R.; Goulopoulou, StylianiMitochondrial dysfunction has been implicated in pregnancy-induced hypertension (PIH). The role of mitochondrial gene dysregulation in PIH, and consequences for maternal-fetal interactions, remain elusive. Here, we investigated mitochondrial gene expression and dysregulation in maternal and placental tissues from pregnancies with and without PIH; further, we measured circulating mitochondrial DNA (mtDNA) mutational load, an index of mtDNA integrity. Differential gene expression analysis followed by Time Course Gene Set Analysis (TcGSA) was conducted on publicly available high throughput sequencing transcriptomic data sets. Mutational load analysis was carried out on peripheral mononuclear blood cells from healthy pregnant individuals and individuals with preeclampsia. Thirty mitochondrial differentially expressed genes (mtDEGs) were detected in the maternal cell-free circulating transcriptome, whereas nine were detected in placental transcriptome from pregnancies with PIH. In PIH pregnancies, maternal mitochondrial dysregulation was associated with pathways involved in inflammation, cell death/survival, and placental development, whereas fetal mitochondrial dysregulation was associated with increased production of extracellular vesicles (EVs) at term. Mothers with preeclampsia did not exhibit a significantly different degree of mtDNA mutational load. Our findings support the involvement of maternal mitochondrial dysregulation in the pathophysiology of PIH and suggest that mitochondria may mediate maternal-fetal interactions during healthy pregnancy.NEW & NOTEWORTHY This study identifies aberrant maternal and fetal expression of mitochondrial genes in pregnancies with gestational hypertension and preeclampsia. Mitochondrial gene dysregulation may be a common etiological factor contributing to the development of de novo hypertension in pregnancy-associated hypertensive disorders.Item Mitochondrial dysfunction and DNA methylation in type 2 diabetes and cognitive impairment(2018-03-14) Phillips, Nicole; Barber, Robert C.; Sun, Jie; O'Bryant, Sid E.; Johnson, Leigh A.; Silzer, Talisa K.Background. Mexican American populations are disproportionately affected by type 2 diabetes (T2D) and Alzheimer’s disease (AD). Although commonly characterized by the accumulation of amyloid plaques and tau tangles, the role of mitochondrial dysfunction (changes in mitochondrial dynamics, apoptosis, and/or oxidative stress signaling) in AD pathophysiology has become further elucidated over recent years. Methylation of key nuclear-encoded genes may be involved in regulation of critical mitochondrial processes. Evidence suggests that differential methylation and expression of mitochondrial related genes (e.g. POLG) may correlate with mitochondrial DNA copy number (mtDNACN). Hypothesis. We tested the following hypotheses: (1) methylation of mitochondrial-related genes is negatively correlated with their respective gene expression, (2) methylation of mitochondrial biogenesis genes (e.g., TFAM, POLG) negatively correlates with mtDNACN per cell, and (3) methylation of genes related to oxidative stress response, mitophagy, endosomal/exosomal trafficking and apoptosis correlates with cell-free mtDNA (mtDNACF) levels. Methods. DNA from 14 female Mexican American subjects enrolled in HABLE, the Healthy Aging Brains of Latino Elders cohort, was used for this study. Subjects were grouped based on T2D diagnosis, and were matched across groups based on age and cognitive status. For mitochondrial-related gene expression, cDNA was synthesized from blood buffy coat RNA and tested using the RT2 Profiler™ Human Mitochondria Array. For methylation analysis, nDNA from the blood buffy coat extract was bisulfite-converted and methylation levels were determined using the MethylationEPIC™ beadchip. Data was analyzed using Genome Studio. Buffy coat mtDNACN and plasma mtDNACF were quantified using TaqMan®-based qPCR. Methylation levels of CpG regions around candidate genes were then correlated with (1) gene expression, (2) mtDNACN, and (3) mtDNACF. Results. Preliminary results indicate that hypomethylation of some mitochondrial-related genes corresponds with increased expression (e.g., COX10); methylation of two sites associated with a known CpG island for POLG are negatively correlated with mtDNA copy number per cell. Conclusions. Significant correlations between mitochondrial phenotypes and candidate gene epigenetic loci may point to novel regulatory mechanisms of mitochondrial function. Future studies will include exploratory analysis at the genome-wide level using a larger cohort.Item Patient genetics is linked to chronic wound microbiome composition and healing(PLOS, 2020-06-18) Tipton, Craig D.; Wolcott, Randall D.; Sanford, Nicholas E.; Miller, Clint; Pathak, Gita A.; Silzer, Talisa K.; Sun, Jie; Fleming, Derek; Rumbaugh, Kendra P.; Little, Todd D.; Phillips, Nicole; Phillips, Caleb D.The clinical importance of microbiomes to the chronicity of wounds is widely appreciated, yet little is understood about patient-specific processes shaping wound microbiome composition. Here, a two-cohort microbiome-genome wide association study is presented through which patient genomic loci associated with chronic wound microbiome diversity were identified. Further investigation revealed that alternative TLN2 and ZNF521 genotypes explained significant inter-patient variation in relative abundance of two key pathogens, Pseudomonas aeruginosa and Staphylococcus epidermidis. Wound diversity was lowest in Pseudomonas aeruginosa infected wounds, and decreasing wound diversity had a significant negative linear relationship with healing rate. In addition to microbiome characteristics, age, diabetic status, and genetic ancestry all significantly influenced healing. Using structural equation modeling to identify common variance among SNPs, six loci were sufficient to explain 53% of variation in wound microbiome diversity, which was a 10% increase over traditional multiple regression. Focusing on TLN2, genotype at rs8031916 explained expression differences of alternative transcripts that differ in inclusion of important focal adhesion binding domains. Such differences are hypothesized to relate to wound microbiomes and healing through effects on bacterial exploitation of focal adhesions and/or cellular migration. Related, other associated loci were functionally enriched, often with roles in cytoskeletal dynamics. This study, being the first to identify patient genetic determinants for wound microbiomes and healing, implicates genetic variation determining cellular adhesion phenotypes as important drivers of infection type. The identification of predictive biomarkers for chronic wound microbiomes may serve as risk factors and guide treatment by informing patient-specific tendencies of infection.Item Population-specific mtDNA indices of mitochondrial stress associated with Alzheimer’s disease in Mexican Americans and Non-Hispanic Whites(2023) Gorham, Isabelle; Reid, Danielle; Sun, Jie; Barber, Robert C.; Phillips, Nicole R.Purpose: Alzheimer’s disease (AD) is the most prevalent form of dementia and is one of America’s leading causes of death. Age is known to be the biggest risk factor for AD, and Mexican Americans are one of the fastest-aging populations in America. Mitochondrial stress and dysfunction are key players in the progression of AD and are also known to be impacted by lifestyle and environmental exposures/stressors. Mitochondrial dysfunction can cause the release of mitochondrial DNA (mtDNA) extracellularly, which can be detected in the peripheral blood (i.e., plasma). MtDNA copy number within the cell can also serve as an indicator of overall mitochondrial health, biogenesis, and/or mitophagy. This project hopes to identify population-specific differences in mitochondrial stress and dysfunction detectable in the blood and identify any relationship between AD risk factors and cognitive impairment. This data may help to further elucidate the role that mtDNA may be playing in population-specific Alzheimer's disease pathogenesis. Methods: DNA was extracted from 200uL of participant plasma and buffy coat using the Mag-Bind® Blood & Tissue DNA HDQ 96 kit (Omega Bio-tek) according to the manufacturer’s specifications. mtDNA and nuDNA copy number was assessed through absolute quantitative PCR (qPCR), targeting the mitochondrial minor arc (MinArc), and the nuclear-encoded beta-2-microglobulin gene (B2M). Data was stratified by population and sample type and linear regressions were performed to adjust for batch effects and identify factors that may influence this phenotype of mitochondrial dysfunction. Results: Population-specific differences in factors contributing to the mtDNA phenotype were observed at the p < 0.05 level. In the Mexican American cohort, there was a significant relationship between cellular mtDNA:nuDNA ratio (quantified from buffy coat) and BMI, Clinical Dementia Rating Sum of Boxes score (CDRSum), and education. Further, there was a relationship between cell-free mtDNA copy number (quantified from participant plasma), education, and CDRSum. In the non-Hispanic white cohort, there was a significant relationship between cellular mtDNA:nuDNA ratio (from buffy coat) and both age and CDRSum. Age was associated with cell-free mtDNA in the non-Hispanic white cohort. Conclusions: Evidence supports that there are population-based differences in which factors may be predictive of this blood-based phenotype of mitochondrial dysfunction. Mexican American populations seem to be more heavily influenced by environmental factors (BMI and education) whereas the non-Hispanic white population seems to be more heavily influenced by non-environmental factors (age). There also seems to be an indication of a relationship between these indicators of mitochondrial dysfunction and AD-related cognitive impairment (when measured through the CDR sum of boxes score).Item Reduced Maternal Circulating Cell-Free Mitochondrial DNA Is Associated With the Development of Preeclampsia(American Heart Association, Inc., 2022-01-11) Cushen, Spencer C.; Ricci, Contessa A.; Bradshaw, Jessica L.; Silzer, Talisa K.; Blessing, Alexandra M.; Sun, Jie; Zhou, Zhengyang; Scroggins, Sabrina M.; Santillan, Mark K.; Santillan, Donna A.; Phillips, Nicole R.; Goulopoulou, StylianiBackground Circulating cell-free mitochondrial DNA (ccf-mtDNA) is a damage-associated molecular pattern that reflects cell stress responses and tissue damage, but little is known about ccf-mtDNA in preeclampsia. The main objectives of this study were to determine (1) absolute concentrations of ccf-mtDNA in plasma and mitochondrial DNA content in peripheral blood mononuclear cells and (2) forms of ccf-mtDNA transport in blood from women with preeclampsia and healthy controls. In addition, we sought to establish the association between aberrance in circulating DNA-related metrics, including ccf-mtDNA and DNA clearance mechanisms, and the clinical diagnosis of preeclampsia using bootstrapped penalized logistic regression. Methods and Results Absolute concentrations of ccf-mtDNA were reduced in plasma from women with preeclampsia compared with healthy controls (P0.05). While the pattern of reduced ccf-mtDNA in patients with preeclampsia remained, DNA isolation from plasma using membrane lysis buffer resulted in 1000-fold higher ccf-mtDNA concentrations in the preeclampsia group (P=0.0014) and 430-fold higher ccf-mtDNA concentrations in the control group (P<0.0001). Plasma from women with preeclampsia did not induce greater Toll-like receptor-9-induced nuclear factor kappa-light-chain enhancer of activated B cells-dependent responses in human embryonic kidney 293 cells overexpressing the human TLR-9 gene (P>0.05). Penalized regression analysis showed that women with preeclampsia were more likely to have lower concentrations of ccf-mtDNA as well as higher concentrations of nuclear DNA and DNase I compared with their matched controls. Conclusions Women with preeclampsia have aberrant circulating DNA dynamics, including reduced ccf-mtDNA concentrations and DNA clearance mechanisms, compared with gestational age-matched healthy pregnant women.Item Role of DNA Methylation in Risk for Alzheimer's Disease and Type 2 Diabetes in a Mexican American Cohort(2021) Barber, Robert C.; Abraham Daniel, Ann; Hall, Courtney; Sun, Jie; Phillips, Nicole; Silzer, TalisaPURPOSE: Age related diseases such as Alzheimer's disease (AD) and type 2 diabetes (T2D) are respectively the 6th and 7th leading cause of mortality in the US. Mexican Americans, the largest ethnic minority group in the US, have an increased likelihood of developing T2D compared to their Caucasian counterparts. With the elderly Mexican American population (≥65 years old) likely to multiply 7-fold by 2050, prevalence of AD alongside T2D is predicted to increase too. Mexican Americans have an earlier onset of AD and a metabolic heavy predisposition for AD compared to Caucasians who develop inflammation-based AD. The risk for T2D and AD is multifactorial involving epigenetic factors such as methylation, which is the addition of a methyl group to the cytosine base of DNA. We aim to establish an epigenetic association between AD and T2D unique to the Mexican American population. METHODS: Participants from the Texas Alzheimer's Research and Care Consortium (TARCC), which consists of Mexican American individuals diagnosed with either AD only, T2D only or AD and T2D matched with a Caucasian counterpart were selected. Peripheral blood was drawn from participants and individual methylation profiles collected using the Illumina Infinium MethylationEPIC chip array. Differential methylation will be assessed using the Chip Analysis Methylation Pipeline (ChAMP) package in R. RESULTS: Results obtained will be analyzed using pathway and gene set enrichment analysis tools. CONCLUSIONS: Identifying possible methylation sites associated with T2D and AD unique to the Mexican American population could contribute towards developing ethnicity-specific biomarkers and treatments.Item Role of DNA Methylation in Risk for Cognitive Impairment and Type 2 Diabetes in a Mexican American Cohort(2022) Daniel, Ann Abraham; Silzer, Talisa K.; Hall, Courtney; Sun, Jie; Zhou, Zhengyang; Phillips, Nicole; Barber, Robert C.Purpose: Alzheimer's disease (AD) and type 2 diabetes (T2D) are among the leading causes of mortality among the aging Mexican American population (≥ 65 years old) in the US. This cohort is expected to be the largest aging ethnic minority group in the US by 2050. In comparison to their non-Hispanic white counterparts who are most likely to develop AD associated with inflammation, aging Mexican Americans have an earlier onset of AD and metabolism related predisposition for AD. Mild cognitive impairment (MCI) is a phenotype that often leads to AD and is also prevalent in this cohort. The presence of T2D is known to double the risk of developing MCI/AD. The risk for AD, MCI and T2D is multifactorial, involving genetics and epigenetics. Methylation is a form of epigenetic regulation whereby a methyl group is added to the cytosine base in DNA. Methylation patterns in DNA can be affected and possibly reversed by a variety of environmental factors such as lifestyle and diet. Targeting changes to methylation patterns through associated lifestyle changes could be a possible prevention method for AD, MCI and T2D in the future, particularly for minority groups affected by health disparities, such as the Mexican American population. We aim to establish an epigenetic association between cognitive impairment (identified here as AD and MCI), and T2D that is unique to the Mexican American population. Methods: For this project, 551 aging participants from the Texas Alzheimer's Research and Care Consortium (TARCC) were selected, following quality control. A cross phenotype study design will be used to assess differential methylation associated with cognitive impairment (CI) alone, T2D alone and then with both CI and T2D simultaneously. For the first stage of this project, 299 Mexican American and 252 non-Hispanic white participants were stratified into groups of individuals diagnosed with CI alone and controls without CI within each ethnic group. In the second stage, this cohort will be stratified into individuals with T2D alone and controls without T2D. The third stage will stratify participants into those with both CI and T2D versus normal healthy controls. Lastly, any differential methylation associated with each ethnic group will be compared and contrasted. Peripheral blood drawn from participants was used to obtain individual methylation profiles using the Illumina Infinium MethylationEPIC chip array. Differential methylation will be assessed using the Chip Analysis Methylation Pipeline (ChAMP), limma and cate packages in R. The Beta MIxture Quantile dilation (BMIQ) method will be used for data normalization. Results: Gene set enrichment and pathway analysis tools will be used to analyze results. Conclusions: Identifying methylation sites associated with CI and T2D could contribute towards developing biomarkers that are ethnicity-specific for the Mexican American population and possibly lead towards more effective medical treatment in the future.Item Role of methylation in risk for cognitive impairment in Mexican Americans(2023) Abraham Daniel, Ann; Silzer, Talisa; Sun, Jie; Zhou, Zhengyang; Hall, Courtney; Phillips, Nicole R.; Barber, Robert C.Purpose: Mexican Americans (MAs) are the largest aging (›65 years old) and growing US ethnic minority group, with a unique risk for cognitive impairment (CI) in comparison to non-Hispanic whites (NHWs). MAs have an earlier age of onset and a risk for CI that is largely metabolism related in contrast to NHWs who have a more inflammation-based risk for CI. CI is defined in this study as individuals diagnosed with either Alzheimer’s disease (AD), or mild cognitive impairment (MCI) (a likely precursor to AD). Risk for CI is multifactorial and involves an epigenetic form of gene regulation called DNA methylation, which involves the addition of a methyl group to the cytosine base of DNA. DNA methylation patterns can be altered or possibly reversed through changes in environmental factors such as diet and lifestyle. Our aim was to identify differentially methylated sites of the genome associated with CI and determine DNA methylation profiles that are specific to MAs and NHWs. Methods: Peripheral blood was drawn from 551 Texas Alzheimer's Research and Care Consortium participants (299 MAs and 252 NHWs) and DNA was typed on the Illumina Infinium MethylationEPIC chip array, assessing >850,000 CpG genomic sites. Participants were compared according to cognitive status (control versus CI(AD/MCI)) among each ethnic group. Beta values that represent relative degree of methylation were normalized using the Beta MIxture Quantile dilation (BMIQ) method. Differential methylation between control and CI was assessed using the Chip Analysis Methylation Pipeline (ChAMP), limma and cate packages within R studio. Results: Two significant differentially methylated sites were associated with CI at an FDR-adjusted p-value threshold <0.05: cg13135255 in MAs and cg27002303 in NHWs. Three differentially methylated sites were suggestively associated with CI at an FDR-adjusted p-value threshold <0.1: cg01887506 and cg10607142 in MAs, and cg13529380 in NHWs. Four of the five significant and suggestively differentially methylated sites were hypermethylated in CI compared to normal controls, except for hypomethylated site cg13529380. The site most significantly associated with CI was cg13135255 within the CREBBP gene in MAs (FDR-adjusted p-value = 0.029). The CREBBP protein is a histone acetyltransferase, involved in epigenetic regulation, and plays a role in memory formation. Conclusion: This is the first study to report these specific CpG sites as either significantly or suggestively associated with CI among MAs and NHWs. These sites may be used in addition to other methylated sites to develop risk assessments that are ethnicity specific for CI. Following further validation and replication in other cohorts these sites may aid development of ethnic specific therapeutics that could deter or delay CI in the future.