Browsing by Author "Reiter, Jill"

Now showing 1 - 5 of 5
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    Integrated Single-Cell Multiomic Profiling of Caudate Nucleus Suggests Key Mechanisms in Alcohol Use Disorder
    (bioRxiv, 2024-08-06) Green, Nick; Gao, Hongyu; Chu, Xiaona; Yuan, Quiyue; McGuire, Patrick; Lai, Dongbing; Jiang, Guanglong; Xuei, Xiaoling; Reiter, Jill; Stevens, Julia; Sutherland, Greg; Goate, Alison; Pang, Zhiping; Slesinger, Paul; Hart, Ronald P.; Tischfield, Jay A.; Agrawal, Arpana; Wang, Yue; Duren, Zhana; Edenberg, Howard J.; Liu, Yunlong; Medical and Molecular Genetics, School of Medicine
    Alcohol use disorder (AUD) is likely associated with complex transcriptional alterations in addiction-relevant brain regions. We characterize AUD-associated differences in cell type-specific gene expression and chromatin accessibility in the caudate nucleus by conducting a single-nucleus RNA-seq assay and a single-nucleus RNA-seq + ATAC-seq (multiome) assay on caudate tissue from 143 human postmortem brains (74 with AUD). We identified 17 cell types. AUD was associated with a higher proportion of microglia in an activated state and more astrocytes in a reactive state. There was widespread evidence for differentially expressed genes across cell types with the most identified in oligodendrocytes and astrocytes, including genes involved in immune response and synaptic regulation, many of which appeared to be regulated in part by JUND and OLIG2. Microglia-astrocyte communication via interleukin-1 beta, and microglia-astrocyte-oligodendrocyte interaction via transforming growth factor beta 1 were increased in individuals with AUD. Expression quantitative trait loci analysis revealed potential driver genes of AUD, including ADAL, that may protect against AUD in medium spiny neurons and interneurons. This work provides a thorough profile of the effects of AUD in the human brain and identifies several promising genes for further study.
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    Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis
    (MDPI, 2023-09-26) Chen, Duojiao; Liu, Sheng; Chu, Xiaona; Reiter, Jill; Gao, Hongyu; McGuire, Patrick; Yu, Xuhong; Xuei, Xiaoling; Liu, Yichen; Wan, Jun; Fang, Fang; Liu, Yunlong; Wang, Yue; Medical and Molecular Genetics, School of Medicine
    Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer–promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism.
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    Peptidoglycan Recognition Proteins in the Pathogenesis of Preeclampsia and Periodontal Disease
    (2015) Dukka, Himabindu; John, Vanchit; Reiter, Jill; Blanchard, Steven B.; Zunt, Susan; Kowolik, Michael
    Background: Pre-eclampsia a potentially life threatening hypertensive disorder occurring in 3-14% of pregnancies. Its etiology is multifactorial involving the placenta. The only “cure” that currently exists is the delivery of the baby, which is often pre-term. There is no early pregnancy screening test to recognize those at risk. Recently, an altered immune-inflammatory responses at the placental level in response to infectious agents (eg., periodontal pathogens) have been proposed to be etiological for this pregnancy complication. A new class of Pattern Recognition Receptors called Peptidoglycan Recognition Proteins (PGRPs) constituting 4 distinct molecules PGRP 1-4 is emerging as a key player in modulating host responses to peptidoglycan and its breakdown products. A critical knowledge gap exists on the role of PGRPs in the innate immune responses that occur at the maternal-fetal interface in response to pathogens and their components that may be present in maternal circulation secondary to chronic infections. Aim: The aim of this pilot study is to investigate the expression PGRPs in the placenta of pre-eclamptic women. The overall goal is to better understand the association of periodontal disease and adverse pregnancy outcomes. Methods and Materials: This case control study consisted of subjects with: (1) normal term pregnancies (n=7) (2) pre-eclampsia (n=7). Preeclampsia was defined as hypertension (systolic blood pressure of ≥ 140 mm Hg or diastolic blood pressure of ≥ 90 mm Hg on at least 2 occasions, 4 hours to 1 week apart) and proteinuria (≥ 300 mg in a 24-hour urine collection or one dipstick measurement of ≥ 2+). A real time quantitative PCR array was used to analyze the relative mRNA expression of TLR2, TLR4, NOD1, NOD2, PGRP1, PGRP2, PGRP3, and PGRP4. Immunohistochemistry was performed to determine the cell type(s) expressing the PGRP proteins in the placental tissue. Summary statistics (mean, standard deviation, range, 95% confidence interval for the mean) were calculated for PGRP 1-4 expression for each group. Results and conclusions: The PCR data showed the expression of PGRPs 1, 3 and 4 in the placental samples. There was an up-regulation of PGRP-1 (1.4 fold) and down regulation of PGRP-3 (1.3 fold) and PGRP-4 (1.6 fold). TLR2, TLR4 and NOD2 mRNA were also elevated in the placental samples. Immunohistochemistry demonstrated positive staining for PGRPs 3 and 4 in the trophoblasts. The results from this novel research could lead to development of salivary and/or plasmatic biomarkers for early detection of PE and warrants further investigation.
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    Role of Peptidoglycan Recognition Proteins in Pathogenesis of Preeclampsia and Periodontitis.
    (04/13/15) Dukka, Himabindu; John, Vanchit; Blanchard, Steven; Reiter, Jill; Dukka, Himabindu; John, Vanchit; Periodontics
    Preeclampsia (PE) is a pregnancy related disease and is the leading cause of maternal and fetal morbidity and mortality. Altered immune-inflammatory responses at the placental level in response to infectious agents (eg: periodontal pathogens) have been proposed to be etiological for this pregnancy complication. A new class of Pattern Recognition Receptors called Peptidoglycan Recognition Proteins (PGRP) constituting 4 distinct molecules PGRP 1-4 is emerging as key player in modulating host responses to peptidoglycan and its breakdown products. A critical knowledge gap exists on the role of PGRPs in the innate immune responses that occur at the maternal-fetal interface in response to pathogens and their components that may be present in maternal circulation secondary to chronic infections. The aim of this pilot study is to investigate the expression PGRPs in the placenta of pre-eclamptic women. This case control study consisted of subjects with: (1) normal term pregnancies (n=20) (2) pre-eclampsia (n=20). A real time quantitative PCR was used to analyze the relative mRNA expression of TLR2, TLR4, NOD1, NOD2, PGRP1, PGRP2, PGRP3, and PGRP4. Immunohistochemistry was performed to determine the cell type(s) expressing the PGRP proteins in the placental tissue. Summary statistics (mean, standard deviation, range, 95% confidence interval for the mean) were calculated for PGRP 1-4 expression for each group. The PCR data showed the expression of PGRPs 1, 3 and 4 when compared with positive controls such as liver, brain, skin and T-cells. This study demonstrated the expression of PGRPs 1, 3 and 4 by the placental samples. There was an up-regulation of PGRP-1 (1.4 fold) and down regulation of PGRP-3 (1.3 fold) and PGRP-4 (1.6 fold). TLR2, TLR4 and NOD2 mRNA were elevated in placental samples. The results from this novel research could lead to development of salivary and/or plasmatic biomarkers for early detection of PE and warrants further investigation. (This project is supported by the Delta Dental Master Thesis Award, No: 141031)
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    VALIDATION OF IMPRINTED GENES ON HUMAN CHROMOSOME 6 EXPRESSED IN THE PLACENTA
    (Office of the Vice Chancellor for Research, 2013-04-05) Brenneman, Anna; Reiter, Jill
    One of the most critical health issues facing women and children is pre-term birth. A major cause of pre-term birth is poor placentation, which results in inadequate blood flow and nutrient transfer to the developing fetus. Genomic imprinting is an epigenetic mechanism that results in allele-specific expression (ASE) that is dependent on the parent of origin. Imprinted genes are critical for placental development and Loss of imprinting (LOI) is associated with aberrant placentation and adverse pregnancy outcomes, such as preterm birth, preeclampsia, and intrauterine growth restriction. LOI refers to re-expression of the silenced allele, which appears to occur in a developmental stage-specific manner in human placenta. Our goal is to better define the set of imprinted genes in the placenta, which would provide the framework for identifying epigenetic mechanisms that are important in human placental development. Imprinted genes are frequently located in clusters on chromosomes. This project will test whether several genes located near two known imprinted genes, PLAGL1 and HYMAI (non-coding RNA), on chromosome 6 are imprinted in the human placenta. The genes that will be examined are PHACTR2, STX11, LTV1, C6orf94, and SF5B3. Our approach involves real-time qPCR and high resolution melt (HRM) analysis for genotyping and determining the relative expression of the maternal and paternal alleles in heterozygous placentas. We have identified several informative single nucleotide polymorphisms (SNPs) with minor allele frequencies >0.1 that are located in the transcribed region of PLAGL1, rs36120645 and rs2076684; HYMAI, rs28364590 and rs12524155; PHACTR2, rs10447447 and rs3734226; and STX1, rs3734227. PCR assays have been designed and optimized for HRM and qPCR assays. Current efforts are in identifying placental DNA samples for heterozygosity of each gene. Future endeavors will examine ASE from each gene, and test whether monoallelic expression is parent-of-origin specific.