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Browsing by Author "McGuire, Patrick"
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Item Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients(Frontiers Media, 2021-04-21) Chen, Duojiao; Abu Zaid, Mohammad I.; Reiter, Jill L.; Czader, Magdalena; Wang, Lin; McGuire, Patrick; Xuei, Xiaoling; Gao, Hongyu; Huang, Kun; Abonour, Rafat; Walker, Brian A.; Liu, Yunlong; Medical and Molecular Genetics, School of MedicineSingle-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown to largely preserve the transcriptome, it is unclear whether the freeze-thaw process might alter gene expression profiles in a cell-type specific manner or whether changes in cell-type proportions might also occur. To address these questions in the context of multiple myeloma clinical studies, we performed single-cell RNA sequencing (scRNA-seq) to compare fresh and frozen cells isolated from bone marrow aspirates of six multiple myeloma patients, analyzing both myeloma cells (CD138+) and cells constituting the microenvironment (CD138-). We found that cryopreservation using 90% fetal calf serum and 10% dimethyl sulfoxide resulted in highly consistent gene expression profiles when comparing fresh and frozen samples from the same patient for both CD138+ myeloma cells (R ≥ 0.96) and for CD138- cells (R ≥ 0.9). We also demonstrate that CD138- cell-type proportions showed minimal alterations, which were mainly related to small differences in immune cell subtype sensitivity to the freeze-thaw procedures. Therefore, when processing fresh multiple myeloma samples is not feasible, cryopreservation is a useful option in single-cell profiling studies.Item CTSA 2 Community: www.ctsa2community.org(2011-08-31) Ackermann, Ronald; Hardwick, Emily; Comer, Karen; Hudson, Brenda; Odell, Jere D.; Arenson, Andrew; Barnett, Bill; McGuire, Patrick; Derr, Michelle; Reid, Tisha; Vandergraff, Donna; Marrero, David G.This poster describes the development an accessible, user-driven, and sustainable web resource for community and academic experts working together to identify, adopt, and implement a wide array of community engaged research infrastructures for enhancing community engagement in all forms of clinical and translational research. CTSA2Community aims to be a storage place for valuable resources referring to the set-up and running of a community engagement program. Resources are provided by experts in the field of community engagement.Item IndianaCTSI and INresearch(Office of the Vice Chancellor for Research, 2012-04-13) McGuire, PatrickThe Indiana Clinical and Translational Sciences Institute (CTSI) is a statewide collaboration of Indiana University, Purdue University and the University of Notre Dame, as well as public and private partnerships, which facilitates the translation of scientific discoveries in the lab into clinical trials and new patient treatments in Indiana and beyond.Item 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 MedicineMesenchymal 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.Item A Pilot Single Cell Analysis of the Zebrafish Embryo Cellular Responses to Uropathogenic Escherichia coli Infection(Case Western Reserve University, 2022-02-04) Rawson, Ashley; Saxena, Vijay; Gao, Hongyu; Hooks, Jenaya; Xuei, Xiaoling; McGuire, Patrick; Hato, Takashi; Hains, David S.; Anderson, Ryan M.; Schwaderer, Andrew L.; Pediatrics, School of MedicineBackground: Uropathogenic Escherichia coli (UPEC) infections are common and when they disseminate can be of high morbidity. Methods: We studied the effects of UPEC infection using single cell RNA sequencing (scRNAseq) in zebrafish. Bulk RNA sequencing has historically been used to evaluate gene expression patterns, but scRNAseq allows gene expression to be evaluated at the single cell level and is optimal for evaluating heterogeneity within cell types and rare cell types. Zebrafish cohorts were injected with either saline or UPEC, and scRNAseq and canonical pathway analyses were performed. Results: Canonical pathway analysis of scRNAseq data provided key information regarding innate immune pathways in the cells determined to be thymus cells, ionocytes, macrophages/monocytes, and pronephros cells. Pathways activated in thymus cells included interleukin 6 (IL-6) signaling and production of reactive oxygen species. Fc receptor-mediated phagocytosis was a leading canonical pathway in the pronephros and macrophages. Genes that were downregulated in UPEC vs saline exposed embryos involved the cellular response to the Gram-negative endotoxin lipopolysaccharide (LPS) and included Forkhead Box O1a (Foxo1a), Tribbles Pseudokinase 3 (Trib3), Arginase 2 (Arg2) and Polo Like Kinase 3 (Plk3). Conclusions: Because 4-day post fertilization zebrafish embryos only have innate immune systems, the scRNAseq provides insights into pathways and genes that cell types utilize in the bacterial response. Based on our analysis, we have identified genes and pathways that might serve as genetic targets for treatment and further investigation in UPEC infections at the single cell level.