Browsing by Subject "Gene Expression"

Now showing 1 - 10 of 22
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    Abnormal PTPN11 enhancer methylation promotes rheumatoid arthritis fibroblast-like synoviocyte aggressiveness and joint inflammation
    (American Society for Clinical Investigation, 2016-05-19) Maeshima, Keisuke; Stanford, Stephanie M.; Hammaker, Deepa; Sacchetti, Cristiano; Zeng, Li-Fan; Ai, Rizi; Zhang, Vida; Boyle, David L.; Aleman Muench, German R.; Feng, Gen-Sheng; Whitaker, John W.; Zhang, Zhong-Yin; Wang, Wei; Bottini, Nunzio; Firestein, Gary S.; Department of Biochemistry & Molecular Biology, IU School of Medicine
    The PTPN11 gene, encoding the tyrosine phosphatase SHP-2, is overexpressed in rheumatoid arthritis (RA) fibroblast-like synoviocytes (FLS) compared with osteoarthritis (OA) FLS and promotes RA FLS invasiveness. Here, we explored the molecular basis for PTPN11 overexpression in RA FLS and the role of SHP-2 in RA pathogenesis. Using computational methods, we identified a putative enhancer in PTPN11 intron 1, which contained a glucocorticoid receptor- binding (GR-binding) motif. This region displayed enhancer function in RA FLS and contained 2 hypermethylation sites in RA compared with OA FLS. RA FLS stimulation with the glucocorticoid dexamethasone induced GR binding to the enhancer and PTPN11 expression. Glucocorticoid responsiveness of PTPN11 was significantly higher in RA FLS than OA FLS and required the differentially methylated CpGs for full enhancer function. SHP-2 expression was enriched in the RA synovial lining, and heterozygous Ptpn11 deletion in radioresistant or innate immune cells attenuated K/BxN serum transfer arthritis in mice. Treatment with SHP-2 inhibitor 11a-1 reduced RA FLS migration and responsiveness to TNF and IL-1β stimulation and reduced arthritis severity in mice. Our findings demonstrate how abnormal epigenetic regulation of a pathogenic gene determines FLS behavior and demonstrate that targeting SHP-2 or the SHP-2 pathway could be a therapeutic strategy for RA.
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    Craniofacial Morphology in familial cases of cleft lip/palate: phenotypic heterogeneity and genetic predisposition in unaffected family members
    (1993) Litz, Stephanie M.; Bixler, David; Fleener, Donald E.; Hennon, David Kent, 1933-; Sadove, A. Michael; Ward, Richard E.; Avery, David R.
    This study investigated familial cases of cleft lip with or without cleft palate to determine whether the unaffected members of each family can be identified as gene carriers for the cleft trait. This research presumes that such carriers will have henotypic features identifiable by cephalometric analysis that are associated with an increased risk to cleft offspring. Using population genetics methodology, a pedigree analysis was made for each family member was assigned to one of four groups: (1) obligate normal, (2) affected, (3) carrier, and (4) unknown. LA and PA cephalographs were taken on each subject and a clinical oral-facial examination carried out on participating family members. Various anatomic landmarks located on the LA and PA films were digitized and from them, a total of 28 linear measurements were made. To eliminate the effect of sex and differential age responses, Z scores were calculated. Through univariate analysis, only one variable, NCR-MO, was shown to be significantly different between the two groups. This variable difference by itself is not adequate to differentiate those in the normal group from the carrier group. Even though only one variable was significant, other differences in the variables between these groups become obvious when the group variables were plotted as Z scores. Since Z scores are pure values with no limits (2--the number of standard deviations in a given variable differs from normal). Thereby, age-related growth differences were minimized. Further information is gained when these Z scores are plotted as pattern profiles, Figures 5-7. These profiles of mean Z scores for each variable pointed out areas of the face in which the differences were so great that specific anatomic areas appeared to be associated with one of the four groups. For example, gene carriers demonstrated specific alterations in facial height that might conceivably be used to discriminate that group from the other three groups. The family normals and carriers were then analyzed by using a stepwise multivariate analysis. By this approach, a discriminant function was generated consisting of six variables (three each from the lateral and frontal headplates), which proved to be significant in distinguishing an individual's phenotype. These variables define facial height, width and depth. The specific findings included a decrease in mid-facial height and depth along with an increased lower facial height and width in the gene carrier population as compared to the normals. The function then was used to predict group membership of the same two groups. Comparing this analytical prediction to that of the grouping system that resulted from the pedigree analysis, all but one individual was classified correctly in both the normal and carrier population. A discriminant score was also determined for the unknown population of family members which were defined as non-cleft blood relatives of cleft probands. Thus, they were a mixture of two types--those unaffected who carried a genetic liability for producing a cleft child and those unaffected who did not. A prediction of their placement into either the normal or carrier group was made with the discriminate function. One-third were classed in the normal group and two-thirds as gene carriers. The results of this study confirm that the phenotype of these unaffected family members designated as obligate gene carriers differs significantly from that of the family normals. This information is not only quite useful for genetic counselling but gives both a better understanding or the genetic control of clefting and can lead to molecular research to identify the specific gene in question.
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    Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats
    (Elsevier, 2008-06) Rodd, Zachary A.; Kimpel, Mark W.; Edenberg, Howard J.; Bell, Richard L.; Strother, Wendy N.; McClintick, Jeanette N.; Carr, Lucinda G.; Liang, Tiebing; McBride, William J.; Department of Psychiatry, IU School of Medicine
    The current study examined the effects of operant ethanol (EtOH) self-administration on gene expression in the nucleus accumbens (ACB) and amygdala (AMYG) of inbred alcohol-preferring (iP) rats. Rats self-trained on a standard two-lever operant paradigm to administer either water-water, EtOH (15% v/v)-water, or saccharin (SAC; 0.0125% g/v)-water. Animals were killed 24 hr after the last operant session, and the ACB and AMYG dissected; RNA was extracted and purified for microarray analysis. For the ACB, there were 513 significant differences at the p < 0.01 level in named genes: 55 between SAC and water; 215 between EtOH and water, and 243 between EtOH and SAC. In the case of the AMYG (p < 0.01), there were 48 between SAC and water, 23 between EtOH and water, and 63 between EtOH and SAC group. Gene Ontology (GO) analysis indicated that differences in the ACB between the EtOH and SAC groups could be grouped into 15 significant (p < 0.05) categories, which included major categories such as synaptic transmission, cell and ion homeostasis, and neurogenesis, whereas differences between the EtOH and water groups had only 4 categories, which also included homeostasis and synaptic transmission. Several genes were in common between the EtOH and both the SAC and water groups in the synaptic transmission (e.g., Cav2, Nrxn, Gabrb2, Gad1, Homer1) and homeostasis (S100b, Prkca, Ftl1) categories. Overall, the results suggest that changes in gene expression in the ACB of iP rats are associated with the reinforcing effects of EtOH.
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    Differential miRNA Expression in Cells and Matrix Vesicles in Vascular Smooth Muscle Cells from Rats with Kidney Disease
    (PLOS, 2015-06-26) Chaturvedi, Praneet; Chen, Neal X.; O’Neill, Kalisha; McClintick, Jeanette N.; Moe, Sharon M.; Janga, Sarath Chandra; Department of BioHealth Informatics, School of Informatics and Computing
    Vascular calcification is a complex process and has been associated with aging, diabetes, chronic kidney disease (CKD). Although there have been several studies that examine the role of miRNAs (miRs) in bone osteogenesis, little is known about the role of miRs in vascular calcification and their role in the pathogenesis of vascular abnormalities. Matrix vesicles (MV) are known to play in important role in initiating vascular smooth muscle cell (VSMC) calcification. In the present study, we performed miRNA microarray analysis to identify the dysregulated miRs between MV and VSMC derived from CKD rats to understand the role of post-transcriptional regulatory networks governed by these miRNAs in vascular calcification and to uncover the differential miRNA content of MV. The percentage of miRNA to total RNA was increased in MV compared to VSMC. Comparison of expression profiles of miRNA by microarray demonstrated 33 miRs to be differentially expressed with the majority (~ 57%) of them down-regulated. Target genes controlled by differentially expressed miRNAs were identified utilizing two different complementary computational approaches Miranda and Targetscan to understand the functions and pathways that may be affected due to the production of MV from calcifying VSMC thereby contributing to the regulation of genes by miRs. We found several processes including vascular smooth muscle contraction, response to hypoxia and regulation of muscle cell differentiation to be enriched. Signaling pathways identified included MAP-kinase and wnt signaling that have previously been shown to be important in vascular calcification. In conclusion, our results demonstrate that miRs are concentrated in MV from calcifying VSMC, and that important functions and pathways are affected by the miRs dysregulation between calcifying VSMC and the MV they produce. This suggests that miRs may play a very important regulatory role in vascular calcification in CKD by controlling an extensive network of post-transcriptional targets.
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    Endurance exercise accelerates myocardial tissue oxygenation recovery and reduces ischemia reperfusion injury in mice
    (PLoS, 2014-12-04) Li, Yuanjing; Cai, Ming; Cao, Li; Qin, Xing; Zheng, Tiantian; Xu, Xiaohua; Sandvick, Taylor M.; Hutchinson, Kirk; Wold, Loren E.; Hu, Keli; Sun, Qinghua; Thomas, D. Paul; Ren, Ju; He, Guanglong; Department of Medicine, IU School of Medicine
    Exercise training offers cardioprotection against ischemia and reperfusion (I/R) injury. However, few essential signals have been identified to underscore the protection from injury. In the present study, we hypothesized that exercise-induced acceleration of myocardial tissue oxygenation recovery contributes to this protection. C57BL/6 mice (4 weeks old) were trained on treadmills for 45 min/day at a treading rate of 15 m/min for 8 weeks. At the end of 8-week exercise training, mice underwent 30-min left anterior descending coronary artery occlusion followed by 60-min or 24-h reperfusion. Electron paramagnetic resonance oximetry was performed to measure myocardial tissue oxygenation. Western immunoblotting analyses, gene transfection, and myography were examined. The oximetry study demonstrated that exercise markedly shortened myocardial tissue oxygenation recovery time following reperfusion. Exercise training up-regulated Kir6.1 protein expression (a subunit of ATP-sensitive K(+)channel on vascular smooth muscle cells, VSMC sarc-K(ATP)) and protected the heart from I/R injury. In vivo gene transfer of dominant negative Kir6.1AAA prolonged the recovery time and enlarged infarct size. In addition, transfection of Kir6.1AAA increased the stiffness and reduced the relaxation capacity in the vasculature. Together, our study demonstrated that exercise training up-regulated Kir6.1, improved tissue oxygenation recovery, and protected the heart against I/R injury. This exercise-induced cardioprotective mechanism may provide a potential therapeutic intervention targeting VSMC sarc-K(ATP) channels and reperfusion recovery.
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    Expand your research: Next-Gen Sequencing, Genotyping, Gene Expression, and Epigenetics at the Center for Medical Genomics at IUSM
    (Office of the Vice Chancellor for Research, 2015-04-17) Xuei, Xiaoling; McClintick, Jeanette; Liu, Yunlong; Edenberg, Howard J.
    The Center for Medical Genomics (CMG) provides Indiana researchers with next-generation sequencing, SNP genotyping, gene expression and epigenetics. We provide expertise in experimental design, carry out the procedures, and assist with analyses and interpretation. These state-of-the-art technologies have enabled a large number of grants to be funded over the years, and have resulted in a very large number of publications. Our next-generation sequencing technology includes SOLiD5500xl, Ion Proton and Ion Torrent PGM (Personal Genome Machine). This set of instruments covers a wide range of nextgeneration sequencing capabilities from small bacterial genomes to the whole human genome, transcriptome (total RNA), small RNA, targeted DNA fragments, exome, ChIP-seq, and methylseq, with high sequencing accuracy. We have generated sequencing data for 74 projects over the past two-three years. Our SNP genotyping facility, using the Sequenom MassArray platform, specializes in targeted genotyping of 20-30 SNPs per assay and is an excellent choice for candidate gene studies and for following up results from GWAS and next-generation sequencing. It has been a central part of several large, multi-site collaborative genetic studies, including Genetics of Alcoholism (COGA), bipolar disorder, osteoporosis and hypertension, as well as many smaller projects; it is most efficient for sets of approximately 370 samples. We have produced more than 20 million targeted SNP genotypes to date. This platform is also capable of measuring allele-specific gene expression, and targeted quantitative DNA methylation for epigenetics study. For many projects, microarrays offer a good alternative to next-generation sequencing for measuring gene expression. We use Affymetrix GeneChip microarrays, capable of measuring expression of nearly all genes in humans (and all exons within them), rats, mice and most model organisms, and can measure expression of miRNAs. We can also use RNA extracted from FFPE samples. We have carried out more than 6,700 GeneChip hybridizations to date in support of many different projects. The CMG partners with the Center for Computational Biology and Bioinformatics for data analysis. We are recognized as a Core Facility of the Indiana CTSI and available to faculty not only from IU and IUPUI, but also from Purdue and Notre Dame Universities.
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    Exploratory genome-wide interaction analysis of non-steroidal anti-inflammatory drugs and predicted gene expression on colorectal cancer risk
    (American Association for Cancer Research, 2020-09) Wang, Xiaoliang; Su, Yu-Ru; Petersen, Paneen S.; Bien, Stephanie; Schmit, Stephanie L.; Drew, David A.; Albanes, Demetrius; Berndt, Sonja I.; Brenner, Hermann; Campbell, Peter T.; Casey, Graham; Chang-Claude, Jenny; Gallinger, Steven J.; Gruber, Stephen B.; Haile, Robert W.; Harrison, Tabitha A.; Hoffmeister, Michael; Jacobs, Eric J.; Jenkins, Mark A.; Joshi, Amit D.; Li, Li; Lin, Yi; Lindor, Noralane M.; Le Marchand, Loïc; Martin, Vicente; Milne, Roger; Maclnnis, Robert; Moreno, Victor; Nan, Hongmei; Newcomb, Polly A.; Potter, John D.; Rennert, Gad; Rennert, Hedy; Slattery, Martha L.; Thibodeau, Steve N.; Weinstein, Stephanie J.; Woods, Michael O.; Chan, Andrew T.; White, Emily; Hsu, Li; Peters, Ulrike; Global Health, School of Public Health
    Background: Regular use of nonsteroidal anti-inflammatory drugs (NSAID) is associated with lower risk of colorectal cancer. Genome-wide interaction analysis on single variants (G × E) has identified several SNPs that may interact with NSAIDs to confer colorectal cancer risk, but variations in gene expression levels may also modify the effect of NSAID use. Therefore, we tested interactions between NSAID use and predicted gene expression levels in relation to colorectal cancer risk. Methods: Genetically predicted gene expressions were tested for interaction with NSAID use on colorectal cancer risk among 19,258 colorectal cancer cases and 18,597 controls from 21 observational studies. A Mixed Score Test for Interactions (MiSTi) approach was used to jointly assess G × E effects which are modeled via fixed interaction effects of the weighted burden within each gene set (burden) and residual G × E effects (variance). A false discovery rate (FDR) at 0.2 was applied to correct for multiple testing. Results: Among the 4,840 genes tested, genetically predicted expression levels of four genes modified the effect of any NSAID use on colorectal cancer risk, including DPP10 (PG×E = 1.96 × 10-4), KRT16 (PG×E = 2.3 × 10-4), CD14 (PG×E = 9.38 × 10-4), and CYP27A1 (PG×E = 1.44 × 10-3). There was a significant interaction between expression level of RP11-89N17 and regular use of aspirin only on colorectal cancer risk (PG×E = 3.23 × 10-5). No interactions were observed between predicted gene expression and nonaspirin NSAID use at FDR < 0.2. Conclusions: By incorporating functional information, we discovered several novel genes that interacted with NSAID use.
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    Gene Expression Analysis Indicates Divergent Mechanisms in DEN-Induced Carcinogenesis in Wild Type and Bid-Deficient Livers
    (Public Library of Science (PLoS), 2016) Yu, Changshun; Yan, Shengmin; Khambu, Bilon; Chen, Xiaoyun; Dong, Zheng; Luo, Jianhua; Michalopoulos, George K.; Wu, Shangwei; Yin, Xiao-Ming; Department of Pathology & Laboratory Medicine, IU School of Medicine
    Bid is a Bcl-2 family protein. In addition to its pro-apoptosis function, Bid can also promote cell proliferation, maintain S phase checkpoint, and facilitate inflammasome activation. Bid plays important roles in tissue injury and regeneration, hematopoietic homeostasis, and tumorigenesis. Bid participates in hepatic carcinogenesis but the mechanism is not fully understood. Deletion of Bid resulted in diminished tumor burden and delayed tumor progression in a liver cancer model. In order to better understand the Bid-regulated events during hepatic carcinogenesis we performed gene expression analysis in wild type and bid-deficient mice treated with a hepatic carcinogen, diethylnitrosamine. We found that deletion of Bid caused significantly fewer alterations in gene expression in terms of the number of genes affected and the number of pathways affected. In addition, the expression profiles were remarkably different. In the wild type mice, there was a significant increase in the expression of growth regulation-related and immune/inflammation response-related genes, and a significant decrease in the expression of metabolism-related genes, both of which were diminished in bid-deficient livers. These data suggest that Bid could promote hepatic carcinogenesis via growth control and inflammation-mediated events.