Showing items 1 - 13 of 13

Best practice data life cycle approaches for the life sciences

- Griffin, Philippa, Khadake, Jyoti, LeMay, Kate, Lewis, Suzanna, Orchard, Sandra, Pask, Andrew, Pope, Bernard, Roessner, Ute, Russell, Keith, Seemann, Torsten, Treloar, Andrew, Tyagi, Sonika, Christiansen, Jeffrey, Dayalan, Saravanan, Gladman, Simon, Hangartner, Sandra, Hayden, Helen, Ho, William, Keeble-Gagnère, Gabriel, Korhonen, Pasi, Neish, Peter, Prestes, Priscilla, Richardson, Mark, Watson-Haigh, Nathan, Wyres, Kelly, Young, Neil, Schneider, Maria

Dysregulation of c-kit expression parallels the development of spontaneous genetic cardiac hypertrophy

- Marques, Francine, Prestes, Priscilla, Lewandowski, Paul, Harrap, Stephen, Charchar, Fadi

  • Authors: Marques, Francine , Prestes, Priscilla , Lewandowski, Paul , Harrap, Stephen , Charchar, Fadi
  • Date: 2015
  • Type: Text , Conference paper
  • Relation: Cardiac Society of Australia and New Zealand Annual Scientific Meeting and the International Society for Heart Research Australasian Section Annual Scientific Meeting; Melbourne, Victoria, Australia; 13th-16th August 2016; published in Heart, Lung and Circulation. Vol. 24, p. S401-S401
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  • Description: Objective: The molecular processes associated with cardiac hypertrophy independent of blood pressure are still largely unknown. The hypertrophic heart rate (HHR) is normotensive and born with a reduced complement of cardiomyocytes that predisposes to cardiac hypertrophy and failure in later life. We investigated the expression of c-kit gene, a marker of cardiac stem cells and myocardial regeneration that could contribute to hypertrophy. Methods: Left ventricular c-kit mRNA expression was measured by real-time PCR in HHR and control strain in neonatal and 38-week old rats (n=7-12/group). We tested for linkage of c-kit expression with neonatal cardiac size in 197 second generation crosses (F2) of HHR and control strain. Results: c-kit mRNA was slightly up-regulated in neonatal (fold change +1.3, P=0.02) and markedly so in 38-week old HHR (+35.5, P=0.0003). Cardiac weight index was positively correlated with neonatal myocardial c-kit mRNA in the F2 population (r=0.19, P=0.007). Conclusions: In HHR hearts c-kit expression appears increased throughout life, but more so in the adult where cardiac hypertrophy is established and leading to failure. In aged hypertrophic hearts, over-expression of c-kit is likely a compensatory mechanism of the failing heart. Previous studies showed an activation of cardiac stem cells in the hypertrophic myocardium. Our study suggests that c-kit might be involved from an early age in mechanisms that lead to cardiac hypertrophy in adulthood.

Experimental and human evidence for Lipocalin-2 (Neutrophil Gelatinase-Associated Lipocalin NGAL ) in the development of cardiac hypertrophy and heart failure

- Marques, Francine, Prestes, Priscilla, Byars, Sean, Ritchie, Scott, Wurtz, Peter, Patel, Sheila, Booth, Scott, Rana, Indrajeetsinh, Minoda, Yosuke, Berzins, Stuart, Curl, Claire, Bell, James, Wai, Bryan, Srivastava, Piyush, Kangas, Antti, Soininen, Pasi, Ruohonen, Saku, Kahonen, Mika, Lehtimaki, Terho, Raitoharju, Emma, Havulinna, Aki, Perola, Markus, Raitakari, Olli, Salomaa, Veikko, Ala-Korpela, Mika, Kettunen, Johannes, McGlynn, Maree, Kelly, Jason, Wlodek, Mary, Lewandowski, Paul, Delbridge, Lea, Burrell, Louise, Inouye, Michael, Harrap, Stephen, Charchar, Fadi

Increased expression of telomere-regulating genes in endurance athletes with long leukocyte telomeres

- Denham, Joshua, O'Brien, Brendan, Prestes, Priscilla, Brown, Nicholas, Charchar, Fadi

  • Authors: Denham, Joshua , O'Brien, Brendan , Prestes, Priscilla , Brown, Nicholas , Charchar, Fadi
  • Date: 2015
  • Type: Text , Journal article
  • Relation: Journal of Applied Physiology Vol. 120, no. 2 (2015), p. 148-158
  • Relation: http://purl.org/au-research/grants/nhmrc/1009490
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  • Description: Leukocyte telomeres shorten with age, and excessive shortening is associated with age-related cardiometabolic diseases. Exercise training may prevent disease through telomere length maintenance although the optimal amount of exercise that attenuates telomere attrition is unknown. Furthermore, the underlying molecular mechanisms responsible for the enhanced telomere maintenance observed in endurance athletes is poorly understood. We quantified the leukocyte telomere length and analyzed the expression of telomere-regulating genes in endurance athletes and healthy controls (both n = 61), using quantitative PCR. We found endurance athletes have significantly longer (7.1%, 208-416 nt) leukocyte telomeres and upregulated TERT (2.0-fold) and TPP1 (1.3-fold) mRNA expression compared with controls in age-adjusted analysis. The telomere length and telomere-regulating gene expression differences were no longer statistically significant after adjustment for resting heart rate and relative (V) over dotO(2 max) (all P > 0.05). Resting heart rate emerged as an independent predictor of leukocyte telomere length and TERT and TPP1 mRNA expression in stepwise regression models. To gauge whether volume of exercise was associated with leukocyte telomere length, we divided subjects into running and cycling tertiles (distance covered per week) and found individuals in the middle and highest tertiles had longer telomeres than individuals in the lowest tertile. These data emphasize the importance of cardiorespiratory fitness and exercise training in the prevention of biological aging. They also support the concept that moderate amounts of exercise training protects against biological aging, while higher amounts may not elicit additional benefits.

Involvement of human monogenic cardiomyopathy genes in experimental polygenic cardiac hypertrophy

- Prestes, Priscilla, Marques, Francine, Lopez-Campos, Guillermo, Lewandowski, Paul, Delbridge, Lea, Charchar, Fadi, Harrap, Stephen

  • Authors: Prestes, Priscilla , Marques, Francine , Lopez-Campos, Guillermo , Lewandowski, Paul , Delbridge, Lea , Charchar, Fadi , Harrap, Stephen
  • Date: 2018
  • Type: Text , Journal article
  • Relation: Physiological Genomics Vol. 50, no. 9 (2018), p. 680-687
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  • Description: Hypertrophic cardiomyopathy thickens heart muscles, reducing functionality and increasing risk of cardiac disease and morbidity. Genetic factors are involved, but their contribution is poorly understood. We used the hypertrophic heart rat (HHR), a unique normotensive polygenic model of cardiac hypertrophy and heart failure, to investigate the role of genes associated with monogenic human cardiomyopathy. We selected 42 genes involved in monogenic human cardiomyopathies to study: 1) DNA variants, by sequencing the whole genome of 13-wk-old HHR and age-matched normal heart rat (NHR), its genetic control strain; 2) mRNA expression, by targeted RNA-sequencing in left ventricles of HHR and NHR at 5 ages (2 days old and 4, 13, 33, and 50 wk old) compared with human idiopathic dilated cardiomyopathy data; and 3) microRNA expression, with rat microRNA microarrays in left ventricles of 2-day-old HHR and age-matched NHR. We also investigated experimentally validated microRNA-mRNA interactions. Whole-genome sequencing revealed unique variants mostly located in noncoding regions of HHR and NHR. We found 29 genes differentially expressed in at least 1 age. Genes encoding desmoglein 2 (Dsg2) and transthyretin (Ttr) were significantly differentially expressed at all ages in the HHR, but only Ttr was also differentially expressed in human idiopathic cardiomyopathy. Lastly, only two microRNAs differentially expressed in the HHR were present in our comparison of validated microRNA-mRNA interactions. These two microRNAs interact with five of the genes studied. Our study shows that genes involved in monogenic forms of human cardiomyopathies may also influence polygenic forms of the disease.

Measurement of absolute copy number variation reveals association with essential hypertension

- Marques, Francine, Prestes, Priscilla, Pinheiro, Leonardo, Scurrah, Katrina, Emslie, Kerry, Tomaszewski, Maciej, Harrap, Stephen, Charchar, Fadi

  • Authors: Marques, Francine , Prestes, Priscilla , Pinheiro, Leonardo , Scurrah, Katrina , Emslie, Kerry , Tomaszewski, Maciej , Harrap, Stephen , Charchar, Fadi
  • Date: 2014
  • Type: Text , Journal article
  • Relation: BMC Medical Genomics Vol. 7, no. (2014), p. 1-8
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  • Description: Background: The role of copy number variation (CNV) has been poorly explored in essential hypertension in part due to technical difficulties in accurately assessing absolute numbers of DNA copies. Droplet digital PCR (ddPCR) provides a powerful new approach to CNV quantitation. The aim of our study was to investigate whether CNVs located in regions previously associated with blood pressure (BP) variation in genome-wide association studies (GWAS) were associated with essential hypertension by the use of ddPCR. Methods: Using a "power of extreme" approach, we quantified nucleic acids using ddPCR in white subjects from the Victorian Family Heart Study with extremely high (n = 96) and low (n = 92) SBP, providing power equivalent to 1714 subjects selected at random. Results: A deletion of the CNVs esv27061 and esv2757747 on chromosome 1p13.2 was significantly more prevalent in extreme high BP subjects after adjustment for age, body mass index and sex (12.6% vs. 2.2%; P = 0.013). Conclusions: Our data suggests that CNVs within regions identified in previous GWAS may play a role in human essential hypertension.

MicroRNA-34a and tert act as epi-drivers of cardiac telomere length and polygenic cardiac hypertrophy

- Booth, Scott, Marques, Francine, Prestes, Priscilla, Curl, Claire, Delbridge, Lea, Lewandowski, Paul, Harrap, Stephen, Charchar, Fadi

  • Authors: Booth, Scott , Marques, Francine , Prestes, Priscilla , Curl, Claire , Delbridge, Lea , Lewandowski, Paul , Harrap, Stephen , Charchar, Fadi
  • Date: 2015
  • Type: Text , Journal article
  • Relation: Heart, Lung and Circulation Vol. 24, no. S3 (2015), p. S180-S181
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  • Description: Cardiac hypertrophy is one of the main risk factors forheart failure. Here we aimed to investigate whether cardiactelomere length contributes to polygenic cardiac hypertro-phy independent of blood pressure. We also investigatedwhether changes in telomere length were due to the telomereregulators microRNA-34a,Ppp1r10(also known asPnuts)and telomerase. We used the hypertrophic heart rat (HHR),a normotensive model of polygenetic cardiac hypertrophy,and compared it to age-matched controls. Telomere length, microRNA levels, gene expression and telomerase activitywere measured in isolated cardiomyocytes and left ventricletissue using real-time PCR. Telomere length was significantlylonger in 2-day and 38-week-old HHR, but shorter at 4-and 13-week HHR. In the HHR, telomere length becameshorter early in development, while in the control straintelomere shortening was only observed in late adulthood.Telomere length was the main determinant of cardiac mass.

Molecular insights into genome-wide association studies of chronic kidney disease-defining traits

- Xu, Xiaoguang, Eales, James, Akbarov, Artur, Guo, Hui, Becker, Lorenz, Talavera, David, Ashraf, Fehzan, Nawaz, Jabran, Pramanik, Sanjeev, Bowes, John, Jiang, Xiao, Dormer, John, Denniff, Matthew, Antczak, Andrzej, Szulinska, Monika, Wise, Ingrid, Prestes, Priscilla, Glyda, Maciej, Bogdanski, Pawel, Zukowska-Szczechowska, Ewa, Berzuini, Carlo, Woolf, Adrian, Samani, Nilesh, Charchar, Fadi, Tomaszewski, Maciej

Muscle-enriched MicroRNAs isolated from whole blood are regulated by exercise and are potential biomarkers of cardiorespiratory fitness

- Denham, Joshua, Prestes, Priscilla

  • Authors: Denham, Joshua , Prestes, Priscilla
  • Date: 2016
  • Type: Text , Journal article
  • Relation: Frontiers in Genetics Vol. 7, no. NOV (2016), p. 1-8
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  • Description: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate gene expression post-transcriptionally. Evidence indicating miRNAs influence exercise-induced health and performance adaptations is mounting. Circulating miRNAs are responsible for intercellular communication and could serve as biomarkers for disease and exercise-related traits. Such biomarkers would contribute to exercise screening, monitoring, and the development of personalized exercise prescription. Accordingly, we investigated the impact of long-term strenuous aerobic exercise training and a single bout of maximal aerobic exercise on five muscle-enriched miRNAs implicated in exercise adaptations (miR-1, miR-133a, miR-181a, miR-486, and miR-494). We also determined linear correlations between miRNAs, resting heart rate, and maximum oxygen uptake (V˙O2 max). We used TaqMan assay quantitative polymerase chain reaction to analyze the abundance of miR-1, miR-133a, miR-181a, miR-486, and miR-494 in resting whole blood of 67 endurance athletes and 61 healthy controls. Relative to controls, endurance athletes exhibited increased miR-1, miR-486, and miR-494 content (1.26- to 1.58-fold change, all p < 0.05). miR-1, miR-133a, and miR-486 were decreased immediately after maximal aerobic exercise (0.64- to 0.76-fold change, all p < 0.01) performed by 19 healthy, young men (20.7 ± 2.4 years). Finally, we observed positive correlations between miRNA abundance and V˙ O2 max (miR-1 and miR-486) and an inverse correlation between miR-486 and resting heart rate. Therefore, muscle-enriched miRNAs isolated from whole blood are regulated by acute and long-term aerobic exercise training and could serve as biomarkers of cardiorespiratory fitness. © 2016 Denham and Prestes.

Telomere dynamics during aging in polygenic left ventricular hypertrophy

- Marques, Francine, Booth, Scott, Prestes, Priscilla, Curl, Claire, Delbridge, Lea, Lewandowski, Paul, Harrap, Stephen, Charchar, Fadi

  • Authors: Marques, Francine , Booth, Scott , Prestes, Priscilla , Curl, Claire , Delbridge, Lea , Lewandowski, Paul , Harrap, Stephen , Charchar, Fadi
  • Date: 2016
  • Type: Text , Journal article
  • Relation: Physiological Genomics Vol. 48, no. 1 (2016), p. 42-49
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  • Description: Short telomeres are associated with increased risk of cardiovascular disease. Here we studied cardiomyocyte telomere length at key ages during the ontogeny of cardiac hypertrophy and failure in the hypertrophic heart rat (HHR) and compared these with the normal heart rat (NHR) control strain. Key ages corresponded with the pathophysiological sequence beginning with fewer cardiomyocytes (2 days), leading to left ventricular hypertrophy (LVH) (13 wk) and subsequently progression to heart failure (38 wk). We measured telomere length, tissue activity of telomerase, mRNA levels of telomerase reverse transcriptase (Tert) and telomerase RNA component (Terc), and expression of the telomeric regulator microRNA miR-34a. Cardiac telomere length was longer in the HHR compared with the control strain at 2 days and 38 wk, but shorter at 13 wk. Neonatal HHR had higher cardiac telomerase activity and expression of Tert and miR-34a. Telomerase activity was not different at 13 or 38 wk. Tert mRNA and Terc RNA were overexpressed at 38 wk, while miR-34a was overexpressed at 13 wk but downregulated at 38 wk. Circulating leukocytes were strongly correlated with cardiac telomere length in the HHR only. The longer neonatal telomeres in HHR are likely to reflect fewer fetal and early postnatal cardiomyocyte cell divisions and explain the reduced total cardiomyocyte complement that predisposes to later hypertrophy and failure. Although shorter telomeres were a feature of cardiac hypertrophy at 13 wk, they were not present at the progression to heart failure at 38 wk. © 2016 the American Physiological Society.

The SNPforID 34-plex-Its ability to infer level of admixture in individuals

- Prestes, Priscilla, Mitchell, Robert, Santos, Carla, Van Oorschot, Roland

  • Authors: Prestes, Priscilla , Mitchell, Robert , Santos, Carla , Van Oorschot, Roland
  • Date: 2013
  • Type: Text , Journal article
  • Relation: Forensic Science International: Genetics Supplement Series Vol. 4, no. 1 (2013), p. e13-e14
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  • Description: Forensic scientists use genetic individualization markers to include or exclude persons of interest in investigations. However, when there are no suspects due to absence of database matches or eye-witness information, prediction of biogeographical ancestry can be a valuable investigative tool. The SNP. forID 34-plex uses 34 autosomal markers to predict ancestry from three geographic regions, Africa, Europe and East Asia. However, its ability to identify levels of admixture within individuals is unclear. We tested the 34-plex assay in 56 individuals from 15 families with varying levels of self-declared Asian/European admixed ancestry. STRUCTURE 2.3.4 was used for population structure analysis and cluster information provided inferences on levels of admixture. Chi-square tests were performed to evaluate the ability of the SNP. forID 34-plex to predict level of admixture. The average/SD Asian and European contribution for individuals self-declared as first generation since admixture was 0.46/0.13 and 0.54/0.13, respectively. As expected, the average European contribution increased for individuals of 1/4, 1/8 and 1/16 Asian/European ancestries - 0.78/0.13, 0.89/0.05 and 0.91/0.03, respectively. There were no significant differences between observed and expected average contribution from each ancestry. However, individual outliers were observed, which could have been misclassified if analyzed separately. These results suggest the 34-plex can be a reliable tool to predict levels of admixture; however caution is required when an individual sample is investigated. A larger number of markers, combined with increased sample sizes comprising varying levels of admixture of different biogeographical ancestries, are required to enhance the ability to predict an individual's level of biogeographical ancestry.

Tripartite motif-containing 55 identified as functional candidate for spontaneous cardiac hypertrophy in the rat locus cardiac mass 22

- Prestes, Priscilla, Marques, Francine, Lopez-Campos, Guillermo, Booth, Scott, McGlynn, Maree, Lewandowski, Paul, Delbridge, Lea, Harrap, Stephen, Charchar, Fadi

  • Authors: Prestes, Priscilla , Marques, Francine , Lopez-Campos, Guillermo , Booth, Scott , McGlynn, Maree , Lewandowski, Paul , Delbridge, Lea , Harrap, Stephen , Charchar, Fadi
  • Date: 2016
  • Type: Text , Journal article
  • Relation: Journal of Hypertension Vol. 34, no. 5 (May 2016), p. 950-958
  • Relation: http://purl.org/au-research/grants/nhmrc/1034371
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  • Description: Background:Left ventricular (LV) hypertrophy is a risk factor for cardiovascular death, but the genetic factors determining LV size and predisposition to hypertrophy are not well understood. We have previously linked the quantitative trait locus cardiac mass 22 (Cm22) on chromosome 2 with cardiac hypertrophy independent of blood pressure in the spontaneously hypertensive rat. From an original cross of spontaneously hypertensive rat with F344 rats, we derived a normotensive polygenic model of spontaneous cardiac hypertrophy, the hypertrophic heart rat (HHR) and its control strain, the normal heart rat (NHR).Methods and results:To identify the genes and molecular mechanisms underlying spontaneous LV hypertrophy we sequenced the HHR genome with special focus on quantitative trait locus Cm22. For correlative analyses of function, we measured global RNA transcripts in LV of neonatal HHR and NHR and 198 neonatal rats of an HHRxNHR F2 crossbred population. Only one gene within locus Cm22 was differentially expressed in the parental generation: tripartite motif-containing 55 (Trim55), with mRNA downregulation in HHR (P<0.05) and reduced protein expression. Trim55 mRNA levels were negatively correlated with LV mass in the F2 cross (r=-0.16, P=0.025). In exon nine of Trim55 in HHR, we found one missense mutation that functionally alters protein structure. This mutation was strongly associated with Trim55 mRNA expression in F2 rats (F=10.35, P<0.0001). Similarly, in humans, we found reduced Trim55 expression in hearts of subjects with idiopathic dilated cardiomyopathy.Conclusion:Our study suggests that the Trim55 gene, located in Cm22, is a novel candidate gene for polygenic LV hypertrophy independent of blood pressure.

Uncovering genetic mechanisms of kidney aging through transcriptomics, genomics, and epigenomics

- Rowland, Joshua, Akbarov, Artur, Eales, James, Xu, Xiaoguang, Dormer, John, Guo, Hui, Denniff, Matthew, Jiang, Xiao, Ranjzad, Parisa, Nazgiewicz, Alicja, Prestes, Priscilla, Antczak, Andrzej, Szulinska, Monika, Wise, Ingrid, Zukowska-Szczechowska, Ewa, Bogdanski, Pawel, Woolf, Adrian, Samani, Nilesh, Charchar, Fadi, Tomaszewski, Maciej

  • Authors: Rowland, Joshua , Akbarov, Artur , Eales, James , Xu, Xiaoguang , Dormer, John , Guo, Hui , Denniff, Matthew , Jiang, Xiao , Ranjzad, Parisa , Nazgiewicz, Alicja , Prestes, Priscilla , Antczak, Andrzej , Szulinska, Monika , Wise, Ingrid , Zukowska-Szczechowska, Ewa , Bogdanski, Pawel , Woolf, Adrian , Samani, Nilesh , Charchar, Fadi , Tomaszewski, Maciej
  • Date: 2019
  • Type: Text , Journal article
  • Relation: Kidney International Vol. 95, no. 3 (2019), p. 624-635
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  • Description: Nephrons scar and involute during aging, increasing the risk of chronic kidney disease. Little is known, however, about genetic mechanisms of kidney aging. We sought to define the signatures of age on the renal transcriptome using 563 human kidneys. The initial discovery analysis of 260 kidney transcriptomes from the TRANScriptome of renaL humAn TissuE Study (TRANSLATE) and the Cancer Genome Atlas identified 37 age-associated genes. For 19 of those genes, the association with age was replicated in 303 kidney transcriptomes from the Nephroseq resource. Surveying 42 nonrenal tissues from the Genotype–Tissue Expression project revealed that, for approximately a fifth of the replicated genes, the association with age was kidney-specific. Seventy-three percent of the replicated genes were associated with functional or histological parameters of age-related decline in kidney health, including glomerular filtration rate, glomerulosclerosis, interstitial fibrosis, tubular atrophy, and arterial narrowing. Common genetic variants in four of the age-related genes, namely LYG1, PPP1R3C, LTF and TSPYL5, correlated with the trajectory of age-related changes in their renal expression. Integrative analysis of genomic, epigenomic, and transcriptomic information revealed that the observed age-related decline in renal TSPYL5 expression was determined both genetically and epigenetically. Thus, this study revealed robust molecular signatures of the aging kidney and new regulatory mechanisms of age-related change in the kidney transcriptome.
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