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  • 1
    In: Theranostics, Ivyspring International Publisher, Vol. 11, No. 11 ( 2021), p. 5346-5364
    Type of Medium: Online Resource
    ISSN: 1838-7640
    Language: English
    Publisher: Ivyspring International Publisher
    Publication Date: 2021
    detail.hit.zdb_id: 2592097-2
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  • 2
    Online Resource
    Online Resource
    Ovid Technologies (Wolters Kluwer Health) ; 2020
    In:  Journal of the American Society of Nephrology Vol. 31, No. 7 ( 2020-7), p. 1539-1554
    In: Journal of the American Society of Nephrology, Ovid Technologies (Wolters Kluwer Health), Vol. 31, No. 7 ( 2020-7), p. 1539-1554
    Abstract: Several microRNAs have been shown to play significant roles in the development of renal injury. The microRNA miR-204-5p is highly enriched in the kidney but its involvement in chronic renal injury is unknown. In this study, the authors report that miR-204-5p abundance is significantly decreased in kidney biopsy samples from patients with hypertension, hypertensive nephrosclerosis, or diabetic nephropathy. They also found, in a rat model of salt-sensitive hypertension, a mouse model of hypertension, and a mouse model of type 2 diabetes, inhibition of miR-204-5p, or deletion of the Mir204 gene results in upregulation of an injurious molecular pathway and substantial exacerbation of renal injury. These findings provide evidence of a prominent role for miR-204-5p in safeguarding the kidneys against common causes of chronic renal injury. Background Aberrant microRNA (miRNA) expression affects biologic processes and downstream genes that are crucial to CKD initiation or progression. The miRNA miR-204-5p is highly expressed in the kidney but whether miR-204-5p plays any role in the development of chronic renal injury is unknown. Methods We used real-time PCR to determine levels of miR-204 in human kidney biopsies and animal models. We generated Mir204 knockout mice and used locked nucleic acid–modified anti-miR to knock down miR-204-5p in mice and rats. We used a number of physiologic, histologic, and molecular techniques to analyze the potential role of miR-204-5p in three models of renal injury. Results Kidneys of patients with hypertension, hypertensive nephrosclerosis, or diabetic nephropathy exhibited a significant decrease in miR-204-5p compared with controls. Dahl salt-sensitive rats displayed lower levels of renal miR-204-5p compared with partially protected congenic SS.13 BN26 rats. Administering anti–miR-204-5p to SS.13 BN26 rats exacerbated interlobular artery thickening and renal interstitial fibrosis. In a mouse model of hypertensive renal injury induced by uninephrectomy, angiotensin II, and a high-salt diet, Mir204 gene knockout significantly exacerbated albuminuria, renal interstitial fibrosis, and interlobular artery thickening, despite attenuation of hypertension. In diabetic db/db mice, administering anti–miR-204-5p exacerbated albuminuria and cortical fibrosis without influencing blood glucose levels. In all three models, inhibiting miR-204-5p or deleting Mir204 led to upregulation of protein tyrosine phosphatase SHP2, a target gene of miR-204-5p, and increased phosphorylation of signal transducer and activator of transcription 3, or STAT3, which is an injury-promoting effector of SHP2. Conclusions These findings indicate that the highly expressed miR-204-5p plays a prominent role in safeguarding the kidneys against common causes of chronic renal injury.
    Type of Medium: Online Resource
    ISSN: 1046-6673 , 1533-3450
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2020
    detail.hit.zdb_id: 2029124-3
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  • 3
    In: Kidney International, Elsevier BV, Vol. 101, No. 4 ( 2022-04), p. 766-778
    Type of Medium: Online Resource
    ISSN: 0085-2538
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2022
    detail.hit.zdb_id: 2007940-0
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  • 4
    Online Resource
    Online Resource
    Ovid Technologies (Wolters Kluwer Health) ; 2018
    In:  Journal of the American Society of Nephrology Vol. 29, No. 10 ( 2018-10), p. 2518-2528
    In: Journal of the American Society of Nephrology, Ovid Technologies (Wolters Kluwer Health), Vol. 29, No. 10 ( 2018-10), p. 2518-2528
    Abstract: In spite of extensive study, the mechanisms for salt sensitivity of BP in humans and rodent models remain poorly understood. Several microRNAs (miRNAs) have been associated with hypertension, but few have been shown to contribute to its development. Methods We examined miRNA expression profiles in human kidney biopsy samples and rat models using small RNA deep sequencing. To inhibit an miRNA specifically in the kidney in conscious, freely moving rats, we placed indwelling catheters to allow both renal interstitial administration of a specific anti-miR and measurement of BP. A rat with heterozygous disruption of the gene encoding endothelial nitric oxide synthase (eNOS) was developed. We used bioinformatic analysis to evaluate the relationship between 283 BP-associated human single-nucleotide polymorphisms (SNPs) and 1870 human miRNA precursors, as well as other molecular and cellular methods. Results Compared with salt-insensitive SS.13 BN26 rats, Dahl salt-sensitive (SS) rats showed an upregulation of miR-214-3p, encoded by a gene in the SS.13 BN26 congenic region. Kidney-specific inhibition of miR-214-3p significantly attenuated salt-induced hypertension and albuminuria in SS rats. miR-214-3p directly targeted eNOS. The effect of miR-214-3p inhibition on hypertension and albuminuria was abrogated in SS rats with heterozygous loss of eNOS. Human kidney biopsy specimens from patients with hypertension or hypertensive nephrosclerosis showed upregulation of miR-214-3p; the gene encoding miR-214-3p was one of several differentially expressed miRNA genes located in proximity to human BP-associated SNPs. Conclusions Renal miR-214-3p plays a functional and potentially genetic role in the development of hypertension, which might be mediated in part by targeting eNOS.
    Type of Medium: Online Resource
    ISSN: 1046-6673 , 1533-3450
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2018
    detail.hit.zdb_id: 2029124-3
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  • 5
    In: Briefings in Bioinformatics, Oxford University Press (OUP), Vol. 24, No. 4 ( 2023-07-20)
    Abstract: DNA methylation plays a crucial role in transcriptional regulation. Reduced representation bisulfite sequencing (RRBS) is a technique of increasing use for analyzing genome-wide methylation profiles. Many computational tools such as Metilene, MethylKit, BiSeq and DMRfinder have been developed to use RRBS data for the detection of the differentially methylated regions (DMRs) potentially involved in epigenetic regulations of gene expression. For DMR detection tools, as for countless other medical applications, P-values and their adjustments are among the most standard reporting statistics used to assess the statistical significance of biological findings. However, P-values are coming under increasing criticism relating to their questionable accuracy and relatively high levels of false positive or negative indications. Here, we propose a method to calculate E-values, as likelihood ratios falling into the null hypothesis over the entire parameter space, for DMR detection in RRBS data. We also provide the R package ‘metevalue’ as a user-friendly interface to implement E-value calculations into various DMR detection tools. To evaluate the performance of E-values, we generated various RRBS benchmarking datasets using our simulator ‘RRBSsim’ with eight samples in each experimental group. Our comprehensive benchmarking analyses showed that using E-values not only significantly improved accuracy, area under ROC curve and power, over that of P-values or adjusted P-values, but also reduced false discovery rates and type I errors. In applications using real RRBS data of CRL rats and a clinical trial on low-salt diet, the use of E-values detected biologically more relevant DMRs and also improved the negative association between DNA methylation and gene expression.
    Type of Medium: Online Resource
    ISSN: 1467-5463 , 1477-4054
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2023
    detail.hit.zdb_id: 2036055-1
    SSG: 12
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  • 6
    In: Genomics, Elsevier BV, Vol. 112, No. 6 ( 2020-11), p. 4567-4576
    Type of Medium: Online Resource
    ISSN: 0888-7543
    RVK:
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2020
    detail.hit.zdb_id: 1468023-3
    SSG: 12
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  • 7
    In: Hypertension, Ovid Technologies (Wolters Kluwer Health), Vol. 78, No. 2 ( 2021-08), p. 434-446
    Abstract: Dietary sodium affects blood pressure (BP) and vascular function. Animal studies suggest epigenetic changes (eg, DNA methylation) are involved. We hypothesized that sodium restriction induces methylation changes in T cells and arterioles in humans. Fifty subjects (49% women) were placed on 1200-mg sodium/day diet for 2 weeks. BP and brachial artery flow-mediated dilation were evaluated. Methylation sequencing (pre- and post-diet) was performed on T-cell (n=50) and biopsied arteriolar (n=10) DNA. RNA sequencing was also performed on arterioles (n=11). Over 2 weeks, mean sodium consumption was 946 mg/day. Average BP reductions after low-sodium intake were −8±13/−4±9 mm Hg ( P 〈 0.001). Flow-mediated dilation improved (5.8±2.9% to 6.8±3.4%; P =0.03). T-cell DNA was substantially more methylated than arterioles. The differentially methylated regions (false discovery rate, 〈 0.05) identified in T cells and arterioles after sodium restriction were located in 117 and 71 genes, respectively. Four genes were identified in both T cells and arterioles ( P =0.009 for the overlap). The dietary effects on methylation in several DNA regions were associated with dietary effects on BP. Several differentially expressed genes in arterioles contained differentially methylated regions at the significance level of P 〈 0.05. In addition, 46 genes contained differentially methylated regions in both human and SS/Mcw rat T cells ( P =0.03 for the overlap). Sodium restriction significantly affected DNA methylation in T cells and arterioles, some of which are associated with BP. Methylation patterns and sodium effects on methylation are largely tissue specific but also have overlaps between tissues and species. These findings may lead to better understanding of dietary sodium interactions with cellular processes and, therefore, novel therapeutic targets.
    Type of Medium: Online Resource
    ISSN: 0194-911X , 1524-4563
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2021
    detail.hit.zdb_id: 2094210-2
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  • 8
    In: Hypertension, Ovid Technologies (Wolters Kluwer Health), Vol. 79, No. Suppl_1 ( 2022-09)
    Abstract: Global knockout of microRNA miR-204 leads to significant attenuation of hypertension in mice treated with uninephrectomy, angiotensin II (AngII), and a high-salt diet. We hypothesize that miR-204 in endothelial cells (EC) contributes to hypertension. We developed Mir204 fl/fl mice and crossed them with VE-Cadherin-Cre mice. The loss of miR-204 was confirmed in isolated endothelial cells (1 ± 0.15, 0.41 and 0.13 ± 0.05, fold in EC- Mir204 +/+ , EC- Mir204 +/- , and EC- Mir204 -/- mice, respectively; n=4, 1, and 4). AngII and 4% NaCl diet increased systolic blood pressure (SBP) by up to 40-50 mmHg in both male and female EC- Mir204 +/- and WT littermates (n=11 and 17). The SBP was significantly decreased by 20-30 mmHg in EC- Mir204 -/- mice (P 〈 0.05, n=10). Vascular function was assessed by pressure myograph in basilar artery following the Ang II and 4% NaCl diet treatment. In EC- Mir204 -/- male mice, the wall thickness (21.5 ± 0.1 vs 30 ± 3.1μm, n=7 and 2) and media/lumen ratio (0.2 ± 0.01 vs 0.51 ± 0.09, n=7 and 2) was significantly reduced compared with EC- Mir204 +/+ mice. Endothelial-dependent vasodilation (response to Ach) was lost in EC- Mir204 +/+ mice but largely preserved in EC- Mir204 -/- mice (P= 0.007). Renal interstitial fibrosis was not influenced by the miR-204 KO in endothelial cells (Cortex: 0.27 ± 0.04, 0.18 ± 0.01 %; Outer medulla: 0.18 ± 0.05, 0.19 ± 0.05 % in EC- Mir204 +/+ and EC- Mir204 -/- male mice, respectively; n=3 and 2). Urinary albumin excretion was increased during the two-week treatment. However, the albuminuria was not significantly affected by the knockout of miR-204 in endothelial cells (2.65 ± 1.13, 3.41 ± 0.86, and 2.86 ± 0.85 mg/24h in EC- Mir204 +/+ , EC- Mir204 +/- , and EC- Mir204 -/- mice, respectively; n=9, 11 and 6). Glomerular filtration rate did not differ among the three groups at baseline or study termination (Baseline: 188.3 ± 30.1, 223.1 ± 34.9, and 185.3 ± 21.3 μl/min, n=4, 2 and 5; Termination: 203.8 ± 22.1, 150.7 ± 30.3, and 193.9 ± 42.5 μl/min, n=6, 2 and 5 in EC- Mir204 +/+ , EC- Mir204 +/- , and EC- Mir204 -/- mice, respectively). The findings suggest that miR-204 in endothelial cells plays an important role in the development of hypertension associated with impaired endothelial-dependent vasodilation and vascular remodeling.
    Type of Medium: Online Resource
    ISSN: 0194-911X , 1524-4563
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2022
    detail.hit.zdb_id: 2094210-2
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  • 9
    Online Resource
    Online Resource
    Ovid Technologies (Wolters Kluwer Health) ; 2018
    In:  Hypertension Vol. 72, No. 5 ( 2018-11), p. 1160-1171
    In: Hypertension, Ovid Technologies (Wolters Kluwer Health), Vol. 72, No. 5 ( 2018-11), p. 1160-1171
    Abstract: Numerous adult diseases involving tissues consisting primarily of nondividing cells are associated with changes in DNA methylation. It suggests a pathophysiological role for de novo methylation or demethylation of DNA, which is catalyzed by DNA methyltransferase 3 and ten-eleven translocases. However, the contribution of DNA de novo (de)methylation to these diseases remains almost completely unproven. Broad changes in DNA methylation occurred within days in the renal outer medulla of Dahl SS rats fed a high-salt diet, a classic model of hypertension. Intrarenal administration of anti-DNA methyltransferase 3a/ten-eleven translocase 3 GapmeRs attenuated high salt-induced hypertension in SS rats. The high-salt diet induced differential expression of 1712 genes in the renal outer medulla. Remarkably, the differential expression of 76% of these genes was prevented by anti-DNA methyltransferase 3a/ten-eleven translocase 3 GapmeRs. The genes differentially expressed in response to the GapmeRs were involved in the regulation of metabolism and inflammation and were significantly enriched for genes showing differential methylation in response to the GapmeRs. These data indicate a significant role of DNA de novo (de)methylation in the kidney in the development of hypertension in SS rats. The findings should help to shift the paradigm of DNA methylation research in diseases involving nondividing cells from correlative analysis to functional and mechanistic studies.
    Type of Medium: Online Resource
    ISSN: 0194-911X , 1524-4563
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2018
    detail.hit.zdb_id: 2094210-2
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  • 10
    In: Hypertension, Ovid Technologies (Wolters Kluwer Health), Vol. 74, No. Suppl_1 ( 2019-09)
    Abstract: Blood pressure (BP) levels are influenced by genetic and environmental factors. Epigenome is the result of interactions between the DNA and the environment. Methylation is a naturally occurring epigenetic modification of genomic DNA and may influence BP levels. We examined the association of DNA methylation in whole blood with 24-hour and clinic BP phenotypes in 281 African Americans; fifty percent were women and fifty percent were hypertensive. Mean age of the participants was 44±7 years and mean body mass index (BMI) was 28±5 kg/m 2 . Clinic BP was obtained in duplicate from both arms and averaged using a standardized protocol as part of screening procedures for a 3-day inpatient clinical study. Blood was obtained for DNA at the time of screening visit. BP medications were discontinued for 1-week after the screening visit and prior to inpatient study. Detailed phenotyping and 24-hour BP measurements were performed during the in-patient study. DNA methylation profiles of these 281 subjects with 24-hour BP measurements were analyzed at single-base resolution with a modified reduced representation bisulfite sequencing (RRBS) method. Analysis of 38,216 DNA methylation regions, representing 1,549,368 CpG sites across the genome, identified up to 72 regions that were significantly associated with 24-hour, daytime or nighttime BPs. Considered jointly, these methylation regions explained up to 66.6% of the BP variance. Methylation regions associated with 24-hour, daytime or nighttime BPs or systolic, diastolic or mean arterial pressure or pulse pressure overlapped partially. No methylation region was significantly associated with clinic BP. Two to three methylation regions were significantly associated with 24-hour BP after adjustment for age, sex, and body mass index. These methylation regions, jointly, explained up to 16.5% of the variance of 24-hour BP, while age, sex and body mass index explained up to 11.0% of the variance. In summary, we have identified several DNA methylation regions in the whole blood that are associated with 24-hour, daytime or nighttime BPs, but not with clinic BP measured at a single point in time. DNA methylation appears to be an excellent marker for the cumulative effect of factors that influence 24-hour, daytime or nighttime BPs
    Type of Medium: Online Resource
    ISSN: 0194-911X , 1524-4563
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2019
    detail.hit.zdb_id: 2094210-2
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