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  • 1
    In: Kidney International, Elsevier BV, Vol. 103, No. 3 ( 2023-03), p. 565-579
    Type of Medium: Online Resource
    ISSN: 0085-2538
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 2007940-0
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  • 2
    In: Journal of the American Society of Nephrology, Ovid Technologies (Wolters Kluwer Health), Vol. 34, No. 11S ( 2023-11), p. 584-584
    Type of Medium: Online Resource
    ISSN: 1046-6673
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2023
    detail.hit.zdb_id: 2029124-3
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  • 3
    In: Diabetes, American Diabetes Association, Vol. 72, No. Supplement_1 ( 2023-06-20)
    Abstract: In abstract 2023-A-3497-Diabetes, we show impaired TCA cycle turnover using 11C acetate PET and lower proximal tubular transcripts of TCA cycle enzymes by single-cell RNA sequencing of kidney biopsies in young adults with T1D vs. healthy controls (HC). Spatial metabolomics analyses of the kidney tissue were conducted to further explore perturbations in kidney oxidative metabolism in T1D. Matrix-assisted laser desorption/ionization-mass spectrometry imaging-based spatial metabolomics was used to analyze metabolites in situ (spatial resolution: 20 μm) in kidney tissues from 8 participants with T1D and preserved kidney function and 5 HC. Univariate analysis (t-test or Wilcoxon Mann Whitney test) demonstrated that 36 of 456 METASPACE annotated metabolites were altered (P & lt;0.05) in T1D vs. HC. Partial least squares-discriminant analysis (PLS-DA) and heatmaps showed clearly separated clusters of metabolites. To identify the most significant discriminators for T1D, a variable importance in projection (VIP) plot from PLS-DA model was applied. Of the top 15 metabolites, two TCA cycle intermediates, succinic acid (m/z 117.0193, -H; P = 0.016) and malic acid (m/z 133.0142, -H; P = 0.026), were reduced in kidney tissues of participants with T1D. Pathway analysis revealed that the TCA cycle, mitochondrial electron transport chain, glutamate metabolism, malate-aspartate shuttle, and purine pathway were the dominant metabolic pathways perturbed in T1D kidney tissue. Spatial metabolomics comparing T1D kidney biopsies vs. HC reveal alterations of TCA cycle intermediates indicating mitochondrial dysfunction in the subclinical stages of diabetic kidney disease. The spatial metabolomics data are consistent with the data from transcriptomics and stable isotope tracing analysis in a subset of same participants. Further analysis with pathologic features will identify potential pathways linked to disease development. Disclosure G.Zhang: None. C.Birznieks: None. I.De boer: Advisory Panel; AstraZeneca, Boehringer Ingelheim and Eli Lilly Alliance, Boehringer Ingelheim International GmbH, Otsuka America Pharmaceutical, Inc., Bayer Inc., Consultant; George Clinical, Gilead Sciences, Inc., Medscape, Research Support; Dexcom, Inc. J.A.Schaub: None. K.J.Nadeau: None. V.Nair: None. F.Alakwaa: None. P.J.Mccown: None. A.Naik: Advisory Panel; CareDx. L.Pyle: None. D.Blondin: None. L.Liu: None. G.Richard: None. M.Kretzler: Research Support; Lilly, Boehringer Ingelheim Inc., Traveere Pharmaceuticals, Novo Nordisk, certa, Chinook Therapeutics Inc., Janssen Research & Development, LLC, AstraZeneca, Moderna, Inc., Gilead Sciences, Inc., Regeneron, Ionis Pharmaceuticals, Angioin, Renalytix. P.Bjornstad: Advisory Panel; AstraZeneca, Novo Nordisk, Lilly, Horizon Therapeutics plc, Boehringer Ingelheim (Canada) Ltd., LG Chem, Consultant; Bayer Inc., Bristol-Myers Squibb Company. K.Sharma: Advisory Panel; Reata Pharmaceuticals, Inc., Otsuka America Pharmaceutical, Inc. I.M.Tamayo: None. N.Garcia ponce de leon: None. T.B.Vigers: None. K.L.Tommerdahl: None. R.G.Nelson: None. P.E.Ladd: None. T.Alexandrov: None. Funding National Institutes of Health (UH3DK114920); JDRF (2-SRA-2019-845-S-B); Diabetes Research Center (P30DK116073)
    Type of Medium: Online Resource
    ISSN: 0012-1797
    Language: English
    Publisher: American Diabetes Association
    Publication Date: 2023
    detail.hit.zdb_id: 1501252-9
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  • 4
    Online Resource
    Online Resource
    American Society for Cell Biology (ASCB) ; 2008
    In:  Molecular Biology of the Cell Vol. 19, No. 1 ( 2008-01), p. 284-296
    In: Molecular Biology of the Cell, American Society for Cell Biology (ASCB), Vol. 19, No. 1 ( 2008-01), p. 284-296
    Abstract: Under certain conditions of nutrient stress, the budding yeast Saccharomyces cerevisiae initiates a striking developmental transition to a filamentous form of growth, resembling developmental transitions required for virulence in closely related pathogenic fungi. In yeast, filamentous growth involves known mitogen-activated protein kinase and protein kinase A signaling modules, but the full scope of this extensive filamentous response has not been delineated. Accordingly, we have undertaken the first systematic gene disruption and overexpression analysis of yeast filamentous growth. Standard laboratory strains of yeast are nonfilamentous; thus, we constructed a unique set of reagents in the filamentous Σ1278b strain, encompassing 3627 integrated transposon insertion alleles and 2043 overexpression constructs. Collectively, we analyzed 4528 yeast genes with these reagents and identified 487 genes conferring mutant filamentous phenotypes upon transposon insertion and/or gene overexpression. Using a fluorescent protein reporter integrated at the MUC1 locus, we further assayed each filamentous growth mutant for aberrant protein levels of the key flocculence factor Muc1p. Our results indicate a variety of genes and pathways affecting filamentous growth. In total, this filamentous growth gene set represents a wealth of yeast biology, highlighting 84 genes of uncharacterized function and an underappreciated role for the mitochondrial retrograde signaling pathway as an inhibitor of filamentous growth.
    Type of Medium: Online Resource
    ISSN: 1059-1524 , 1939-4586
    Language: English
    Publisher: American Society for Cell Biology (ASCB)
    Publication Date: 2008
    detail.hit.zdb_id: 1474922-1
    SSG: 12
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  • 5
    In: Journal of the American Society of Nephrology, Ovid Technologies (Wolters Kluwer Health), Vol. 34, No. 11S ( 2023-11), p. 606-606
    Type of Medium: Online Resource
    ISSN: 1046-6673
    Language: English
    Publisher: Ovid Technologies (Wolters Kluwer Health)
    Publication Date: 2023
    detail.hit.zdb_id: 2029124-3
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  • 6
    Online Resource
    Online Resource
    Cold Spring Harbor Laboratory ; 2022
    In:  RNA Vol. 28, No. 9 ( 2022-09), p. 1172-1184
    In: RNA, Cold Spring Harbor Laboratory, Vol. 28, No. 9 ( 2022-09), p. 1172-1184
    Abstract: Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could regulate the formation of these triple helices is through RNA modifications. With over 140 naturally occurring RNA modifications, we hypothesize that some modifications stabilize RNA•DNA-DNA triple helices while others destabilize them. Here, we focus on a pyrimidine-motif triple helix composed of canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays and microscale thermophoresis to examine how 11 different RNA modifications at a single position in an RNA•DNA-DNA triple helix affect stability: 5-methylcytidine (m 5 C), 5-methyluridine (m 5 U or rT), 3-methyluridine (m 3 U), pseudouridine (Ψ), 4-thiouridine (s 4 U), N 6 -methyladenosine (m 6 A), inosine (I), and each nucleobase with 2′- O -methylation (Nm). Compared to the unmodified U•A-T base triple, some modifications have no significant change in stability (Um•A-T), some have ∼2.5-fold decreases in stability (m 5 U•A-T, Ψ•A-T, and s 4 U•A-T), and some completely disrupt triple helix formation (m 3 U•A-T). To identify potential biological examples of RNA•DNA-DNA triple helices controlled by an RNA modification, we searched RMVar, a database for RNA modifications mapped at single-nucleotide resolution, for lncRNAs containing an RNA modification within a pyrimidine-rich sequence. Using electrophoretic mobility shift assays, the binding of DNA-DNA to a 22-mer segment of human lncRNA Al157886.1 was destabilized by ∼1.7-fold with the substitution of m 5 C at known m 5 C sites. Therefore, the formation and stability of cellular RNA•DNA-DNA triple helices could be influenced by RNA modifications.
    Type of Medium: Online Resource
    ISSN: 1355-8382 , 1469-9001
    Language: English
    Publisher: Cold Spring Harbor Laboratory
    Publication Date: 2022
    detail.hit.zdb_id: 1475737-0
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  • 7
    In: Diabetes, American Diabetes Association, Vol. 72, No. Supplement_1 ( 2023-06-20)
    Abstract: IR has been linked to kidney injury in T1D. Animal models show that IR associates with impaired TCA cycle turnover and oxidative phosphorylation, collectively termed oxidative metabolism, but little is known about this relationship in humans with T1D. Thirty young adults with T1D (age: 23±3 years, diabetes duration: 13±5 years, 53% female, HbA1c: 7.9±1.1%, BMI: 25±3 kg/m2, UACR: 5 [3, 8] mg/g) and 20 healthy controls (HC) (age: 25±3, 50% female, HbA1c: 5.2±0.3%, BMI: 23±2 kg/m2, UACR: 5 [3, 9] mg/g) underwent hyperinsulinemic-euglycemic clamps to assess whole-body insulin sensitivity (IS), and MRI to assess kidney perfusion. A subset underwent voxel-wise and region-of-interest (ROI) pharmacokinetic (PK) 11C-acetate PET analyses (n=16 T1D; n=10 HC) to quantify kidney cortical oxidative metabolism (k 2), and research kidney biopsies with single-cell RNA sequencing (n=28 T1D; n=13 HC). Compared to HC, participants with T1D exhibited lower IS (7.8±2.6 vs. 14.3±4.0 mg/kg/min, p & lt;0.0001), cortical perfusion (196±68 vs. 243±46 ml/min/100g, p=0.01) and lower cortical k 2 (0.16±0.02 vs. HC 0.18±0.02 min-1, p=0.04) in voxel-wise models, although significance was not reached in the ROI PK analyses. IS associated with cortical k 2 (r:0.43, p=0.03) and the associations remained significant after adjusting for age, sex, and HbA1c (p=0.04). No significant interaction observed between T1D and HC for IS and cortical k2 (p=0.78). Proximal tubular transcripts of the enzymes catalyzing the proximal steps of the TCA cycle (e.g., ACO1, IDH1, SUCLG1) were lower in T1D vs. HC (all FDR-adjusted p & lt;0.0001). Kidney oxidative metabolism is impaired in young people with T1D and is linked to lower whole-body IS. Statistical differences in k 2 from ROI and voxel-wise analyses suggest regional variations in kidney oxidative metabolism that may not be apparent in global analysis. Spatial metabolomic analyses of kidney tissue in a subset of these participants are shown in abstract #2023-A-3407-Diabetes. Disclosure G.Richard: None. S.Gross: None. V.N.Shah: Advisory Panel; LifeScan Diabetes Institute, Medscape, Consultant; DKSH, Research Support; Novo Nordisk, Tandem Diabetes Care, Inc., Dexcom, Inc., Insulet Corporation, JDRF, National Institutes of Health, Speaker's Bureau; Dexcom, Inc., Insulet Corporation. L.Pyle: None. T.B.Vigers: None. J.K.Snell-bergeon: None. I.De boer: Advisory Panel; AstraZeneca, Boehringer Ingelheim and Eli Lilly Alliance, Boehringer Ingelheim International GmbH, Otsuka America Pharmaceutical, Inc., Bayer Inc., Consultant; George Clinical, Gilead Sciences, Inc., Medscape, Research Support; Dexcom, Inc. D.Van raalte: Consultant; Boehringer Ingelheim and Eli Lilly Alliance, AstraZeneca, Merck & Co., Inc., Research Support; Boehringer Ingelheim and Eli Lilly Alliance, AstraZeneca, Merck & Co., Inc. L.Li: None. P.V.Prasad: None. P.E.Ladd: None. C.Birznieks: None. B.B.Chin: None. D.Cherney: Other Relationship; Boehringer Ingelheim-Lilly, Merck, AstraZeneca, Sanofi, Mitsubishi-Tanabe, Abbvie, Janssen, Bayer, Prometic, BMS, Maze, Gilead, CSL-Behring, Otsuka, Novartis, Youngene, Lexicon and Novo-Nordisk, Research Support; Boehringer Ingelheim-Lilly, Merck, Janssen, Sanofi, AstraZeneca, CSL-Behring and Novo-Nordisk. P.J.Mccown: None. F.Alakwaa: None. M.Kretzler: Research Support; Lilly, Boehringer Ingelheim Inc., Traveere Pharmaceuticals, Novo Nordisk, certa, Chinook Therapeutics Inc., Janssen Research & Development, LLC, AstraZeneca, Moderna, Inc., Gilead Sciences, Inc., Regeneron, Ionis Pharmaceuticals, Angioin, Renalytix. K.Sharma: Advisory Panel; Reata Pharmaceuticals, Inc., Otsuka America Pharmaceutical, Inc. F.C.Brosius: Advisory Panel; Gilead Sciences, Inc. R.G.Nelson: None. K.J.Nadeau: None. P.Bjornstad: Advisory Panel; AstraZeneca, Novo Nordisk, Lilly, Horizon Therapeutics plc, Boehringer Ingelheim (Canada) Ltd., LG Chem, Consultant; Bayer Inc., Bristol-Myers Squibb Company. G.Zhang: None. L.Driscoll: None. K.L.Tommerdahl: None. J.A.Schaub: None. A.Naik: Advisory Panel; CareDx. V.Nair: None. A.A.Macdonald: None. Funding JDRF; National Institute of Diabetes and Digestive and Kidney Diseases
    Type of Medium: Online Resource
    ISSN: 0012-1797
    Language: English
    Publisher: American Diabetes Association
    Publication Date: 2023
    detail.hit.zdb_id: 1501252-9
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  • 8
    Online Resource
    Online Resource
    Elsevier BV ; 2014
    In:  Chemistry & Biology Vol. 21, No. 7 ( 2014-07), p. 880-889
    In: Chemistry & Biology, Elsevier BV, Vol. 21, No. 7 ( 2014-07), p. 880-889
    Type of Medium: Online Resource
    ISSN: 1074-5521
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2014
    detail.hit.zdb_id: 2019089-X
    SSG: 12
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  • 9
    In: Diabetes, American Diabetes Association, Vol. 72, No. Supplement_1 ( 2023-06-20)
    Abstract: Introduction: VSG attenuates early diabetic kidney disease (DKD) in youth with T2D, yet the molecular mechanisms of VSG on kidney health are unknown. We analyzed single-cell RNA sequencing data from paired kidney biopsies obtained from youth with T2D before and 1-year after VSG. Methods: Data from 5 youths with T2D who underwent kidney biopsies before and after VSG were included in this analysis (pre-VSG:17±2 years, HbA1c 7.5±2.6%, BMI 41±3 kg/m2, 40% with albuminuria (UACR≥30mg/g). A total of 23598 cells were profiled from the five paired kidney biopsies, with 19735 cells from 12 HC. Cell selective differentially expressed genes in disease (T2D vs. HC) were computed. Disease genes that reversed directionality post-VSG were termed "suppressed by VSG" or "upregulated by VSG," depending on the direction of the reversal. Results: VSG resulted in the normalization of HbA1c and UACR in all cases at 12 months. Post VSG, 73% of proximal tubule (PT) genes that were upregulated in T2D vs. HC were suppressed in VSG vs. T2D. These suppressed genes were enriched for glycolysis, gluconeogenesis, and TCA cycle pathways (Figure). Gene and pathway changes in the PT were similar to what was recently demonstrated with SGLT2i in T2D youth. Conclusion: VSG, like SGLT2i, is associated with reduced central carbon metabolism in the PT and other nephron segments. Disclosure A.Naik: Advisory Panel; CareDx. K.N.Z.Fuller: None. P.E.Ladd: None. D.A.Sandoval: Consultant; Metis Therapeutics. S.Gross: None. P.Zeitler: Consultant; Eli Lilly and Company, Boehringer Ingelheim Inc., Johnson & Johnson. K.J.Nadeau: None. J.R.Ryder: None. T.Inge: None. J.B.Hodgin: None. F.C.Brosius: Advisory Panel; Gilead Sciences, Inc. F.Alakwaa: None. R.G.Nelson: None. M.Kretzler: Research Support; Lilly, Boehringer Ingelheim Inc., Traveere Pharmaceuticals, Novo Nordisk, certa, Chinook Therapeutics Inc., Janssen Research & Development, LLC, AstraZeneca, Moderna, Inc., Gilead Sciences, Inc., Regeneron, Ionis Pharmaceuticals, Angioin, Renalytix. P.Bjornstad: Advisory Panel; AstraZeneca, Novo Nordisk, Lilly, Horizon Therapeutics plc, Boehringer Ingelheim (Canada) Ltd., LG Chem, Consultant; Bayer Inc., Bristol-Myers Squibb Company. J.A.Schaub: None. P.J.Mccown: None. V.Nair: None. S.Eddy: None. L.Pyle: None. T.B.Vigers: None. M.M.Kelsey: Other Relationship; Boehringer Ingelheim Inc., Janssen Pharmaceuticals, Inc., Rhythm Pharmaceuticals, Inc., Lilly. Funding Boettcher Foundation; National Institute of Diabetes and Digestive and Kidney Diseases (K23116720, R01DK129211); JDRF (2-SRA-2019-845-S-B)
    Type of Medium: Online Resource
    ISSN: 0012-1797
    Language: English
    Publisher: American Diabetes Association
    Publication Date: 2023
    detail.hit.zdb_id: 1501252-9
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  • 10
    Online Resource
    Online Resource
    MDPI AG ; 2019
    In:  International Journal of Molecular Sciences Vol. 20, No. 22 ( 2019-11-09), p. 5610-
    In: International Journal of Molecular Sciences, MDPI AG, Vol. 20, No. 22 ( 2019-11-09), p. 5610-
    Abstract: Human metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is an abundant nuclear-localized long noncoding RNA (lncRNA) that has significant roles in cancer. While the interacting partners and evolutionary sequence conservation of MALAT1 have been examined, much of the structure of MALAT1 is unknown. Here, we propose a hypothetical secondary structural model for 8425 nucleotides of human MALAT1 using three experimental datasets that probed RNA structures in vitro and in various human cell lines. Our model indicates that approximately half of human MALAT1 is structured, forming 194 helices, 13 pseudoknots, five structured tetraloops, nine structured internal loops, and 13 intramolecular long-range interactions that give rise to several multiway junctions. Evolutionary conservation and covariation analyses support 153 of 194 helices in 51 mammalian MALAT1 homologs and 42 of 194 helices in 53 vertebrate MALAT1 homologs, thereby identifying an evolutionarily conserved core that likely has important functional roles in mammals and vertebrates. Data mining revealed that RNA modifications, somatic cancer-associated mutations, and single-nucleotide polymorphisms may induce structural rearrangements that sequester or expose binding sites for several cancer-associated microRNAs. Our findings reveal new mechanistic leads into the roles of MALAT1 by identifying several intriguing structure–function relationships in which the dynamic structure of MALAT1 underlies its biological functions.
    Type of Medium: Online Resource
    ISSN: 1422-0067
    Language: English
    Publisher: MDPI AG
    Publication Date: 2019
    detail.hit.zdb_id: 2019364-6
    SSG: 12
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