2
|
de Almeida RMC, Clendenon SG, Richards WG, Boedigheimer M, Damore M, Rossetti S, Harris PC, Herbert BS, Xu WM, Wandinger-Ness A, Ward HH, Glazier JA, Bacallao RL. Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. Hum Genomics 2016; 10:37. [PMID: 27871310 PMCID: PMC5117508 DOI: 10.1186/s40246-016-0095-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 11/04/2016] [Indexed: 12/18/2022] Open
Abstract
Background Autosomal dominant polycystic kidney disease (ADPKD) causes progressive loss of renal function in adults as a consequence of the accumulation of cysts. ADPKD is the most common genetic cause of end-stage renal disease. Mutations in polycystin-1 occur in 87% of cases of ADPKD and mutations in polycystin-2 are found in 12% of ADPKD patients. The complexity of ADPKD has hampered efforts to identify the mechanisms underlying its pathogenesis. No current FDA (Federal Drug Administration)-approved therapies ameliorate ADPKD progression. Results We used the de Almeida laboratory’s sensitive new transcriptogram method for whole-genome gene expression data analysis to analyze microarray data from cell lines developed from cell isolates of normal kidney and of both non-cystic nephrons and cysts from the kidney of a patient with ADPKD. We compared results obtained using standard Ingenuity Volcano plot analysis, Gene Set Enrichment Analysis (GSEA) and transcriptogram analysis. Transcriptogram analysis confirmed the findings of Ingenuity, GSEA, and published analysis of ADPKD kidney data and also identified multiple new expression changes in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways related to cell growth, cell death, genetic information processing, nucleotide metabolism, signal transduction, immune response, response to stimulus, cellular processes, ion homeostasis and transport and cofactors, vitamins, amino acids, energy, carbohydrates, drugs, lipids, and glycans. Transcriptogram analysis also provides significance metrics which allow us to prioritize further study of these pathways. Conclusions Transcriptogram analysis identifies novel pathways altered in ADPKD, providing new avenues to identify both ADPKD’s mechanisms of pathogenesis and pharmaceutical targets to ameliorate the progression of the disease. Electronic supplementary material The online version of this article (doi:10.1186/s40246-016-0095-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Rita M C de Almeida
- Biocomplexity Institute and Department of Physics, Indiana University, Bloomington, IN, 47405, USA.,Instituto de Física and Instituto Nacional de Ciência e Tecnologia, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Sherry G Clendenon
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, USA
| | | | | | - Michael Damore
- AMGEN Inc., One Amgen Center Drive, Thousand Oaks, CA, 91320-1799, USA
| | - Sandro Rossetti
- Division of Nephrology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Peter C Harris
- Division of Nephrology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA
| | - Britney-Shea Herbert
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Wei Min Xu
- Division of Nephrology, Department of Medicine, Richard Roudebush VAMC and Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Angela Wandinger-Ness
- Department of Pathology MSC08-4640 and Cancer Research and Treatment Center, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - Heather H Ward
- Division of Nephrology, Department of Medicine, University of New Mexico Health Sciences Center, Albuquerque, NM, 87131, USA
| | - James A Glazier
- Biocomplexity Institute and Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, 47405, USA
| | - Robert L Bacallao
- Division of Nephrology, Department of Medicine, Richard Roudebush VAMC and Indiana University School of Medicine, Indianapolis, IN, 46202, USA.
| |
Collapse
|
5
|
Adachi JI, Totake K, Shirahata M, Mishima K, Suzuki T, Yanagisawa T, Fukuoka K, Nishikawa R, Arimappamagan A, Manoj N, Mahadevan A, Bhat D, Arvinda H, Indiradevi B, Somanna S, Chandramouli B, Petterson SA, Hermansen SK, Dahlrot RH, Hansen S, Kristensen BW, Carvalho F, Jalali S, Singh S, Croul S, Aldape K, Zadeh G, Choi J, Park SH, Khang SK, Suh YL, Kim SP, Lee YS, Kim SH, Coberly S, Samayoa K, Liu Y, Kiaei P, Hill J, Patterson S, Damore M, Dahiya S, Emnett R, Phillips J, Haydon D, Leonard J, Perry A, Gutmann D, Epari S, Ahmed S, Gurav M, Raikar S, Moiyadi A, Shetty P, Gupta T, Jalali R, Georges J, Zehri A, Carlson E, Martirosyan N, Elhadi A, Nichols J, Ighaffari L, Eschbacher J, Feuerstein B, Anderson T, Preul M, Jensen K, Nakaji P, Girardi H, Monville F, Carpentier S, Giry M, Voss J, Jenkins R, Boisselier B, Frayssinet V, Poggionovo C, Catteau A, Mokhtari K, Sanson M, Peyro-Saint-Paul H, Giannini C, Hide T, Nakamura H, Makino K, Yano S, Anai S, Shinojima N, Kuroda JI, Takezaki T, Kuratsu JI, Higuchi F, Matsuda H, Iwata K, Ueki K, Kim P, Kong J, Cooper L, Wang F, Gao J, Teodoro G, Scarpace L, Mikkelsen T, Schniederjan M, Moreno C, Saltz J, Brat D, Cho U, Hong YK, Lee YS, Lober R, Lu L, Gephart MH, Fisher P, Miyazaki M, Nishihara H, Itoh T, Kato M, Fujimoto S, Kimura T, Tanino M, Tanaka S, Nguyen N, Moes G, Villano JL, Nishihara H, Kanno H, Kato Y, Tanaka S, Ohnishi T, Harada H, Ohue S, Kouno S, Inoue A, Yamashita D, Okamoto S, Nitta M, Muragaki Y, Maruyama T, Sawada T, Komori T, Saito T, Okada Y, Omay SB, Gunel JM, Clark VE, Li J, Omay EZE, Serin A, Kolb LE, Hebert RM, Bilguvar K, Ozduman K, Pamir MN, Kilic T, Baehring J, Piepmeier JM, Brennan CW, Huse J, Gutin PH, Yasuno K, Vortmeyer A, Gunel M, Perry A, Pugh S, Rogers CL, Brachman D, McMillan W, Jenrette J, Barani I, Shrieve D, Sloan A, Mehta M, Prabowo A, Iyer A, Veersema T, Anink J, Meeteren ASV, Spliet W, van Rijen P, Ferrier T, Capper D, Thom M, Aronica E, Chharchhodawala T, Sable M, Sharma MC, Sarkar C, Suri V, Singh M, Santosh V, Thota B, Srividya M, Sravani K, Shwetha S, Arivazhagan A, Thennarasu K, Chandramouli B, Hegde A, Kondaiah P, Somasundaram K, Rao M, Santosh V, Kumar VP, Thota B, Shastry A, Arivazhagan A, Thennarasu K, Kondaiah P, Shastry A, Narayan R, Thota B, Somanna S, Thennarasu K, Arivazhagan A, Santosh V, Shastry A, Naz S, Thota B, Thennarasu K, Arivazhagan A, Somanna S, Santosh V, Kondaiah P, Venneti S, Garimella M, Sullivan L, Martinez D, Huse J, Heguy A, Santi M, Thompson C, Judkins A, Voronovich Z, Chen L, Clark K, Walsh M, Mannas J, Horbinski C, Wiestler B, Capper D, Holland-Letz T, Korshunov A, von Deimling A, Pfister SM, Platten M, Weller M, Wick W, Zieman G, Dardis C, Ashby L, Eschbacher J. PATHOLOGY. Neuro Oncol 2013. [DOI: 10.1093/neuonc/not184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
7
|
Negoro H, Kobayashi H, Teng B, Schafer I, Starker G, Miller E, Mao Y, Park JK, Haller H, Schiffer M, Lu Y, Zhong F, Zhou Q, Hao X, Li C, Guo S, Wang W, Chen N, Okano K, Jinnai H, Iwasaki T, Miwa N, Kimata N, Akiba T, Nitta K, Chen CA, Cheng YC, Hwang JC, Chang JMC, Guh JY, Chen HC, Garcia-Sanchez O, Lopez-Novoa JM, Lopez-Hernandez FJ, Hirai Y, Iyoda M, Shibata T, Kuno Y, Akizawa T, Shimizu H, Bolati D, Niwa T, Kim YK, Nam SA, Kim WY, Park SH, Song HC, Choi EJ, Kim J, Sirolli V, Giardinelli A, Morabito C, Di Cesare M, Di Pietro N, Di Liberato L, Amoroso L, Mariggio MA, Formoso G, Pandolfi A, Bonomini M, Shalhoub V, Shatzen E, Ward S, Damore M, Boedigheimer M, Campbell M, Pan Z, Davis J, Henley C, Richards W, Yoshida T, Yamashita M, Hayashi M, Bodor C, Nemeth A, Berzsenyi V, Vegh B, Sebe A, Rosivall L, Koken T, Hunkerler Z, Kahraman A, Verzola D, Villaggio B, Tosetti F, Cappuccino L, Gianiorio F, Simonato A, Parodi E, Garibotto G, Chai Y, Liu J, Sun B, Zhao X, Qian J, Xing C. Cell signalling. Clin Kidney J 2011. [DOI: 10.1093/ndtplus/4.s2.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|