The kidney transcriptome and proteome defined by transcriptomics and antibody-based profiling

PLoS ONE

Volumn 9, Issue 12, 2014, Pages

  Habuka, Masato ^a,c   Fagerberg, Linn ^a   Hallström, Björn M ^a   Kampf, Caroline ^b   Edlund, Karolina ^b   Sivertsson, Asa ^a   Yamamoto, Tadashi ^c   Pontén, Fredrik ^b   Uhlén, Mathias ^a   Odeberg, Jacob ^a,d  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c NIIGATA UNIVERSITY   (Japan)

^d KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; TRANSCRIPTOME;

ADULT; AGED; ARTICLE; FEMALE; GENE EXPRESSION; GENE IDENTIFICATION; GLOMERULUS; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; KIDNEY; KIDNEY COLLECTING TUBULE; KIDNEY DISTAL TUBULE; KIDNEY PROXIMAL TUBULE; MALE; NORMAL HUMAN; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; TISSUE MICROARRAY; TRANSCRIPTOMICS; CYTOLOGY; GENE EXPRESSION PROFILING; GENETICS; METABOLISM; MIDDLE AGED; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

AGED; BASE SEQUENCE; FEMALE; GENE EXPRESSION PROFILING; HUMANS; KIDNEY; KIDNEY GLOMERULUS; KIDNEY TUBULES, COLLECTING; KIDNEY TUBULES, DISTAL; KIDNEY TUBULES, PROXIMAL; MALE; MIDDLE AGED; PROTEOME; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84920434621     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0116125     Document Type: Article

References (41)

1. Kestila M, Lenkkeri U, Mannikko M, Lamerdin J, McCready P, et al. (1998) Positionally cloned gene for a novel glomerular protein-nephrin-is mutated in congenital nephrotic syndrome. Molecular cell 1: 575-582.
2. Yamamoto T, Sasaki S (1998) Aquaporins in the kidney: emerging new aspects. Kidney international 54: 1041-1051.
3. Schlessinger A, Yee SW, Sali A, Giacomini KM (2013) SLC classification: an update. Clinical pharmacology and therapeutics 94: 19-23.
4. Morrissey KM, Wen CC, Johns SJ, Zhang L, Huang SM, et al. (2012) The UCSF-FDA TransPortal: a public drug transporter database. Clinical pharmacology and therapeutics 92: 545-546.
5. Takemoto M, He L, Norlin J, Patrakka J, Xiao Z, et al. (2006) Large-scale identification of genes implicated in kidney glomerulus development and function. The EMBO journal 25: 1160-1174.
6. Miyamoto M, Yoshida Y, Taguchi I, Nagasaka Y, Tasaki M, et al. (2007) In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. Journal of proteome research 6: 3680-3690.
7. Fagerberg L, Hallstrom BM, Oksvold P, Kampf C, Djureinovic D, et al. (2014) Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics. Molecular & cellular proteomics: MCP 13: 397-406.
8. Uhlen M, Oksvold P, Fagerberg L, Lundberg E, Jonasson K, et al. (2010) Towards a knowledgebased Human Protein Atlas. Nature biotechnology 28: 1248-1250.
9. Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (Oxford, England) 25: 1105-1111.
10. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28: 511-515.
11. Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, et al. (2013) Ensembl 2013. Nucleic acids research 41: D48-55.
12. Anderson CM, Thwaites DT (2010) Hijacking solute carriers for proton-coupled drug transport. Physiology 25: 364-377.
13. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13: 2498-2504.
14. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome biology 11: R106.
15. Ponten F, Jirstrom K, Uhlen M (2008) The Human Protein Atlas-a tool for pathology. The Journal of pathology 216: 387-393.
16. Kampf C, Olsson I, Ryberg U, Sjostedt E, Ponten F (2012) Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas. Journal of visualized experiments: JoVE.
17. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature genetics 25: 25-29.
18. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC bioinformatics 10: 48.
19. Bleyer AJ, Zivna M, Kmoch S (2011) Uromodulin-associated kidney disease. Nephron Clinical practice 118: c31-36.
20. Serafini-Cessi F, Malagolini N, Cavallone D (2003) Tamm-Horsfall glycoprotein: biology and clinical relevance. American journal of kidney diseases: the official journal of the National Kidney Foundation 42: 658-676.
21. Lhotta K (2010) Uromodulin and chronic kidney disease. Kidney & blood pressure research 33: 393-398.
22. He L, Vasiliou K, Nebert DW (2009) Analysis and update of the human solute carrier (SLC) gene superfamily. Human genomics 3: 195-206.
23. Zhou Y, Holmseth S, Hua R, Lehre AC, Olofsson AM, et al. (2012) The betaine-GABA transporter (BGT1, slc6a12) is predominantly expressed in the liver and at lower levels in the kidneys and at the brain surface. American journal of physiology Renal physiology 302: F316-328.
24. Usener D, Schadendorf D, Koch J, Dubel S, Eichmuller S (2003) cTAGE: a cutaneous T cell lymphoma associated antigen family with tumor-specific splicing. The Journal of investigative dermatology 121: 198-206.
25. Andley UP (2009) Effects of alpha-crystallin on lens cell function and cataract pathology. Current molecular medicine 9: 887-892.
26. Litt M, Kramer P, LaMorticella DM, Murphey W, Lovrien EW, et al. (1998) Autosomal dominant congenital cataract associated with a missense mutation in the human alpha crystallin gene CRYAA. Human molecular genetics 7: 471-474.
27. Kumar R, Schaefer J, Grande JP, Roche PC (1994) Immunolocalization of calcitriol receptor, 24- hydroxylase cytochrome P-450, and calbindin D28k in human kidney. The American journal of physiology 266: F477-485.
28. Moser M, Dahmen S, Kluge R, Grone H, Dahmen J, et al. (2003) Terminal renal failure in mice lacking transcription factor AP-2 beta. Laboratory investigation; a journal of technical methods and pathology 83: 571-578.
29. Eladari D, Chambrey R, Peti-Peterdi J (2012) A new look at electrolyte transport in the distal tubule. Annual review of physiology 74: 325-349.
30. Schafer JA (1979) Response of the collecting duct to the demands of homeostasis. The Physiologist 22: 44-53.
31. Ruotsalainen V, Ljungberg P, Wartiovaara J, Lenkkeri U, Kestila M, et al. (1999) Nephrin is specifically located at the slit diaphragm of glomerular podocytes. Proceedings of the National Academy of Sciences of the United States of America 96: 7962-7967.
32. Schwarz K, Simons M, Reiser J, Saleem MA, Faul C, et al. (2001) Podocin, a raft-associated component of the glomerular slit diaphragm, interacts with CD2AP and nephrin. The Journal of clinical investigation 108: 1621-1629.
33. Donoviel DB, Freed DD, Vogel H, Potter DG, Hawkins E, et al. (2001) Proteinuria and perinatal lethality in mice lacking NEPH1, a novel protein with homology to NEPHRIN. Molecular and cellular biology 21: 4829-4836.
34. Sato T, Okumura F, Ariga T, Hatakeyama S (2012) TRIM6 interacts with Myc and maintains the pluripotency of mouse embryonic stem cells. Journal of cell science 125: 1544-1555.
35. Faber JJ, Anderson DF (2010) The placenta in the integrated physiology of fetal volume control. The International journal of developmental biology 54: 391-396.
36. Beall MH, Amidi F, Gayle DA, Wang S, Beloosesky R, et al. (2005) Placental and fetal membrane Nephrin and Neph1 gene expression: response to inflammation. Journal of the Society for Gynecologic Investigation 12: 298-302.
37. Cui Z, Yoshida Y, Xu B, Zhang Y, Nameta M, et al. (2013) Profiling and annotation of human kidney glomerulus proteome. Proteome science 11: 13.
38. Curthoys NP, Taylor L, Hoffert JD, Knepper MA (2007) Proteomic analysis of the adaptive response of rat renal proximal tubules to metabolic acidosis. American journal of physiology Renal physiology 292: F140-147.
39. Walmsley SJ, Broeckling C, Hess A, Prenni J, Curthoys NP (2010) Proteomic analysis of brushborder membrane vesicles isolated from purified proximal convoluted tubules. American journal of physiology Renal physiology 298: F1323-1331.
40. Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, et al. (2014) State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology- and disease-driven Human Proteome Project. Journal of proteome research 13: 60-75.
41. Griffin NM, Schnitzer JE (2011) Overcoming key technological challenges in using mass spectrometry for mapping cell surfaces in tissues. Molecular & cellular proteomics: MCP 10: R110000935.