Applied Systems Biology Core Publications

Gene expression analyses of kidney biopsies: the European renal cDNA bank--Kröner-Fresenius biopsy bank.
Cohen CD, Kretzler M. Pathologe. 2009 Mar;30(2):101-4. German.

Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays.
Moll AG, Lindenmeyer MT, Kretzler M, Nelson PJ, Zimmer R, Cohen CD. PLoS One. 2009;4(3):e4702. Epub 2009 Mar 11.

Role of basic fibroblast growth factor (FGF-2) in diabetic nephropathy and mechanisms of its induction by hyperglycemia in human renal fibroblasts.
Vasko R, Koziolek M, Ikehata M, Rastaldi MP, Jung K, Schmid H, Kretzler M, Müller GA, Strutz F. Am J Physiol Renal Physiol. 2009 Jun;296(6):F1452-63. Epub 2009 Mar 11.

Patients with IgA nephropathy exhibit high systemic PDGF-DD levels.
Boor P, Eitner F, Cohen CD, Lindenmeyer MT; ERCB-Consortium, Mertens PR, Ostendorf T, Floege J. Nephrol Dial Transplant. 2009 Sep;24(9):2755-62. Epub 2009 Apr 8.

Urine podocyte mRNAs mark progression of renal disease.
Sato Y, Wharram BL, Lee SK, Wickman L, Goyal M, Venkatareddy M, Chang JW, Wiggins JE, Lienczewski C, Kretzler M, Wiggins RC. J Am Soc Nephrol. 2009 May;20(5):1041-52. Epub 2009 Apr 23.

Renal gene and protein expression signatures for prediction of kidney disease progression.
Ju W, Eichinger F, Bitzer M, Oh J, McWeeney S, Berthier CC, Shedden K, Cohen CD, Henger A, Krick S, Kopp JB, Stoeckert CJ Jr, Dikman S, Schröppel B, Thomas DB, Schlondorff D, Kretzler M, Böttinger EP. Am J Pathol. 2009 Jun;174(6):2073-85. Erratum in: Am J Pathol. 2009 Sep;175(3):1349.

How to build a tight but permeable glomerular junction.
Martini S, Kretzler M. J Am Soc Nephrol. 2009 Jul;20(7):1420-1. Epub 2009 Jun 11. No abstract available.

The peroxisome proliferator-activated receptor gamma agonist pioglitazone improves cardiometabolic risk and renal inflammation in murine lupus. 
Zhao W, Thacker SG, Hodgin JB, Zhang H, Wang JH, Park JL, Randolph A, Somers EC, Pennathur S, Kretzler M, Brosius FC 3rd, Kaplan MJ. J Immunol. 2009 Aug 15;183(4):2729-40. Epub 2009 Jul 20.

Mouse models of diabetic nephropathy.
Brosius FC 3rd, Alpers CE, Bottinger EP, Breyer MD, Coffman TM, Gurley SB, Harris RC, Kakoki M, Kretzler M, Leiter EH, Levi M, McIndoe RA, Sharma K, Smithies O, Susztak K, Takahashi N, Takahashi T; Animal Models of Diabetic Complications Consortium. J Am Soc Nephrol. 2009 Dec;20(12):2503-12. Epub 2009 Sep 3. Review.

Network analysis of genes regulated in renal diseases: implications for a molecular-based classification.
Bhavnani SK, Eichinger F, Martini S, Saxman P, Jagadish HV, Kretzler M. BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S3.

The ubiquitin-like protein FAT10 mediates NF-kappaB activation.
Gong P, Canaan A, Wang B, Leventhal J, Snyder A, Nair V, Cohen CD, Kretzler M, D'Agati V, Weissman S, Ross MJ. J Am Soc Nephrol. 2010 Feb;21(2):316-26. Epub 2009 Dec 3.

Human nephrosclerosis triggers a hypoxia-related glomerulopathy.
Neusser MA, Lindenmeyer MT, Moll AG, Segerer S, Edenhofer I, Sen K, Stiehl DP, Kretzler M, Gröne HJ, Schlöndorff D, Cohen CD. Am J Pathol. 2010 Feb;176(2):594-607. Epub 2009 Dec 17.

The management of diabetic neuropathy in CKD. 
Pop-Busui R, Roberts L, Pennathur S, Kretzler M, Brosius FC, Feldman EL. Am J Kidney Dis. 2010 Feb;55(2):365-85. Epub 2009 Dec 30. Review. No abstract available.

BASP1 promotes apoptosis in diabetic nephropathy. 
Sanchez-Niño MD, Sanz AB, Lorz C, Gnirke A, Rastaldi MP, Nair V, Egido J, Ruiz-Ortega M, Kretzler M, Ortiz A. J Am Soc Nephrol. 2010 Apr;21(4):610-21. Epub 2010 Jan 28.

NFkappaB promotes inflammation, coagulation, and fibrosis in the aging glomerulus.
Wiggins JE, Patel SR, Shedden KA, Goyal M, Wharram BL, Martini S, Kretzler M, Wiggins RC. J Am Soc Nephrol. 2010 Apr;21(4):587-97. Epub 2010 Feb 11.

Loss of collagen-receptor DDR1 delays renal fibrosis in hereditary type IV collagen disease.
Gross O, Girgert R, Beirowski B, Kretzler M, Kang HG, Kruegel J, Miosge N, Busse AC, Segerer S, Vogel WF, Müller GA, Weber M. Matrix Biol. 2010 Jun;29(5):346-56. Epub 2010 Mar 20.

Linking variants from genome-wide association analysis to function via transcriptional network analysis.
Keller B, Martini S, Sedor J, Kretzler M. Semin Nephrol. 2010 Mar;30(2):177-84. Review.

Systematic analysis of a novel human renal glomerulus-enriched gene expression dataset.
Lindenmeyer MT, Eichinger F, Sen K, Anders HJ, Edenhofer I, Mattinzoli D, Kretzler M, Rastaldi MP, Cohen CD. PLoS One. 2010 Jul 12;5(7):e11545.

The detrimental effects of IFN-a on vasculogenesis in lupus are mediated by repression of IL-1 pathways: potential role in atherogenesis and renal vascular rarefaction.
Thacker SG, Berthier CC, Mattinzoli D, Rastaldi MP, Kretzler M, Kaplan MJ. J Immunol. 2010 Oct 1;185(7):4457-69. Epub 2010 Aug 30.

A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue.
Hodgin JB, Borczuk AC, Nasr SH, Markowitz GS, Nair V, Martini S, Eichinger F, Vining C, Berthier CC, Kretzler M, D'Agati VD. Am J Pathol. 2010 Oct;177(4):1674-86. Epub 2010 Sep 16.

Intrarenal production of B-cell survival factors in human lupus nephritis.
Neusser MA, Lindenmeyer MT, Edenhofer I, Gaiser S, Kretzler M, Regele H, Segerer S, Cohen CD. Mod Pathol. 2011 Jan;24(1):98-107. Epub 2010 Oct 1.

A molecular signature of proteinuria in glomerulonephritis. 
Reich HN, Tritchler D, Cattran DC, Herzenberg AM, Eichinger F, Boucherot A, Henger A, Berthier CC, Nair V, Cohen CD, Scholey JW, Kretzler M. PLoS One. 2010 Oct 18;5(10):e13451.

Integrative biology of renal disease: toward a holistic understanding of the kidney's function and failure.
Kretzler M, Cohen CD. Semin Nephrol. 2010 Sep;30(5):439-42. No abstract available.

Discovering hidden relationships between renal diseases and regulated genes through 3D network visualizations. 
Bhavnani SK, Ganesan A, Hall T, Maslowski E, Eichinger F, Martini S, Saxman P, Bellala G, Kretzler M. BMC Res Notes. 2010 Nov 11;3:296.

Bone Morphogenetic Protein (BMP)-7 expression is decreased in human hypertensive nephrosclerosis.
Bramlage CP, Tampe B, Koziolek M, Maatouk I, Bevanda J, Bramlage P, Ahrens K, Lange K, Schmid H, Cohen CD, Kretzler M, Müller GA. BMC Nephrol. 2010 Nov 16;11:31.

The role of bone morphogenetic protein-5 (BMP-5) in human nephrosclerosis.
Bramlage CP, Müller GA, Tampe B, Bevanda J, Maatouk I, Koziolek M, Lange K, Ahrens K, Schmid H, Cohen CD, Bramlage P, Kretzler M, Strutz F. J Nephrol. 2011 Feb 8. pii: B9752D67-46BE-43BF-AF09-C3A0390FFAA5. [Epub ahead of print]

Kindlin-2 regulates podocyte adhesion and fibronectin matrix deposition through interactions with phosphoinositides and integrins.
Qu H, Tu Y, Shi X, Larjava H, Saleem MA, Shattil SJ, Fukuda K, Qin J, Kretzler M, Wu C. J Cell Sci. 2011 Feb 15. [Epub ahead of print]

A unique hybrid renal mononuclear phagocyte activation phenotype in murine systemic lupus erythematosus nephritis. 
Bethunaickan R, Berthier CC, Ramanujam M, Sahu R, Zhang W, Sun Y, Bottinger EP, Ivashkiv L, Kretzler M, Davidson A. J Immunol. 2011 Apr 15;186(8):4994-5003. Epub 2011 Mar 16. PMID: 21411733

A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology. 
Mirel B, Eichinger F, Keller BJ, Kretzler M. J Biomed Discov Collab. 2011 Mar 21;6:1-33. doi: 10.5210/disco.v6i0.3410. PMID: 21455901

Role of mTOR in podocyte function and diabetic nephropathy in humans and mice.
Gödel M, Hartleben B, Herbach N, Liu S, Zschiedrich S, Lu S, Debreczeni-Mór A, Lindenmeyer MT, Rastaldi MP, Hartleben G, Wiech T, Fornoni A, Nelson RG, Kretzler M, Wanke R, Pavenstädt H, Kerjaschki D, Cohen CD, Hall MN, Rüegg MA, Inoki K, Walz G, Huber TB. J Clin Invest. 2011 May 23. pii: 44774. doi: 10.1172/JCI44774. PMID: 21606591

mTORC1 activation in podocytes is a critical step in the development of diabetic nephropathy in mice.
Inoki K, Mori H, Wang J, Suzuki T, Hong S, Yoshida S, Blattner SM, Ikenoue T, Rüegg MA, Hall MN, Kwiatkowski DJ, Rastaldi MP, Huber TB, Kretzler M, Holzman LB, Wiggins RC, Guan KL. J Clin Invest. 2011 May 23. pii: 44771. doi: 10.1172/JCI44771. PMID: 21606597

Netting Neutrophils Induce Endothelial Damage, Infiltrate Tissues, and Expose Immunostimulatory Molecules in Systemic Lupus
rythematosus.

Villanueva E, Yalavarthi S, Berthier CC, Hodgin JB, Khandpur R, Lin AM, Rubin CJ, Zhao W, Olsen SH, Klinker M, Shealy D, Denny MF, Plumas J, Chaperot L, Kretzler M, Bruce AT, Kaplan MJ. J Immunol. 2011 May 25. PMID: 21613614

Transcriptional Profiling of Diabetic Neuropathy in the BKS db/db Mouse: A Model of Type 2 Diabetes.
Pande M, Hur J, Hong Y, Backus C, Hayes JM, Oh SS, Kretzler M, Feldman EL. Diabetes. 2011 May 26. PMID: 21617178

{alpha}-Actinin-4 and CLP36 Deficiences Contribute to Podocyte Defects in Multiple Human Glomerulopathies.
Liu Z, Blattner S, Tu Y, Tisherman R, Wang J, Rastaldi M, Kretzler M, Wu C. J Biol Chem. 2011 Sep 2;286(35):30795-805. Epub 2011 Jun 16.

CKD in Hispanics: Baseline Characteristics from the CRIC (Chronic Renal Insuffiency Cohort) and Hispanic-CRIC Studies.
Fischer MJ, Go AS, Lora CM, Ackerson L, Cohan J, Kusek JW, Mercado A, Ojo A, Ricardo AC, Rosen LK, Tao K, Xie D, Feldman HI, Lash JP; CRIC and H-CRIC Study Groups. Am J Kidney Dis. 2011 Aug;58(2):214-27. Epub 2011 Jun 25.

Periostin is induced in glomerular injury and expressed de novo in interstitial renal fibrosis.
Sen K, Lindenmeyer MT, Gaspert A, Eichinger F, Neusser MA, Kretzler M, Segerer S, Cohen CD. Am J Pathol. 2011 Oct;179(4):1756-67. Epub 2011 Aug 18.

Alteration of forkhead box O (foxo4) acetylation mediates apoptosis of podocytes in diabetes mellitus.
Chuang PY, Dai Y, Liu R, He H, Kretzler M, Jim B, Cohen CD, He JC.PLoS One. 2011;6(8):e23566. Epub 2011 Aug 17.

Cardiovascular disease among hispanics and non-hispanics in the chronic renal insufficiency cohort (CRIC) study.
Ricardo AC, Lash JP, Fischer MJ, Lora CM, Budoff M, Keane MG, Kusek JW, Martinez M, Nessel L, Stamos T, Ojo A, Rahman M, Soliman EZ, Yang W, Feldman HI, Go AS; CRIC and HCRIC Investigators. Clin J Am Soc Nephrol. 2011 Sep;6(9):2121-31.

Activation of innate immune defense mechanisms contributes to polyomavirus BK-associated nephropathy.
Ribeiro A, Wörnle M, Motamedi N, Anders HJ, Gröne EF, Nitschko H, Kurktschiev P, Debiec H, Kretzler M, Cohen CD, Gröne HJ, Schlöndorff D, Schmid H. Kidney Int. 2012 Jan;81(1):100-11. doi: 10.1038/ki.2011.311. Epub 2011 Sep 14.

The identification of gene expression profiles associated with progression of human diabetic neuropathy.
Hur J, Sullivan KA, Pande M, Hong Y, Sima AA, Jagadish HV, Kretzler M, Feldman EL. Brain. 2011 Nov;134(Pt 11):3222-35. Epub 2011 Sep 16.

A systems view of genetics in chronic kidney disease.
Keller BJ, Martini S, Sedor JR, Kretzler M. Kidney Int. 2012 Jan;81(1):14-21. doi: 10.1038/ki.2011.359. Epub 2011 Oct 19.

Inflammasome activation of IL-18 results in endothelial progenitor cell dysfunction in systemic lupus erythematosus.
Kahlenberg JM, Thacker SG, Berthier CC, Cohen CD, Kretzler M, Kaplan MJ. J Immunol. 2011 Dec 1;187(11):6143-56. Epub 2011 Nov 4.

Urine glycoprotein profile reveals novel markers for chronic kidney disease.
Vivekanandan-Giri A, Slocum JL, Buller CL, Basrur V, Ju W, Pop-Busui R, Lubman DM, Kretzler M, Pennathur S. Int J Proteomics. 2011;2011:214715. Epub 2011 Oct 10.

The NIH National Center for Integrative Biomedical Informatics (NCIBI).
Athey BD, Cavalcoli JD, Jagadish HV, Omenn GS, Mirel B, Kretzler M, Burant C, Isokpehi RD, Delisi C; the NCIBI faculty, trainees, and staff. J Am Med Inform Assoc. 2012 Mar 1;19(2):166-170. Epub 2011 Nov 19.

Bcl-2-modifying factor induces renal proximal tubular cell apoptosis in diabetic mice.
Lau GJ, Godin N, Maachi H, Lo CS, Wu SJ, Zhu JX, Brezniceanu ML, Chénier I, Fragasso-Marquis J, Lattouf JB, Ethier J, Filep JG, Ingelfinger JR, Nair V, Kretzler M, Cohen CD, Zhang SL, Chan JS. Diabetes. 2012 Feb;61(2):474-84. Epub 2011 Dec 30.