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Microgravity Science and Technology

, Volume 30, Issue 6, pp 951–963 | Cite as

Gene Pathways Analysis of the Effects of Suspension Culture on Primary Human Renal Proximal Tubular Cells

  • Timothy G. HammondEmail author
  • Patricia L. Allen
  • Holly H. Birdsall
Original Article

Abstract

Drug-induced acute kidney injury causes massive morbidity and mortality at exorbitant cost, yet there is currently no effective method for preclinical in vitro testing for nephrotoxicity. Proximal tubule cells are a key target for nephrotoxins, but heretofore, it has been a challenge to maintain their differentiation in vitro. One promising approach is to culture them in suspension, under physiological levels of shear, so as to induce and maintain structural and functional differentiation. Advances in materials, additive manufacturing, and injection molding have reduced the complexity and cost of suspension cultures hardware by orders of magnitude, making it a viable alternative for high throughput screening. This study defines the global transcriptome responses of human renal proximal tubular cells to suspension culture. GSEA/Cytoscape/ClueGO analysis showed near perfect concurrence with GPS-SIGORA analysis in the areas of mineral absorption and ribosome assembly, and defined the nucleic acid and protein mechanisms underlying the transcriptome response to suspension culture. Proximal tubular cells in suspension culture showed increased growth and viability assayed as reducing potential compared to cells cultured under static conditions. Suspension culture of human renal proximal tubular cells now allows investigations in basic cell biology, toxicology, drug screening, and tissue engineering, free of artificial matrices, feeder layers, fetal gene expression, or the need for complex engineering technologies.

Keywords

Human renal proximal tubular cells Kidney Gene array Space flight, drug toxicity 

Abbreviations

ABC

ATP-binding cassette

FDR

False Discovery Rate

FWER

Family Wise Error Rate

GAPDH

glyceraldehyde 3-phosphate dehydrogenase

GO

Gene ontology

GPS

Gene-Pair Signatures

GSEA

Gene Set Enrichment Analysis

NES

Normalized Enrichment Scores

OAT

Organic anion transporter

OCT

Organic cation transporter

RFU

Relative fluorescence units

SIGORA

Signature Over-Representation Analysis

SLC

Solute carrier

Notes

Acknowledgements

NASA Grants NNX13AN32G, NNX12AM93G, and NNX10AP01G supported these studies. This material is the result of work supported with resources and the use of facilities at the Durham Veterans Affairs Medical Center and the Veterans Health Administration Office of Research and Development in the Department of Veterans Affairs. Contents do not represent the views of the Department of Veterans Affairs or the United States of America. We thank the Medical College of Georgia for performing gene arrays. We thank David Corcoran Ph.D. and the Duke Genomic Analysis and Bioinformatics Shared Resource for performing Gene Array analysis. We thank Erica Acton and Corey Nislow of the University of British Columbia for performing analysis both by Cytoscape using ClueGO and SIGORA. The authors declare that there is no conflict of interest regarding the publication of this paper.

Compliance with Ethical Standards

Conflict of Interest

The authors declare that they have no conflict of interest.

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2018

Authors and Affiliations

  1. 1.Medicine and Research & Development ServiceDurham VA Medical CenterDurhamUSA
  2. 2.Nephrology Division, Department of Internal MedicineDuke University School of MedicineDurhamUSA
  3. 3.Space Policy Institute, Elliott School of International AffairsGeorge Washington UniversityWashington, DCUSA
  4. 4.Department of Veterans Affairs Office of Research and DevelopmentWashington, DCUSA
  5. 5.Departments of Otorhinolaryngology, Immunology, and PsychiatryBaylor College of MedicineHoustonUSA

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