High density gene expression microarrays and gene ontology analysis for identifying processes in implanted tissue engineering constructs.
The in vivo performance of tissue-engineered constructs is often based on generally accepted read-out parameters, like (immuno)histology. In this study, high-density gene expression microarrays and gene ontology (GO) analysis were used as a read-out tool to identify the biological processes occurring after implantation of an acellular collagen-based skin construct using a rat full-thickness wound model. A freely-available program (DAVID) was used to identify up/downregulated biological processes (GO-terms) and results were compared to wound healing/regeneration without a construct. The entire process from RNA isolation to biological interpretation is explained step-by-step. Conventional (immuno)histology was used to validate the biological processes identified and indicate that microarray analysis may provide a valuable, fast and unbiased tool to evaluate the in vivo performance of tissue-engineered constructs. However, challenges remain e.g. with regards to the development of specific GO-terms and annotation of the (rat) genome.
Lammers
Gerwen
G
Department of Biochemistry 280, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands.
Gilissen
Christian
C
Nillesen
Suzan T M
ST
Uijtdewilligen
Peter J E
PJ
Wismans
Ronnie G
RG
Veltman
Joris A
JA
Daamen
Willeke F
WF
van Kuppevelt
Toin H
TH
D000818:Animals; D020869:Gene Expression Profiling / Q000295:instrumentation; D005786:Gene Expression Regulation; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation; D012313:RNA / Q000235:genetics / Q000302:isolation & purification; D051381:Rats; D017208:Rats, Wistar; D012867:Skin / Q000378:metabolism / Q000648:ultrastructure; D017768:Skin, Artificial; D023822:Tissue Engineering
D012313:RNA