Functional profiling: from microarrays via cell-based assays to novel tumor relevant modulators of the cell cycle.
Cancer transcription microarray studies commonly deliver long lists of "candidate" genes that are putatively associated with the respective disease. For many of these genes, no functional information, even less their relevance in pathologic conditions, is established as they were identified in large-scale genomics approaches. Strategies and tools are thus needed to distinguish genes and proteins with mere tumor association from those causally related to cancer. Here, we describe a functional profiling approach, where we analyzed 103 previously uncharacterized genes in cancer relevant assays that probed their effects on DNA replication (cell proliferation). The genes had previously been identified as differentially expressed in genome-wide microarray studies of tumors. Using an automated high-throughput assay with single-cell resolution, we discovered seven activators and nine repressors of DNA replication. These were further characterized for effects on extracellular signal-regulated kinase 1/2 (ERK1/2) signaling (G1-S transition) and anchorage-independent growth (tumorigenicity). One activator and one inhibitor protein of ERK1/2 activation and three repressors of anchorage-independent growth were identified. Data from tumor and functional profiling make these proteins novel prime candidates for further in-depth study of their roles in cancer development and progression. We have established a novel functional profiling strategy that links genomics to cell biology and showed its potential for discerning cancer relevant modulators of the cell cycle in the candidate lists from microarray studies.
Arlt
Dorit
D
Division of Molecular Genome Analysis, German Cancer Research Center, Heidelberg, Germany.
Huber
Wolfgang
W
Liebel
Urban
U
Schmidt
Christian
C
Majety
Meher
M
Sauermann
Mamatha
M
Rosenfelder
Heiko
H
Bechtel
Stephanie
S
Mehrle
Alexander
A
Bannasch
Detlev
D
Schupp
Ingo
I
Seiler
Markus
M
Simpson
Jeremy C
JC
Hahne
Florian
F
Moosmayer
Petra
P
Ruschhaupt
Markus
M
Guilleaume
Birgit
B
Wellenreuther
Ruth
R
Pepperkok
Rainer
R
Sültmann
Holger
H
Poustka
Annemarie
A
Wiemann
Stefan
S
D000818:Animals; D002453:Cell Cycle / Q000235:genetics; D004261:DNA Replication; D020869:Gene Expression Profiling / Q000379:methods; D018816:Genes, cdc; D006801:Humans; D020935:MAP Kinase Signaling System / Q000235:genetics; D051379:Mice; D041681:NIH 3T3 Cells; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000096:biosynthesis / Q000235:genetics
D012333:RNA, Messenger