The uncovering of genes involved in susceptibility to the sporadic cancer types is a great challenge. It is well established that the way in which an individual deals with DNA damage is related to the chance to develop cancer. Mutagen sensitivity is a phenotype that reflects an individual’s susceptibility to the major sporadic cancer types, including colon, lung and head and neck cancer. A standard test for mutagen sensitivity is measuring the number of chromatid breaks in lymphocytes after exposure to bleomycin. The aim of the present study was to search for the pathways involved in mutagen sensitivity. Lymphoblastoid cell lines of seven individuals with a low mutagen sensitivity were compared with seven with a high score. RNA was isolated from cells exposed to bleomycin (4 hr) and unexposed cells. Micro-array analysis (19K) was used to compare gene expression of insensitive and sensitive cells. The profile of most altered genes after bleomycin exposure, analyzed in all fourteen cell lines, included genes involved in multiple processes, most prominent in cell proliferation and DNA repair. When comparing the insensitive and sensitive individuals other differentially expressed genes were found, that were involved in proliferation (e.g. BUB1) and signal transduction (e.g. DUSP4). This difference in expression profiles between mutagen sensitive and insensitive individuals justifies further studies aiming to elucidate the genes responsible for the development of sporadic cancers. Keywords: exposure to dna damaging agent, comparison of phenotypic response to dna damaging agent
Overall design
We analyzed 14 lymphoblastoid cell lines without and with exposure to bleomycin for 4hr. Seven of these fourteen were insensitive to bleomycin, meaning that few chromatide breaks were examined after exposure to bleomycin. The other seven were sensitive, meaning that in these cell lines a relatively high number of chromatide breaks could be detected after exposure to bleomcyin.
Supplementary information #1. Genes with a statistically different expression as a result of exposure to bleomycin, analyzed in 14 lymphoblastoid cell lines header descriptions
GENE
Genes responsive to bleomycin exposure
DESCRIPTION
Bleomycin-responsive gene descriptions
Data table
GENE
DESCRIPTION
INCREASED EXPRESSION BY BLEOMYCIN TREATMENT
CAMK1
Calcium/calmodulin-dependent protein kinase I
CDKN1A
Cyclin-dependent kinase inhibitor 1A (p21, Cip1)
XPC
Xeroderma pigmentosum, complementation group C
H2AFZ
H2A histone family, member Z
POLH
Polymerase (DNA directed), eta
FDXR
Ferredoxin reductase
RGS16
Regulator of G-protein signalling 16
FRDA
Frataxin
TNFSF7
Tumor necrosis factor (ligand) superfamily, member 7
TNFSF9
Tumor necrosis factor (ligand) superfamily, member 9
UBR1
Ubiquitin protein ligase E3 component n-recognin 1
BBC3
BCL2 binding component 3
CD37
CD37 antigen
ANKFY1
Ankyrin repeat and FYVE domain containing 1
CX3CL1
Chemokine (C-C motif) ligand 22
PPM1D
Protein phosphatase 1D magnesium-dependent, delta isoform
COL4A4
Collagen, type IV, alpha 4
DDB2
Damage-specific DNA binding protein 2, 48kDa
TKTL1
Transketolase-like 1
Total number of rows: 207
Table truncated, full table size 9 Kbytes.
Supplementary information #2. Genes with a differential expression between mutagen sensitive and insensitive lymphoblastoid cell lines header descriptions
GENE
Genes differentially expressed in bleomycin-sensitive cell lines
DESCRIPTION
Descriptions of bleomycin sensitivity-related genes
Data table
GENE
DESCRIPTION
HIGHER EXPRESSION IN SENSITIVE LINES
CDCA8
Cell division cycle associated 8
PPAT
Phosphoribosyl pyrophosphate amidotransferase
APRIN
Androgen-induced proliferation inhibitor
KCNJ14
Potassium inwardly-rectifying channel, subfamily J, member 14
BUB1
BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast)
MYO7A
Myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))
Cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa
USP47
Ubiquitin specific protease 47
MTCP1
Mature T-cell proliferation 1
RBPSUH
Recombining binding protein suppressor of hairless (Drosophila)
GRK1
G protein-coupled receptor kinase 1
CDC10
Septin 7
PTGER4
Prostaglandin E receptor 4 (subtype EP4)
JIK
Ribosomal protein S2
Total number of rows: 104
Table truncated, full table size 4 Kbytes.
Supplementary information #3. Z-normalized 4 0ver 4 hr ratios of the genes differently expressed when sensitive and insensitive persons were compared. On these figures the cluster of Figure 1 has been based header descriptions
GENE
Genes differently expressed when bleomycin-sensitive and -insensitive persons were compared
SENSITIVE 1
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 1
SENSITIVE 2
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 2
SENSITIVE 3
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 3
SENSITIVE 4
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 4
SENSITIVE 5
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 5
SENSITIVE 6
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 6
SENSITIVE 7
The 4- over 0-hour Z ratios of the 101 genes differently expressed in sensitive person 7
INSENSITIVE 1
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 1
INSENSITIVE 2
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 2
INSENSITIVE 3
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 3
INSENSITIVE 4
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 4
INSENSITIVE 5
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 5
INSENSITIVE 6
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 6
INSENSITIVE 7
The 4- over 0-hour Z ratios of the 101 genes differently expressed in insensitive person 7
Less...
More...