Biology Reference
In-Depth Information
Germline DNA repair genetic variations may impact
upon DNA repair capacity by altering protein function
in cells. Genetic variations may include mutations and
single nucleotide polymorphisms (SNPs). SNPs are
single-base differences in the DNA sequence that can
be observed between individuals and are defined as
the least common allele occurring in 1% or more of
the population, whereas mutations occur in less than
1% (21). SNPs can alter amino acid sequence of the
encoded protein or affect RNA splicing and gene tran-
scription, resulting in either over or under expression
or altered functional activity of the encoded proteins.
In somatic tumors, a large body of preclinical and clin-
ical evidence indicate that altered DNA repair protein
expression may be involved in pathogenesis of tumors
and may impact on response to treatment. For example,
suboptimal DNA repair due to germline polymor-
phisms or mutations not only lead to genomic insta-
bility and predispose to cancer development but may
also lead to increased susceptibility to anticancer
DNA damaging agents. On the other hand, protein
overexpression in somatic tumors may contribute to
resistance to therapy.
In this chapter we will review the current status of
DNA repair predictive biomarkers in cancer. To facilitate
discussion of complex clinical data we will also provide
a brief overview of essential DNA repair pathways that
operate in man. Several recent reviews are available for
a detailed discussion of individual biochemical
pathways.
7
e
20
We have taken a pathway-specific
approach to describe clinical studies that have investi-
gated DNA repair factors at a genetic level (e.g. poly-
morphisms), transcriptional level (mRNA expression)
or at the protein level.
DNA polymerase
b
(Pol
b
) then adds the first nucleo-
tide to the 3
0
-end of the incised AP site and also
removes the 5
0
-sugar phosphate residue (by the process
of
b
-elimination) and DNA ligase III-XRCC1 hetero-
dimer (or DNA ligase I) then completes the repair. If
the 5
0
-sugar phosphate is resistant to
b
-elimination,
the repair process proceeds through the long-patch
pathway where proliferating cell nuclear antigen
(PCNA) is loaded onto the DNA by replication factor
C. PCNA functions as a DNA sliding clamp for Pol
d
/
3
which performs DNA synthesis to displace the 5
0
-
sugar phosphate as part of a flap. The flap is then
removed by flap endonuclease (FEN1) and long-patch
repair is completed by ligation of the DNA ends by
DNA ligase I. Another alternative branch exists within
the short-patch pathway that involves processing of
a damaged base by a bifunctional glycosylase endowed
with an AP lyase activity which cleaves the phospho-
diester backbone on the 3
0
-side of an AP site, leaving
a fragmented sugar derivative at the 3
0
-side of the
resulting strand break. The 3
0
-phosphodiesterase
activity of APE1 removes this polymerase-blocking
lesion in order for Pol
b
to fill in the gap and DNA
ligase III-XRCC1 heterodimer then completes the repair
process.
7,13,22,23
Members of the poly (ADP-ribose)
polymerase (PARP) family of proteins also have a
role in BER. These enzymes catalyze the addition of
poly (ADP-ribose) polymers to target proteins,
affecting protein
e
protein interactions and catalytic
activities.
24
PARP-1 and -2 have roles in the repair of
DNA damage, binding to both single- and double-
strand breaks.
25
e
29
Human AP Endonuclease (APE1)
APE1 is a ubiquitous multifunctional protein.
30
e
32
The
N-terminal domain is essential for the redox activity of
APE1 while the C-terminus is essential for the DNA
repair activity.
33
APE1 accounts for over 95% of the total
AP endonuclease activity in most cultured human cell
lines.
30,31,34,35
APE1 is a member of the highly conserved
exonuclease III family of AP endonucleases, named after
the E. coli homolog of APE1.
36
The C-terminal DNA
repair domain of APE1 cleaves the phosphodiester bonds
hydrolytically in a Mg
2
รพ
-dependent manner, leaving
a3
0
-hydroxyl group and a 5
0
-deoxyribose phosphate
(d RP) group flanking the nucleotide gap. APE1 also
performs roles in DNA repair other than AP
site elimination
37
such as 3
0
-phosphodiesterase,
38
3
0
-
phosphatase, 3
0
-5
0
exonuclease, and RNaseH
activity.
37,39,40
APE1 is also intimately involved in the
coordination of BER by interacting directly or indirectly
with other BER enzymes.
41
e
52
A separate domain in
APE1, located close to the N-terminus, performs a role
unrelated to the direct repair of DNA damage. This
BASE EXCISION AND SINGLE-STRAND
B
REAK REPAIR (
TABLE 12.
1
)
Base excision repair (BER) is essential for the
removal of bases that have been damaged by alkyl-
ation, oxidation or ring-saturation. This pathway also
deals with a variety of other lesions including deami-
nated bases. DNA single-strand breaks induced by
chemotherapeutic agents such as topoisomerase I
inhibitors are processed by single-strand break repair
(SSBR), a pathway related to BER. Although the
short-patch BER and long-patch BER sub-pathways
differ from each other in the length of the repair
patch and in the subsets of enzymes involved, both
sub-pathways are initiated by a damage-specific DNA
glycosylase, which removes the damaged base creating
an abasic site (apurinic/apyrimidinic, AP site). The AP
site is then cleaved by an AP endonuclease generating
a nick with 5
0
-sugar phosphate and 3
0
-hydroxyl group.
