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DNA damage, repair and diseasesProf. Tsai-Kun (TK) Li,
Dept. & Grad. Inst. of Microbiology,
National Taiwan University College of Medicine
88287/88294; tsaikunli@ntu.edu.tw
DNA
synthesis
Growth
Growth
Parental
cell
Offspring
cells
Mitosis
Cell division
G0: somatic cells
Genome integrity
2015: The Year of Repair (Molecular Cell vol.60)
Dept. Biochemistry and
Molecular Biology
National Taiwan University
College of Medicine
Prof. Jing-Jer Lin
Dept. Clinical Laboratory
Sciences and Medical
Biotechnology
National Taiwan University
College of Medicine
Prof. Jing-Jer Lin
DNA damage response and signaling
Cell cycle Transcription DNA repair Cell death
checkpoint control program activation * direct reversal * apoptosis
* NER * necrosis
* MMR
* HR .… etc. …. etc.
Genome instability diseases & death
Endogenous Exogenous
3’
5’
Cellular replication Ionization Chemical UV light metabolism errors radiation damage exposure
Mitoticfailure
Local structure alteration created by DNA damage--- potential sources/substrates for detection
DNA damage, corresponding signaling & responses
Sources
Activation
Processing
Impacts
DSBSSB
Protein-
capped SSBBulky
adduct
MismatchChromatin
alteration
Telomere
dysfunctionRadio- and
chemotherapy
Alkylating
agentsReplication
errors
X-raysAID
UV light
Topoisomerase
3’
5’
U
GT^T
CH3
G8oxo
Oxidants
Sensors
Transducers
Effectors
DNA repair
Transcription
SOS
Apoptosis
Cell cycle
transitionsSTOP
Hiden
DSB
recognition
transduction
amplification
exo or endo
Types of DNA damage and corresponding repairs
Causes
Damages
Repair
pathways
DSBSSB
Protein-
capped SSBBulky
adduct
MismatchChromatin
alteration
Telomere
dysfunctionRadio- and
chemotherapy
Alkylating
agentsReplication
errors
X-raysAID
UV light
Topoisomerase
3’
5’
U
GT^T
CH3
G8oxo
Oxidants
MMR
BERHR
NHEJHR
NHEJ
Ub/
proteasome
SSA
BER
HR
NHEJ
NER
BER
removal
Chromatin
remodeling ?
Reversal ?
HR
NHEJ
Hiden
DSB
In prokaryotic cells
Bacterial DNA damage responses --- transcription activation and gene expression
SOS response Adaptive response Oxidative response
www.scielo.br/cgi-bin/wxis.exe/
?IsisScript=Sc...DNA repair and mutagenesis
(1995) Friedberg EC et al
SOS genes: uvrA/B/D
recN/F
ftsK, sulA
The network of SOS response to DNA damage
sensing
checkpoint
checkpoint
Recombination repair proteins in bacteria
Base excision repair (BER)
Nucleotide excision repair (NER)
Mismatch repair (MMR)
www.mun.ca/.../4103/topics/mutagenesis.htmlModified from
G TO6 O4
meme
The adaptive response to alkylating agents
G T
NTD CTD
meme
me
methyl
trasnfer
Induction of the OxyR regulon
In eukaryotic cells
Local structure alteration created by DNA damage:
--- sources/substrates for damage detection
Local chromatin alteration created by DNA damage:--- detection and repair accessibility
Isoforms
& tails
Histone modification after DNA damage:--- accessibility & signaling for downstream events
Cancer Science 97 (10), 984-989
H3 K56 acetylation H4K methylation
H2A & H2AX
ubiquitination
Enhanced P-P interactions
--- specificity
The general outline of DNA damage response --
- signal-transduction pathway in eukaryotic cells
Organization of DNA damage
response/pathway in mammalian cells
DNA-PK
Conserved recruitment of ATM, ATR and
DNA-PKcs to sites of DNA damage
ATMATR
DNA-PKcs
Oncogene (2005) 24, 2871–2876
ssDNA/RPA acts as a ligand for activation of
the ATR-CHK1 checkpoint pathway
ssDNA and RPA act
as an activation ligand
recruitment of
911 complex/ ATRIP
Claspin ?
focus formation:
cytological marker
5’ 3’ resection
Key kinase
molecule
for DDR
Formation of DNA damage foci --- an important cytological DNA damage marker ---
untreated
DNA
damage
signaling
recombination repair*
Watching the DNA repair ensemble dance
Cell. 2004 Sep 17;118(6):666-8
kinase
cascade
Cell. 2004 Sep 17;118(6):699-713
Model for recruitment of checkpoint and recombination proteins to a DSB
--- Choreography of checkpoint activation and DNA repair ---
Driving forces:--- phosphopeptide-binding molecules
FHA domain BRCT domainRad53 - pThrXXAsp BRCA1 - gH2AX (pSXXF)
pS/TQ
DNA damage: --- ubiquitin marks the damaging spot on chromatin
Nature Structural & Molecular Biology 15, 20 - 22 (2008)
Turning off DNA damage checkpoints
1. Reversal of activating phosphorylations: Protein phosphatases
could act to reverse the DNA damage induced phosphorylations.N.R. den Elzen, M.J. O’Connell, EMBO J. 23 (4) (2004) 908–918.
2. Proteolysis of activated checkpoint proteins: Ubiquitin-dependent
proteolysis of activated checkpoint proteins ---
phosphorylation/activation acts as a mark for ubiquitination
Y.W. Zhang, et al., Mol. Cell 19 (5) (2005) 607–18.
I. Mamely, et al., Curr. Biol. 16 (19) (2006) 1950–5.
3. Checkpoint antagonists: Independent pathways could antagonize
the cell cycle arrest induced by checkpoint activation.T.R. Coleman, Z. Tang, W.G. Dunphy, Cell 72 (1993) 919–29.
4. De-ubiquitination (DUB): USP13 & Brcc36.F. Nicassio et al. Curr. Biol. 17 (2007) 1972-7.
Nature Structural & Molecular Biology 15 (2008) 20-2.
Modification of the ubiquitin signal:not yet finished off
Nature Structural & Molecular Biology 15, 20 - 22 (2008)
USP28
DeUb EnzymeUSP28 in Control of the DNA-
Damage Response, Cell 126, 529–542, 2006
TAP-53BP1 IP USP28
Activation of repair pathway --- ssDNA and RPA act as a substrate for HR ---
Oncogene (2005) 24, 2871–2876
recruitment of
BRCA2/ DSS1
Homologous recombination (HR)Non-homologous
end joining (NHEJ)
Double strand break (DSB) repair
Mismatch Repair (MMR)
PLoS Biology June 2006 | Volume 4 | Issue 6 | e203
Nucleotide excision repair (NER)
ub
PLoS Biology June 2006 | Volume 4 | Issue 6 | e203
Transcription-coupled repair (TCR)
TFIIH Is a multi-functional protein complex--- Linking transcription and repair ---
PLoS Biology June 2006 | Volume 4 | Issue 6 | e203
Poly ADP-ribose polymerase-1 (PARP-1) in
transcription and repair
DNA damage, genome instability, cancer
development and aging
Colorectal cancer as an example
Parallel pathways of tumorigenesis
--- Hallmarks of cancer/where we stand in the fight against cancer
Emerging hallmarks & enabling characteristics
An evolving hallmark
Just accelerating?
Cancer arises from a series of genetic alterations that
promote resistance to apoptosis, self-sufficiency in
growth, cellular immortalization and escape from cell-
cycle-exit. Hanahan and Weinberg, Cell (2011) 144:646-74
Microenvironment
Genome instability and Cancer development
On and off Mis-regulation Genome instability Cancer
development
Cancer Types Inter-tumor heterogeneity Intra-tumor
heterogeneity
Many oncogenic mutations confer a cell-autonomous fitness
+ microenvironment (non-cell-autonomous driving of growth) ???
Genome instability Mutations Dysfunctions Diseases & Death
Endogenous Exogenous
3’
5’
Cellular replication Ionization Chemical UV light metabolism errors radiation damage exposure
Cell cycle Transcription DNA repair Cell death checkpoint control program activation * direct reversal * apoptosis
* NER * necrosis
Mitotic failure
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