Genome Instability and Mutation
Genome Instability and Mutation
Genome Instability and Mutation
and Mutation
Not all cancer cells are equal, they evolve in response to selective pressure driven by accumulation of mutations.
Cancer cells have to out-compete nearby cells for nutrients and other resources, avoid immune cell attack, and
suppress apoptotic self-destruction.
Due to the aberrant proliferation associated with cancer cells, there is an increased tendency of genomic changes
and mutations that contribute to the damage of multiple genes regulating cell division and tumor suppression. This
is known as genomic instability. Genomic instability has the tendency to compound in cancer cells, since survival-
enhancing mutations increase the probability that those mutations will propagate in future cells.
A mutation is an alteration of an organism’s DNA sequence. The nucleotides that compose our DNA can be added,
replaced, or deleted, and single- or double-stranded breaks can occur within the DNA strand. Complete sections of
DNA can also swap positions, be inadvertently replicated, or deleted. Most of these mutations are not cancer-related.
They can either be spontaneous or the result of environmental insults like chemicals and radiation. Despite the high
probability that such mutations can occur, our DNA is maintained relatively error-free. Our genome surveillance and
maintenance systems, mitotic checkpoints and DNA repair mechanisms are always working to mitigate common
daily factors that attempt to mutate our genetic code. A defect in any of these systems can increase the DNA’s
susceptibility to mutations, resulting in genomic instability and an increased risk of malignancy.
ne such mechanism is the G2/M DNA damage checkpoint, which serves to prevent the cell from entering mitosis
O
(M-phase) with genomic DNA damage, facilitating genome surveillance and DNA repair. There are several key
proteins involved:
• D
NA-dependent protein kinase (DNA-PK), a serine/threonine kinase complex composed of a heterodimer of
Ku proteins (Ku70/Ku80) and the catalytic subunit DNA-PKcs, is deployed to the site of double-stranded DNA
breaks almost instantly to initiate repair via non-homologous end joining.
• B RCA1 and BRCA2, two tumor suppressors that are found in breast and other tissue, contribute to DNA repair,
chromosomal stability and transcriptional regulation in response to DNA damage. Studies have shown that,
in response to DNA damage, BRCA1 is hyperphosphorylated and translocated to specific sites within the
replication fork. BRCA1 has also been shown to regulate the expression levels of several genes activated in
response to DNA damage. In addition, BRCA1 is required for the S-phase and G2/M-phase mitotic checkpoints.
BRCA2 plays a slightly different role than BRCA1 and is predominantly active in maintaining chromosomal
stability and mitotic recombination. Both BRCA1 and BRCA2 have been shown to repair double-stranded DNA
breaks via homologous recombination.
• C
hk1 and Chk2 are key signaling transducers that are part of a complex network of gene integrity checkpoints,
damage detectors and tumor suppressors.
• p 53 is also known as the “guardian of the genome” for its role in conserving genomic stability. p53 plays a
central role in in a pathway that recognizes and mitigates oncogenic stress by halting proliferation and inducing
apoptosis/senescence in an attempt to allay accumulating DNA damage that could lead to malignancy. (Fun
fact, elephants have over 20 copies of the p53 gene to protect them from mutations.)
14
Aside from the genomic instability that arises from compounding DNA mutations, aberrant epigenetic modifications
can also dramatically change functional protein levels and affect genomic integrity. Two epigenetic mechanisms
that play an important role in genomic instability are DNA methylation and histone modifications. Hyper- and/or
hypomethylation of regulatory regions within genes can mimic DNA mutations and promote tumor progression. In
addition, the remodeling of chromatin structure via epigenetic modifications to histones can permit chromosomal
rearrangements that lead to chromosomal instability. Together, these epigenetic changes can also affect cell cycle
progression and checkpoint regulation, further contributing to genomic instability and cancer progression.
References:
1. Hanahan D, Weinberg RA (January 2000). “The Hallmarks of Cancer”. Cell. 100 (1): 57–70. doi:10.1016/S0092-8674(00)81683-9
2. Hanahan D, Weinberg RA (March 2011). “Hallmarks of Cancer: the next generation”. Cell. 144 (5):646-74. doi: 10.1016/j.cell.2011.02.013.
3. Rogakou, E.P. et al. (1998) J Biol Chem 273, 5858-68.
4. Burma, S. et al. (2001) J Biol Chem 276, 42462-7.
5. Rogakou, E.P. et al. (1999) J Cell Biol 146, 905-16.
Heterochromatin
UHRF1
Transcriptionally Inactive
Chromatin
Transcriptionally Active
Chromatin
UHRF1
DMAP1 DMAP1
HDAC2
NU PTF
Me
DNMT1 DNMT1
RF
NU PTF
B Me
Me
IR
RF
B Me
UV
PCNA
PCNA
Me Me
Repair n
Pericentric Heterochromatin tio
M
yla me on
H ethy
NBS1
D
eth 4
yla
ti
4K la
DNA Repair
em
Mre11 M 3K yla
tio
H eth
M 1 hV
M 1 hV
M 1 hV
M 1 hV
n
SU
HP SU
SU
SU
Transcription Initiation
39
39
39
39
ATM/ (MRN) em
e
De novo Cytosine Methylation
ATR D
HP
HP
HP
e
e
HIPK2 DNA-PK
Caffeine TF
BRCA1
Methylation Methylation Me
Me
TSS Me
Me
Active Gene TET1/2/3 TF TF H3K9me H3K36me
BRCA1 Demethylation Demethylation
WIP1 c-Abl Rad51
MDM4 Nucleosome Depleted Region Pericentric Heterochromatin
Nuclear Export, Inactive X Chromosome
Ubiquitination MDM2 p53 Chk2 Rad52 Rb-Mediated Repression M
eth
H
m n
Chk1 3 yla
tio
Transcription Elongation
em K7 tio
D
yla
e
eth 9m n
eth
n
27
tio
Nucleolar HDAC1 HDAC1
PC C1
PC C1
PC C1
PC C1
Inactive Gene
14-3-3 yla e
M
cdc25A
PR
PR
PR
PR
p19Arf
yla
3K
Sequestration
eth
tio
H
M
M
or MDM2 DNMT3L DNMT3A/B DNMT3A/B DNMT3L TSS n
em
p53 Stabilization
D
TRIP12 p300/ cdc25A/C Me
p53 PCAF cdc25
Nuclear Exclusion Me
Ubiquitination
cdc25A/B Inactive Genes MBD1 MeCP2 MBD2/4 Me Me
WIP1 AurA
HDAC
Bora
PLK1 NuRD Complex Inactive X Chromosome
TopoII BRCA1 14-3-3σ Reprimo GADD45 p21Cip1 CDK7 SCF SETDB1 CoREST Sin3A HDAC Hox Gene Repression Anti-Silencing
HP1 MCAF MBD1 SUV39H1 MeCP2 MBD2/4 ATP
p90RSK TSS Methylation Degree: + Mono † Di ‡ Tri
Myt1
Nuclear H4K20me H3K9me H3K27me H3K4me H3K36me H3K79me
Exclusion Methylases: Methylases: Methylases: Methylases: Methylases: Methylases:
SCF SET8 / KMT5A (+) PRDM3 / KMT8E (+) Ezh2 / KMT6 (+,†,‡) MLL1 / KMT2A (+,†,‡) NSD1 / KMT3B (+,†) DOTIL / KMT4 (+,†,‡)
Tet-Mediated Cytosine Demethylation NSD1 / KMT3B (+,†) PPRDM16 / KMT8F (+) NSD2 / KMT3G (+,†,‡) MLL2 / KMT2B (+,†,‡) SMYD2 / KMT3C (+,†) Demethylases:
ASH1L / KMT2H (+,†,‡) G9a/EHMT2 / KMT1C (+,†) NSD3 / KMT3F (†,‡) MLL3 / KMT2C (+) NSD2 / KMT3G (+,†) ???
Wee1 Ubiquitination Cytosine SUV420H1 / KMT5B (†,‡) EHMT1 / KMT1D (+,†) Demethylases: MLL4 / KMT2D (+) SET2 / KMT3A (‡)
DNMT BER ASH1L / KMT2H (+,†,‡) JHDM1D / KDM7A (+,†) SET1A / KMT2F (+,†,‡)
cdc2 Key SUV420H2 / KMT5C (†,‡) Demethylases:
NSD2 / KMT3G (+,†) PRDM2 / KMT8A (+,†,‡) PHF8 / KDM7B (+,†) SET1B / KMT2G (+,†,‡) JMJD1A / KDM2A (+,†)
—Cytosine
SE Cyclin B M-P Demethylases: PRDM8 / KMT8D (†) UTX / KDM6A (†,‡) NSD3 / KMT3F (+,†) JMJD1B / KDM2B (+,†)
PH A
5-Methylcytosine
H ASE —Methylcytosine JMJD3 / KDM6B (†,‡) NSD2 / KMT3G (+,†) JMJD2A / KDM4A (†,‡)
G2 -
JHDM1D / KDM7A (+,†) SUV39H1 / KMT1A (†,‡)
—5-Hydroxy PHF8 / KDM7B (+,†) SUV39H2/ KMT1B (†,‡) SET7 / KMT7 (†) JMJD2B / KDM4B (†,‡)
Methylcytosine Tet 1/2/3 TDG ESET / KMT1E (†,‡) SMYD3 / KMT3E (†,‡) JMJD2C / KDM4C (†,‡)
—H3K9me3 CLLD8 / KMT1F (†,‡) ASH1L / KMT2H (+,†,‡) JMJD2D / KDM4D (†,‡)
5-Hydroxy Demethylases: PRDM9 / KMT8B (‡) KDM4DL / KDM4E (†,‡)
—H3K4me0 Methylcytosine 5-Carboxycytosine
AOF1 / KDM1B (+,†) Demethylases:
—H3K36me3 JMJD1A / KDM3A (+,†) LSD1 / KDM1A (+,†)
—H3K27 Acetyl Tet 1/2/3 Tet 1/2/3 JMJD1B / KDM3B (+,†) AOF1 / KDM1B (+,†)
5-Formylcytosine JMJD1C / KDM3C (+,†) JARID1A / KDM5A (†,‡)
JHDM1D / KDM7A (+,†) JARID1B / KDM5B (†,‡)
PHF8 / KDM7B (+,†) JARID1C / KDM5C (†,‡)
JMJD2A / KDM4B (†,‡) JARID1D / KDM5D (†,‡)
JMJD2B / KDM4B (†,‡)
JMJD2C / KDM4C (†,‡)
rev. 06/14/18 JMJD2D / KDM4D (†,‡)
KDM4E / KDM4DL (†,‡)
16
Once a tumor is established, it can circumvent immune detection through various mechanisms including antigen loss,
down-regulation of major histocompatibility molecules, alteration of the endogenous antigen presentation pathways, and
immune suppression via cytokine secretion. Along with their ability to evade detection by the immune system, tumors
can also hijack immune cells to promote self-growth and metastasis. Immune suppression and subversion by a tumor
generally occur in a step-wise manner.
Immune Checkpoints
Immune checkpoints refer to the built-in control mechanisms of the immune system that maintain self-tolerance and
help to avoid collateral damage during a physiological immune response. Research has shown that tumors engineer
microenvironments to evade immune surveillance and attack, particularly by modulating certain immune checkpoint
pathways3.
Because T cells are the primary effector immune cells, they express multiple autoinhibitory cell surface receptors, such
as lymphocyte-activation gene 3 (LAG-3), programmed cell death protein 1 (PD-1) and cytotoxic T-lymphocyte-associated
protein 4 (CTLA-4), that modulate their response. Within the tumor microenvironment, tumor cells can upregulate the
ligands to these receptors to enhance tumor tolerance and evade eradication by the immune system.
In recent years, pharmacological modulators of these ligand-receptor interactions, known as immune checkpoint
therapies, have been intensely researched and deployed as novel immunotherapy agents to treat cancers. Of particular
interest are monoclonal antibodies against PD-1 and CTLA-4. Given the early success of these immune checkpoint
therapies in activating anti-tumor immune responses, creating immunotherapies targeting other co-inhibitory and co-
stimulatory receptors and their ligands in order appears to be a compelling therapeutic strategy.
Learn more about the pathways and proteins involved in Tumor-promoting Inflammation:
• NF-κB Signaling
• Inflammasome Signaling
• Tumor-infiltrating Markers
• Immune Checkpoints in the TME
References
1. Hanahan D, Weinberg RA (January 2000). “The Hallmarks of Cancer”. Cell. 100 (1): 57–70. doi:10.1016/S0092-8674(00)81683-9
2. Hanahan D, Weinberg RA (March 2011). “Hallmarks of Cancer: the next generation”. Cell. 144 (5):646-74. doi: 10.1016/j.cell.2011.02.013.
3. Sharma P, Allison JP. The future of immune checkpoint therapy. 2015;348(6230):56-61
IKKβ IKKα ub β-TrCP IKKα IKKβ NEK7 hCasp-4,5 CD16+and (M) MDSCs DCs CD86+or T Cells (Th) NKT (iNKT) NK Cells Switched
ub CD66b+or CD15–and CD1c+ CD80+or CD4+ TCR Vα24 Vβ11+ CD56 low and Memory
SHARPIN IKKγ/ NEMO NLRP3 CD15/SSEA1+ CD14+and iNOS+ CD16+ IgD –and
NEMO HLA-DR – CD1c–and Th1 Type II Cytotoxic CD27+
ub IKKα IKKα Mitochondria Eosinophils CD141–or M2-like T-Bet+ NKT
ub ub Granzyme+
β-TrCP • mtDNA Gasdermin D CD193+and
Siglec-8+and
Polymorphonuclear
(PMN) MDSCs
CLEC9A–
DCs
CD163+or
CD206+
Th2 or Perforin+
Unswitched
IgD+and
• mtROS cleavage CD16 – CD15+and CD1c –and
GATA-3+
JNK
CD27+
CD14–and CD141– or Th17 PB Immature
ub ub • NLRP3 NAIPs NLRC4
p65/ ASC Basophils HLA-DR – CLEC9A – or RORγt+ / Regulatory
IKKγ/
Nucleus NF-κB p65/ ac CBP/ NEMO IKKα IKKα
p50/52 RelA p300 Gasdermin pyroptosis Myeloid Cells Lymphoid Cells
Class
PIASγ ATM PARP1 Siglec-H+and CD11c+and F4/80 high CD14+and CD3+ CD3+and NK1.1+or CD19+ BCMA+or
NOX2 phagosome maturation CD317+ MHCII + F4/80 – NK1.1+ NKp46+or Naïve CD138+
Survival, Proliferation, Inflammation, Immune Regulation Lymphogenesis, B Cell Maturation us
Activated NKG2D+and
IgD+and
cle CD3 –
Nu glycolytic enzymes metabolism Neutrophils Monocytic CD83+ XCR1/ M1-like Helper Type I Activated
CD27 –
F4/80 med and (M) MDSCs CLEC9A+ CD86+or T Cells (Th) NKT (iNKT) Switched
Ly-6G+ Ly6C+and DCs CD80+or CD4+ TCR Vα14-Jα18+ CD69+ Memory
p65/RelA NLRP3 Ly6G–and (excel at cross- iNOS+ IgD –and
NF-κB Eosinophils Arginase+ presentation) Th1 Type II Cytotoxic
pro-IL-1β IL-1β XCR1+or CD27+
CD193+and M2-like T-Bet+ NKT
inflammation F4/80 med and Polymorphonuclear CLEC9A+ CD163+or Th2
Granzyme+
or Perforin+
Unswitched
pro-IL-18 IL-18 Siglec-F+ (PMN) MDSCs
CD8α+
CD206+or GATA-3+ IgD+and
Ly6C lowand Arginase+ CD27+
Basophils Resident
Ly6G+and Th17
FcεR1α+and DCs RORγt+
Arginase+
CD117 – CD8α+
Treg
FoxP3+and
Subtypes
rev. 12/19/18
Learn more about Adherens Junction Signaling and the proteins involved.
References
1. Hanahan D, Weinberg RA (January 2000). “The Hallmarks of Cancer”. Cell. 100 (1): 57–70. doi:10.1016/S0092-8674(00)81683-9
2. Hanahan D, Weinberg RA (March 2011). “Hallmarks of Cancer: the next generation”. Cell. 144 (5):646-74. doi: 10.1016/j.cell.2011.02.013.
3. G
arcia, Miguel A. (April 2018). “Cell-Cell Junctions Organize Structural and Signaling Networks to Regulate Epithelial Tissue Homeostasis”. Cold
Spring Harb Perspect Biol. 2; 10(4): a029181.
4. H
artstock A, Nelson WJ (March 2008). “Adherens and Tight Junctions: Structure, Function and Connections to the Actin Cytoskeleton”. Biochim
Biophys Acta. 1778(3): 660–669.
Adherens Junction
Signaling
Cytoplasm
Nectin
Maintenance
Extracellular
Space Disassembly
Formation
Cadherin PTPµ
Nectin
Cadherin
δ-cat Rac
Fyn Gβ1 δ-cat δ-cat
Clathrin
p190 RhoA IQGAP
α-cat β-cat Afadin Afadin
δ-cat β-cat Caveolin
SH2D1A Vinculin α-cat Ub UbUb
Cytoplasm c-Cbl E3
β-cat Tiam1
α-cat Vin β-cat
cu LAMTOR1 γ-cat
lin
Rac PRK1 Rac Formin WASP
Par3/6 aPKC α-cat Axin1
PI3K CK2 Ajuba
RhoA
Actin bundles Cip4
ARHGAP1
IQGAP
Src
δ-cat PTP1B
Akt α α
Ect2 Cortactin
cdc42 mDIA
β-cat α-cat
IQGAP α α-actinin
Centralspindlin
ndocytosis
Remodeling
herin
β-cat
Src
Cad
α-cat β-cat
• Actin Nucleation ROCK Cadherin APC
RaIA
• Actin Dynamics Recycling Ub
6
5
10
8 9
1. GITR (D9I9D) Rabbit mAb (IHC Preferred) #68014 (lung). 2. PD-1 (D4W2J) XP® Rabbit mAb #86163 (colon). 3. TIM-3 (yellow), CD8α (magenta), PD-1 (green),
CD68 (Red), LAG3 (orange), Pan-Keratin (cyan) on FFPE NSCLC. 4. PD-L1 (E1L3N®) XP® Rabbit mAb #13684 (lung). 5. PD-L2 (orange), PD-L1 (E1L3N®) (red), CD68
(green), PD-1 (yellow), CD8α (magenta) & Pan-Keratin (cyan) on FFPE tonsil. 6. PD-1 (green), CD68 (yellow), PD-L1 (E1L3N®) (magenta), PD-L2 (red), CD8α (orange),
Pan-Keratin (cyan), DAPI (blue) on FFPE NSCLC. 7. IDO (D5J4E™) Rabbit mAb #86630 (breast). 8. PD-1 (green), TIM-3 (yellow), B7-H4 (negative), LAG3 (magenta), B7-
H3 (red) & VISTA (orange) on FFPE NSCLC. 9. PD-L1 (E1L3N®) (red), PD-1 (green), TIM-3 (yellow), CD8α (magenta), LAG3 (orange), Pan-Keratin (cyan) on FFPE breast
adenocarcinoma. 10. TIM-3 (D5D5R™) XP® Rabbit mAb #45208 (tonsil).
TRUST
CST
970K commuter miles
offset
10K+ hours
mentoring/year 145,810 Ab
product citations
$3M in
green energy
$1M in small
grant awards
6/10
top-cited Abs
SCIENCE
$2.5M in charitable
donations
For the next 20, we’ll keep delivering the most Consistent, Sensitive, and
Trustworthy antibodies possible because we believe every antibody should create
a pathway to success.
cst-science.com/20
19-CEL-85764-BKL