DNA damage and repair Flashcards
(32 cards)
DNA damage
DNA can be hit by both endogenous sources like a DNA replication stress or through metabolic reactions, reactive oxygen species.
There are also external sources that can cause DNA damage and this can be through
Radiation- different types, ionizing radiation ultraviolet radiation through the sunlight.
And of course the chemotherapies often act by inducing DNA damage.
and through various other environmental chemicals carcinogenics and food, etc
So they cause all sorts of lesions
- there are many different types of lesions that the DNA can get inflicted
DNA repairs
most lesions are rapidly repaired
these repair mechanisms are highly specialized to the type of lesion
- there are the lesion specific DNA repair Pathways that deal with different lesions in a very much evolved and optimized way
- you have for instance mismatch repair which deals with base mismatches
- base excision repair that deals with single strand breaks
- nucleotide excision repair deals with adducts and intrastrand crosslinks
- homologous recombination and non homologous eng joining deal with double strand breaks and interstrand cross links
the DNA damage response
- DNA damage sensor proteins
- recruitment of mediator proteins
- signal amplification:
- effector proteins mediate downstream responses
- DNA repair
- chromatin changes
- gene expresison
- apoptosis, senescence
when do different repairs happen
there is a few different Pathways And these Pathways don’t act at the same time on different DNA double strand breaks and they’re very much directed by the cell cycle stage for which pathway is chosen
- and that’s critical because these Pathways have different advantages and disadvantages.
double stranded breaks activate different repair an signalling pathways depending on cell cycle stage
DNA repairs - G1 phase
You have different players that act on the break that are present like the Upstream signaling sensor protein ATM
- . It’s a major Upstream signaling kinase, and it leads to Downstream signaling for inducing G1 checkpoints via check 2 p 53 pathways.
DNA repairs - G2
if you encounter a double strand break in G2 or S phase There’s a the critical difference because you have a homologous sequence present
- in these cell cycle stages You have a sister chromatid present, which means that also in this stage there is a different type of signaling mechanism.
- This is a largely coordinated through an upstream protein kinase called ATR which is related to ATM and you have a all sorts of different proteins that are signalling these breaks
homologous recombination repair in S phase and G2
- in sg2 the sister chromatid is present and this gives the cell a huge Advantage because a break has the potential to take that information from the homologous sequence and repair it in an accurate way.
- So this is a fantastic mechanism because you can repair the DNA to what it was before without any mutations that could cause trouble
non homologous pathway in G1
in G1 you don’t have that homologous sequence present.
- And in that case you have NHEJ - It’s a non-homologous pathway.
- So it essentially involves very little processing of the DNA ends and just joining them together, but that means that you can induce mutations in that pathway
○ but it’s still better than leaving this Break unrepaired to cause trouble later on.
lesions
these lesions are not necessarily static. So they
might start as 1 type of lesion, but due to the cell being very active and having all sorts of chemical processes going on they can transition into a different lesion
and this can happen between single Strand breaks and double strand breaks
PARP enzymes
function of PARP enzymes is crucial for single-strand break repair
single strand break repair
usually it is repaired very quickly and then that’s fine.
- It’s not as a cytotoxic as a double strand break can be but if there is a problem with repairing it means that the cell will go into DNA replication in s-phase and that single strand break will cause problems with that.
- And in fact, this single strand brea will become a double strand break and because of its nature of being single-ended It has to be repaired by homologous recombination.
DNA damage that is not bad - Meiotic recombination
- the formation of gametes during meiosis.
- this happens in a way that you have to pair the homologous chromosomes
- and the way this happens relies on Having these chiasma forming
- there has a been a break that has been induced in the chromosome and is linked to the other Homologous chromosome to form the chiasma
- and by doing that you can pair them very tightly together And this is a entirely crucial for allowing that re combination to occur in a in an effective Manner
- and it is therefore required for the subsequent steps of accurate segregation of the homologous chromosomes.
DNA damage that is not bad - immune system - VDJ recombination
- diversity in antibody specificity is achieved during B cell development inside bone marrow
- double strand break induction and repair facilitate random arrangement of variable (V), diverse (D) and joining (J) genes that make up the variable, antigen recognising region of the antibodies
DNA double strand breaks and their repair is critical for antibody diversification and thus, a well functioning immune system
DNA damage that is not bad - Immune system - class switch recombination
there are different types of antibodies that are different in the time that they act after you have been infected.
- they’re optimized for the different stages of fighting off an infection.
- for each antibody class you need to Loop out and remove the different sections that don’t belong to the Antibody class that you you want to achieve
- So for doing that again, the DNA needs to be cut, its looped out and then it’s reconnected and you get the sequence aligned in a way that it can be transcribed to form the correct antibody class.
- So in that sense the DNA double strand breaks and their repair are important for switching to the different types of antibody classes.
- And this is important for facilitating a well functioning course at the different stages during an immune response.
DNA damage that is not bad - neural plasticity
recent findings indicate that the neuronal activity can induce DNA damage and that DNA damage and repair can alter neuronal transmission.
- So by doing that, DNA repair really modulates the neural plasticity and Alters the synaptic connections and transmission thereby contributing to neural plasticity.
Alterations in the DNA damage response
there are sometimes alterations in the DNA damage response
- This can be through hereditary Gene defects or mutations in different DNA damage response genes
Often This is so critical that is it is incompatible with life but some mutations can lead to these hereditary syndromes
mutation in ATM
ATM, - this Upstream kinase that starts signaling DNA double strand breaks in certain contexts.
- if you have a mutation in that Gene, it can have drastic effects that can lead to neurodegeneration, immune defects and Exquisite radio sensitivity, because they can’t repair the breaks properly
DNA damage in cancer
- It’s a very much a double-edged sword
- . So on the one hand, it’s one of the major Hallmarks of cancer - genome instability and mutation.
○ So in that sense, it leads to an increased mutational burden and can lead to oncogene activation, can lead to loss of tumor suppressors and tumorigenesis - but on the other hand this can also be exploited.
So the fact that there is genome instability and that these cells are rapidly proliferating as cancer cells means that They take on a lot of stress and they tend to have especially DNA replication stress.
DNA replication stress in cancer cells
- This is the prime target that is being exploited through most of the therapies that we have at the moment against cancer.
- So most of the common chemotherapies, radio therapies, they target this stress that is caused by this increased mutational burden genome instability
- The reason they do that is because it can tip the balance. So from slightly increased mutational burden that makes these cells flourish and develop cancers, It can completely lead to an overload and that is not good for the cancer cells either. So in fact if that balance is tipped enough it can cause the cells to die. So that’s what’s being exploited here with these types of Therapies.
side effectes that come with these therapies
hey are still quite untargeted, So that means normally proliferating cells are are also affected and of course that explains the side effects that come with these therapies
germline mutations
there are mutations that can happen in in the germ line and that can happen somatically
- for a germline variant, The variant/ pathogenic mutation is present in the gamete
- which means that because every cell arises from those the variation is present in every cell in the body including those in the germ line
- and because it persists in The Germ line, it is also passed on to The Offspring
for a recessive gene, that means when only 1 of the Alleles is affected by this pathogenic variant, the mutation is masked so you still have a functionality of that Gene because it’s sufficient to act from one allele.
somatic mutations
it’s absent in the gamete and it can occur in a foetal development or any time after birth in any cell of the body except those of the germ line,
which means that this is not passed on to The Offspring.
how can differences in cancer cells be targeted
a big group of these cancers has a defect that is related - BRCA defect
- it can be exploited
- There is an inhibitor that targets PARP enzymes
- and these PARP Inhibitors, the first one that was approved olaparib was found to specifically cause synthetically lethality with BRCA Alterations
- selective targeting is facilitated by a mechanism called synthetic lethality.
Was approved in 2014 and it has formed a paradigm for targeted cancer Therapeutics.
mechanism of synthetic lethality
you can imagine that 1 Gene is inactivated, but it’s a non-essential Gene. So the cell can still survive. And you have this for 2 different types of genes
- So inactivation of each gene individually is not harmful
- now if you inactivate both genes It causes a synthetic lethality.
○ So the cell dies and this forms the crucial foundation for targeted therapies like the ones exploited by olaparib.
