Note for: The DNA-damage response in human biology and disease

Note for: The DNA-damage response in human biology and disease

(doi: 10.1038/nature08467)

DNA damage response detection is very essential process in living organism to maintain the right balance between the diversity (fit well to the external) and the disease (unfit to the external).

1.DNA lesion can occur either both physiological and pathological condition.

2.physilogical lesion -- DNA mismatch//break by topo-i and topo-ii

Damage occurs through:

1.oxidative respiration

2.redox-cycling (membrane of mitochondria)

3.Fenton reaction (redox reaction catalyzed by Fe)

4.NOS and ROS produce during inflammation and infection

DNA double-strand break is rarely found but very toxic once it is generated.

DNA damage responses differentially occur depending on the classes of DNA lesions. The process could be separated as follow;

1.damage or stalled replication/transcription

2.detection by sensors

3.recruitment of mediators

4.amplifying the signal

5.transduce the signal

6.execute by effectors

Fig. Core process of DDR – the detailed molecules will be different according to the cellular physiology (type - stem cell or fully differentiate/state - divide or non-dividing).

DNA repair;

MMR-

1.detect the mismatch repair

2.SS incision

3.nuclease -->polymerase-->ligase-->lesion is fixed

Base-excision repair

1.recognized by glycosylase (remove base)

2.nuclease -->polymerase-->ligase-->lesion is fixed

NER -- 2 sub pw depending on lesions (remove 22-30 bases)

1.transcription-coupled NER

2.global-genome NER

Some lesions have been by-passed using less stringent base-pairing polymerase

DNA double strand break;

NHEJ-

KU - recognize the lesion and activating DNA-PK -->end-processing --> polymerases --> Lig4

Alt-NHEJ (microhomology-mediated end-joining MMEJ)

Both -- NHEJ and MMEJ create err0r prone but can occur in every cell cycle.

HR- restrict to S and G2 since it requires sister chromatid as template

Step for HR --> recognize by MRN cpx --> generate the ssDNA to invade the correct strand --> synthesis --> ligate --> resolve

HR helps restarting the stalled replication as well as the inter strand-cross link

Table informs the key proteins involving in DNA damage and repair

DNA damage;

1.recognize by RPA (replication protein A)

2.activate either ATM (db) or ATR (ss)

3.telling either CHK1 or CHK2 to inform CDK to slow down the replication process in order to fix the DNA lesion first!

3 check points throughout the replication; G1-S, intra-S and G2-M

Role of ATM and ATR; to send out the signal --

1.enhance transcription of DNA repair proteins

2.post-modification like phosphorylation, acetylation, ubiquitylation and SUMOylation.

If DNA damage cannot be solved -->signal cell to undergo apoptosis or senescence state (permanent stop dividing) -- after I have listened to the talk from PhD student, actually the senescence can be reversed, like it occurs in the cancer cells.

Structure of chromatin is another factor contributing to DDR. Once there is the db break, H2Ax is phosphorylated.

Upon ATM activation, the chromatin chain starts to relax at the site of DSB.

Besides Ser-139 is phosphorylated, a new discovery showed Tyr-142 is phosphorylated and modulate DDR.

There are much more gap to put the jigsaw on the DDR modulation, especially during the signal amplification through the post-modification process which requires better technology to explore the complexity.

Physiological DDR

1.immune class switching

2.hyper-mutation to generate the diversity

The recombination of VDJ segments (exon which exists separately) require NHEJ process. The sequences flanked between these exons are recoginzed by RAG1-RGA2 protein clpx --> generating DSB. Hence, defect in NHEJ caused severe combined immune-deficiency.

For the class switching, requires different mechanism called AID (activation-induced deaminase) -->change C to U --> initiate MMR/BER --> error-prone repair and NHEJ is also required for the class-switching.

3. Another physiological break --> producing the gametes;

During the HR of M1 -- it requires Topo-II related enzyme, Spo11, which generates DSBs -->DSB resection -->MRN clp --> exchange genetic material between "homologous chromosome".

The process needs all mitotic HR component plus meiosis-specific RAD51-like protein DMC1.

4.Telomere homeostasis and ageing;

normal cell -- ribonucleoprotein complex telomerase

some cancer cells -- using HR-based "alternative lengthening of telomeres"; if the telomere structure is defective -->chromosome fusions and chromosomal instability.

Except stem cells, the normally maintains the low amount of telomerase that causing the cell to be able to replicate in certain rounds. If the process is defected the shortening telomere structure will be recognized as DBS --> chronic DDR activation --> apoptosis/senescence --> ageing (therefore, any kinds of challenges that causes the cell to keep dividing on the environment that shortage of telomerase --> very risky to cause premature ageing or chromosomal fusion/chromosomal instability)

Different physiological state of cell requires different level of DDR. Less DNA repair activity along the cell differentiation.

Example;

DBS repair requirement is changed according to the developmental process of nervous system. HR is important during the proliferative period and NHEJ becomes major when neuron fully differentiated.

Consideration of physiological state;

Stem-cell -- highly proliferative, highly depending of DDR - defect in the repair system impair the stem cell function. Defect in NER and NHEJ --> induce aging in hematopoietic stem cell.

There is the linkage between the circadian genes and DDR. There are more evidents show some DNA repair pathways have been modulated by the circardian gene. They proposed that it may help our body to response the external damage directly. Like, NER is important for removing dimer from thymine which causes by the sunlight. It is found out that NER is regulated by circadian genes -- so in the morning/afternoon the genes related to NER might be highly expressed to prevent the severe damage from the sunlight.

Pathogens are using the recombination process to manipulate their own genetic materials to be beneficial for themselves.

Some viruses activate DDR to integrate their genomes to the hos cells.

Actually, human has the restriction factors which can fight against the viral infection and in the other way round viruses have developed the tool to win these barriers.

Cancer and DNA damage with examples;

1. MMR --> microsatellite instability --> predispose to colorectal and endometrial cancers

2.inherited DDR defects -->predispose to cancer -->involve in mutator phenotype

Neurodegenerative disorder;

The neuronal cells are very prone to the damage due to very high-mitochondrial respiration which will create lots of ROS. Besides, most of the neuronal cells are fully differentiated, less choice for DNA repair pws available, esp. fixing DSB which NHEJ (error-prone) is the major pw.

Also, the neuronal cells rely heavily on the transcription and highly oxidative state can block the transcription.

Genome instability;

Repetitive sequence is very prone to the mistake due to the DNA-secondary structure that could form during the DNA replication and repair.

Immune defect and infertility;

- esp. VDJ recombination --> reduce the diversity of immune cells

- meiosis defect can cause the defect in reproduction due to improper production of germ cells

Ageing; -- accumulation of DNA damage. As the time goes by the lesion gets accumulate as well as the DDR and repair system start to decline --> decline of the cell activity (and sometimes cause ageing related disease like cancer).

Exhausted stem cell --> senescent/apoptosis.

Targeted substrate of DDR kinase include those involved with glucose metabolism and insulin-AKT kinase signalling network. 

Though, there is no clear direct evident on the relation between the control of DDR over the energy metabolism, but the author believes that there might be such a relationship in some aspects.

Treating disease based on the knowledge from DDR;

it is believed that cancer cells lack particular DNA damage and repair in order to support their characteristic by dividing very fast (selective pressure toward tumour evolution). However, the same process can cause the cancer cells become resist to the treatment.

Example of synthetic lethality. Finding the key repair or DDR which cancer cells rely on and inhibit that pathway à be able to kill the cancers.

Ischaemia-reperfusion injury and ageing;

Too much DDR --> during the reoxigenate process can reduce the substrate to create the energy --> ATP deplete --> necrosis mostly (causing organ dysfunction). Drug inhibit PARP1 --> prevent cell death due to the over activation of DDR.

The author suggests the possibility to use DDR in bacteria as the target to develop drug.

Future perspectives;

DDR is the complex process, yet, important in living organism. Much defined details require to be discovered on how the process modulate such the response. Which molecules have been involved and how do they play role in the different physiological state of cell. This could lead us to promote human health, prevent and cure the disease.

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