Nucleic acid, protein, and lipids are continuously damaged in our body by various sources like radiation, diet, chemical instability, etc. error of normal metabolism give rise to reactive oxygen species (ROS) and damage in DNA during replication and repair. DNA injuries include base modification, single-strand breaks (SSBs), double-strand breaks (DSBs), and interstrand cross-links (ICLs). Important DNA repair pathways in mammalian cells are                                                                                      

  • base excision repair (BER) cut out mostly oxidation and alkylation of DNA damage,                                                                                                                                                  
  • nucleotide excision repair (NER) removes bulky DNA lesion formed by UV light.                                                                                                          
  • mismatch repair (MMR) repairs replication errors, 
  • double-strand break repair (DSBR) specifically repair DSBs mainly by either error-prone rejoining of the broken DNA ends.
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FIGURE 1: Mammalian DNA repair pathways, various types of genotoxic agent result in DNA damage and repaired by specific DNA repair pathways. Disease are shown in red; the black arrow show RecQ helicases signify these enzymes are involved in several DNA repair pathways. SSBR (single-stand break repair); TCR (transcription coupled repair); Alt-NHEJ, alternative nonhomologous end joining pathway; AID, activation-induced cytidine deaminase; MM, mismatch of DNA bases. 

Unrepaired DNA damage gives rise to genetic instability and via cascade method leads to cell deaths which associated with aging. And as DNA repair ability decreased with time and DNA lesion gives rise to mutation and in this mutation can be oncogenic. Unrepaired DNA damage may reduce the capacity for tissue self-renewal, thus inhibiting recovery from acute stress or injury. Stem cells appear has a very capable at DNA repair thus apoptosis in those cells is not seen.

NEURODEGENERATIVE DISEASE AND PREMATURE AGING


Mitochondrial DNA (mtDNA) damage, mitochondrial dysfunction, and defects in base excision repair BER can adversely affect neuronal functions, and increase the chances of neurodegenerative disease. Oxidation damage to neuronal cells may be important component of neurodegeneration, BER is important in preventing neurodegeneration. 

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Fig: How ROS damage brain cells

Defects in DNA repair leads to genetic instability and it accumulated with age and sometime leads to accelerated aging include 

  • Werner syndrome (WS) in this Werner protein is mutated in WS patient is a member of RecQ helicase family, this helicase has a role in unwind DNA, DNA repair, replication and recombination. 
  • Cockayne syndrome (CS) in this mutation in CSA and CSB gene occur 80% of CS cases happens because of mutation in CSB gene, CSB play a role in base excision repair (BER) and maintenance of mitochondrial function. 
  • Hutchinson-Gilford progeria syndrome (HGPS) occur due to point mutation in lamin A gene, and lamin A promotes DNA repair especially DSBR. 

THEORIES OF AGING

Theory of aging say that genetic program give rise to aging processes, and evolutionary terms aging is the random process with decline in natural selection.

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Fig: four major theories of aging. Each theory has DNA damage accumulation and DNA repair as a major component. 
  • DNA Damage/Repair Theory of Aging

This theory say that unrepaired DNA damage leads to genetic instability and accumulation of this instability leads to aging. Age-associated DNA damage could include DNA breaks, cross-links and modified bases (oxidation lesions). DNA damage by various methods if not perfectly repaired leading to mutation. And if this mutation in germline leads to mutations drive evolutionary changes through natural selection. And sometimes this mutation leads to tumor formation. But we see less mutation in germline because of more efficient DNA repair system and hence lower level of DNA damage. 

  • The Mitochondrial and Free Radical Theories of Aging  

This theory states that DNA damage to mitochondrial DNA leads to physiological dysfunction and eventually to pathological disease. And with time mitochondrial became leaky and release ROS with may contribute to nuclear genomic instability. mtDNA mutates at faster rate and therefore accumulates more damage than nuclear DNA. And if somehow, we increase the anti-oxidant leads to increase the life span. When aging related to organ system is considered then oxidative stress/ free radical theory is appropriate, any single type of damage like oxidative damage is not enough to explain aging. 

  • Telomere Theory of Aging

Cellular senescence or improper maintenance of telomeres leading to cell-cycle exit after a number of cell cycle (Hayflick limit), Telomere prevent chromosomes ends from being recognized as DSBs. When telomeres became shorten, then DNA damage response increase. Human telomeric DNA includes 2-15kb of tandem repeats of TTAGGG. The ssDNA tail folds back and invades the dsDNA and forming a  T-loop is needed for telomere capping. Telomerase is specialized DNA polymerase responsible for telomere replication. Somatic cells have less expression of telomerase is insufficient to compensate for telomere loss. Telomerase reactivation leads to elongated telomere and reverse age-related pathology in mice. DNA glycosylases remove damage bases from oxidation at telomeres, but this enzyme does this so imperfectly that DNA damage still accumulated in telomeres and contribute to aging. A protein RecQl4 which interact with human telomeric DNA and present in mitochondria and suggest that mitochondrial dysfunction can lead to telomere wearing down. 

  • Cellular Senescence during Aging 

Random damage can lead to cellular senescence. The senescence cellular stress response now considers as a major factor of aging. Example fibroblast from progeroid patients (rare genetic disease characterized by an aged appearance at birth) have accelerated senescence. Whereas fibroblast from long-lived mice show resistance to oxidative stress. Senescent cell accumulates in tissue when their death or removal is less than their formation. Indeed, tumor suppressor p53 plays an important role in regulatory mechanism between DNA repair, apoptosis, and senescence. Senescence appear because of another demonstration of imperfect homeostasis as basis of aging. 

MITOCHONDRIAL DYSFUNCTION AND ENERGY HOMEOSTASIS

The importance of mitochondria is by conserved pathway that ensure proper function of organelles, and mtDNA transcription, translation, replication and OXPHOS are essential for organismal survival. Mitochondria is the primarysource of superoxide formation to tackle this ROS aerobic organisms have several antioxidant defense systems include Superoxide, dismutase, catalase, and peroxiredoxins. And dietary antioxidants include glutathione, vitamin E and vitamin C. ROS induce expression of antioxidant gene such as NRF2 and PGC-1α, if ROS not scavenged that it can oxidize molecules like lipids, proteins, and DNA. mtDNA is particularly prone to damage by ROS because it is source of ROS. Oxidatively damaged mtDNA is repaired primarily through BER, 

  • First damage is recognized by glycosylase, then the resultant abase side recognized by 
  • Apyrimidinic endonuclease1 (APE1) leaving a gap in the DNA strand
  • The gap is then subsequently filled by mtDNA polymerase γ (POL- γ) and then DNA sealed by ligase III.

If mitochondria became damage beyond repair then is degraded by autophagy termed as mitophagy. In which double layer structure formed around the damaged mitochondria, such that it is engulfed in a vesicle, the autophagosome. After fusion with lysosome it starts degradation. 

Two mitophagy pathways can lead to mitochondrial degradation.

  1. Programmed mitophagy through up-regulation of mitochondrial receptor NIX leading to removal of all mitochondria necessary for erythropoiesis.
  2. Selective mitophagy whereby single mitochondria are degraded. This occur by loss of inner mitochondrial membrane potential. Inner membrane depolarization leads to accumulation of kinase PINK1 on outer membrane. PINK1 phosphorylates a number of proteins in the outer mitochondrial membrane leas to activation of parkin which is a E3-ubiquitin ligase ubiquitinates outer membrane protein and facilitates the association of mitochondria with a growing autophagosome membrane. 

Defects in mitophagy is associated with Parkinson disease through mutation in PINK1 and parkin. And mitochondria dysfunction is symbol of β-amyloid-induced neural toxicity in Alzheimer’s disease. Increased production of ROS is associated with cardiovascular disease, and reduction of ATP generation appears to have a causal role in features of type 2 diabetes. Scientist believed that mitochondrial dysfunction is crucial in aging, to prove this hypothesis they created a database which proves that Cockayne syndrome (CS) and xeroderma pigmentosum group A (XPA) [a disorder with deficient nucleotide excision repair] associated with mitochondrial disease. To prove that whether XPA cells displayed altered mitochondrial properties. Both XPA-knockdown and XPA-deficient patient cells show mitochondrial changes includes high membrane potential, altered mitophagy, high basal oxygen and ATP consumption rates, this suggest that normal aging shares many features with mitochondrial dysfunction, corroborating the mitochondrial theory of aging.

DNA damage is sense by poly (ADP-ribose) polymerase 1 (PARP1) to recruit DNA repair proteins and fix the damage DNA. It plays a major role in PARylation, a process by which it does 

  • DNA repair
  • Transcription,
  • Replication, 
  • Chromatin modification and 
  • Cell death

PARP1 play role in genome maintenance, hyperactivation of PARP1 with aging, abnormal metabolism, neurodegeneration and specific form of cell death known as parthanatos, is a caspase independent pathway of programmed cell death depend on the nuclear translocation of mitochondrial-associated apoptosis-inducing factor (AIF), hyperactivation of PARP1 also associated with stock and neurodegeneration in some premature aging disorder such as XPA, CSB and ATM. 

There are two pathway PARP1 and SIRT1-NAD+ and when PARP1 is hyperactive then SIRT-1 and in DNA repair defect disease show lower level of NAD+ levels because of PARP1 hyperactivation in XPA leads to reduced SIRT1 deacetylation because of loss of NAD+. SIRT1 regulate PGC-1α and this PGC-1α consequently leads to mitochondrial dysfunction. Persistent DNA damage also activate nuclear  DNA-damage response which include kinases and PARP. This enzyme uses high level of ATP and NAD+ and to complete this high amount of energy so mitochondria become coupled, and more coupled will give more ROS production. And also, when PARP hyperactivation also decreased NAD+ level and for maintaining homeostatic NADH/NAD+ and may account for increase oxygen and ATP consumption observed in cell. So mitochondrial dysfunction is important strategy for investigating potential mechanisms of neurodegeneration in disorder as well as aging. 

FUTURE DIRECTIONS: INTERFERENCES 

From these studies we get to know that agents that alter DNA repair may have therapeutic potential. For example, if we able to inhibit endogenous DNA repair mechanism in cancer cell then cancer cell will die. And this genotoxic agent also affects the healthy cell, so scientist have to save the normal cells as well from this genotoxic agent. So, agents which do DNA repair in normal cell useful for cancer chemotherapy. Let’s discuss some of promising approaches involving agents that stimulates DNA repair. 

BER

Ligase are protein that seal the DNA ends. Ligase 3 is only ligase found in mitochondria and component of BER pathway. Reduced level of ligase 3 can be seen in many neurodegenerative diseases, including ataxia telangiectasia and Alzheimer’s disease. So somehow scientist have to increase the ligase 3 concentration. And this increase also helps in tackling increased oxidation stress. For example, one protein USP47 (a de-ubiquitylating enzyme) can regulate the BER process, so USP47 can be interesting druggable target to regulate BER pathway. 

PARP1

NAD+ metabolism is of great importance in health and disease, boosting NAD+ level can be effective in antiaging studies and some neurodegenerative DNA repair. Pharmacological approach taken here is to increase NAD+ level by decreasing NAD+ consumption and therefore inhibition of PARPs and increase NAD+ precursors like nicotinamide riboside (NR) and nicotinamide mononucleotide (NMN). Supplement with NR is overall improved mitochondrial fitness, NR is stable at room temperature and water soluble so it is good candidate for further clinical trials. 

CONCLUSION

Throughout this blog, scientist told us the current understanding of the role of DNA repair in preventing aging-associated disease, like the mechanism by which DNA damage leads to aging, and use this knowledge in therapeutic approaches to prevent aging, cancer and neurodegenerative disease. And it is clear that DNA repair mechanism, nuclear and mitochondrial, are essential for a long and healthy life. Regulation of DNA repair and of mitochondrial health as discussed above could be promising strategic intervention in future. 

Reference

Maynard, S., Fang, E.F., Scheibye-Knudsen, M., Croteau, D.L. and Bohr, V.A., 2015. DNA damage, DNA repair, aging, and neurodegeneration. Cold Spring Harbor perspectives in medicine5(10), p.a025130

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