🌟 Master-Level Summary: DNA Repair, Aging & the Brain

(Applied Molecular Biology – Day 5, Part 2)

🧬 1. Why Repair Capacity Differs Between Cell Types

Dividing vs. non-dividing tissues

Cells that divide frequently must be excellent at repairing DNA — otherwise mutations accumulate during replication. → Thus, tissues with high proliferation (e.g., testis) show strong repair activity, while slowly dividing tissues (e.g., neurons, especially in some brain regions) show lower repair capacity.

Example: 8-oxoG repair across tissues

• Testis = very high repair (protect the germline!).
• Kidney = moderate.
• Brain = surprisingly low, despite high ROS from mitochondrial activity.

This suggests repair efficiency is not proportional to ROS load, leading to deeper questions about tissue-specific resilience.

🧠 2. Different Brain Regions ≠ Same Repair Profile

The brain is not one homogeneous tissue. Regions behave differently.

Cerebellum (CE)

• Young mice: very high repair of 8-oxoG.
• Aged mice: strong decline, especially in oxidative DNA repair.

Brainstem

• Also relatively high in youth, drops with age.

Cortex & hippocampus

• More mixed patterns depending on lesion type.

The main message: ➡️ DNA repair in the brain is region-specific AND lesion-specific. ➡️ You cannot homogenize whole-brain lysates and assume it represents the brain as a whole.

🔬 3. Different Lesions = Different Glycosylases = Different Aging Patterns

Studied lesions included:

• Uracil in DNA (from cytosine deamination)
• 5-hydroxyuracil
• 8-oxoG
• Lesions in single-stranded DNA “bubbles”, relevant for transcription

Each lesion type has its own glycosylase in the BER pathway.

Key insight:

• Aging does not change all glycosylases equally.
• Some show increases, some decreases, some no change — depending on both region and substrate.

This destroys the idea of “DNA repair goes up/down with age” as a general statement.

🧩 4. Neurons: Mitochondria at Synapses vs. Cell Bodies

Neurons contain mitochondria in:

• Cell body
• Axon
• Synapses (the major site of energy consumption ⚡)

Researchers separated synaptic mitochondria from non-synaptic ones and tested BER activity.

Finding

👉 With aging, synaptic mitochondria show a strong decline in repair activity. 👉 The soma/axon mitochondria do not decline significantly.

Interpretation: ➡️ Synapses may be especially vulnerable to accumulated DNA damage with age. ➡️ This might contribute to cognitive decline.

🩸 5. Human Blood Cells: Repair Declines With Age

Using lymphocytes from:

• Young individuals
• Centenarians (~100 years old)

Even with individual variation, the pattern is clear: 👉 Young individuals have higher BER activity than centenarians.

Because centenarians are “survivors,” the difference might be even stronger between 20-year-olds and 80-year-olds.

🧪 6. Human Brain Tissue (Post-Mortem)

Brains from ages 20–99 (N=55) were analyzed by microarray to quantify expression of all nuclear-encoded genes.

Four regions were examined separately.

Finding:

• BER-related genes show broad downregulation with age (heat-maps mostly blue).
• Exception: UNG (uracil glycosylase) — likely because it participates in many processes beyond BER.

Thus: ➡️ Expression of BER components tends to decrease in the aging human brain.

🧠 7. What Controls BER Expression? The BDNF → CREB Pathway

BDNF (Brain-Derived Neurotrophic Factor)

A neurotrophic factor that declines with age.

Mechanism:

1. BDNF binds TrkB receptor.
2. Receptor dimerizes → activates multiple kinase cascades.
3. These phosphorylate CREB (a transcription factor).
4. pCREB activates transcription of many neuronal genes.

Hypothesis:

Maybe CREB also regulates BER genes.

🧬 Evidence (Step-by-step)

a) In-silico promoter analysis

Most BER gene promoters contain CREB binding sites.

b) Mobility-shift assays

CREB was shown to physically bind promoters of nearly all BER genes (except XRCC1 and one glycosylase).

c) Mouse model with reduced BDNF (heterozygotes)

• BDNF ↓ → CREB activation ↓
• BER proteins ↓ (especially at protein level; mRNA reduction less clear)

d) Adding BDNF to cultured neurons

Within 1–24 hours:

• CREB phosphorylation ↑
• BER proteins ↑
• BER activity ↑

Therefore: 👉 BDNF positively regulates BER through CREB. 👉 Declining BDNF in old age likely contributes to reduced BER in neurons.

🏃‍♂️ Exercise boosts BDNF

Physical activity reliably increases BDNF and may therefore boost BER indirectly. This is one reason exercise protects cognitive health.

🧪 8. Post-Translational Regulation of BER: The Case of NEIL2

NEIL2 is a glycosylase specialized for single-stranded DNA lesions (important during transcription).

Researchers asked:

• Is NEIL2 regulated by phosphorylation?
• If so, which kinase?

Findings

1. NEIL2 is phosphorylated (radioactive phosphate incorporated).
2. Candidate kinases: PKC and CK5.
3. Purified PKC phosphorylates NEIL2 in vitro.
4. But phosphorylated NEIL2 has lower activity.

Conclusion: 👉 NEIL2 must be dephosphorylated for optimal function. Another fine-tuned layer of BER regulation.

👶🧓 9. Cockayne Syndrome (CS): Failure of Transcription-Coupled Repair

CS is a rare progeroid (premature aging) disorder. Patients exhibit:

• Growth defects
• Neurological impairment
• Photosensitivity
• Aging-like facial features (sunken eyes, cataracts)

Known defect: Transcription-coupled nucleotide excision repair. New finding: They also have defective BER, especially during transcription.

Key protein: CSB

• Interacts with NEIL2
• Enhances incision activity on SS lesions
• Interacts with several BER components

Thus CSB is a central coordinator in repairing transcription-associated oxidative DNA damage. Its failure contributes to neurodegeneration.

🎂 10. Centenarians: Does Repair Correlate With Cognitive Health?

In the 1915 Danish birth cohort:

• Blood was collected at age 100
• Cognitive tests administered (MMSE, etc.)

Researchers tested:

• BER activity (AP endonuclease assays, incorporation assays)
• Mitochondrial function
• Plasma BDNF
• Expression/activity of key BER proteins

🔍 Result:

Individuals with higher BER activity had:

• Better MMSE scores
• Better cognitive performance overall

Correlation ≠ causation, but the link is strong.

🧠 11. Alzheimer's Disease and BER

When comparing:

• Controls
• MCI (mild cognitive impairment)
• AD patients

Patterns:

• Controls → highest BER
• MCI → intermediate
• AD → lowest

Implication: 👉 Reduced BER is associated with neurodegeneration, but directionality unclear:

• Does reduced BER predispose to AD?
• Or does AD pathology suppress BER?

Both possibilities remain open.

🧠✨ 12. Aging, Repair & Biology: Big-Picture Conclusions

1. BER declines with age

But specific patterns depend on:

• Organ
• Brain region
• Lesion type
• Subcellular location (e.g., synapses!)

2. Regulation occurs at multiple levels

• Transcription (BDNF → CREB)
• Translation
• Post-translational modification (e.g., NEIL2 phosphorylation)
• Protein localization
• Protein-protein interactions (e.g., CSB)

3. BER capacity strongly correlates with brain health

• Cognition
• Neurodegeneration
• “Biological age” markers

4. Exercise is one of the few interventions that reliably improves BDNF → CREB → BER signaling