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DNA Damaging Agents and Their Lesions: * X-rays: Lead to single-strand breaks and double-strand breaks. * Oxygen Radicals: Cause the formation of 8-Oxoguanine and abasic sites. * Alkylating Agents: Result in abasic sites and single-strand breaks. * Spontaneous Reactions: Frequently produce Uracil and abasic sites. * UV Light: Induces (6-4)PP ((6-4) photoproducts) and CPD (Cyclobutane pyrimidine dimers). * Polycyclic Aromatic Hydrocarbons: Create bulky adducts. * Anti-tumour Agents (e.g., Cis-Pt, MMC): Cause interstrand cross-links and double-strand breaks. * Replication Errors: Result in $A-G$ mismatches, $T-C$ mismatches, insertions, and deletions.
Cellular Consequences of DNA Damage: * (Transient) Cell-Cycle Arrest: Occurs at $M$ and $G1$ phases. * Inhibition: Affects transcription, replication, and chromosome segregation. * Apoptosis: Programmed cell death if damage is irreparable. * Long-term Effects: Include mutations, cancer, chromosome aberrations, ageing, and inborn repair diseases.
Primary Repair Processes: * Base-Excision Repair (BER). * Nucleotide-Excision Repair (NER). * Recombinational Repair (Homologous Recombination [HR]; End-Joining [EJ]). * Mismatch Repair (MMR).

Awarded in $2015$ for mechanistic studies of DNA repair to three key scientists: * Tomas Lindahl. * Paul Modrich. * Aziz Sancar.

Mechanism: Removes damaged DNA bases (e.g., adducts or oxidized bases) and excises the affected DNA sections. It replaces the gap with "new" DNA using the existing undamaged strand as a template.
Types of Excision Repair: * Nucleotide Excision Repair (NER): Targets bulky lesions such as UV photoproducts and BPDE adducts. * Base Excision Repair (BER): Targets small base damages like $8-oxoguanine$ . * Transcription Coupled Repair (TCR): Facilitates faster repair of DNA damage specifically in the transcribed strands of expressed genes.

Scope: A multi-stage and versatile mechanism dealing with "bulky" DNA damage, including adducts and UV-induced cross-links.
Six Major Stages of NER: 1. Lesion Recognition: Identifying the damage on the DNA strand. 2. DNA Unwinding and Scaffolding: Opening the double helix around the lesion. 3. Incision: Cutting the damaged DNA strand on both sides of the lesion. 4. Excision: Removing a patch containing the damaged DNA, typically measuring $24-32$ nucleotides. 5. Repair Replication: DNA polymerase fills the gap using the opposite strand as a template. 6. Ligation: DNA ligase seals the remaining nick.
Functions of NER Proteins: * XPC/hHR23B: Performs lesion recognition for most NER substrates (e.g., 6-4 photoproduct). * XPE (UV/DDB or p48/p125): Recognizes non-helix distorting lesions such as CPD. * XPB/XPD: Responsible for local unwinding; they function as helicases within the TFIIH complex. * XPA: Functions as a scaffold to maintain the structural integrity of the repair complex and performs damage verification. * XPF/ERCC1 and XPG: Nucleases that perform incision to remove the repair patch ( $24-32$ nucleotides). * Standard Cellular Machinery: Used for repair replication (e.g., DNA polymerase $\delta$ or $\epsilon$ , PCNA, RF-C) and ligation (DNA ligase I).

Gene	No. of Exons	Chromosomal Location	Protein Size (aa)	Protein Function	Defective Pathway
XPA	$6$	$9q22.33$	$273$	Damage verification	NER
XPB/ERCC3	$15$	$2q14.3$	$782$	Helicase	NER
XPC	$16$	$3p25.1$	$940$	Damage recognition	NER (GGR)
XPD/ERCC2	$23$	$19q13.32$	$760$	Helicase	NER
XPE/DDB2	$10$	$11p11.2$	$427$	Damage recognition	NER (GGR)
XPF/ERCC4	$11$	$16q13.12$	$916$	Nuclease	NER
XPG/ERCC5	$15$	$13q33.1$	$1186$	Nuclease	NER
XPV/POLH	$11$	$6p21.1$	$713$	Polymerase	Translesion Synthesis (TLS)

Definition: XP means "dry pigmented skin."
Primary Defect: Defective in global genome NER (GGR).
Symptoms and Risks: * Extremely high sensitivity to sunlight. * Freckle-like pigmentation in sun-exposed areas. * $10,000$ -fold increase in non-melanoma skin cancer. * $2,000$ -fold increase in melanoma.
Complementation Groups: * XP-A through XP-G correspond to mutations in the respective XPA-XPG genes. * Severity depends on the specific complementation group. * Some groups feature neurological problems. * XP-C and XP-E exhibit the mildest phenotypes and typically have no neurological disorders.

Global Genome Repair (GGR): * Works throughout the genome. * Utilizes XPC, HHR23B, and XPE for recognition.
Transcription Coupled Repair (TCR): * Provides more rapid repair of transcribed strands of active genes. * Does not work on the non-transcribed strand or non-transcribed genes. * Triggered by the obstruction of RNA polymerase II (RNAPII) at a lesion. * Requires TCR-specific factors: CSA and CSB. * XPA interacts strongly with CSA, serving as a central junction between TCR and GGR pathways.

Etiology: Results from a defect in TCR due to mutations in CSA and CSB genes.
Clinical Presentation: * Premature ageing. * Photosensitivity. * Impaired neurological development. * Crucial Distinction: Unlike XP, CS patients have no increased risk of cancer.
Overlap: Some XP patients with specific mutations in XPB, XPD, and XPG also exhibit Cockayne Syndrome features.

Individual Variation: Polymorphisms in repair genes may influence subtle cancer risks. * XPD (761 amino acids): * $Lys751Gln$ : Associated with enhanced risk for esophageal cancer. * $Asp312Asn$ : Associated with enhanced risk of bladder cancer.
Impact on Cancer Therapy: * Cisplatin: Used to treat testicular and ovarian cancer. * Resistance: Can occur via enhanced NER efficiency. Resistant cell lines often exhibit enhanced ERCC1 expression. Conversely, RNAi knockdown of ERCC1 enhances sensitivity to cisplatin and reduces the repair of cross-links.

Research by Wang et al. ( $2009$ ) highlighted PTEN mutations in XP patients: * Total melanomas sequenced: $59$ (Invasive: $12$ ). * Melanomas with PTEN mutations: $33$ (Frequency: $56\%$ ). * Frequency of UV-type PTEN mutations among those with PTEN mutations: $91\% - 100\%$ .