Mutations: Types, Causes, and Effects Explained

• These are study notes on cancers

Cancer and the Genome

• Genome: the complete set of genes or genetic material in a cell or organism.
• Carcinogen: A substance, organism, or agent capable of causing cancer.
• Mutagen: A reagent, like radiation or a chemical substance, that causes genetic mutation.

Types of Mutations

• Genetic mutation.
• Substitutions: a base being replaced by a base of the same kind.
• Point mutations: affect a single base pair.
• Transversions substitution: a purine being replaced by a pyrimidine or vice versa.
• Silent mutation: a codon still codes for the same amino acid due to the degeneracy of the gene code.
• Missense mutation: a substitution results in a codon for a different amino acid.
• Nonsense mutation: a substitution in the formation of a stop codon.
• Insertions and Deletions: shift the reading frame.
• Frameshift mutations: shift the reading frame.
• Translocation: a piece of DNA from one chromosome moves to another chromosome or to another region of the same chromosome.
• Germline mutations: changes to inherited DNA from egg and sperm cells.
• Somatic mutations: changes to DNA after conception happen in cells other than egg and sperm cells.
• Epigenetic change: a reversible mechanism regulating genome function.
• Extrachromosomal DNA (ecDNA): distinct pieces of DNA that don't reside on a chromosome and are circular.
• Small ecDNAs (kilobase size) are typically not amplified and don't contain whole genes.
• Large ecDNAs (megabase size) are cancer cell-specific, amplified, and contain many genes and regulatory regions.

Factors Causing Cancer

• Genetics: less than 0.3% of population carriers of a cancer-related genetic mutation.
• Cancer syndrome: a genetic disorder is inherited genetic mutations in one or more genes.
• Mutations in the genes BRCA1 and BRCA2 carry a higher than 75% risk for breast and ovarian cancer.
• Physical and chemical agents: Inhaled asbestos, certain dioxins, and tobacco smoke.
• Lifestyle considerations include alcohol consumption, diet, and obesity.
• Hormones can contribute to cancers of the breast, endometrium, prostate, ovary, and testis, as well as thyroid and bone cancers.
• Infection and inflammation: Viruses (HPV; cervical cancer), Bacteria and parasites (helicobacter pylori; gastric carcinoma), and Chronic inflammation.
• Non-ionizing radiation: a form of radiation with less energy than ionizing radiation, non-ionizing radiation does not remove electrons from atoms or molecules of materials that include air, water, and living tissue.
• Forms: Ultraviolet radiation, radiofrequency, and microwave radiation

Ionizing Radiation

• This is high-energy radiation that removes electrons from atoms and molecules of materials
• Consists of subatomic particles or electromagnetic waves.
• Subatomic particles may include alpha and beta particles, and neutrons.
• The new international system (SI) unit of radiation dose is Gray, the absorbed energy per unit mass of tissue.
• Biological effects of radiation measured in units of "sievert".
• Linear Energy Transfer (LET): the rate at which energy is transferred per unit length of track (keV/µm).
• Higher LET radiation particles (alpha particles, protons, and neutrons) produce greater damage.
• Secondary effects caused by ionizing radiation are the generation of reactive oxygen species (ROS), which oxidize proteins and lipids and induce damages to DNA, such as generation of abasicsites and single strand breaks (SSB).

DNA Damage and Repair

• DNA-damaging agents include toxins, alkylating agents, base deamination, and replication errors.
• Oxidative damage and electrophiles also contribute.
• Ionizing radiation, UV radiation, crosslinking agents, aromatic compounds, and extreme temperatures can damage DNA.
• Damaged DNA may contain mismatches, uracil, abasic sites, lesions, adducts, bulky lesions, single-strand breaks, double-strand breaks, intra-strand crosslinks, and inter-strand crosslinks.
• DNA repair pathways include mismatch repair and base excision repair.

DNA Repair Pathways

• Nucleotide excision repair, inter-strand crosslink repair, single-strand break repair, double-strand break repair, and translesion synthesis.
• Direct reversal repair/one-step repair pathways: DNA synthesis isn't required to correct the error, making repair mechanisms error-free.
• Homologs of 06-methylguanine-DNA methyltransferase (MGMT) and the alkylated DNA repair protein B (AlkB) carry out direct reversal repair in humans.
• MGMT mediates a stoichiometric reaction which methyl and other alkyl groups bound to the 06 position of guanine in DNA.
• The process involves a thioester linkage to a cysteine residue in the active site, leading to the protein's degradation rate.

Base Excision Repair

• 8-oxoG is excised by 8-oxoguanine DNA glycosylase (OGG1), which leaves an apurinic site (AP site)
• Short patch base excision repair is constituted by polymerase beta (Polβ)replacing the single missing base, ligase III (LigIII) ligation of the DNA backbone, and X-ray repair cross- complementing protein 1 (XRCC1) aiding the process.
• Long patch base excision repair replaces the base and some additional nucleotides are.
• Activity is dependent on the activity of polymerase delta (Polo) and epsilon (Pole) which work together with proliferating cell nuclear antigen (PCNA).

Recombinational Repair

• Double-strand breaks within DNA can be repaired through non-homologous end-joining or homologous recombination.
• Non-homologous end joint (NHEJ): Direct resealing of DNA ends.
• Homologous recombination: relies on the presence of homologous DNA sequences for DSB repair.
• Process: DSB recognition, 5'-3' end resection (initiated by MRN complex and CtIP), further resection by Exo1, DNA2, and Sgs1 proteins, ends bound byRPA, strand exchange is executed by Rad51, and final step of junction resolution executed by helicases including Bloom syndrome and RecQ helicase-like (BLM) helicase.

Apoptosis vs Necrosis

• Apoptosis: an active, programmed process of autonomous cellular dismantling to avoid inflammation.
• Necrosis: passive, accidental cell death from environmental perturbations releasing inflammatory cellular contents.

Epidermal Growth Factor Signaling

• Extracellular module consists of four domains (I, II, III, IV)
• Domains | and III sandwich the ligands between them.
• Domain II bridges ligand-binding domains, containing the 'dimerization arm’ loop which mediates prime interaction on the other subunit in an activated dimer
• Transmembrane helix
• An asymmetric dimer of kinase domains
• Juxtamembrane segment
• Ligand-binding head.
• C- terminal tail

SH2/SH3 Domains

• Recognize amino acid motifs with phosphotyrosine and polyproline, respectively.
• PH2 domains: 100 amino acids organized into a modular structure that recognizes phosphotyrosine-containing sequences on protein tyrosine kinases and their substrates.
• SH3 domains: 50 amino acids in size and bind to proline-rich consensus sequence PXXP.
• Unlike SH2 domains, SH3 domains remain constitutively associated with their cognate ligands, making their function less dependent on tyrosine phosphorylation.

RAS & SOS

• RAS is attached to the membrane via a prenyl group.
• In the absence of growth factors, it's in an inactive guanosine diphosphate (GDP) bound conformation.
• To be activated it needs the SOS protein that can promote exchange of GDP.
• SOS normally forms a complex with growth factor receptor-bound protein 2 (GRB2), held together by proline-rich regions and SH3 domains in GRB2.
• Dimerizing the growth factor receptor, promotes tyrosine phosphorylation.
• Some tyrosine-containing peptides have affinity for the GRB2 SH2 domain, re polarizing them the GRB2 -SOS. This relocalizes the SOS to the membrane
• The activation of RAS is triggered by RAF/MEK/ERK phosphorylation.

EGFsignaltransduction Pathway

• RAS activates RAF
• RAF activates MEK
• MEK activates MAPK

RAF Proteins

• Raf proteins: initiating enzymes in the three-tiered extracellular signal-regulated kinase (ERK) cascade.
• Mammalian cells have three: A-Raf, B-Raf, and C-Raf (also known as Raf-1).
• Regulatory and carboxy-terminal kinase domains divide the Raf kinases containing three conserved regions: CR1, CR2, and CR3.

The Hedgehog (Hh) Signaling Pathway

• Canonically operates in vertebrates.
• The transmembrane receptor PTCH1 suppresses Hhsignaling.
• SMO is intrinsically linked to PTCH1.
• The binding of Hhligands to PTCH1 allows for SMO release.
• With no PTCH bound, SMO moves to the primary cilium.
• Within the cilium, SMO disinhibits suppressor of fused (SUFU), increasing transcription of glioma-associated oncogene (Gli).
• In the absence of ligand, Glis is phosphorylated/ cleaved which prevents downstream Hhsignaling.

The TOR Pathway

• The target of rapamycin (TOR): an essential protein that is conserved in eukaryotes.
• TOR directly or indirectly regulates the translation of ribosomal proteins.
• It controls cap-dependent translation initiation by phosphorylating inactivating eukaryotic initiation factor 4E.
• TOR functions as a sensor and gatekeeper of 5′-untranslated regions.
• Regulating pathways are complex, involving positive regulators (AKT) and negative regulators (tuberin(TSC2))
• Pathways upstream of TOR occur through increased activity of phosphatidylinositol-3-kinase-AKT or kinases that regulate TSC2.

Kinases

• Receptor tyrosine kinase (RTK): EGFR, PDGFR, FGFR
• Non-receptor tyrosine kinase (NRTK): SRC, ABL, FAK, and Janus kinase (JAK)
• Protein Serine-Threonine Kinases: AKT, RAF, ERK

Mechanisms of Oncogene Activation

• Activation involves genetic changes to cellular protooncogenes, giving the cell a growth advantage.
• The three genetic mechanisms are mutation, gene amplification, and chromosome rearrangements.
• Gene amplification: The transcribed portion can be duplicated 100-fold.
• Single amino acid substitutions can alter the biochemical properties of gene products, causing constitutive enzymatic activation.
• Chromosome rearrangements, such as translocation and inversion, generate fusion transcripts resulting in chimeric oncogenic proteins.
• H-ras (Harvey rat sarcoma), K-ras(Kirsten rat sarcoma), N-ras (Neuroblastoma Ras), M-ras (Muscle Ras), R-ras (Related Ras)
• Common mutations of Ras include G12V, G12S, G12A, G13D, Q 61R.

RAS

• RAS mutations the incidence is mutation through isoforms. KRAS, NRAS, and HRAS.
• KRAS mutations at the 12th codon are prevalent in LUAD (32%), CRC (41%), and PDAC (86%).
• NRAS mutations occur at the 61st codon in 29% of melanomas.

Targeting Driver Mutations

• Targeted agent is indicated by the type of agent and its structure (e.g., monoclonal antibodies).
• Antibody nomenclature ends w "-mab, molecules end "-ib
• Added substems designate source of the compound, eg: x-x-imab for chimeric antibodies, -z for humanized
• Some drugs have side effect of Tumor Reogenesis

Tyrosine Kinase Targeted Therapy

• Crizotinibis an inhibitor with multiple targets, including ALK,c-MET, and ROS1.
• Criz binds to the nonphosphorylatedstate of the c-MET kinase domain in an autoinhibitory kinase conformation.

Hhsignaling Pathway Targeted

• Vismodegibis, first class is selectively targets, Hhsignaling with locally advanced and metastatic basal cell carcinoma.
• The drug targets the pathway to prevent aloss of function mutationin PTCH1 orag of function mutationin SMO.
• Vismodegib and sonidegibact binds to preventing migration to other cells.

Drugging KRAS

• Is an derived covalent inhibitor of KRAS that cysteine in mutated
• Bind Kras- 1 reversible

RB (RB1) Gene Family and Pathway

• The protein family exist in cells —RB (retinoblastoma), p107 and They contain an binds domain to all a numbers. is mostly

P53 Cellular Functions

• The P53 function is regulated
• CHIP,COP1, ,

PTEN

• The domain includes PBD, and PT domain.

The PTEN-P13K-AKT-mTOR Pathway

• The the functions
• following, (phospharidylinositol-345, 5 kinase Inhibators include: and
• ErbB2 Herceptin and Lapatinib inhibits.
• MEI kinase or
• RTK cell.

BRCA1 and 2 function

• The protein role is in and and strand
• Contains *REV7, C20orf196,35A, and CTC534A2.2
• It also *CSTI, and

Tumor Suppressor

• The vHL linked in development of spinal retina factor

VHL

• The 3 gene transfers 81 is
• RBX1 also
• This contains E3 and

Explore different types of mutations, including point mutations, frameshift mutations, and substitutions. Understand how these mutations can alter the genetic code and lead to various effects. Learn about mutagens and the differences between genetic and epigenetic changes.