classes of cancer genes

1=Oncogenes (accelerate growth)-activated proto-oncogenes2=Tumour suppressor genes (brakes)3=DNA repair genes4=Apoptosis genes (cell death)5=Normal genes which become abnormal6=Somatic or germline mutations

DNA damage response

0

types of DNA damage

Single-strand breakDouble-strand breakMis-match basesDamaged baseIntra / Inter -strand crosslink

DNA damaging factors

1=Exogenous (extracellular)-UV light, x-rays, natural isotopes, chemicals (natural, man-made)2=Endogenous (intracellular)-Oxygen, water, reactive metabolism intermediates

How UV damages DNA

1=Cyclobutane pyramidine dimers(Thymine dimers, CC dimers) 2=6-4 photoproducts3=Cause DNA to distort4=CC can mis-pair at replication with AA5=CC to TT mutation 'signature

ATM deficiency in ataxia-telangiectasia

Human autosomal recessive disorder causing: A. Progressive neurodegeneration B. Cancer predisposition C. Aspects of premature ageingD. Radiosensitivity- Impairment in triggering cell cycle checkpoints in response to DNA damage (double strand breaks)

role of ATM in the dna damage response pathway

Is a major surveillance protein- Looks for DNA damage - checks integrity of genome

role of p53 in the DNA damage response pathway

Once ATM recognises damage in genome, p53 accumulates:- Normally p53 has a very short 1⁄2 life in cell-once signalling pathway is activated it accumulates (to pass on signal for cell cycle arrest)• Cell cycle arrest=no replication&DNA repair occurs to make sure damage doesn't remain in the genomeCell cycle resumes once DNA is repairedIf repair is not possible: cell apoptosis pathway is activated = cell death

exogenous causes of p53 mutations

1=UV sunlight-Skin cancer (CC to TT pyrimidine dimers)2=Aflatoxin B1 in diet-Liver cancer (codon 249 AGG to AGT)3=Benxoapyrene in tobacco smoke-Lung cancer (hotspot codons 157, 248, 273)

endogenous causes of p53 mutations

1=Most mutations occur at CpG sites2=Methylation of C at CpG (gene promotor regions) spontaneous deamination 5-meC to T3=Deamination of cytosine to uracil can be repaired4=Deamination of 5-methylcytosine to thymine cannot be repaired5=G-C to A-T transition

DNA repair systems

1=Repair of alkylation damage2=Base Excision Repair (BER)3=Nucleotide Excision Repair (NER)4=Double Strand Break (DSB) Repair

repair od alkylation damage

1=Uses MGMT 'suicide' enzyme to directly reverse damage on DNA2=A covalent transfer of alkyl group from modified base to a cysteine residue on enzyme3=Tumours with reduced MGMT expression are responsive to treatment with alkylating agents

base excision repair

1=Can be a short patch repair (single base) or a long patch repair (2-10 nucleotides)2=DNA glycosylases remove base where DNA damage is, this produces an empty gap(AP site)3=AP endonuclease repairs AP sitee.g: 8-oxoG (DNA glycosylase(hOGG1)for 8-oxoG oppositeC B. AP endonuclease(hAPE/HAP1/REF1)

What are reactive oxygen species?

1=AP sites also occur spontaneously2=It is estimated that the human genome sustains about 10,000 oxidative 'hits' per cell per day

nucleotide excision repair

Differs from base excision repair, many forms of DNA damage aren't recognised byDNA glycosylases =can't be repaired by BER2=NER removes an oligonuclotide fragment that contains the damaged bases instead of a single base as in BER3=NER works on bulky lesions such as chemical crosslinks, pyramidine dimers, 6-4photoproducts, and large chemical adducts

e.g of ner

Xeroderma pigmentosum (XP):1=Genetic disorder2=Defect is in nucleotide excision repair of UV damage3=Extreme sensitivity to sunlight4=>1000x higher risk of skin cancer by the age of 8

double stranded break repair

-done by: non-homologous end-joining (NHEJ)1=DBS's can arise spontaneously and through exposure to ionising radiation2=Unlike other systems-Cannot use the complementary DNA strand to provide information to restore the break3=NHEJ or homologous recombination

DNA mismatch repair

1=Errors at DNA replication2=Repeated DNA (microsatellite) sequence expansion/contraction3=There are a few different terms for the mutated phenotype:4=Microsatellite instability (MSI)5=Replication error (RER) phenotype6=Mutator phenotype7=This type of repeated sequence we can use as DNA markers

Xeroderma pigmentosum (cancer predisposition syndromes linked to genetic instability

XPA-G Nucleotide excision repair

Ataxia Telangiectasia (cancer predisposition syndrome linked to genetic instability)

Ataxia telangiectasia: ATM Checkpoint Signaling and DSB Repair

HNPCC (Cancer Predisposition Syndromes linked to Genetic Instability)

HNPCC: hMSH2 hMLH1 Mismatch Repair• Hereditary colorectal cancer

early onset breast/ovarian cancer (Cancer Predisposition Syndromes linked to Genetic Instability)

Early Onset Breast and Ovarian Cancer: BRCA1,2 homologous recombination repair of DSBand Checkpoint Signaling

blooms (Cancer Predisposition Syndromes linked to Genetic Instability)

Blooms: BLM Helicase Replication/Repair

werners (Cancer Predisposition Syndromes linked to Genetic Instability)

Werners: WRN Helicase Replication/Repair

Li-Fraumeni syndrome(Cancer Predisposition Syndromes linked to Genetic Instability)

Li-Fraumeni: p53, Chk2 Checkpoint Signaling and Apoptosis

Franconi Anemia (Cancer Predisposition Syndromes linked to Genetic Instability)

Fanconi Anemia: Fanc Proteins DNA Repair and Checkpoint Signaling

Nijmegen breakage syndrome (Cancer Predisposition Syndromes linked to Genetic Instability)

Nijmegens Breakage Syndrome: NBS1 Checkpoint Signaling and Repair

Biotransformation

1=The enzymatic process that transforms chemicals into entities that can be readily excreted from the body2=Metabolism of a wide range of compounds including medicinal drugs/ carcinogens3=Some drugs undergo biotransformation to pharmacologic active agents4=In some cases the metabolites can be toxic, carcinogenic, or teratogenic5=In the liver, cytochrome p450 family start the process6=Then a second phase renders the chemical soluble7=Intermediates may cause DNA damage

e.g of biotransformation

aflatoxin1=Cytochrome p450 adds a highly reactive epoxide group2=If not immediately disarmed with glutathione it can attack DNA

how many cancer related genes have been identified so far

570+

2 types of mutations

1=Somatic-Affect only that individual, we see this type of mutation in sporadic cancer2=Germline-In all cells of the body including germ cells, can be inherited and passed on, can give an increased risk of particular cancers

the 2 hits of the tumour suppressor gene

1st hit-Mutation (somatic or germline), second copy of the gene is still sufficient2nd hit-Mutation, allele loss (deletion), hypermethylation; silences gene transcription (gene turned off)

retinoblastoma

1=Malignant tumour of retinal cells2=RB1 is a tumour suppressor gene, normally activated by phosphorylation and releases E2F (transcription factor) which allows the expression of genes which control cell proliferation3=In hereditary cases, first mutation 'hit' present in germline and second occurs in retina, early onset, bilateral4=In sporadic cases, both mutation 'hits' occur in retina, late onset, unilateral

problems with RB

can't sequester E2F so it is free to allow the cell cycle to progress without being signalled

Colorectal adenoma-carcinoma sequence

1=Sessile polyp (precursor lesion, has the possibility of becoming malignant)2=Pedunculated polyp3=Adenocarcinom

2 types of colorectal cancer

-sporadic (75%)-inherited (25%)

sporadic cancers subtypes

a=85% CIN (chromosome instability)-Tumour suppressor genes and oncogenes affectedb=15% CIMP (microsatellite instability)-Defect in mismatch repair, hMLH1silencing2=Familial colorectal cancer20%3=Hereditary colorectal cancer syndromes (NHPCC 5-8%, FAP <1%)

2 types of inherited colorectal cancer

1=Familial adenomatous polyposis (FAP)2=Hereditary non polyposis colon cancer (HNPCC)

difference between FAP and HNPCC

FAP Vs HNPCC:1=Polyposis VS No polyposis2=Autosomal dominant inheritance VS Early onset colorectal cancer3=Cytogenetically visible deletion 5q, linkageanalysis VS Predominantly right colon 4=APC gene-negative regulator of beta catenin VS Synchronous colorectal cance

FAP: APC gene

1=Involved in the Wnt signalling pathway2=If no APC then beta catenin is free and can bind to TCF whether or not there is a signal for cell growth, causes polyp growth

HNPCC: defective mismatch repair

1=Mismatch repair complex hMSH2, hMLH12=DNA repair/genome stability3=Repair of-Single base mismatch, replication errors at short repeats4=Defects lead to-Genome wide mutations, base alterations, expansion and contraction of repeated DNA sequences, mutator phenotype, rapid accrual of further mutation

gatekeepers in colorectal cancer

1=Inhibit growth/promote death2=E.g. APC (polyposis)3=Cancer initiated if mutation of 2nd allele4=Tumour initiation accelerated in FAP (APC) leading to progression

caretakers in colorectal cancer

1=E.g. hMSH2, hMLH12=Mutator phenotype, cancer initiated if mutate gatekeeper3=Tumour progression accelerated in HNPCC (mutator phenotype

Subtypes of Colorectal Cancer at molecular level

CMS1-4