Epigenetics + Cancer

Question 1

CpGs
- how many?

• where are they?
• methylation status?

Answer 1

2.8 x 10^7 CpGs in mammalian genomes
60-80% methylated
10% in CpG islands

usually at promoters
predominantly unmethylated

Question 2

De novo methylation

Answer 2

By Dnmt3b + Dnmt3a

DNA methyltransferases

Question 3

Maintenance methylation

Answer 3

Maintaining methylation marks when cells divide

Dnmt1 binds to heavily methylated DNA
- adds methyl groups to strand during heme-methylation

Question 4

Active demethylation

Answer 4

When methyl marks are removed by enzymes

Question 5

Passive demethylation

Answer 5

When methyl marks aren’t maintained by Dmnt1

Question 6

DNA methylation in embryonic reprogramming

• pre-fertilisation
• fertilisation

Answer 6

PGCs
- global demethylation 
Mature GCs
- Remethylation 
Fertilisation 
- Active demethylation of male pronucleus

Question 7

DNA methylation in embryonic programming

- post-fertilisation

Answer 7

Males: DNA remethylated
(ensures meiosis)

Spermatogenesis impaired if methylation defective

Females: DNA fully remethylated after meiosis 1 + sexual maturation

Defective methylation in oocyte doesn’t hinder fertilisation

Question 8

PGC migration

Answer 8

PGCs migrate to genital ridge

- removes methyl groups

Question 9

PGCs stuck during migration

Answer 9

Need to die or be removed

• > have stem cell properties
• -> tumours

Question 10

DNA demethylation cycle

Answer 10

C

• > 5-mC (via DNMTs)
• > 5-hmC (via TETs)
• > C (via TETs)

Question 11

TET enzymes

- define

Answer 11

= Ten-eleven translocation enzymes

Oxidise methyl group -> OH

Question 12

TET enzymes
- levels

5mc levels

Answer 12

1 + 2 = increases 4 cell -> blastocyst
3 = decreases zygote -> 2 cell

5mC =
decreases Zygote -> blastocyst

5hmC =
increases zygote -> 2 cel
Decreases 2 cell -> 4 cell
Increases 4 cell -> blastocyst

Question 13

De novo methylation of pluripotency factors

Answer 13

Silences Oct4 + Nanog

Question 14

ICM -> ES cells –>?

Answer 14

ectoderm
(brain, skin)

mesoderm
(muscle, blood, bone)

endoderm
(lung, gut)

germline
(sperm + egg)

Question 15

Add TFs to fibroblasts
–> ?

Which TFs?

Answer 15

iPS cells
-> smooth muscle cells, RBCs, neurones etc

Oct4
Sox2
Klf4
Myc

Question 16

TET1 in iPS cells

Answer 16

TET1 promotes Oct4 demethylation
= reactivation

TET1 can replace Oct4 to generate fully pluripotent iPS cells

Question 17

Changes in pluripotency-related genes in reprogramming

leads to..?

Answer 17

Expression of Oct4, Sox2 + Nanog

Activation of silent X

Upregulation of telomerase

Question 18

Pathological PGC migration

• can lead to?
• e.g.

Answer 18

Ectopic localisation
(= abnormal)

e.g. intracranial region

Question 19

Germ cell cancers

• caused by
• unusual tumours?

Answer 19

Arise from PGCs
- have failed to mature into pre-spermatogonia or oogonia

Have no/few genetic mutations

Question 20

Germ cell cancers

- mimic?

Answer 20

embryonal development
- express Oct4 + Sox2
= over demethylated

Question 21

Germ cell tumours

Answer 21

Emerge during puberty

66% are benign

Most children are cured
- could kill if affects heart + prevents blood flow

45 cases/yr in UK

Question 22

classification of germ cell cancers

Answer 22

> Germinoma
= in GC stage

• Seminoma
  = in testes
• Dysgerminoma
  = in ovary

> Embryonic tumours
Extra-embryonic tumours

> Teratoma
= tissue/organ components resemble normal derivatives of more than 1 germ layer

Question 23

Tattan-Brown-Rahman Syndrome (TBRS)

Answer 23

Mutation in Dnmt3A

Overgrowth syndrome
- growth rate increased before + after birth

Question 24

Sotos syndrome

Answer 24

Haplo-insufficiency of NSD1
= histone methyltransferase that catalyses demethylation of H3 at K36
(H3K36me2)

Overgrowth syndrome

Question 25

SOTOS + TBRS
- risk of?

• what do their molecular abnormalities lead to?

Answer 25

Both have high risk of tumours due to epigenetic modification

Genome-wide K27me3 accumulation