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Precision Cancer Medicine > Epigenetics and circulating biomarkers > Flashcards

Epigenetics and circulating biomarkers Flashcards

1
Q

Integrated genomic analysis (4)

A

DNA methylation
DNA sequence
Copy number analysis
Rna expression

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2
Q

Promoter and methylation

A

Promoter hypermethylation is associated with reduced transcription

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3
Q

GENE body and methylation

A

GENE body hypermethylation is associated with increased transcription

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4
Q

Epigenetic dysregulation in CRC

A

Global DNA methylation changes
CIMP
SEPT9

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5
Q

CIMP

A

Present in 20% of CRC
Negative prognostic marker
Affects response to treatment- 5-FU CIMP high has better response

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6
Q

How is SEPT9 methylation detected?

A

Circulating DNAm biomarker

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7
Q

SEPT 9- why is it circulating?

A

In early stages of CRC, SEPT9 is hypermethylated and released into circulation by apoptotic cells

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8
Q

What is SEPT 9 (protein)

A

SEPTIN 9 is a GTP binding protein

It is a scaffolding protein - structural support

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9
Q

Physiological role of SEPT9

A

Actin dynamics, angiogenesis, motility, proliferation

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10
Q

SEPT9 in CRC

A

Underexpressed in CRC

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11
Q

5 challenges of using cfDNA biomarkers

A

Mutated cfDNA diluted by normal cfDNA (allele frequency)

Duration of marker in circulation

Needs stable methylation pattern and stable levels in circulation

Mutation detection cannot identify tumour location

Requires adequate sensitivity and specificity

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12
Q

What are miRNAs

A

Small non coding RNA

Function in RNA silencing and post transcriptional regulation of gene expression

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13
Q

What is the mechanism of miRNAs? 4

A

Complementary base pairing with mRNA leading to:

Cleavage of mRNA strand into 2 pieces
Destabilisation of mRNA through shortening of the poly(A) tail

Less efficient translation of mRNA into proteins by ribosomes

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14
Q

4 types of circulating biomarkers

A

Circulating tumour cells
Cell feee DNA
MicroRNAs
Exosomes

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15
Q

3 ways to methodologically isolate CTCs:

A

Antibody based capture
Physical characteristics
CD45 depletion and culture

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16
Q

How to capture CTCs with antibodies?

A

EPCAM AND MUC1

17
Q

How to capture CTCs by their physical characteristics

A

Size filtration
Flow dynamics
Membrane capacitance

18
Q

What is CellSearch?

A

EPCAM based selection

19
Q

How to capture cells with EPCAM?

A

Use ferrofluid conjugated EPCAM Ab

20
Q

How to capture CTCs by CK?

A

PE-conjugated CK antibody

21
Q

How to capture by CD45?

A

APC Conjugated CD45 Ab

22
Q

What are the therapeutic options for neuroendocrine tumours? 5

A 
Somatostatin analogies
Chemo
Targeted radiotherapy
TACE 
Radioembolisation
23
Q

Applications of CTCs:

5

A 
See response to treatment 
Drug target expression
Pharmacodynamic marker
Genetic heterogeneity
Biology of metastases
24
Q

Steps for whole genome amplification of DNA from a single CTC? 7

A 
Proteinase k digests single cell
Preannealing of adaptors
Ligation
Removal of unligated small primers
Filling reaction at 3'
Primary PCR amplification
25
Q

Concentration of cell free DNA in blood

A

1000-2000 copies of genome per ml

26
Q

Cell free DNA half life

A

1 hour

27
Q

Cell free DNA pro and con

A

Good response marker

Tumour must be of a certain size

28
Q

Optimal ctDNA collection

A

If blood is collected into EDTA tubes it should be centrifuges within a short time frame

Alternatively use a stabilisation tube

29
Q

Top 5 cancers with ctDNA:

A 
Bladder 
Colorectal
Gastric
Ovarian 
Pancreatic
30
Q

2 ways to use ctDNA

A

Detecting and tracking single mutations

Sequencing ctDNA to detect mutations

31
Q

Why sequence a tumour scone from plasma?

A

Can’t always get to tumour tissue

To understand tumour relapse

32
Q

6 ways to use ctDNA as a biomarker

A 
Early detection
Molecular stratification
Treatment response
Residual disease
Tumour evolution
Differing treatment response
33
Q

What biofluids can cancer DNA be detected in?

A 
Blood plasma 
Csf
Cyst fluid
Urine
Stool
34
Q

Cancer DNA detection in oesophageal/ gastric cancer:

A

Cystosponges

35
Q

What cancer is already being stratified by ctDNA

A

Lung

36
Q

Ctc > ctDNA (4)

A

Validated prognostic marker
Heterogeneity at single cell level
Look at rna and protein expression
Study cancer biology

37
Q

CtDNA>CTCs

A

More sensitive
Bigger dynamic range
Cheaper

Precision Cancer Medicine (10 decks)

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