Liquid Biopsy

Question 1

Diagnostic, prognostic and predictive markers

Answer 1

Diagnostic: likely presence of cancer
Prognostic: likely course of disease in an untreated individual (how agressive)
Predictive: likely to respond to a given therapy (how will respond)

Question 2

liquid biopsy markers (5) - explain the less relevant 3

Answer 2

circulating tumour cells (CTCs)
circulating tumour DNA (ctDNA)

micro RNA (miRNA) - small non coding RNA that regulate gene expression (oncogenes or tumour supressors)

exosomes - shed out by cells (remodel tumour
microenvironment, pre metastic niches and immune escape)

platelets- absorb RNA and DNA from tumour

Question 3

CTC (definition, 4 types, problems, applications)

Answer 3

cells detached from main tumour - represent tumour heterogeneity, metastisis (seeds for metastic growth)
easy but difficult to find

traditional- large irregular, viable nucleus, CK+/CD45-

small - CK+/CD45-, similar size WBC, progressive disease

CK- - cancer STEM or EMT, more malignant and metastic, resistant to treatment

apoptic- information about therapy efficacy

Question 4

CTCs isolation and analysis (applications)

Answer 4

Cytometric/protein analysis - immunostaing, FACS/FISH/CGH, chip/array screening

PCR - PCR, qPCR, RT-PCR, qRT-PCR, NGS

pre clinical ex vivo - ex vivo omics, CDX models, CTC drug screening

Question 5

CTC pre clinic (3) and clinical (2)

Answer 5

pre-clinic:
1- patient - CTC ex vivo (omics or drug screening)
2- model - CDX (omics, biomarker proffiling, in vivo trial study)
3- CDX ex vivo (drug screening, in vivo implant, genome editing fluo)

clinic:
1. CTC enumeration
- baseline: - treatment de-escalation; + treatment intensification
- during therapy: + treatment change
- after therapy: residual - intensification; therapy efficacy in clinical trial

2. molecular characteristcs
   -response to treatment
   -resistance to treatment

Question 6

ctDNA and cfDNA

Answer 6

tumour derived fraction in cfDNA (plasma)
blood, urine, cerebral spinal fluid, pleural fluid, saliva
apoptisis, necrosis, secretion - apoptic bodies, point mutations, copy nº alterations, rearrangements, methylation changes, exosomal DNA
plasma - DNA or RNA

Question 7

new ctDNA analysis

Answer 7

fragmentatomics- length and nucleosomal footprinting
methylation - what tissue is comming from, signature of how it is when there´s cancer
topology- shape