Lecture 4 Biomarkers in Clinical Studies

Question 1

What is a biomarker?

Answer 1

• A defined characteristic that is measured as an indicator of normal biological processes, pathogenic processes, or responses to an exposure or intervention, including therapeutic interventions.
• A biomarker is NOT an assessment of how an individual feels, functions, or survives.

Question 2

What is the purpose of having biomarkers?

Answer 2

Slide 7, 8

Question 3

What characteristics does an ideal biomarker have?

Answer 3

• Expression is significantly increased especially in the related disease condition.
• Readily quantifiable in accessible biological fluid or clinical samples
• Shown to correlate with an interested outcome progression
• Economical, quick and consistent.

Question 4

What are the different type of BM and how does it correlate with the disease pathology?

Answer 4

Slide 11 and 12

Question 5

What are some BM for hypertension + consequences for HBP/HTN

Answer 5

Slide 14, 15, 16, 17, 18

Question 6

What are some methods to diagnose cancer?

Answer 6

Slide 23

Question 7

How to diagnose for breast cancer?

Answer 7

Slide 24 + Slide 26 (What is cytological analysis?)
- Cytological analysis: Examining a few cells instead of the entire tissue (biopsy)

Question 8

How can FISH be used as diagnostic BM?

Answer 8

Slide 27, 28, 29, 30-32

Question 9

How do you detect for oncogenes using blots?

Answer 9

Slide 37
!!! NoRthen blot - RNA
Southern blot - DNA
WB - Protein

Question 10

How do you perform gene expression profiling of many genes?

Answer 10

Slide 38
Microarray, comparing heatmap

Question 11

How do you identify single mutations in a genome?

Answer 11

Slide 39
NGS

Question 12

How do you develop a good biomarker?

Answer 12

Slide 43

Question 13

What is a non-invasive diagnosis BM and what is the difference compared to traditional biopsy?

Answer 13

Slide 44 + 45

Question 14

What can EVs be used to diagnose cancers?

Answer 14

Slide 46 (ECV)

Question 15

What is the purpose of mass spectrometry?

Answer 15

Slide 47
- MS: Identify proteins in the EV lysate using mass analysis
- Quantitative MS: Abundance of each protein in the mixture to facilitate protein expression comparison

Question 16

What assays/methods do you use to detect surface protein on EVs?

Answer 16

• Flow cytometry and ELISA
  Slide 48
• EVs does not contain chromosomes so we cannot use FISH
• Cannot use WB/Immunostaining as they are not sensitive enough for EVs

Question 17

What is an example of using BM for cancer prognosis

Answer 17

Slide 49, 50, 51
- Evaluating cancer
- Integrins, associated with ECM -> Often increased in cancer as it is involved in cell migration which correlates with more metastatic properties -> hence higher expression in CA1 cells which are more aggressive (as seen in luciferase imaging)
- Slide 51: Late stage cancer correlates with higher ITGAV (Integrin alpha V levels)

Question 18

What is the process of developing a good BM for use?

Answer 18

Slide 52