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LSM4221 > L6: Biomarkers in clinical studies > Flashcards

L6: Biomarkers in clinical studies Flashcards

1
Q

define biomarkers

A

a defined characteristic that is measured as an indicator of:
1. a normal biological process
2. pathogenic process
3. response to (therapeutic) intervention

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2
Q

are biomarkers the same as symptoms?

A

no. biomarkers are more quantitative

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3
Q

state the 7 categories of biomarkers
hint: dm ppp and ss

A
  1. diagnostic biomarker
  2. monitoring biomarker
  3. pharmacodynamic biomarker
  4. predictive biomarker
  5. prognostic biomarker
  6. safety biomarker
  7. susceptibility/risk biomarker
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4
Q

what is diagnostic biomarkers? +examples

A

used to identify individuals WITH the disease/condition OR to define a subset of the disease

eg. blood sugar in diabetes
eg. ejection failure in heart failure

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5
Q

what is monitoring biomarker? +examples

A
  • biomarker measured repeatedly and used to detect a change in the degree of disease
  • can also be used to indicate toxicity or assess safety or provide evidence of exposure to eg. medical products

eg. PSA in prostate cancer; CA-125 in ovarian cancer

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6
Q

what is a predictive biomarker? example?

A

-used to identify indivs who are MORE LIKELY than indivs without biomarker to experience favourable/unfavourable effect from a specific intervention/exposure
- usually checked before giving patient treatment to predict gauge likelihood of response

eg. EGFR mutation in lung cancer for anti-EGFR drugs
eg. PD1 expression in tumour for anti-PD1 therapy

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7
Q

what is prognostic marker? example?

A

used to identify likelihood of CLINICAL EVENT, DISEASE recurrence or progression.

eg. BRCA1/2 mutation in breast cancer patients for likelihood of second breast cancer
eg. Ch17p deletions in Chronic lymphoblastic leukemia for likelihood of death
eg. PSA in prostate cancer -> likelihood of cancer progression

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8
Q

what is safety biomarker? + 2 examples

A

used to indicate the presence/extent of TOXICITY related to an intervention/exposure

eg. hepatic aminotransferase in hepatotoxicity
eg. serum creatinine in nephrotoxicity

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9
Q

what is susceptibility/risk biomarker?

A

biomarker that indicate the POTENTIAL for developing disease/medical condition or sensitivity to an exposure in an indiv without clinically apparent disease or medical condition –> * no symptom for disease yet

eg. BRCA1/2 mutation -> risk of getting breast cancer
eg. APOE gene variations-> risk of earlier onset of Alzheimers
eg. infection of HPV subtypes in likelihood for cervical cancer

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10
Q

whats the difference between susceptibility and diagnostic marker?

A

diagnostic markers once present = 100% have disease

susceptibility markers not 100%, just indicative of POTENTIAL

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11
Q

difference between diagnostic and monitoring biomarker

A

diagnostic: IDENTIFIES disease in individuals; done once
monitoring: measured repeated over a period to detect CHANGE IN DEGREE/extent of disease

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12
Q

difference between predictive and prognostic biomarker

A

predictive: to determine likelihood of patient having favourable/unfavourable effects from intervention/drug
prognostic: identify likelihood of clinical event (death, disease recurrence or progression)

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13
Q

what is a pharmacodynamic marker? example?

A

used to show that a biological response has occurred in individual who has received intervention

eg. blood pressure in hypertension patients treated with anti-ypertensives
eg. viral load in covid patients

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14
Q

can a marker fall into more than 1 category?

A

yes

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15
Q

what kind of marker is blood pressure?

A

diagnostic, monitoring, pharmacodynamic marker

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16
Q

methods for cancer diagnosis [6]

A
  1. self examination
  2. blood/urine screening
  3. biopsy
  4. x-rays, CT scans, MRI scans, PET scans and ultrasound
  5. molecular diagnostic tests
  6. next gen sequencing
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17
Q

how is breast cancer diagnosed? [3]

A
  1. self-examination
  2. cytological analysis [get a breast tissue and analyse
  3. mammography
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18
Q

what are double minute chromosomes?

A

they are derived from chromosomal segments that have broken loose from original sites and have been replicated repeatedly as extrachromosomal genetic elements

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19
Q

what is a homogeneously staining region (HSR)?

A

when a marker gene gets amplified, it can cause an entire stretch of chromosome to stain the same

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20
Q

what is FISH?

A

in situ hybridisation of genes along chromosomes –> used to get a physical mapping of genes on chromosome

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21
Q

cancer can manifest itself through abnormalities in chromosomes, such as:

A
  • inversion
  • deletion
  • translocation
  • aneuploidy [change in number of chromosomes]
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22
Q

can cancer be diagnosed through histopathology?

A

yes

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23
Q

differentiate hyperplasia and dysplasia

A

hyperplasia: growth contain normal cells in excessive numbers
dysplasia: cells w abnormal appearance eg. nuclear size and shape

24
Q

how are oncogenes detected? [2] compare the 2.

A

via immunoprecipitation/western blot and immunohistochemistry

both can detect proteins.
immunoprecipitation/western blot can show molecular weight of protein

immunohistochem: cannot see molecular weight but can see localisation changes in tissue [to validate that DNA/protein expression led to disease as it is not alws the case]

25
Q

what is a new form of biopsy that is non-invasive?

A

liquid biopsy, where sample is derived from body fluids

26
Q

pros of liquid biopsy [4]

A
  1. non-invasive
  2. less risk and pain
  3. easy to obtain, can repeat easily
  4. real time detection and comprehensive profile
27
Q

can cancer be diagnosed with extracellular vesicles from the blood?

A

yes. EVs are secreted by many cell types

28
Q

HOW can cancer be diagnosd by EVS?

A
  • EVs are membrane vesicles secreted by cell
  • EVs from cancer cells can be purified from blood –> detect biomarkers through RNA [eg. sequencing, microarray, qRT-PCR] or protein detection [mass spec, flow cytometry, ELISA]
29
Q

EVs can be classified into: [3]

A
  1. apoptotic bodies: vesicle containing parts of a dying cell
  2. exosomes: small vesicles released out of cell from a multi-vesicular body
  3. micro-vesicles: proteins bud away from cell -> small vesicles formed
30
Q

what methods can be used to identify cancer by detecting proteins on EVs?

A

flow cytometry and ELISA

31
Q

when detecting surface proteins on EVs, to diagnose cancer, EVs are immobilised on latex/magnetic beads because _____

A

EVs are very small, required alot of EVs at one area so that when protein-binding antibodies conjugated with fluorescent dye give off fluorescent, can be detected

32
Q

western blot/immunostaining can be used to detect proteins on EVs. T/F?

A

False. EV too small, western blot not sensitive enough to detect

33
Q

do EVs contain chromosomes?

A

no, but they have RNA and DNA that can be detected using qRT-PCR

34
Q

differentiate between southern blot and western blot.

A

southern: for DNA
Western: for protein

35
Q

how do we find a new biomarker? [3]

A
  1. start w clinical sample. or if we have gene candidate in mind we can go gene profiling for that specific gene. compare disease vs normal to check if theres a difference
  2. validate biomarker by checking for precision, sensitivity, accurcy, dynamic rnage
  3. proceed to do on large clinical study to confirm evaluation from step 2
36
Q

best method for detecting PROTEINS on EVs [2]

A

ELISA & flow cytometry

37
Q

why is western blot and immunostaining not recommended for detecting proteins on EVs?

A

EV very small, need alot of EVs to detect presence of protein or for band to appear

38
Q

why is qRT-PCR not the best for detecting RNA on EVs?

A

EVs contain little DNA and RNAs

39
Q

we validate biomarker using ____ curve which help to ____

A

receiver operating characteristic (ROC); determine responsiveness of biomarker [sensitivity and specificity]

40
Q

HCV-RNA is a ____ marker for chronic hepatitis C

A

monitoring

41
Q

CA-125 is a ____ marker for ovarian cancer

A

monitoring

42
Q

APOE gene variation is a ____ marker for _____.

A

susceptibility; alzheimer’s disease

43
Q

infection of HPV subtypes is a ____ marker for ____

A

susceptibility; cervical cancer

44
Q

hepatic aminotransferase levels is a ____ marker for ____

A

safety; hepatotoxicity

45
Q

serum creatinine is a ____ marker for _____.

A

safety; nephrotoxicity

46
Q

which is worse, hyperplasia or dysplasia?

A

dysplasia. cells not only in excessive numbers but have abnormal appearance

47
Q

n-myc is a ____ marker for _____.

A

prognostic; neuroblastoma

48
Q

HER-2 is a ____ marker for ___

A

predictive; HER2 cancers + drugs that target these cancers

49
Q

how are proteins in EVs detected/measured? [3]

A
  1. mass spec
  2. flow cyto
  3. ELISA
50
Q

how are DNA/RNA in EVs detected?

A

sequencing, microarray, qRT-PCR

51
Q

northern blot is for?

A

RNA

52
Q

southern blot is for?

A

DNA (rmb btS-DNA)

53
Q

western blot is for?

A

proteins

54
Q

HCV-RNA is what kind of marker?

A

monitoring marker for chronic hep C

55
Q

CA-125 is what kind of marker?

A

monitoring marker for ovarian cancer

56
Q

APOE gene variation is what kind of marker?

A

susceptibility/risk marker for Alzheimer’s

LSM4221 (13 decks)

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