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EXMD504 > 11. MicroRNAs in Cancer > Flashcards

11. MicroRNAs in Cancer Flashcards

1
Q

what organism was miRNA found in?

A

C. elegans

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2
Q

what are lin mutants?
why are they used?

A

lineage defective mutants

diff larval stages have diff fates so can trace development thru Lin mutants and map mutations

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3
Q

what is Lin4?

A

miRNA

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4
Q

Lin4L vs Lin4S

A

Lin4L base pairs with itself to form hairpin

Lin4S has shorter, linear sequence

there must be precursor and mature form

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5
Q

relationship btwn Lin4 and Lin14, how does it work?

A

Lin4 represses Lin14

Lin4 matches Lin14 sequence at 3’ and 5’ ends –> base pairing contributes to repression

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6
Q

describe miRNA across organisms

A

miRNA are conserved across organisms

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7
Q

how did we find that miRNA are conserved across organisms?

A

Let7 miRNA matches in many organisms

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8
Q

are miRNA encoding RNA?

A

no!! don’t encode things

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9
Q

what do miRNA do?

A

just control genes

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10
Q

how have miRNA evolved with mRNA?

A

miRNA and mRNA have co-evolved since the beginning

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11
Q

describe Let7 mutants in V cells

A

normally V cells divide finite number of times

Let7 mutants divide continuously and never differentiate like cancer

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12
Q

why do Let7 mutants in V cells cause continuous division?

A

division of V cell is controlled by Ras

Regions of Let7 match 3’ region of Ras to suppress Ras (dose-response relationship)

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13
Q

describe Let7 and Ras in cancer cells vs normal cells

what does this mean about the function of Let7?

A

in cancer cells:
-Let7 is reduced and Ras is increased

in normal cells:
- Let7 is increased and Ras is reduced

therefore, Let7 may have TUMOUR SUPPRESSIVE function –> lose Let7 in tumour

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14
Q

where are miRNA usually found in genome?

A

at fragile sites

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15
Q

what are fragile sites

A

region of genome in tumour cells where chunk of info is lost or amplified

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16
Q

how do we know that fragile sites are not random?

A

fragile sites contain fusions between oncogenes and promoters, as well as miRNA tumour suppressors/oncogenes

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17
Q

what do we see at fragile site if miRNA is oncogene?

A

would see region amplified (multiple copies) in tumour

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18
Q

what do we see at fragile site if miRNA is tumour suppressor?

A

region would be lost

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19
Q

is miRNA-17-92 oncogene or tumour suppressor?

A

oncogene

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20
Q

how did they find that miR-17-92 is oncogene?

A

found RNA from amplicon highly expressed in lymphoma

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21
Q

what oncogene does miR-17-92 interact with?

A

Myc

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22
Q

Describe 17-92 in Myc driven cancer

A

17-92 is amplified in Myc-driven cancer

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23
Q

what happens if you transduced 17-92 in mice with overexpressed Myc?

what can you conclude from this?

A

gives tumour with same profile as Burkitt’s Lymphoma

therefore 17-92 involved in lymphomas

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24
Q

describe survival in mice with:
A. overexpressed Myc
B. overexpressed Myc + 17-92

A

A. overexpressed Myc = survival

B. overexpressed Myc + 17-92 = survival drops quickly

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25
Q

what does miRNA depend on? why?

example with Let7/Ras
example with 17-92/Myc

A

miRNA depends on TARGET because it is just a regulator

If you have Let7 but no Ras –> nothing will happen

If you have 17-92 but no Myc –> nothing will happen

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26
Q

where are miRNA encoded?

A

in genome

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27
Q

what transcribes miRNA ?

A

miRNA is transcribed by Pol II

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28
Q

how many miRNA does 1 miRNA transcript make?

A

can make 1 or multiple miRNA

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29
Q

describe the biogenesis of miRNA (5 steps)

A
  1. primary transcript made by pol II in nucleus
  2. pri-miRNA is substrate for DROSHA (RNAse) which makes sequences with overhang –> produces pre-miRNA
  3. pre-miRNA exported to cytoplasm to meet DICER (RNAse) which makes 2 strands with overhang
  4. pre-miRNA captured by Argonaute which cleaves the 2 strands
  5. 1 strand is used as a guide to find mRNA targets with miRISC complex
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30
Q

pre-miRNA vs pri-miRNA

A

pri-miRNA = primary transcript transcribed from genome

pre-miRNA = cleaved after DROSHA

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31
Q

purpose of argonaute?

A

normally, the 2 strands cleaved from pre-miRNA would be degraded but argonaute cleaves one of the strand

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32
Q

why does the miRISC complex have specific scanning mechanism to find targets?

A

most contacts btwn miRISC complex and targets are non-prouctive

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33
Q

what is GW182?

A

piggybacks on miRISC to help find targets and enacts silencing

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34
Q

how did they crystallize the argonaute structure?

A

use traces of phenol

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35
Q

shape of argonaute

A

crescent shape with 2 lobes

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36
Q

describe the domains in the 2 lobes of argonaute

A

LOBE 1: mid domain and PIWI domain

LOBE 2: PAZ domain and N terminal domain

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37
Q

which 3 argonaute domains are well-conserved?

A

Mid, PIWI, PAZ

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38
Q

which argonaute domain is more variable/less conserved?

A

N-terminal

39
Q

which domain of argonaute binds the 5’ end of miRNA?

A

Mid domain

40
Q

what allows specificity for miRNA and argonaute interaction?

A

1st nucleotide at 5’ end embedded in pocket at mid domain allows specificity

41
Q

which domain of argonaute binds the 3’ end of miRNA?

A

PAZ domain

42
Q

describe the interaction of miRNA with argonaute in terms of domains

A

5’ end at Mid domain
3’ end at PAZ domain

the rest of miRNA is in the cleft

43
Q

what is the significance of the non-5’/3’ parts of miRNA being in the cleft?

A

since the miRNA is in the cleft, the mRNA is also in the cleft

44
Q

what does the PIWI domain of argonaute resemble?

A

RNAse H

45
Q

what does the PIWI domain do?

A

cleaves mRNA when there’s an RNA-DNA/RNA-RNA hybrid

46
Q

when does the PIWI domain cleave?

A

only cleaves when the miRNA is fully base paired with mRNA

47
Q

where does the PIWI domain cleave?

A

cleaves exactly at the 10th nt

48
Q

why does the argonaute scan mRNA in the cell?

A

to find complementarity btwn miRNA and mRNA

49
Q

in animals, do miRNA perfectly base pair with mRNA targets?

example with Lin4 and Lin14

A

miRNA INCOMPLETELY base-pair with mRNA

Lin4 stops base-pairing with Lin 14 by 10th nt

50
Q

since miRNA and mRNA don’t completely base-pair, what does indicate about the argonaute cleavage mechanism?

A

if the goal was to cleave, the co-evolution of the miRNA and mRNA would favour base-pairing in the middle

51
Q

what did ppl initially think was the mechanism for miRNA-mediated silencing?

A

the cleavage by argonaute

52
Q

what are the names of the 2 current models for miRNA-mediated silencing

A
  1. Deadenylation, Decapping, and Decay
  2. mRNA Translation Repression
53
Q

describe the Deadenylation, Decapping, and Decay model of miRNA-mediated silencing

3 steps

A
  1. CCR-NOT is deadenylation complex that removes polyA tail of mRNA
  2. loss of polyA tail stimulates enzymes to remove 5’ cap
  3. deadenylation AND decapping = mRNA loses stability
54
Q

describe the mRNA translation repression model of miRNA-mediated silencing

A

RISC shuts down transcription initiation and prevents ribosome assembly

55
Q

why is deadenylation bad for mRNA?

A

polyA tail is important for initiation bc interacts with 5’ end and important for stability of 3’ end bc acts as protection

56
Q

why are the 2 current models of miRNA-mediated silencing better than the cleavage/slicing model?

A

these mechanisms allow for better regulation and control bc they can be tuned –> if you just slice, the activity is fully gone

57
Q

if not for miRNA-mediated silencing, what is the role of the slicing mechanism?

A

2 miRNA are made but must get rid of 1 so it can base pair with its target

58
Q

what are P bodies?

A

biological condensates –> segregate from cytoplasm and concentrate specific enzymes

may be a storage place for mRNA with polyA tail and cap –> then upon exit, the mRNA becomes deadenylated and decayed

59
Q

what is targetscan?

A

database with all matching sequences in transcriptome for miRNA-mRNA interactions

60
Q

how are many miRNA’s organized?

A

as cluster/polycistron

61
Q

do the pri-miRNAs have the same functions as the mature miRNA?

how do we know?

A

pri-miRNA may contain info for diff functions than mature miRNA

many intermediates are made as pri-miRNA is processed –> last intermediate miRNA-19 is most oncogenic

62
Q

can miRNA profile predict cancer patient survival?

A

yes

63
Q

in profiling of miRNA, what causes miRNA expression to increase or decrease?

A

miRNA expression varies with cell fate and state, i.e. depending on nutrients/conditions

64
Q

how can we use miRNA to detect cancer

A

look at changes in miRNA expression and predict origin of cell

if you sequence all miRNA in tumour, can determine where it came from, which subtype of cancer it is, and find NEW subtypes of cancer

65
Q

survival curve with Let7

what does this tell us about using miRNA to predict outcome?

A

data shows high Let7 has best outcome –> Let7 is tumour suppressor

just 1 miRNA can help us predict outcome, even if you didn’t know what it does

66
Q

how can we profile miRNA?

A

with NGS

67
Q

what are heatmaps used for?

what is clustering?
what does red/blue mean?

A

heatmaps are used to analyze multiple variations in gene expression and represent increases/decreases

clustering = grouping genes based on similarities

red = increased expression
blue = decreased expression

68
Q

relationship between Myc and p53

A

Myc oncogene will activate p53

69
Q

in cancer with increased Myc, what happens if 17-92 is removed?

A

17-92 removal –> pre-B cells will survive bc no self-tolerance and lead to autoimmunity

17-92 cannot activate Myc so p53 is inactive

70
Q

in cancer with increased Myc, what happens if 17-92 is expressed?

A

17-92 expressed –> B cells will die

17-92 activates Myc so p53 is active

71
Q

comparing 2 patients with Burkitt’s Lymphoma, 1 with high 17-92 and 1 with low 17-92, which has worst outcome after treatment?

A

patient with HIGH 17-92 –> tumour cells won’t die

72
Q

what happens to PTEN if 17-92 is lost?

A

PTEN increases –> increased tumour suppressor activity

73
Q

if you knockdown PTEN, what is the outcome?

A

very bad bc removing tumour suppressor

74
Q

what is BIM?

A

Induces apoptosis

75
Q

relationship btwn 17-92 and BIM

A

17-92 allows promotion of proliferation and growth as an oncogene and REPRESSES BIM

76
Q

in lymphoproliferative disease with high 17-92, what happens with PTEN and BIM?

A

Both decrease

77
Q

why do tumour cells develop oncogene addiction?

A

cancer causes the loss of many genes –> can maintain a pathway via synthetic lethality but there is strain in the background –> cells lose flexibility and are less adaptable

78
Q

describe 17-92 oncogene addiction

A

tumour cell relies on 17-92 to survive with Myc overexpression

normal cell would be fine if 17-92 was removed

79
Q

why is the DICER heavily oncogenic?

A

required for 17-92

80
Q

why is 17-92 a good drug target?

A

tumour is addicted so will die if removed

81
Q

3 ways for RNA to be used as a drug

A
  1. use siRNA with full base-pairing to target gene to slicing activity
  2. can mimic miRNA to replaces tumour suppressor
  3. inhibit miRNA with modified oligonucleotide
82
Q

give an example of an miRNA mimic that can replace a tumour suppressor

A

normally, Let7 tumour suppressor suppresses Ras

so if Let7 can be restored in tumour cells, tumour will die

83
Q

describe inhibiting oncogenic miRNA with modified oligonucleotide

A

oligonucleotide can base pair with miRNA and prevent miRNA function

84
Q

what is the main problem with using RNA as a drug?

A

delivery

85
Q

2 types of overcoming the issue with RNA drug delivery

A
  1. aerosol helpful for lung cancer
  2. lipid nanoparticles
86
Q

why must RNA drugs have chemical modifications?

A

exogenous RNA is normally not taken up and is seen as foreign by innate immunity –> chemical modifications hide the RNA from innate immune system

87
Q

what can determine whether miRNA will function or not?

A

depends on whether target site is in 3’ UTR

88
Q

describe dynamics of 3’ UTR

A

UTRs change with cell state as miRNA changes with cell state

89
Q

describe relationship btwn 3’ UTR and cancer

A

cancer can avoid control by miRNA due to the dynamics of 3’ UTR

90
Q

how does 3’ UTR change in proliferating cancer cells?

A

3’ UTR can get shorter due to alternative polyadenylation

91
Q

describe short vs long UTR

A

long UTR has many miRNA binding sites

short UTR has fewer miRNA binding sites

92
Q

how can cancer avoid control by miRNA via UTR?

A

Cancer can shorten the UTR by alternative polyadenylation in proliferating cells

93
Q

in retinoblastoma what happens if you shut down the 17-92 dicer? is this true in all tumours?

A

tumour dies

in other cases, if you shut down drosha or dicer to lose the miRNA, there is greater proliferation

EXMD504 (12 decks)

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