Biology of non-coding RNAs in cancer

Question 1

Mir-17-92 controls the expression of :
a) PTEN
b) TP53
c) Ras
d) BRCA1
e) Rb1

Answer 1

a) PTEN

Question 2

MicroRNA profiling is informative of:
a) Tumor origin
b) Tumor type and sub-type
c) Mutations that can be targeted by targeted therapy
d) a and b are correct
e) All of the above

Answer 2

d) a and b are correct

Question 3

P-bodies are:
a) sites in the cytoplasm where pre-miRNA are processed by Drosha
b) potential targets for miRNA-mediated anti-cancer therapy
c) proteins that bind mature, single-stranded siRNAs and miRNAs
d) sites in the cytoplasm where there is high activity of enzymes dedicated to mRNA turnover
e) none of the above

Answer 3

d) sites in the cytoplasm where there is high activity of enzymes dedicated to mRNA turnover

Question 4

Who were the researchers involced in studying C-Elegans development, and discovering the lin4 gene

Answer 4

Rosalin Lee and Victor Ambros

Question 5

What change did Rosalind Lee and Victor Ambros observe in C.Elegrans development that affected all cells

Answer 5

They observed that a change in one cell resulted in the same change in all cells

Question 6

What was the focus of the search for mutations by Lee and Ambros, and what gene did they identify

Answer 6

They were looking for mutations influencing the lin-14 gene and identified the lin-4 gene, which encodes small RNA

Question 7

What was the relationship between the variants of lin-4 namely lin-4S and lin-4L

Answer 7

They postulated that lin-4S was derived from lin-4L due to size differences

Question 8

How did lin-4 interact with lin-14 and what was its effect on lin-14

Answer 8

Lin-4 was found to bind to seven sites in the 3’UTR of lin-14 suppresing its expression

Question 9

What significant discovery was made eight years after identifying lin-4 and lin-14’s interaction

Answer 9

The discovery of let-7 miRNA in C.Elegans, which showed homology in drosophila and humans, indicating conservation acroess species

Question 10

What was the observed consequence of let-7 mitations in C.elegans and what resemblance did it show?

Answer 10

C-elegans let-7 mutants exhibited continuous cell division and failure to differentiate, resembling traits seen in cancer

Question 11

How did let-7 miRNA control the expression of RAS gene in both C elegans and human cells

Answer 11

Let-7 could bind multiple times to the homolog of Ras in C.elegans and human cells, effectively shutting down Ras expression, which is a proto-oncogene

Question 12

Where are human miRNA genes frequently located and what is their association with cancer

Answer 12

Human miRNA genes are often found at fragile sites and in genomic regions associated with cancers

Question 13

What is the significance of the miR-17-92 amplicon in relation to lymphoma

Answer 13

It represents a piece of the genome that is amplified in lymphomas, particularly at the 13q31locus, and collaborates with c-Myc, accelerating lymphoma progression, as seen in Burkitt’s lymphoma

Question 14

What is the source of miRNAs in the genome and which enzyme transcribes them

Answer 14

miRNAs are transcribed from the genome by RNA pol II

Question 15

What is the initial transcript of miRNAs and what is its name

Answer 15

The primary transcript is knows as pri-miRNA

Question 16

Where does the processing of miRNA occur, and what enzyme is involved in this step

Answer 16

processing occurs in the nucleus by the microprocessor complex, which cleaves the hairpin structure of pri-miRNA to form pre-miRNA, which is then transported to the cytoplasm

Question 17

What role does Dicer play in miRNA biogenesis

Answer 17

Dicer enzyme chews a loop in pre-miRNA, releasing a 21-nucleotide complex

Question 18

After Dicer processing, where does the complex from pre-miRNA go, and what happens?

Answer 18

the complex is loaded onto the RNA-induced silencing complex (RISC) where the Argonaute protein binds the small RNA and cleaves one of the two strands via slicing

Question 19

What challenges were faced in determining the structure of Human Argonaute 2, and what does its structure compromise

Answer 19

It was challenging du to crystallization difficulties. The structure includes 2 lobes : one with PIWI and MID domains folded together and the other PAZ+N domains.

Question 20

What specific function does the PIWI domain of Argonaute proteins serve in miRNA functionality

Answer 20

PIWI domains functions as a RNAse domain and carries out the slicing activity by cleaving target RNAs

Question 21

Why do the majority of mRNA targets not fully base-pair with miRNAs and can you provide an example

Answer 21

its intentional, for instance the middle genes of the lin-14 mRna did not fully base-pair with the lin-4 microRNA

Question 21

How do miRNAs impact gene expression and what are the mechanisms through which they act

Answer 21

miRNAs can repress tranlsation, recreuit CCR4-NOT to degrade mRNA, and destabilize mRNA leading to its decay

Question 22

What is the different mechanisms through which miRNA mediates gene silencing

Answer 22

miRNA, along with co-factors like GW182, can repress translation. It can also recruit CCR4-NOT, which deadenylates the mRNA’s 3’end (poly A tail) and it can induce mRNA decapping leading to destabilization and decay

Question 23

What are P bodies, and why are they suspected as a site for miRNA function

Answer 23

P bodies are regions within the cytoplasm of eukaryotic cells containing enzymes involved in mRNA turnover. They are suspected sites for miRNA function because miRNA-targeted mRNAs are recruited to P bodies, where they can be destabilized or sequestered from the translational machinery

Question 24

What are some activities associated with P Bodies concerning mRNA regulation, although not yet directly demonstrated

Answer 24

Activities include decapping and mRNA degradation, storing mRNA until needed for translation, aiding in translational repression by miRNA and association with chromatin in the nucleus

Question 25

Name a few platforms used for microRNA target prediction besides Targetscan

Answer 25

Other platforms used for microRNA target prediction include RNAhybrid, Pictar, Miranda, and miRWIP

Question 26

According to the statement, what is proposed as the primary purpose of microRNAs

Answer 26

microRNAs primarily function to connect networks and serve as information nexuses, potentially regulating gene expression across various pathways

Question 27

What is the significance of polycistrons concerning microRNA clusters, particularly in the context of lymphomas

Answer 27

Polycistrons which are microRNA clusters can saturate the microprocessor, leading to the downregulation of miRNAs. This downregulation is considered important in lymphomas

Question 28

Explain the purpose and function of a heat map in relation to miRNA expression and tumor classification

Answer 28

Heat maps visually represent relative gene expression. they cluster similar sequences and libraries, allowing identification of miRNA profiles. These profiles can differentiate types of tumors base on miRNA expression, enabling the recognition of new classes of tumors, followed by analysis of affected genes.

Question 28

Name a few methods used for profiling miRNAs in cancer research

Answer 28

qRT-PCR and microarrays

Question 29

How ca microRNA profiles predict cancer patient survival, and what technology is commonly used for this prediction

Answer 29

MicroRNA prolifes can predict cancer patient survival using Next generation Seq, TruSeq kits, involving steps like ligating adapters, making cDNA, amplifying and sequencing libraries, are commonly used. These profiles have greater prognostic power compared to normal genes

Question 30

Explain the purpose of heatmap in miRNA profiling and how clurstering is achieved

Answer 30

Heatmaps integrate large arrays of expression profiles into a matrix, while clurtering regroups profiles based on their similarity in expression

Question 30

What information can miRNA profiliing offer in cancer studies, regardless of our knowledge about specific miRNA function

Answer 30

miRNA profiling can provide information about tumor origin, type, sub-type, patient outcomes, treatment responses and can be intrumental in personalized medecine

Question 31

How can miRNA profiling be employed in personalized medicine

Answer 31

It helps tailor treatment by providing detailed information about the tumor, enabling the customization of therapies

Question 32

Discuss the role of the miR-17-92 cluster in conferring resistance to chemotherapy

Answer 32

miR-17-92, an oncogenic gluster, target PTEN, a tumor suppressor gene involved in regulating cell growth and survival. Higher mir-17-92 levels, lead to PTEN suppression, which promotes cell survival and resistance to programmed cell death induced by chemotherapy

Question 33

What is synthetic lethality and how can it be exploited in cancer therapy

Answer 33

Synthetic lethality occurs when two otherwise non-lethal mutations result in cell death. This concept helps identify essential genes for tumor viability, offering potential targets for drugs that selectively affect cancer cells without harming normal cells

Question 34

In what way does the genetix contect influence the role of microRNAs in cancer

Answer 34

Genetic context influences miRNA function by affecting the expression of their targets, the importance of these targets in gene networks and the state of progression of tumorous cells

Question 35

How can RNAi and miRNA oriented therapy be utilized in cancer treatment

Answer 35

Used de novo RNAi programming, mimicking natural mRNA targeting, and specifically inhibiting miRNA functions. however, a major challenge in RNA-based thepeutic is the delivery due to the insability of the RNA and RNA analogs