Biology of non-coding RNAs in cancer Flashcards
Mir-17-92 controls the expression of :
a) PTEN
b) TP53
c) Ras
d) BRCA1
e) Rb1
a) PTEN
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
d) a and b are correct
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
d) sites in the cytoplasm where there is high activity of enzymes dedicated to mRNA turnover
Who were the researchers involced in studying C-Elegans development, and discovering the lin4 gene
Rosalin Lee and Victor Ambros
What change did Rosalind Lee and Victor Ambros observe in C.Elegrans development that affected all cells
They observed that a change in one cell resulted in the same change in all cells
What was the focus of the search for mutations by Lee and Ambros, and what gene did they identify
They were looking for mutations influencing the lin-14 gene and identified the lin-4 gene, which encodes small RNA
What was the relationship between the variants of lin-4 namely lin-4S and lin-4L
They postulated that lin-4S was derived from lin-4L due to size differences
How did lin-4 interact with lin-14 and what was its effect on lin-14
Lin-4 was found to bind to seven sites in the 3’UTR of lin-14 suppresing its expression
What significant discovery was made eight years after identifying lin-4 and lin-14’s interaction
The discovery of let-7 miRNA in C.Elegans, which showed homology in drosophila and humans, indicating conservation acroess species
What was the observed consequence of let-7 mitations in C.elegans and what resemblance did it show?
C-elegans let-7 mutants exhibited continuous cell division and failure to differentiate, resembling traits seen in cancer
How did let-7 miRNA control the expression of RAS gene in both C elegans and human cells
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
Where are human miRNA genes frequently located and what is their association with cancer
Human miRNA genes are often found at fragile sites and in genomic regions associated with cancers
What is the significance of the miR-17-92 amplicon in relation to lymphoma
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
What is the source of miRNAs in the genome and which enzyme transcribes them
miRNAs are transcribed from the genome by RNA pol II
What is the initial transcript of miRNAs and what is its name
The primary transcript is knows as pri-miRNA
Where does the processing of miRNA occur, and what enzyme is involved in this step
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
What role does Dicer play in miRNA biogenesis
Dicer enzyme chews a loop in pre-miRNA, releasing a 21-nucleotide complex
After Dicer processing, where does the complex from pre-miRNA go, and what happens?
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
What challenges were faced in determining the structure of Human Argonaute 2, and what does its structure compromise
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.
What specific function does the PIWI domain of Argonaute proteins serve in miRNA functionality
PIWI domains functions as a RNAse domain and carries out the slicing activity by cleaving target RNAs
Why do the majority of mRNA targets not fully base-pair with miRNAs and can you provide an example
its intentional, for instance the middle genes of the lin-14 mRna did not fully base-pair with the lin-4 microRNA
How do miRNAs impact gene expression and what are the mechanisms through which they act
miRNAs can repress tranlsation, recreuit CCR4-NOT to degrade mRNA, and destabilize mRNA leading to its decay
What is the different mechanisms through which miRNA mediates gene silencing
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
What are P bodies, and why are they suspected as a site for miRNA function
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
What are some activities associated with P Bodies concerning mRNA regulation, although not yet directly demonstrated
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
Name a few platforms used for microRNA target prediction besides Targetscan
Other platforms used for microRNA target prediction include RNAhybrid, Pictar, Miranda, and miRWIP
According to the statement, what is proposed as the primary purpose of microRNAs
microRNAs primarily function to connect networks and serve as information nexuses, potentially regulating gene expression across various pathways
What is the significance of polycistrons concerning microRNA clusters, particularly in the context of lymphomas
Polycistrons which are microRNA clusters can saturate the microprocessor, leading to the downregulation of miRNAs. This downregulation is considered important in lymphomas
Explain the purpose and function of a heat map in relation to miRNA expression and tumor classification
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.
Name a few methods used for profiling miRNAs in cancer research
qRT-PCR and microarrays
How ca microRNA profiles predict cancer patient survival, and what technology is commonly used for this prediction
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
Explain the purpose of heatmap in miRNA profiling and how clurstering is achieved
Heatmaps integrate large arrays of expression profiles into a matrix, while clurtering regroups profiles based on their similarity in expression
What information can miRNA profiliing offer in cancer studies, regardless of our knowledge about specific miRNA function
miRNA profiling can provide information about tumor origin, type, sub-type, patient outcomes, treatment responses and can be intrumental in personalized medecine
How can miRNA profiling be employed in personalized medicine
It helps tailor treatment by providing detailed information about the tumor, enabling the customization of therapies
Discuss the role of the miR-17-92 cluster in conferring resistance to chemotherapy
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
What is synthetic lethality and how can it be exploited in cancer therapy
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
In what way does the genetix contect influence the role of microRNAs in cancer
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
How can RNAi and miRNA oriented therapy be utilized in cancer treatment
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
