Aberrant gene expression in cancer biology Flashcards
A nucleosome is an octomer made up of which 4 histones?
1. H2A, H2B,H3,H4
2. H1,H2A, H2B, H3
3. H1A, H2B, H3A, H4B
4. H1, H2, H3, H4
H2A, H2B, H3, H4
The first highly recurrent non-coding somatic even observed across multiple cancer types was:
1. Mutations within the promoter of the TP53 gene
2.Mutations within the promoter of the TERT gene
3.Mutations within the promoter of the BRCA1 gene
4.Mutations within the promoter of the Rb gene
Mutations within the promoter of the TERT gene
Enhancer hijacking can occur through which of the following mechanism :
1. Insulator deletion
2. Interchomosomal translocation
3. Intrachromosomal inversion
4.Intrachromosomal deletion
5. all of the above
All of the above
Which of the following statements is false regarding CpG islands?
a. 25% of CpG islands are found in the main gene body
b. Are notably associated with regions of the genome that are devoid of protein-coding genes
c. Approximately 50% of CpG islands are found in the vicinity of known transcriptional start
sites
d. CGIs associated with transcriptional start sites remain unmethylated even when the gene is not
being transcribed.
e. CpG islands are important because they are areas of the gnome that have been protected from
mutating properties of methylation through evolutionary time
b. Are notably associated with regions of the genome that are devoid of protein-coding genes
True or false: 25% of CpG islands are found in the main gene body
True
True or false: Approximately 50% of CpG islands are found in the vicinity of known transcriptional start
sites
True
True or false: CGIs associated with transcriptional start sites remain unmethylated even when the gene is not
being transcribed.
True
True or false: CpG islands are important because they are areas of the gnome that have been protected from
mutating properties of methylation through evolutionary time
True
Whats the epigenetic control of gene expression?
involves modifications to DNA or associated proteins that regulate which genes are turned on or off without altering the underlying DNA sequence.
How somatic cancer driver genes are identified using genomics
CRISPR/Cas9, Whole genome sequencing
what are key features of cancer
Aberrant gene function and altered proteins
True or false: the disruption of epigenetic regulatory mechanisms is prevalent in cancer
True
True or false: both genetic and epigenetic alterations ultimately lead to abnormal gene expression
true
What are the 4 subgroups of medullablastoma
1- Wnt
2- Sonic hedgehog
3 - group 3
4 - group 4
What is epigenetic?
how environmental factors can change gene activity without altering the DNA sequence
True or false: different cell types are programmed to express different sets of genes but they have the same DNA/set of chromosome
True
How do we get different types of cells in the first place?
The estabilishment of different cell lineages and cell differentiation involves different gene expression programmes during development, which do not depend on the DNA sequence itself, but on epigenetic factors
What are the 2 types of epigenetic gene regulation?
1- Histone modification
2- DNA methylation or modifying the DNA itself
The expression state of a gene is determined by the … or … of its DNA regulatory regions, promoters or enhancers, in … and by the presence of … and …
packaging or accessibility
in chromatin
Transcription factors
Chromatin modifying enzymes
Accessibility of chromatin to transcriptional regulation is controlled by …
modification to the DNA itself or by modification/rearrangement of nucleosomes
Features of the nucleosomes:
X turns of DNA wrapped around…and two subunits, and N-terminal tails of histone protrude out of …
2 turns of DNA wrapped around a histone octamer
the nucleosome
True or false: 4 histone proteins that make up the nucleosomes but its actually an octamer
True
True or false: Tails can be pos-translationally modified..by additions of acetyl groups or methyl groups to those histones
True
What are the different groups of the epigenetic code?
Writers, erasers, readers, movers
Writers will..
add modifications
Erasers will
remove post-translational modification
Reader are…
proteins that read histone modification, such as acetylated or methylated residues
Movers are..
chromatin-remodeling proteins that move nucleosomes and allow gene transcription
What is the variant of H3 histone and what does it do
H3.3 and its important in transcriptional activation
True or false: epigenetic modifications allowed us to annotate non-coding regions of the genome
True
H3K4me1 is an
H3K27ac marks…
enhancer
active elements or strong enhancers and promoters
To map the epigenome, we use…
It’s a way to…
Chipseq (way to enrich DNA)
In chip-Seq of histone modification, they use an…to pull down those histones post-translational modification and sequence the DNA attached to those histones
-then they pile those reads up in the genome
- Get … in the locatioin where that particular histone is marked
-antibody to pull down those histones post-translational modification and sequence the DNA attached to those histones
-then they pile those reads up in the genome
- Get peaks in the locatioin where that particular histone is marked
True or false: Epigenetic annotations reveal the cell type-specificity of Non-coding elements
True
H3K4me1 (monomethylation) is an…
active enhancer
H3K4me3 (trimethylation) is an…
active promoter
H3K27ac is an…but if its trimethylated its an
active promoter
inactive promoter
True or false: Instead of profiling the histone marks, we can also profile open region, where the transcriptional machinery is present and theres multiple assets
TrueT
True or false: ATAC-sec is an assay for transposase-accessible chromatin using sequencing
True
Can we use ATAC-seq for mapping the open chromatin regions? if yes, how?
ATAC-seq usise a transposease which will insert into regions where there are no nucleosomes essentially and we can sequence those regions.
Whats the common trait and difference between Chip-seq and ATAC-seq
- they both study chromatin
2.ChIP-seq pinpoints where specific proteins bind to DNA, showing their interactions and regulatory roles, while ATAC-seq maps open chromatin regions, revealing accessible areas of the genome involved in gene regulation.
True or false: Chromatin accessibility profiles reveal distinct molecular subtypes of cancers
True
Whats DNA methylation?
Addition of methyl group at CpGs
True or false: Epigenetic mechanisms act to change the accessibility of chromatin to transcriptional regulation via modification to DNA or by modification/rearrangement of nucleosomes (histones)
true
Does DNA methylation vary between different cells types and different stages in development
Yes
Whats the general roles of DNA methylation (4)
1-gene expression silencing
2- Genomic imprinting
3- X-chromosome inactivation
4- Suppression of retrotransposon elements
True or false; DNA methylation has writers and erasers
true
True or false: DNA methylation is limited to cytosines and occurs with the context of the dinucleotide CG
True
Name the two de novo methyltransferases that methylate CG dinucleotides
DNMT3A and DNMT3B (theyre writers)
Whats the name of the enzyme that maintains existing DNA methylation patterns
DNMT1
Whats TET
Ten eleven translocation - an enzyme that are methylcytosine transferase and initiate demethylation
True or false: DNA methylation is a source of mutations
True
true or false: C–>T mutations are common in human DNA : demaination of cytosine is a common reaction inc ells and normall produces uracil
True
True or false: Uracil is in DNA not RNA
False, its in RNA
What are some features of CpG islands (CGI) (3 features)
1- have a G+C-rich base composition
2- high density of the dinucleotide CpG
3- 1kb or less in lenght and are associated with genes
Which region is more prone to deamination?
CpGs=
Unmethylated regions
True or false: Approximately 50% of CpG islands are located in the vicinity of known transcriptional start sites
True
True or false: CGIs is association with transcriptional start sites and remain unmethylated even when the gene is not being transcribed
True
Whats deamination? removal of?
it refers to the removal of an amino group from a cytosine base, leading to the conversion of cytosine to uracil, which can cause changes in the DNA
True or false: CpG islands are important because they represent areas of the genome that have been protected from the mutation properties of methylation through evolutionary time (deamination)
True
What does deamination of cytosine cause?
produces uracil, and its normally found in RNA, so leads to alterations in DNA and changes the functions
True or false: In normal cell we see CpG islands that are hypomethylated, and in cancer, we see an hypermethylation
True
What are the Role of DNA methylation in cancer (3)
Gene silencing
Gene instability
Tumor heterogeneity
True or false: Change in the chromatin structure are not depend of changes in DNA. methylation, histone modification and the positionning of nucleosomes
False, changes in the chromatin structure is dependent of changes in DNA methylation, histone modification and positioning of nucleosomes
True of false: oncogenes are activated by gain-of-function mutations
True
True or false: Tumor suppressors are recessively acting cancer genes in which the inactivation of both alleles promotes cell proliferation or inhibits apoptosis
True
What the single nucleotide variants (SNV)
are alterations in the DNA sequence where a single nucleotide (A, T, C, or G) is substituted by another at a specific position in the genome.
True or false : Mutations in cancer driver genes are under negative selection and confer a proliferative advantage to cancer cells
False, theyre under a positive selection
What kind of mutations make you predisposed to cancers
germline cancers
How do we detect driver mutations (somatic)
By sequencing normal VS tumor sample and look at variant in tumor genome that arent present in normal gene
In sequences of normal vs tumor samples.. half the reads are mutations, not all of them.. why?
Because we have two chromosomes, and these mutations tend to be heterozygous (one parents gives the mutation)
How do we detect cancer driver genes?
Sequence a bunch of tumor samples, map them to genes, and calculate some background mutation rate
By sequencing tumor sample vs control sample, what does the sequencing say about the function of the driver genes
Nothing, it doesn’t say anything interesting about the function, or if its an oncogene or tumor suppressor
True or false: Oncogenes differ from tumor suppressor genes in the distribution of cancer-associated mutations
True
Whats a truncation?
Loss of function due to shortening or premature stop in protein, so tumor suppressor
Hotspot mutations = oncogene or tumor suppressor?
Oncogene
What are IDH1/IDH2 cancer-associated mutations : Theyre specific missense mutations producing mutant enzymes that convert … to… and that can inhibit … and lead to this hypermethylation in tumors.
Theyre specific missense mutations producing mutant enzymes that convert 2-oxoglutarate to 2-hydroxyglutarate and that can inhibit TET enzymes and lead to this hypermethylation in tumors.
CNVs- copy number variants : are alterations in the DNA that involve …being duplicated or deleted, resulting in an abnormal number of copies of certain sections of DNA
Are alteration in the dNA that involves segments of the genome being duplicated or delete, resulting in an abnormal number of copies of certains sections of DNA
How can you detect CNVs?
Next generation sequencing (analyzing read-depth), FISH (fluorescent probes to visualize and identify CNVs)
True or false: In detection of DNA copy number variation, coverage is not necessarily equal across the genome
True
True or false: Many low-level amplifications occur on circular extrachromosomal DNA (ecDNA)
False, high-level amplification
True or false: When we look at copy numbers variance to find drivers… were interested in recurrance, so we want to see multiple patients with a similar gained region because we hypothesize in those regions ; the genes within those regions are potential oncogenes because these gains would lead to an increase in expression
True
True or false: For recurrent copy number loss (deletions) we’re looking for recurrence across patients that show some type of selective advantage for that gene being either gain or loss
True
What are you calculating when analyzing tumors
background mutations rate, or amplification rate, or copy number rate
What are the 4 subgroups for detection of cancer driver genes and actionable genomic alterations
- Wnt
- SHH
- Group 3
- Group 4
True or false: a major, unanticipated outcome of cancer genome sequencing projets is that roughly 50% of human cancers harbour mutations/alterations in chromatin-related proteins
True
True or false: mutations in pediatric glastoma where they see recurrent mutations in K27 or H3Lysine27 and G35R
True, G34R is likely resulting and inhibiting the lysine36 position which is nearby, but its also recurrent, showing that the histone tails are important to these cancers
Complete: Mutations in histone H3.3 (encoded by H3F3A or H3F3B) commonly occur at three residue: ….
K27, K36, G34
Complete: H3.3K27M and H3.3-K36M mutations are … and reduce the genome wide … of H3K27 and H3K36
dominant negative and reduce the genome wide mthylation
True or false: For H3K36, we see mutations to SETD2, and NSD1, NSD2
True
EZH2 is part of which complex?
Part of PRC2 complex, and its mutated, amplified and deleted in cancer
Whats the SWI/SNF complex?
SWI/SNF chromatin remodeling complex is a group of proteins that alter the structure of chromatin, allowing access to DNA and influencing gene expression by modifying how tightly DNA is packed around histone proteins.
True or false: 20% of all cancers harbour mutations in SWI/SNF-encoding genes
True
True or false: Nine different genes encoding subunits of the SWI/SNF family of chromatin-remodelling complexes are recurrently mutated in cancer
True
Whats the most mutated complex accross all cancers
SWI/SNF
True or false: SWI/SNF is involved in moving the nucleosomes so either sliding them, evicting them or opening them. Theyre chromatin remodelers, and allow access for transcription factors or the transcriptional machinery to bind to the chromatin DNA
True
Is there a competition between SWI/SNF and PRC complex?
yes, theres antogonism between them so you cant have all components mutated in the same tumor. Theres some synthetic lethal relationship between SWI/SNF and PRC which may be exploited for cancer
True or false: You can mutate ARID1A and EZH2 loss.
you cant see mutations with these two, they would kill the cell
Whats the Cis-effect
the cis-effect describes how genetic elements or changes affect nearby genes on the same DNA strand
True or false; The majority of the genome is non-coding regions
True
True or false: about 2% of the genome actually codes for protein coding genes and the rest is non-coding
True
True or false: the majority of the mutations are outside of the coding regions, majority are passenger and regions that are not active within the tumor
True
True or false : The majority of the genome is non-coding
True
Non-coding regulatory elements harbor a larger…
fraction of somatic mutations
True or false: non-coding enhancers outside of oncogenes (MYC, MYCN, AE, KLF5, EGFR) are selectively amplified with or without their respective oncogenes
True
Enhancers are selectively amplified with or without their respective oncogenes
WITH
Do all CNVs (copy number variants) target the genes within them
Not all CNVs affect genes directly; some impact non-gene regions of the DNA, influencing how genes function without changing the genes themselves.
How do we assign enhancers to their target genes?
3D chromatin structure analysis = Even if we look at the genome as a linear thing, in reality, inthe nucleus, its organized in 3D, and theres a method to indicate which regions are in close physical contact with each other, and theyre all based of this chromatin confirmation capture approach
What are TAD domains
Topologically associated domains ; neighborhoods in the genome that keep certain genes and their controls together, separate from others, helping regulate gene activity.
True or false: TADs are regions in the genome that tend to interact with themselves but they dont interact with each other (boundaries)
True
True or false: Enhancer hijacking event can explain aberrant gene expression patterns
true
Is MYCN is amplified in many different tumors
Yes
Whats GFI1B, and its link to TAD boundaries
GF1B is important for the development of blood cells (patelet)
If also marks boundaries in TADS
True or false: SNCAIP duplication is highly recurrent in Group4 medulloblastoma
True, there’s focal amplification or duplication of SNCAIP
True or false: If you duplicate TAD boundary, you create new TADs that include enhancers from neighbour TAD within that regions allowing them to activate those potential cancer genes /
True
ecDNA enables distal DNA interactions ….what are ecDNA
circular DNA structures separate from the main chromosomal DNA, often found in cancer cells.
Whats th interplay between the genome and the epigenome drives aberrant gene expression in cancer
Changes in the epigenome (chemical modifications to DNA and proteins) alongside genetic alterations can disrupt normal gene control, leading to abnormal gene behavior in cancer.