20_Solid Tumors Flashcards
What types of somatic changes may occur in cancer?
- Activating muts/amplification/etc. of one allele of proto-oncogene,
- LOF of two alleles or dominant negative effect of one allele of tumor suppressor
- Gene amplifications
- Gene Fusions and Translocations
- Mutation reversion
Do begin tumors ever carry cytogenetic abnormalities?
Yes, It is possible for begin tumors to carry cytogenetic abnormalities or translocations.
How does activating muts/amplification/etc. of one allele of proto-oncogene cause cancer?
By converting the proto-oncogene to oncogene.
Mention examples of activting mutations/amplfications which cause cancer:
- G12V leads to constitutional activation of RAS-GTP;
- RET can have activating missense muts in cysteine residues which activates the receptor in the absence of ligand;
- MYCN (n-MYC) is frequently amplified in high risk neuroblastoma (associated with poor px);
- Her-2/Neu/c-ERBB2 amp is frequent in breast cancers (therapeutic target: Herceptin [Trastuzumab])
Mention examples of metabolic genes involved in cancer.
- IDH1/2: their GOF muts are seen in many somatic cancers;
- Some other Kerb cycle proteins, like fumarate hydratase
What do “double minutes” refer to?
- Double minutes are an example of gene amplifications;
- They have no centromere;
- Sometimes they are attached to a chr end.
What do “homogenously staining regions” refer to?
- They are examples of gene amplifications;
- They are long stretches of gene amplification within a chromosome.
What are the highlighted features of Gene Fusions and Translocations?
- Chromosomal translocations generate novel chimeric genes or change their expression;
- all somatic!
- Chr3 translocations are amongst the very few examples where an inherited translocation leads to cancer predisposition (AD renal cell cancer)
What are the different types of Gene Fusions and Translocations?
- Imprecise translocations
- Precise translocations
- Interchromosomal dels/inv
What is the outcome of “imprecise translocations”? Give an example.
- Imprecise translocations lead to an oncogene being moved to near a transcriptionally active gene;
- Like t(8;14), fusing MYC to IgG in Burkitt’s lymphoma
What is the outcome of “precise translocations”? Give an example.
- Precise translocations result in precise joining of two genes to make a novel fusion gene, with 5’ end of the fusion gene controlling expression and the other end controlling function;
- Like Philadelphia chr in CML
Mention examples of “Interchromosomal dels/inv” in cancer.
- An interstitial Del on chrX fuses P2RY8 ex1 to CRLF2 ex1 (a growth factor) and activates CRLF2 transcription in high risk ALL & DS-ALL.
- Activation of ALK kinase in 3% of lung cancers happens by an inversion in chr2, leading to EML4-ALK fusion. This responds to Crizotinib (ALK inhibitor).
What are the three mechanisms for elevation of CRLF2 expression?
1) translocation of CRLF2 (in pseudoautosomal X/Y) to IgH enhancer region t(X|Y;14)(IGH-CRLF2),
2) 2) recurrent ~320kb interstitial Del in PAR upstream of CRLF2, juxtaposing it to P2RY8 promoter (P2RY8-
CRLF2)
3) gain of function muts (rare).
Note: All these scenarios are cryptic by karyotype and u need FISH/NGS/PCR.
Inhibition of which signaling pathway could attenuate CRLF2 overexpression?
CRLF2 overexpression can be targeted by JAK/STAT pathway inhibitors.
What does “mutation reversion” refer to?
It is a second change that restores the wildtype genotype
What are the different mechanisms for mutation reversion?
- back mutation which means a second mutation happening in the same locus
- suppressor mutation which means a second mutation at a different locus reverts the effect of the first mut (like an LOF before an activating mut).
- mitotic gene conversion/recombination
- compensatory mutations
FISH for detection of rearrangements in cancer
Wha are the commonly used FISH designs for detection of rearrangements in cancer?
- Dual color single fusion: probes just before or after breakpoints; one of the probes is moved next to the other in the case of fusion, leading to 1R, 1G, and 1 fusion; not commonly used these days.
- Dual color dual fusion: like in BCR-ABL1
- Dual color break-apart
- Dual color single fusion with extra signal
What type of FISH design has been used in this image? Make diagnosis based on the observed information.
- Dual color dual fusion;
- BCR-ABL FISH: nuc ish (ABL1x2,BCRx3)(ABL1 con BCRx1): one fusion is missing; it can mean many things: del of ABL1 from
derivative 9 (relatively common), translocation of all of ABL1 to 22, variable translocation breakpoint, etc. - In reality for this case there’s a t(9;22) but ABL gene
is not involved. The breakpoint is distal to ABL. Only
BCR is broken. This means the patient doesn’t have
AML with t(9;22);
Note: FISH doesn’t always give correct answers; you need Karyotype.
What type of FISH design has been used in this image? Describe your observations.
- Dual color dual fusion;
- classical fusion example;
- If ABL was translocated to another gene instead of BCR, you’d see an extra red probe;
- because ABL is still split (due to 2 events happening
in this probe design, the NL cutoff is very low).
What type of FISH design has been used in this image? Describe your observations.
- Dual color extra signal
- Break does not happen on the green probe.
- Translocation breaks red and moves half of it to the other Chr, while moving all green next to red.
Note the breakpoints.
What type of FISH design has been used in this image?
Dual color single fusion design
What type of FISH design has been used in this image?
Dual color dual fusion
What type of FISH design has been used in this image?
Dual color dual fusion – complex case
What type of FISH design has been used in this image?
Dual color break-apart design:
(L is NL and R is abnl)
What type of FISH design has been used in this image? Describe your observations.
- Break-apart probe design for CRLF2;
- the red probe is on P2RY8, upstream of CRLF2 and the green probe is downstream of CRLF2.
- FISH shows deletion of red signal from one of the fusions.
- This happens when an interstitial Del brings the promoter of P2RY8 near CRLF2, which also deletes the binding site of the red probe.
- Nomen would be: nuc ish(3’CRLF2x2,5’CRLF2x1)(3’CRLF2 con 5’CRLF2x1);
- note that 3’ is listed ahead of 5’ due to it being on reverse strand.
What type of FISH design has been used in this image?
- Triple color dual fusion – Three colors because there is an enumeration probe added (cen8)
Does FISH rule out abnormalities? Why?
- FISH does not rule out.
- You only mention you didn’t see. You don’t rule out.
- There can be any type of rearrangement underneath that changes your signal patterns;
- A break-apart probe may not split for example if there is an insertion of the red region in the green which always moves with it and leaves the result negative; see page 65 of Marylin’s lecture for example.
A FISH study on a myeloma patient by using CCND1/IGH XT probe showed 2R3G2F signal pattern. (R is on chr11 and G is
on chr14). Which of the following is the correct FISH nomenclature?
a) nuc ish(MYEOV/CCND1x4,IGHx5)(MYEOV/CCND1 con IGHx2)[200]
b) nuc ish(MYEOV/CCND1x2,IGHx3)(MYEOV/CCND1 con IGHx2)[200]
c) nuc ish(MYEOV/CCND1x2,IGHx3),(MYEOV/CCND1 con IGHx2)[200]
d) nuc ish(MYEOV/CCND1x4,IGHx5),(MYEOV/CCND1 con IGHx2)[200]
The first one is correct. Note that comma shouldn’t be there.
Which of the following is the correct FISH nomenclature for IGH break-apart probe showing 1R1G3F signal pattern? (3’ is
centromeric, 5’ is telomeric)
a) nuc ish(IGHx3)(3’IGH sep 5’IGHx1)
b) nuc ish(IGHx4)(3’IGH sep 5’IGHx1)
c) nuc ish(3’IGH,5’IGH)x4(3’IGH con 5’IGHx3)
d) nuc ish(3’IGH,5’IGH)x4(3’IGH con 5’IGHx1)
You don’t use con when 3’ and 5’ have the same count. Otherwise, con wou
Which of the following is the correct FISH nomenclature for IGH break-apart probe showing 1R2G signal pattern? (3’ is
centromeric, 5’ is telomeric)
a) nuc ish(3’IGHx1,5’IGHx2)
b) nuc ish(3’IGHx1,5’IGHx2)(3’IGH sep 5’IGHx1)
c) nuc ish(IGHx2)(3’IGH sep 5’IGHx1)
d) nuc ish(IGHx2)(3’IGH sep 5’IGHx2)
The second one is correct.
