20.06.20 Soft tissue tumours and translocation analysis Flashcards
What are soft tissue tumours
- A form of sarcoma (muscle, bone, nerve, cartilage, blood vessels, fatty and fibrous tissue)
- Rare (<1% of all cancers)
- Usually benign with high cure rate after surgical excision.
Review of rhabdomyosarcoma
- Sarcoma of connective tissue
- Most common paediatric soft tissue sarcoma (5%).
- 2 Histological subtypes:
1. Embryonal rhabdomyosarcoma (ERMS) - 70-80% cases
- No recurrent chromosomal rearrangements. Numerical gains in chr 2, 8, 11, 12, 13 and 20
2. Alveolar rhabdomyosarcoma (ARMS) - 20-30%
- 60% have (2;13)(q35;q14) (PAX3/FOXO1) balanced reciprocal translocation.
Review of synovial sarcoma
- Rare and aggressive soft tissue sarcoma. Usually sporadic.
- Usually occur in joints of arm, leg or neck
- Reciprocal translocation t(X;18)(p11.2;q11.2) in 80% of cases (SYT and SSX gene)
Review of clear cell sarcoma
- Very rare in young adults.
- Often involves tendons of lower extremities.
- t(12;22)(q13;q12) (EWSR1-ATF1) in 90% of cases
Review of Extraskeletal myxoid chondrosarcoma (EMC)
- Rare with a unique histology (abundant myxoid matrix) and characteristic translocation
- t(9;22)(q22;q12.2), (EWSR1-NR4A3) in 90% cases
What are lipomas
- Benign tumours composed of fat cells
- Most common soft tissue neoplasm
- 4 major subtypes basesd on cytogenetics
1. 12q13-q15 rearrangements (65% cases). HMGA2 gene.
2. Loss of q13 (10%)
3. 6p21-p23 (5%)
4. Supernumary ring chromosomes
Review of myxoid liposarcoma
- 15-20% of liposarcomas
- t(12;16)(q13;p11) (FUS-DDIT3) in >95% of cases.
Review of Well differentiated (WD) liposarcoma
- 40-45% of liposarcomas
- DO not metastasise unless they differentiate to atypical lipomatous tumor (ALT)
- Characterised by supernumerary ring and giant marker chromosomes containing amplified MDM2 gene (12q15)
- MDM2 inactivates TP53
Review of cytogenetic analysis of fresh tumour sample
- Benefits: additional abnormalities can be detected alongside characteristic changes. Detects different clones in a tumour. Aids diagnosis. Can be done quickly (direct slides for interphase FISH)
- Disadvantages: Fresh tumour not always available. Tumour can degrade quickly and necrotic tissue can compromise growth. Normal cells could contaminate culture. Unexpected rearrangements could be from tumour or acquired during culture. Labor intensive, variable growth rates so culturing can take time. Usually poor quality metaphases (could miss subtle re-arrangements).
Review of FISH analysis of FFPE
- FFPE done to prevent tissues from degrading.
- Advantages: sample preserved so less time pressure. Archive samples can be investigated if required. FISH can be done on very small samples. FFPE slides can be shared easily between labs. Low levels of tumour cells can be detected on a normal background.
-Disadvantages: No metaphases present so hard to interpret non -standard rearrangement patterns. Cell morphology and layering can make analysis difficult. Analysis is labor intensive. Only specific rearrangements can be detected. Break apart probes (target one side of breakpoint) can detect all rearrangements but not the partner gene. Not successful on some tumour types- osteosarcomas.
Review of RT-PCR
- Can detect fusion transcripts resulting from recurrent translocations.
- RNA is extracted and reverse transcribed and PCR carried out (F in one gene and reverse in partner gene). PCR product will only form if fusion is present
- Advantages: Only a small amount of tissue is required. Can be done on fresh/frozen or FFPR. Cheaper and quicker than FISH and cytogenetic analysis. Can distinguish between different partner genes. Can be multiplexed so can analyse several fusions simultaneously. Could be used for MRD.
- Disadvantages: low level of fusion transcript may be hard to detect. RNA less stable than DNA so could give false negatives
