Hot topic - solid tumours Flashcards by Helen Savage

What are the three type of Solid tumour?

Carcinoma
Sarcoma
Lymphoma

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What are Sarcomas derived from?

Muscle, neurons, bone, cartilage, fatty tissue, fibrous tissue, tendons, blood vessels.

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What are carcinomas derived from?

Epithelial cells

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How frequent are soft tissue tumours?

<1% of all cancers

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Which gene is involved in Ewing’s sarcomas?

EWS

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What are the two most common rearrangements in Ewing’s sarcoma?

t(11;22)(q24;q12) EWS-Fli1

t(21;22)(q22;q12) EWS-ERG

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What is a Rhabdomyosarcoma? What are the two histological subtypes?

A tumour of connective tissue.

Embryonal RMS (better prognosis), 70% of RMS, commoner in children. No recurrent structural rearrangements, loss of 11p15.5 imprinted region, MYCN++ = poor prognosis

Alveolar RMS (worse prognosis), 30% of RMS, two common translocations:
t(1;13) PAX7-FOXO1
t(2;13) PAX3-FOXO1
MYCN++ = poor prognosis

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What are synovial sarcomas? What are the common translocation partners?

Tumours of the synovial fluid, usually occuring in the joints of the arm, leg or neck.

SYT pairs with SSX1 or SSX2

t(X;18)(p11.2;q11.2)

SSX1 may be associated with a poorer prognosis.

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Why is translocation analysis important?

Soft tissue tumours can be biologically heterogeneous and very similar on histo.

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What methods are available to test soft tissue tumours?

Cyto: Karyotype - can properly characterise, multiple deletions/translocations/different clones detected. BUT need dividing cells, fresh samples not always available, normal cells might outgrow tumour cells, labour intensive, long culture time, poor quality preps.

FISH of FFPE - preserved sample won’t degrade, rapid, archived samples can be assessed, sharing of slides, can detect low levels of abn cells BUT need marked slide to analyse, no metaphases, cell layering can make analysis difficult, targeted test.

RT-PCR - only need small amount of tissue, fresh or frozen or FFPE, cheaper and quicker, can be used to detect variant partner genes (SYT-SSX1/2 in synovial sarcoma), multiplex reactions, MRD monitoring BUT RNA unstable, low levels of fusion transcript present.

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What translocations are commonly seen in Clear Cell Sarcoma?

t(12;22) EWS-ATF1 (90%)
t(2;22)(q32.2;q12) EWS-CREB1 (6%)

Associated with a poor prognosis.

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What fusions are a hallmark of extraskeletal myxoid chondrosarcomas?

NR4A3 fusions only seen in EMCs, an aggressive neoplasm

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What two type of lipoma are there? What rearrangements are they associated with?

Myxoid liposarcoma:
t(12;16) FUS-CHOP
t(12;22) EWS-CHOP

Well Differentiated Liposarcoma
MDM2 amplification on ring chromosomes (12q15)

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Why are brain tumours not classified as benign or malignant?

The space-occupying effects of non-metastatic tumours can have severe consequences

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What are the two main cell types in the CNS?

Neuron
Glial cells

Glial cells further differentiated into astrocytes and oligodendrocytes,

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What are medulloblastomas?

The most common malignant intercranial tumour seen in children.

4 molecular subgroups: WNT, SHH, Group 3, Group 4

Aggressive

High grade.

Classed as low risk ~5 year survival
High risk <2 year survival

Multiple pathways involved - Wnt pathway activation is associated with lower risk
SHH activation is associated with lower risk
MYC++ are associated with poor prognosis and metastasis - results needed quickly - RT-qPCR

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What are Gliomas?

Tumours of the glial cells.

There are multiple types: astrocytomas, oligodendrogliomas, ependymomas, glioblastoma

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Which glioma subtype has the best prognosis?

Oligodendrogliomas

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What is the common mutation seen in 80% of oligodendrogliomas? How can the identification of this be used clinically?

1p/19q loss.

Confirms a diagnosis, associated with better overall survival.

ID by FISH, SNP array, MLPA

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Which genes are commonly mutated in oligodendroglioma? (see in conjunction with the common mutation)

TP53
IDH1/2
PIK3CA

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What is the prognosis of patients with glioblastoma?

Very poor - 14 months survival

What are the common findings seen in glioblastomas?

7p+ (contains EGFR)
9p- (CDKN2A)
10q- (PTEN)
13q- (RB1)
Amplification of MDM4, MDM2, CDK4, PDGFRA
Loss of NF1, TP53, IDH1/2

What are the two profiles seen in glioblastomas?

TP53 inactivation. May also see MDM2 amplification or CDKN2A silencing
EGFR amplification or PTEN mutation

What common epigenetic findings are associated with glioblastoma?

MGMT hypermethylation: More sensitive to alkylating drugs, so can be used to target treatment. Associated with better progression free and overall survival

CASP8 hypermethylation - poor outcome
GATA6 hypermethylation - increased survival in younger patients.

What are the risk factors for brain tumour development?

``` Ionising radiation Other disease: NF1, Li-Fraumeni, VHL, TS, Gorlin syndrome, Turner synrome, Turcot syndrome Previous cancers Obesity Diabetes Smoking Nitrite content of diet ```

Name some malignant small round cell tumours

``` Wilm's tumour (Nephroblastoma) Ewing's Sarcoma Medulloblastoma Synovial sarcoma Rhabdoid tumours Rhabdomyosarcoma Desmoplastic Small Round Cell Tumours Retinoblastoma etc. ```

What is a Wilm's Tumour?

Renal tumour, incidence 1/10,000.

What syndromes is Wilm's tumour associated with?

WAGR - WT1 and PAX6 deletion (11p13) Beckwith (Paternal UPD for 11p15.5) - occurs in 7% of BWS children Denys-Drash - ambigous genitalia, renal anomalies, mostly missense mutations in exons 8 and 9 of WT1

How is Wilm's tumour diagnosed?

Sequence WT1, imprinting of 11p15.5, CGH or CNV analysis for 11p13

What is retinoblastoma?

Tumours at the rear of the eye. present in 1/15,000 children. Caused by mutation in RB1 (40% hereditary), and also sporadic. Hereditary = AD, second hit required for tumour.

Where is RB1 located?

13q14

How do patients with herditary retinoblastoma present?

With an average of 3 tumours per eye. Mostly bilateral cases. Present in first year of life.

What is also associated with Retinoblastoma, apart from mutation/deletion of RB1?

Hypermethylation of a CpG island in the 5' region of the RB1 gene 13q14 deletion syndrome (retinoblastoma, microcephaly, dysmorphic features, ID)

How should carriers of a RB1 mutation be screened? What is the prognosis?

Regular ophthalmological examination, from birth until 3yo 99% cured; 90% have vision in at least one eye.

What is the diagnostic strategy for RB testing?

Mutation analysis for germline - sequence and MLPA. Screen tumour for second hit, if possible msMLPA of promoter.

What are desmoplastic small round cell tumours?

rare, high grade tumours. Highly malignant. Common mutation t(11;22)(p13;q12) WT1-EWS fusion Detect by RT-PCR

What proportion of patients with EWS present with mets?

15-25%

What does the EWS-FLI1 fusion produce?

An aberrant transcription factor driving cell proliferation.

What can genetic testing of tumours be used for?

Diagnosis/classification Prognosis Target therapy

What methods of tumour characterisation are there?

``` IHC FISH qPCR pyrosequencing sequencing expression arrays ```

List some challenges of tumour testing

Tumours are highly heterogenous Mixed with normal cells FFPE tissue produces poor quality DNA Tumour tissue isn't always available

What are some problems associated with FFPE tissue?

Low quality, low concentration DNA extracted The longer in formalin, the worse the DNA Deamination of cytosine can cause false positives Low percentage tumour Heterogeneous tumour Labour intensive processing

List some clinically useful genetic testing on solid tumours

EGFR - NSCLC - exons18-21 - erlotinib PIK3CA in BRCA - exons 9 and 20 - avoid Herceptin EML4-ALK in Lung cancer (FISH) - Crizotinib KRAS in CRC and Lung cancer - residues 12, 13, 61, 146 - Cetuximab BRAF - V600E in CRC and melanoma - Vemurafinib Her2 amplification in BRCA (FISH) - Herceptin

Why is the panel approach still common in testing labs? (WES and WGS not yet)

Much of the information from WES and WGS is clinically useless at the moment Validation of WGS/WES for FFPE still under development BIX is challenging Cost TAT Low coverage can be a problem

Name some commercial panels available for tumour testing

TruSight Cancer panel (inherited) SureSeq cancer panel (OGT) - tests 60 genes and lung cancer panel for CRUK SMP TrueSeq panel for somatic cancer

Why is aCGH limited in the analysis of tumour samples?

Can't detect balanced translocations May not be sensitive enough to detect low level mutations Can't distinguish between clones

Name some SNP array kits for solid tumours

OGT CystoSure Haematological Cancer Illumina Cancer SNP panel Oncoscan FFPE (Affymetrix) - uses MIP technology optimised for FFPE samples

What can expression arrays be used for?

To quantify transcript expression in tumours - to generate a gene profile/signature Alternative splicing Non-coding transcriptome - miRNAs

What are the two main disadvantages of gene expression arrays?

Not optimised for FFPE | High cost

Which clinical applications are currently making used of ctDNA screening?

EGFR mutations and EML4-ALK in NCSLC. | BRAF mutations in melaona

What method is used to accurately detect ctDNA in the plasma?

ddPCR currently used for EGFR testing in NSCLC patients with no biopsy available.