Tumorigenesis and Leukaemias Flashcards
Name the common rearrangement associated with Burkitt Lymphoma
t(8;14)(q24;q32) MYC-IGH
(also see t(2;8)(p12;q24) MYC-IGK and t(8;22)(q24;q11) MYC-IGL
Name the common rearrangement associated with Follicular Lymphoma
t(14;18)(q32;q21) - IGH-BCL2
Name the common rearrangement associated with Mantle Cell Lymphoma
t(11;14)(q13;q32) - IGH-CCND1
Name 2 rearrangements associated with Diffuse Large B Cell Lymphoma
t(14;18)(q32;q21) - IGH-BCL2
t(3;14)(q27;q32) - IGH-BCL6
Name 2 rearrangements associated with MALT Lymphoma
t(11;18)(q21;q21) - BIRC3-MALT1
t(14;18)(q32;q21) - IGH-MALT1
What is characteristic of B-cell lymphoma, unclassifiable, with features intermediate between diffuse large B-cell lymphoma and Burkitt lymphoma?
Double Hit involving MYC
Commonly BCL2+/MYC+, also BCL6+/MYC+ or BCL2+/BCL6+/MYC
Name 4 rearrangements with a POOR prognosis in ALL
t(9;22)(q34;q11) BCR-ABL1
t(4;11)(q21;q23) AFF1-KMT2A
Hypodiploidy
t(17;19)(q22;p13) HLF-TCF3
Name 2 rearrangements with a FAVOURABLE prognosis in ALL
t(12;21)(p13;q22) ETV6-RUNX1
High Hyperdiploidy
Name a rearrangement with an INTERMEDIATE prognosis in ALL
t(1;19)(q23;p13) PBX1-TCF3
Name the commonest ALL rearrangement associated with:
a) Infant ALL
b) Childhood ALL
c) Adult ALL
a) KMT2A rearrangement
b) ETV6-RUNX1
c) BCR-ABL1
Name 3 partner genes for KMT2A in B-Cell ALL
t(4;11)(q21;q23) KMT2A-AFF1 (40-50% infant ALL, i7q common secondary abn)
t(9;11)(q22;q23) KMT2A-MLLT3 (10% infant ALL)
t(11;19)(q23;p13.3) KMT2A-MLLT1 (10% infant ALL)
Describe the t(12;21) seen in childhood ALL
Fusion protein acts in dominant negative fashion to interfere with normal TF RUNX1
t on its own not enough to cause cancer, often lose functional RUNX1 too or have secondary abns
Name 4 significant prognostic indicators in adult B-Cell ALL
t(9;22)(q34;q11) BCR-ABL1 - POOR
t(4;11)(q21;q23) KMT2A-AFF1 - POOR
Complex karyotype (5 or more abns) - POOR
Ploidy - High hyper - FAVOURABLE
- hypo - POOR
t(17;19)(q22;p13) TCF3-HLF - POOR
iAMP21 - POOR
ETV6-RUNX1 fusion - GOODWhere is TCF3? Name two partners in B-Cell ALL
19p13.3
t(1;19)(q23;p13) PBX1-TCF3
t(17;19)(q22;p13) HLF-TCF3
Where is KMT2A? What does the gene do?
11q23.3 - Histone demethylase
Encodes nuclear protein thought to be positive regulator of gene expression in early embryonic development and haematopoeisis. Over 80 partners described so far.
Describe RUNX1T1-RUNX1 Rearrangement in AML
t(8;21)(q22;q22) - 5% AML - FAB Class M2
Associated with Auer rods - seen predom in younger patients
GOOD prognosis with high dose cytarabine in consolidation phase
Describe abnormalities associated with t(8;21) in AML
5% have complex translocation
70% have secondary abns, -X, -Y, del(9q)
KRAS/NRAS mutns
KIT mutns
Describe CBFB-MYH11 rearrangement in AML
inv(16)(p13.1q22) or t(16;16) - 5-8% AML - FAB Class M4
Myeloid sarcomas may be present at diagnosis/relapse
GOOD prognosis with high dose cytarabine in consolidation phase
+22 as secondary abn improves outcome
Describe abn associated with APML
t(15;17)(q24;q21) PML-RARA - GOOD prognosis, very sensitive to ATRA
Describe APML resistant to ATRA
Variant RARA translocations
t(11;17)(q23;q21)
t(5;17)(q35;q21)
t(11;17)(q13;q21)
Describe PML-RARA Fusion protein
Dominant negative form of RARA - binds to DNA and represses transcription of retinoic acid target genes but doesn’t respond to the transcriptional signal induction of the genes - gene remains repressed. Function of PML disrupted - normally blocks cell growth/proliferation and induces apoptosis
How does ATRA work in APML
Ligand for RARA - binds to fusion protein with co-repressor complex, engagement of co-activation complexes by the chemical receptor and subsequent degredation of the fusion protein PML-RARA
What is the most common KMT2A rearrangement in AML?
t(9;11)(p22;q23) MLLT3-KMT2A
INTERMEDIATE prognosis, better than AML with other KMT2A rearrangements
What is the prognosis of t(6;9)(p23;q34) in AML
Generally POOR
DEK-NUP214
Describe the 3 phases of CML
Chronic - 3-4 yrs but can last 10, 40% asymptomatic
Accelerated - Accumulate further mutations, cell proliferation increases, symptoms more severe
Blast crisis - >20% blast cells in blood/BM. Infiltrate other tissues
Describe the BCR-ABL1 fusion protein
5’ end of BCR fuses with 3’end of ABL1 - fusion oncogene on der(22) has elevated and disregulated tyrosine kinase activity –> uncontrolled cellular proliferation and inhibition of apoptosis
Describe clinical aspects of CLL
Proliferation and accumulation of monomorphic b-lymphocytes in PB, BM, spleen and lymph nodes - prevents haematopoeisis of other normal blood cells –>cytopaenias
Describe the FISH investigations carried out in Liverpool on CLLs and their prognostic significance
ATM deletion - 11q23 - POOR prognosis
TP53 deletion - 17p13.1 - POOR prognosis
Trisomy 12 - INTERMEDIATE prognosis
13q14.3 deletion (mono/biallelic) - FAVOURABLE prognosis
20% CLL have IGH rearrangement - give some examples
t(11;14)(q13;q32) IGH-CCND1 t(14;19)(q32;q13) BCL3 locus often with +12 t(2;14)(p13;q32) IGH-BCL11A t(14;18)(q32;q21) IGH-BCL2 t(8;14)(q24;q32) IGH-MYC
Describe the clinical presentation of Multiple Myeloma
Bone disease (lytic bone lesions, hyperCalcaemia, fractures, osteoporosis)
Impaired Renal function - proteinuria
Anaemia
CRAB
What are the two broad categories of MM?
Hyperdiploid - 48-75 chrms, more favourable prog (often gains of odd numbered chrms)
Non-hyperdiploid - 75 chrms - generally unfavourable
Name the 5 major IGH rearrangements in MM
4p16.3 FGFR3 - POOR 11q13 - CCND1 - GOOD 16q23 - MAF - POOR 6p21 - CCND3 - GOOD 20q11 - MAFB - POOR (may be very poor)
Give 3 genetic changes associated with disease progression in MM
Monosomy/del13q - close associated with t(4;14)
Del17p/TP53 - rare, late event, very poor prognosis
Loss 1p/Gain 1q
Translocations +/- amplifications of MYC - late events in tumour progress
What are the three main checkpoints in cell cycle regulation?
1) G1/S (restriction) checkpoint
2) G2/M checkpoint
3) Metaphase/Spindle checkpoint
How does the G1/S (restriction) checkpoint work?
- Cell growth enables CDK-cyclin D formation
- Phosphorylates Rb protein
- Relieves inhibition of E2F transcription factor
- Cyclin E now expressed - binds to CDK2
- Allows G1-S transition
How does the G2/M checkpoint work?
- CDK1 activated by phosphorylation and dephosphorylation of specific amino acids by cyclin-activating kinases (CAKs) and the wee1 protein
- Enables CDK1-cyclinB production (aka MPF)
- Allows G2/M transition
How does the Metaphase/Spindle checkpoint work?
- Chromosomes assemble on metaphase plate
- Anaphase promoting complex (APC) activated
- Degrades cyclin B-MPF disassembly
- Relieves inhibition of ‘separase’ - spindles cut
- Sister chromatid separation - anapahse entry
What are the heterodimeric protein kinases that regulate cell cycle control made up of?
1) Cyclins - No catalytic activity
2) Cyclin dependent Kinases (CDKs) - Inactive without cyclins, catalytic
How does the heterodimeric protein kinases that regulate cell cycle control work?
Heterodimer phosphorylates target proteins to orchestrate coordinated entry into next phase of the cell cycle
Describe the expression of CDKs and cyclins
CDKs - Constitutively expressed
Cyclins - synthesised at specific stages in response to stimuli
In simple terms - what prevents tumourigenesis?
Arrest of cell cycle proliferation where the genome has been compromised
Where do oncogenes generally exert the most influence?
Over G1 phase progression
- During G1 cell responds to extracellular signals moving it towards division or back to G0
- Cancer cells abandon controls and remain in cell cycle - tend to lose exit pathways too
What does overexpression of Cyclin D1 lead to?
Inappropriate activation of CDKs - can be induced by Ras and P13 kinase signalling pathways - force cell through G1 checkpoint
What is the location of TP53 and what does it do (in simple terms)?
17p13.1 - encodes p53 - Tumour supressor gene that regulates cell cycle - GUARDIAN OF THE GENOME!
When is TP53 activated?
Potent transcription factor activated in response to stressors –> cell cycle arrest/apoptosis/senescence
How is the level of p53 maintained?
Kept at low level in double negative feedback loop by MDM2.
p53 –> Induces expression of MDM2 –> promotes degredation of p53
Name 3 anti-cancer mechanisms of p53
1) Activate DNA repair proteins when damage sustained
2) Arrest growth by holding cell cycle at G1/S in DNA damage
3) Initiate apoptosis if DNA damage too severe
What percentage of human cancers possess a mutated form of TP53?
50% - MDM2-p53 interaction major target for cancer therapies
What percentage of tumours exhibit MDM2 amplification?
17% - MDM2-p53 interaction major target for cancer therapies
What disease is associated with constitutional mutations of TP53?
Li Fraumeni Syndrome
Describe Li Fraumeni Syndrome
Multiple primary tumours, typically soft tissue carcinomas, osteosarcomas, tumours of breast, brain and adrenal cortex, and leukaemia
What is the location of RB1?
13q14.2
How is RB1 activated and what is its role?
Activated by dephosphorylation - binds and inactivates cellular transcription factor E2F1
Are you going to pass this exam?
HELL YES!!!
Describe the role of RB1
2-4 hours before cell enters S-Phase pRB is phosphorylated which releases inhibition of E2F1 and allows cells to progress through to S Phase
What governs the phosphorylation of RB1?
Cascade of cyclins, CDKs and CKIs
RB1 gene mutations produce what?
Sporadic/inherited retinoblastoma - most often frameshifts/dels –> premature introduction of stop codon
What is the location of CDKN2A and what does it encode?
9p21.3
Encodes CDKN2A and ARF
Where in the cell cycle does pCDKN2A function?
Upstream of RB1 protein - inhibiting kinases that phosphorylate pRB
Was function does ARF serve in the cell cycle?
Mediates G1 arrest by destabilising MDM2
What cancer do inherited mutations of CDKN2A cause?
Multiple melanoma
How does blocking MDM2 expression work as a therapeutic target in cancer?
Limits interaction with p53 –> increased levels of p53 which is a tumour suppressor gene
What difficulties are encountered inhibiting the MDM2-p53 binding as a therapeutic target in cancer?
Targeting protein-protein interactions problematic - simple framework of 3 amnio acid residues used to design therapeutic molecules
Name three targets of the MDM2-p53 pathways for cancer therapies
1) Blocking MDM2 expression
2) Inhibiting the MDM2-p53 binding
3) Curtailing E3 ubiquiting ligase activity of MDM2
Give 4 characteristics of myelodysplastic syndromes
1) Clonal expansion of BM myeloid cells with
2) Impaired differentiation
3) Development of peripheral cytopenias
4) Increased risk towards development of AML
Why do we see development of peripheral cytopenias in MDS?
Ineffective haematopoeisis and dysplasia of one or more myeloid lineages - ineffective blood cell production
How does the bone marrow present in MDS?
Hypercellular, dysplastic features, may involve multiple lineages +/- blasts
Name the 3 myeloid lineages involved in MDS
Erythrocytic, granulocytic and megakaryocytic
Where is EVI1 and what is its significance in MDS?
3q36 - associated with poor survival and high risk of transformation to AML
Describe the significance of 5q- in MDS
Proximal 5q31.2 assoc with high risk of transformation, distal 5q33.1 - lower risk of transformation, RPS14 (5q33) found to contribute to abnormal erythroid differentiation and apoptosis. Long survival when isolated finding - low risk of transformation
What is the prognosis of Monosomy 7 and -7q in MDS
POOR
What is the only recurrent amplification in MDS? What is its significance?
+8 - Intermediate risk factor
What is the risk of progression of MDS in 20q-?
Low risk of progression
What is the risk of progression in MDS of complex karyotypes? (>/= 3 abn’s)
High risk of transformation
How do myeloproliferative neoplasms distinguish themselves from MDS?
Increased number of mature cells in BM - normal proliferation and effective maturation
What is constitutively activated in MPN?
Tyrosine kinase/similar –> abnormal proliferation
What is the role of JAK2?
Non-receptor tyrosine kinase involved in JAK/STAT signalling pathway. Acts as signal transducer and activator for the MAPK and P13K pathways to promote transformation and proliferation
What at the most common mutations seen in JAK2?
V617F - gain of function releasing inhibition - also see mutations in exon 12 and LOH of 9p
Name 2 MPNs associated with CALR mutations?
ET and MF - generally considered mutually exclusive of JAK2 mutations
Name 3 types of Burkitt Lymphoma
Sporadic - global and usually presents with abdominal masses,
Endemic - equatorial Africa - predominantly affects jaw and other facial bones,
Immunodeficiency related - AIDS patients
Describe the function of the MYC protein
Involved in regulation, differentiation and apoptosis
How is Burkitt Lymphoma caused?
Juxtaposition with regulatory elements of immunoglobulin loci –> constitutive expression of MYC oncogene or mutns in MYC 5’ regulatory regions - AA substituted in exon 2
What is the cytogenetic characteristic of Burkitt Lymphoma?
Genetically simple - no complex karyotypes
Give 3 favourable abnormalities in adult AML
t(8;21)(q22;q22) RUNX1T1-RUNX1
inv(16)(p13q22) CBFB-MYH11
t(15;17)(q21;q24) PML-RARA
Give 2 examples of therapy related AML
5/7 years post irradiation/alkylating agents with abn 5q/abn 7q, 2/3 year post therapy targeting topoisomerase II often associated with translocations associated with KMT2A or RUNX1
Name 2 therapies used in MDS
Lenalidomide in cases with isolated del(5q) and Azacitidine with chromosome 7 abnormalities
What translocation is commonly associated with Ewing’s Sarcoma?
t(11;22)(q24;q12) EWS/FLI
Name the 3 types of Rhabdomyosarcoma
Embryonal (ERMS), Alveolar (ARMS) and Pleomorphic (PRMS)
What are the recurrent chrm gains seen in Embryonal Rhabdomyosarcomas?
2 8 11 12 13 and 20
Name the two chromosome rearrangements associated with Alveolar Rhabdomyosarcomas
t(1;13)(p36;q14)(PAX7;FOXO1) (20%)
t(2;13)(q35;q14)(PAX3;FOXO1) (60%)
Name 4 alternate Ewing Sarcoma translocations
t(21;22)(q22;q12)(EWS;ERG) (5%)
t(7;22)(p22;q12)(EWS;ETV1) (1%)
t(17;22)(q12;q12)(EWS;ETV4) (
What are the common losses seen in Oligodendrogliomas?
1p/19q
Name 4 common genetic findings in Glioblastoma
Gain of 7p (EGFR at 7p11.2)
Loss of 9q (CDKN2A at 9q21.3)
Loss of 10q (PTEN at 10q23.31)
Loss of 13q (RB at 13q14)
Name 3 common epigenetic findings in Glioblastoma
Hypermethylation of MGMT, GATA6 and CASP8
What are the treatment options in Glioblastoma with hypermethylated MGMT?
Cells more sensitive to alkylating agents - silenced MGMT that repairs DNA damage post alkylating agent damage
What are the outcomes of glioblastoma with Hypermethylated:
CASP8
GATA6
CASP8 - Worse outcome
GATA6 - Increased survival
What can you tell me about Glioblastoma?
Most common primary brain tumour, very poor outcomes, median survival months from diagnosis
Discuss 5q- in MDS
Better prognosis, high rate of response to lenalidomide
Discuss -7/7q- in MDS
Poor prognosis, more common in therapy related MDS
Discuss +8 in MDS
Can help predict response to immunosuppression, some evidence as a marker of progression to AML
Discuss -20q in MDS
Better prognosis
Discuss -Y in MDS
May be a useful as a marker of clonal haematopoiesis - always consider age-related Y chromosome loss
Discuss complex karyotypes (3 or more abnormalities) in MDS
Poor, may be very poor, often include abnormal chromosome 17 - TP53
Common chromosome considerations in MDS
1q, 3q36 (EVI1), 5q-, monosomy 7 and 7q-, +8, KMT2A, del(12p) (loss of ETV6), del(13q), 17p- (TP53), 20q-, -Y, complex karyo
Name 3 Myeloproliferative Neoplasms other than CML
Polycythemia Vera
Essential Thrombocytopenia
Primary Myelofibrosis
What is PCV?
Polycythemia Vera
Expansion of the erythrocytes lineage characterised by high peripheral blood red cell count numbers
What is Essential Thrombocytopenia?
Sustained increase in platelets with associated effects
What is PMF?
Primary Myelofibrosis
Colonial disorder cause by transformation of early haematopoietic progenitor cells resulting in bone marrow fibrosis
What 3 genes are commonly mutated in PCV, ET and PMF?
JAK2 - V617F and exon 12
CALR - Frameshift mutns, 5bp insertion (50%) and 52bp del (35%)
MPL - Hotspot at W515 but others exist
What rearrangements do the European Myeloma Network recommend FISHing for?
t(4;14) - IGH/FGFR3 t(14;16) - IGH/MAF 17p13 deletions - TP53 1p/1q telomeres Extended: t(11;14) - IGH/CCND1 t(14;20) - IGH/MAFB Ploidy status Chrm 12 and 13 abn’s
Give 3 Personalised Medicine examples
Herceptin - HER2 amplification in breast cancer
PARP Inhibitors - BRCA1 and BRCA2
Gefitinib - EGFR Over expressed in lung cancer
Crizotinib - EML4/ALK rearrangement in lung cancer
ATRA - PML/RARA in AML
Cytarabine - RUNX1T1/RUNX1 in AML
What are some of the issues associated with convention needle biopsies for tumour profiling?
High failure rate (10-30% fail to yield suitable DNA for genomic profiling)
Genetic heterogeneity of tumour missed
Tumours hard to get to in some cases
Invasive procedure
What genes would you include on MPN NGS panel
JAK2, CALR, MPL, ASXL1, TET2, SRSF2
