Tumor Cytogenetics. Department of Pathology & Cell Biology & Institute for Cancer Genetics. Vundavalli Murty. Sept 24, 2017

Transcription

1 Tumor Cytogenetics Vundavalli Murty Department of Pathology & Cell Biology & Institute for Cancer Genetics Sept 24, 2017

2 Reference Material 1. Cancer Cytogenetics: Text Book: Heim S and Mitelman F, Recurrent Chromosome Aberrations in Cancer Web site RecurrentAberrations 3. Atlas of Genetics and Cytogenetics in Oncology and Haematology Web site: September 24, 2018 Page 2

3 Overview - Chromosomes in human tumors are widely abnormal: David von Hansemann 1890: nuclear and mitotic abnormalities in tumors Boveri 1914: Chromosome abnormalities play a central role in transformaton - Controversy: Early 1950s Whether the chromosome changes are primary events or merely secondary phenomena? - Changed view: Recurring chromosome aberrations associated with leukemia, lymphoma, sarcoma, carcinoma Proto-oncogenes identified at the breakpoints Experimental evidence for these genes in transformation Targeted drugs that inhibit gene product: e.g. STI571 for BCR-ABL September 24, 2018 Page 3

4 Methods of Chromosome Preparations Actively dividing cells can be arrested at metaphase or prometaphase stages using mitotic arresting agegns (eg. Colcemid) Direct preparations or short-term cultures to represent in vivo conditions Hypotonic treatment & fixation A variety of methods: Giemsa-banding FISH (Fluorescence in situ hybridization) Probes to detect translocations, inversions, deletions, amplification Chromosomal CGH, SKY, array CGH, Microarray September 24, 2018 Page 4

5 Methods Employed in Recognizing Chromosome Aberrations" Banding methods: Trypsin-Giemsa Chromosome painting: FISH: Comparative Genomic Hybridization CGH): Spectral Karyotyping (SKY): Ref. Rao PH et al. Molecular cytogenetic applications in analysis of the cancer genome. Methods Mol Biol. 2007;383:

6 September 24, 2018 Page 6

7 Idiograms of G-band for normal Human Chromosomes Nomenclature " p Region Band Number e.g., 1p34.1" Centromere q September 24, 2018 Page 7

8 Symbols and Abbreviated Terms: ISCN, 2009" Important designations to describe cancer karyotype cen centromere del deletion der derivative chromosome dic dicentric chromosome dmin double minute chromosome dup duplication hsr homogeneously staining region i isochromosome ins insertion inv inversion mar marker chromosome minus (-) loss plus (+) gain p short arm parenthesis()surround structurally altered chromosoems and breakpoints ph Philadelphia chromosome q long arm r ring chromosome semicolon(;)separates altered chromosomes t translocation A translocation between chromosomes " 9 and 22 in CML at bands 9q34 " and 22q11.2" 46,XX,t(9;22)(q34;q11.2)[20]" A deletion of long arm of chromosome 5 at band 5q31 in a leukemia patient" 46,XY,del(5)(q31)[10]/46,XY[10]" September 24, 2018 Page 8

9 Types & Consequences of Major chromosome changes Ploidy (e.g., haploid, triploid, tetraploid): Unclear" Aneuploidy (e.g.,tri-,tetra-, monosomy): Increased or decreased expression of set of genes" Reciprocal or non-reciprocal translocations (inversions): " "Overexpression/fusion gene" Deletions: Loss of expression" Duplications and Amplifications: Increased gene expression" Insertions: Loss or gain of function of genes" Ref. Mitelman, F et al.,the impact of translocations and gene fusions on cancer causation. Nat. Rev. Cancer 7, (2007).! September 24, 2018 Page 9

10 Chromosomal Translocations in Leukemia and Lymphoma Consequences: Altered Expression and/or Fusion Proteins" Gain of function; BCR/ABL Over 420 genes associated with translocations have been identified in human cancer. Ref. Rowley JD. Chromosome translocations: dangerous liaisons revisited. Nature Reviews Cancer 1, , September 24, 2018 Page 10

11 Chronic Myelogenous Leukemia (CML) t(9;22)(q34;q11.2) BCR/ABL fusion Ref. Goldman JM1, Melo JV. Chronic myeloid leukemia--advances in biology and new approaches to treatment. N Engl J Med Oct 9;349(15): September 24, 2018 Page 11

12 CML: Karyotyping and FISH t(9;22)(q34;q11.2) t(9;22)(q34;q11.2) t(9;22)(q22;q11.2) t(9;22) partial karyotype BCR/ABL FISH

13 Chromosome changes in CML progression A: Karyotype: 47,XX,t(9;22)(q34;q11.2),+8,i(17)(q10) B: FISH--BCR/ABL C: FISH--CEP 8 (green) and D20S108 (red) D: FISH TP53 (red) and ATM (green)

14 Chromosomal changes in Myelodysplatic Syndrome (MDS): Clinical significance Heterogenous group" Primary and secondary MDS" Cytogenetic changes have prognostic implications" The classification of MDS is based on clinical data (previous history, age) and biologic characteristics (morphology, cytochemistry, immunophenotype, cytogenetic and molecular alterations) 5q- syndrome Single defect; favorable with low risk of transformation (distinct morphologic entity; high prevalence in elderly females; RPS 14, CTNNA1 as target genes del(5q)/- 5 Favorable as sole abnormality Additional abnormalities, therapy related--poor prognosis del(7q)/-7 Trisomy 8 del(20q) Unfavorable outcome Intermediate Good prognosis (as sole change) Intermediate/unfavorable (with other abnormalities)

15 Acute Myeloid Leukemia (AML) The classification of acute myeloid leukemia (AML) similar to myelodysplasic syndromes (MDS) is based on clinical data (previous history, age) and biologic characteristics (morphology, cytochemistry, immunophenotype, cytogenetic and molecular alterations) >85% karyotypic abnormalities Translocations, deletions, and inversions Diagnostic and classification of risk groups September 24, 2018 Page 15

16 Recurring Chromosome Abnormalities in AML Morphologic Subset Chromosome change Genes Prognosis M2 t(8;21)(q22;q22) ETO-AML1/RUNX1 (attenuates spindle checkpoint) M3 t(15;17)(q22;q12-q21) PML-RARA Favorable (No adverse for additional changes) Favorable Variants: PLZF, NPM, NUMA M4Eo M1,M2, M4, M5a, therapy-related (Topoisomerase inhibitors) inv(16)(p13q22)" t(16;16)(p13;q22)" del(16)(q22)" CBFß/MYH11 (core binding factor/myosin heavy chain) Favorable 11q23 abnormalities" MLL (KMT2A) Poor, generally Variable, translocationbased Biphenotypic leukemia (BAL) t(9;22)(q34;q11), 11q23 abnormalities" BCR/ABL, MLL Worse Many other categorized, Uncategorized, and Treatment-related September 24, 2018 Page 16

17 Inversion 16 in AML: Good prognostic AML" 9/24/18 Page 17

18 t(15;17) is a charcteristic chromosome change in APML

19 Therapy Related MDS and AML

20 An AML patient with complex karytoype and MLL amplification predicts poor prognosis Diagnosis: "AML" Age: " "74 years (Female) "" Karyotype: 45,XX,-4,der(5)t(5;17)(q11.2-q21;q11.2),+6,+8, der(11)dup(11)(q13q23)ins(11;4)(q23;q22q28)hsr(11)(? 23),-17,-18[cp35] Amplification: MLL, ATM: Deletion: EGR1, TP53 " MLL gene amplified" Treatment: "Mylotarg, ATRA " Survival: "5 days after diagnosis"

21 A patient of P. vera transformed to AML with complex karytoype Diagnosis: "taml" Age: " "70 years (Male) "" Karyotype: 61-63,<3N>,XY,-2,-3,-4,-5,-7,der(8)t(2;8) (?;p21),-9,+der(9)(?)x6,-10,-12,-13,-14,-15,-17, -18,+der(18)t(11;18)(q13;p11.2),+21[25] Treatment: Survival: "No data" "No data"

22 Myeloid neoplasms with complex karyotypes predict poor prognosis" No Diagnosis (age) Treatment Karyotype Amplificatio n Increase d copies Deletion Survival 1 AML (74) Mylotarg, ATRA Complex MLL, ATM - EGR1, TP53 5 days 2 MDS/AML (65) Doxorubicin, AraC HU " Complex MLL TP53 EGR1, AML1, TEL 3 MDS (74) NA Complex MLL ATM EGR1, TP53 NA 8 months 4 AML (87) No RX Complex MLL, ATM - EGR1, TP53 <5 days 5 MDS/AML (69) 6 MDS/AML (69) Ida/Ara C refractory disease failed induction " Topotecan/Ara C G- CSF persistent leukemia " Complex MLL ATM EGR1, TEL 1 month Complex MLL, ATM - EGR1, TEL 8 months 7 p.veraàaml NA Complex MLL ATM EGR1, TEL NA 8 AML (49) Ara C/Ida R " Complex - - EGR1, TP53 1 month 9 CML (69) HU, Ida/Ara " Complex MLL ATM EGR1, TP53 1 month 10 AML (65) No RX Complex MLL, ATM - EGR1, TEL 4 days 11 MDS/AML (75) No RX Complex MLL - EGR1, TEL 1 month

23 Cytogenetic abnormalities in therapy-related myeloid neoplasms (t-mn) vs. de novo acute myeloid leukaemia (AML)" *Can co-occur in various combinations From: McNerney ME, Godley LA, & Le Beau MM. Nature Reviews Cancer 17, (2017) 9/24/18 Page 23

24 Acute Lymphoblastic Leukemia (ALL): Cytogenetics Diagnostic and prognostic significance" Accumulation of malignant and immature lyphoid cells in marrow Chromosome change Genes involved Subtype Diagnosis/Prognosis High hyperdiploidy (>55 chromosomes) Not known (+4,+6,+8,+10,+14,+21) Pre-B Good (>90% cure in children) Near haploidy (26-28) Not known Pre-B Poor (short complete remission) Normal Poor t(9;22)(q34;q11.2) BCR/ABL (p210 or p190) B-cell (stem cell or progenitor) t(4;11)(q21;q23) AF4/MLL B-cell (biphenotypc) (also AML M5) t(11;19)(q23;p13.3) MLL (KMT2A)/MLLT1 B-cell (biphenotypc) Poor Short CR and prompt relapse Generally Poor Very Poor t(12;21)(p12;q22) ETV6(TEL)/RUNX1(AML1) B-cell Excellent t(8;14)(q24;q32) MYC/IGH B-cell ALL(L3) Diagnostic and Adverse t(2;8)(p12;q24) MYC/IGK /NHL(BL) t(8;22)(q24;q11) MYC/IGL t(1;19)(q23;p13) PBX/E2A ALL Adverse September 24, 2018 Page 24

25 Chromosomal abnormalities in ALL: T-Cell Diagnostic and prognostic significance Chromosome change Genes Subtype Diagnosis/ involved Prognosis t(10;14)(q24;q11) HOX11/TCRA T-cell Favorable (Adult) t(7;10)(q34;q24) TCRB/HOX11 T-cell Not known t(11;14)(p13;q11) LMO2/TCRA T-cell Not known t(8;14) (q24;q11) MYC/TCRA T-cell Poor t(7;9)(q34;q34) TCRB/NOTCH1 T-cell Not known inv(14)(q11q32.1) TCRA-TCRD/TCL1 T- PLL Aggressive course t(14;14)(q11;q32.1) AT T-cell leukemia /lymphoma NUP214/ABL1 amplificawon ABL1 and NUP214(CAN) T-cell SensiWve to Tyrosine Kinase inhibitor Gleevac September 24, 2018 Page 25

26 Cytogenetic Subsets in Pediatric ALL" Excellent prognosis Poor outcome Poor outcome Favorable outcome Poor prognosis Mullighan CG. J. Clin Invest. 122; 3407, 2012

27 Karyotype showing near haploid chromosomes in an ALL patient Karyotype: 27<1N>,XY,+14,+18,+21

28 t(4;11)(q21;q23) in ALL A: Karyotype--46,XY,t(2;19)(q23;q13.4),t(4;11)(q21;q23) B: FISH: MLL break apart probe

29 Prognostic Impact of Diagnostic Karyotypes in Pediatric ALL" Event Free Survival (%) Karyotype 2 yrs 5 yrs >50 chromosomes chromosomes Normal karyotype t(1;19)(q23;p13) t(9;22)(q34;q11.2) t(8;14)(q24;q32) q23 abnormalities Hypodiploid (<46) t(4;11)(q21;q23) Heim and Mitelman, 1995 September 24, 2018 Page 29

30 Cytogenetics: Mature B- and T-Cell Lympoma

31 Chromosome Translocations: Lymphocyte Development Translocations are considered to arise as errors during intragenic physiologic rearrangements that assemble productive copies of IG and TCR genes during normal B- and T-cell development Translocations tend to be specific for breakpoints and show a high degree of association with histologic subsets Three Main Subsets of NHLs: -- B-Cell -- T-Cell/Natural Killer (NK) Cell -- Hodgkin s Lymphoma (HL) First description of karyotype in BL in 1963 (Jacobs et al., 1963) Identified as t(8;14)(q24;q32) in 1972 (Manolov and Manolova, 1972) t(8;14) was shown that MYC rearranges with IGH (Dalla-Favera et al., 1987) September 24, 2018 Page 31

32 Burkitt s Lymphoma" Primary Chromosome change: --t(8;14)(q24;q32) MYC/IgH Variant translocations: -- t(8;22)(q24;q11) (MYC/IgL) -- t(2;8)(p11;q24) (IgK/MYC) Duplication 1q: progression September 24, 2018 Page 32

33 Follicular Lymphoma Primary Chromosome Change: t(14;18)(q32;q21) (IgH/BCL2)(>75%) variant translocations involving 18q21 break point (BCL2)» 3q27 rearrangements (BCL6)» 6q21 deletions t/der(1q), +7, del(6q), del(17p): Progression/transformation t(14;18) negative tumors do exist, which exhibit complex and heterogeneous breakpoints (3q27; 8q24, ect) September 24, 2018 Page 33

34 Diffuse Large B-Cell Lymphoma (DLBCL) Generally complex, hyperdiploid t(14;18)(q32;q21) (IgH/BCL2) followed by 3q27 rearrangements (BCL6)(many partners) t(8;14)(q24;q32) (MYC/IgH) Correlations with chromosome changes contradictory -- der(1)(q21), +7, del(6q), del(17p) Associate with progression/transformation; predict adverse outcomes --Chromosome amplifications frequent September 24, 2018 Page 34

35 Mantle Cell Lymphoma (MCL) t(11;14)(q13;q32): The cytogenetic hallmark found in 70% of cases (CCND1/IgH) Monosomy 13/del(13q) September 24, 2018 Page 35

36 Chronic lymphocytic leukemia (CLL/SLL) A chronic lymphoproliferative disorder of mature B-lymphocytes Tumor cells are inert with only a small proliferative compartment 50-60% abnormal by karyotype (>80% by FISH) Chromosome change Prognosis OS (mo) del (17p13) (TP53) (v)" del(11q22-q23) (ATM) (iv)" Trisomy 12 (ii)" Normal (iii)" Adverse Progression " Intermediate" Intermediate" 30 " 80 " 115 " 110" del(13q14.3)(sole) (i)" Favorable" FISH panel targeting all the above changes " 135 Absence of IGHV mutation: Aggressive course

37 Prognosis of deletions in CLL" Dal Bo M et al. GENES, CHROMOSOMES & CANCER (2011)

38 Multiple Myeloma Karyotype detects only 30-50% cases with abnormalities Cytogenetic change" Genes" Prognosis" Hyperdiploidy (3, 5, 9, 11, 15, and 19)" Not known" Good" 1p deletions" Not known" Poor" 14q32 rearrangements" IGH" Poor" (at least 5 partners)" (partners: FGFR3, cmaf)" 11q13, t(11;14)" IGH/CCND1" Favorable outcome" 6q deletions" MYB" --" Del(13q)/-13" D13S319" Adverse outcome; shorter survival" September 24, 2018 Page 38

39 Overall survival according to chromosome abnormality in multiple myeloma Hervé Avet-Loiseau et al., J Clin Oncol: 30 (16): , 2012

40 Mature T-cell Neoplasms Entity" Chromosome change" Anaplastic large cell lymphoma t(2;5)(p23;q35) (NPM/ALK) Other partners exists; favorable prognosis T-cell prolymphocytic leukemia (T-PLL)" inv(14)(q11q32), t(14;14)(q11;q32)" (TCRa/d-TCL1)" 7q34-36 translocation (TCRB)" Angioimmunoblastic T-cell lymphoma" (EBV+ve in >75%)" Trisomy 3 or i(3q), +5, +X, del(6q)"

41 Chromosome change in Anaplastic Large Cell Lymphoma (ALCL) Ref. Amin HM, Lai R. Pathobiology of ALK+ anaplastic large-cell lymphoma. Blood. 110(7): , 2007.

42 Genetic hallmark of T-PLL is inv(14)(q11.2q32) or t(14;14)(q11.2;q32) TCL1 gene at 14q32 juxtapose next to TCRA/D locus at 14q11.2 resulting in up regulation of the TCL1 expression. The TCR-associated translocations are regarded as the primary oncogenic events in T-PLL. T-PLL are generally very aggressive tumors among T-cell lymphomas and poorly responsive to chemotherapy.

43 Karyotype Changes in NHL: diagnostic and prognostic significance Type Diagnostic Change Progression/ Transformation Poor outcome Good outcome B-CLL/SLL - +12,del(11q23),t(14q 32) +12, del(11q) del(13q) MM/LPL t(9;14)(p13;q32) - -13/del(13q) - MALT t(11;18)(q21;q21) FL t(14;18)(q32;q21) +7,del(q),t(8;14) t(8;14) - MCL t(11;14)(q13;q32) - del(17p) - DLBCL - der(1q21), +7,del(6q),del(17p) der(1q21),del(6q),de l(17p BL t(8;14)(q24;q32) dup(1q) - - ALCL (anaplastic) t(2;5)(p23;q35) t(2;5)(p23;q35) Chromosome abnormalities of 1, 6, and 17 are virtually seen in all lineage NHLs: Associated with poor clinical outcome September 24, 2018 Page 43

44 Solid Tumor Cytogenetics

45 Ewing sarcoma/primitive neuroectodermal tumor" Heterogeneous group of distinct histologic types 90% cases with t(11;22)(q24;q12); in all histologic types Translocation results in the fusion of the EWS with FLI1, forming a chimeric protein variant translocations: t(21;22)(q12;q12)[ews- ERG] and t(7;22)(p22;q12) [EWS-ETV1 in 5% cases EWSR1 is also rarely rearranged in other soft tissue tumors (Myxoid chondrosarcoma, Desmoplastic small round cell tumor, malignant melanoma of soft parts) Ref. Crompton BD. et al. The genomic landscape of pediatric Ewing sarcoma. Cancer Discov. 4(11): , September 24, 2018 Page 45

46 Other soft tissue tumors- Karyotypic Changes Tumor Chromosome translocation Myxoid liposarcoma" t(12;16)(q13;p11)" Variant: t(12;22)" Genes DDIT3 (CHOP)- FUS (TLS)" DDIT3/EWS" Comments Fusion protein; oncogenic" Alveolar rhabdomyosarcoma (A-RMS)" t(2;13)(q35;q14) (~80%)" t(1;13)(p36;q14) (~15%)" Variants" PAX3 - FOXO1 (FKHR)" PAX7-FKHR" Poorer survival than ERMS" ARMS and ERMS are two distinct genetic entities" Synovial sarcoma" t(x;18)(p11.2;q11.2)" Variants" SSX1, SSX2, SSX4-SYT (SS18)" Hybrid protein" Poor prognosis" Page 46

47 Neuroblastoma Sympathetic neuronal precursor: Embryonic origin Common Extracranial pediatric tumor of infancy Classified as low, intermediate, and high-risk groups " Two major types of Cytogenetic abnormalities: Segmental chromsome aberrations 1p and 11q deletion (LOH) High-risk Amplification of NMYC is the most robust prognostic factor in NB Page 47

48 Gene Amplification: Double Minute Chromosomes September 24, 2018 Page 48

49 Landscape of genetic changes in neuroblastoma" Pugh TJ et al., Nat Genet 45: 279, 2013 Page 49

50 Tumors of Nervous System Gliomas Oligodendrogliomas 1p36/1q25" 19q13/19p13" 1p36/1q25" 19q13/19p13" 1p36 and 19q13 co-deletion occur in over 75% both grade II and III oligodendrogliomas Correlate with response to chemotherapeutic drugs and radiation Page 50

51 Renal Epithelial Neoplasms: Origin and Genes Involved -- Morphologically and behaviorally heterogeneous group, epithelial Hereditary form Origin (Fumarate hydratase) (Brit Hogg Dubé September 24, 2018 Page 51

52 Clear Cell RCC Characteristic feature: Loss of 3p due to deletions or unbalanced translocations Number of common regions of deletions identified: 3p14, 3p21, and 3p25 (3q21 is essential) Trisomy 5q21-qter (partial trisomy): Predictive of good prognosis +12, +20 Germ line mutation in VHL gene at 3p25 in familial cases No consensus on tumor suppressor on 3q21(Candidates: RASSF1A, FHIT, DUTT1, TTRC1, NRC1) September 24, 2018 Page 52

53 Papillary RCC Tri- or Tetrasomy of 17, 7, 16, 20, 12 Loss of Y in men Loss of Y, +7, +17 may correspond to papillary adenomas Additional changes diagnostic papillary RCC Inherited form of prcc--missense mutations in MET oncogene September 24, 2018 Page 53

54 Chromophobe RCC Chromosome modal number 38-39" Loss of chromosomes 1, 2, 6, 10, 13, 17, and 21" Difficulties in differential diagnosis from Oncocytoma" Karyotype (FISH) is useful in differential diagnosis September 24, 2018 Page 54

55 CCND1 rearrangement of 11q13 in Oncocytoma September 24, 2018 Page 55

56 Seminoma and Non-seminoma Over representation of 12p --85% with one or more copies of i(12p) --tandem duplications of 12p (10%) --Rarely, 12p amplification Testicular Germ Cell Tumors September 24, 2018 Page 56

57 Her-2/neu (ERRB) Amplification in Breast Cancer ERBB2 gene is amplified and overexpressed in 20-25% of breast tumors Tumors showing ERBB2 amplification have predominantly lost estrogen receptor expression (ER-) Worsened course of the disease Target for therapeutically approaches using engineered anti-erbb2 antibodies September 24, 2018 Page 57

58 Utilities of Tumor Cytogenetics To Establish Malignant Clone (normal karyotype doesn t rule out) To Clarity/Establish Diagnosis To Indicate Prognosis (some changes associated with poor response) To Assist in Choice of Treatment Strategy To Monitor Response to Treatment To Establish Engraftment Status and Monitor Number of targeted therapies already exists against specific genetic changes that patient s tumor uniquely possesses. " " September 24, 2018 Page 58