Case 1 Sa A.Wang, MD UT MD Anderson Cancer Center Houston, TX
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Case presentation A 54 year old man with no significant past medical history, presented with low grade fever and night sweats, 6 weeks and was found to have blasts in peripheral blood WBC: 9.9K with 52% blasts Hb 9.2 g/dl Platelets 93K
Peripheral blood smear
Bone marrow biopsy and aspirate smear
Flow cytometry immunophenotyping 262144 196508 CD45dim gate = 61.0% Singlet F S CD19 BV 421 V450-A 10 5 10 4 10 3 10 2-10 2 CD22 APC-A 10 5 10 4 10 3 10 2-10 2 SSC-A 130872-10 2 10 2 10 3 10 4 10 5 CD34 PE-Cy7-A -10 2 10 2 10 3 10 4 10 5 CD10 PE-A 65236-400 -10 2 10 0 10 2 10 3 10 4 10 5 CD45 V500-A CD19 APC-A 10 5 10 4 10 3 10 2-10 2 CD19 BV 421 V450-A 10 5 10 4 10 3 10 2-10 2-10 2 10 3 10 4 10 5 cy79a PE-A -10 2 10 3 10 4 10 5 CD20 APC-A
Flow cytometry immunophenotyping 10 5 10 5 10 5 CD33 PE-A 10 4 10 3 10 2-10 2 CD19 PE-Cy7-A 10 4 10 3 10 2-10 2 CD19 PE-Cy7-A 10 4 10 3 10 2-10 2-10 2 10 2 10 3 10 4 10 5 CD13 APC-A -10 2 10 3 10 4 10 5 CD25 PE-A -10 2 10 3 10 4 10 5 CD15 V450-A 10 5 95.4% 0.2% 10 5 1.8% 93.9% CD19 APC-A 10 4 10 3 CD19 APC-A 10 4 10 3 10 2 10 2-10 2 1.3% 3.1% -10 2 3.1% 1.2% -10 2 10 2 10 3 10 4 10 5 MPO PE-A -10 2 10 2 10 3 10 4 10 5 TDT FITC-A
Cytogenetic and molecular study Chromosomal analysis: 46,XY[20] FISH: nuc ish(abl1,bcr)x2[500] Leukemia Translocation: NEGATIVE t(8;21)(q22;q22); RUNX1-RUNX1T, inv(16)(p13.1q22) or t(16;16)(p13.1q22); CBFB-MYH1 t(15;17)(q22;q12); PML-RARA BCR-ABL1 b2a2, b3a2, e1a2, t(12;21)(p13;q22); ETV6-RUNX1, t(1;19)(q23;p13.3); E2A-PBX1(TCF3-PBX1) t(4;11)(q21;q23); MLL-AF4 t(6;9)(p23;q34); DEK-NUP214
Classification of B-ALL (the 2008 WHO) B lymphoblastic leukemia/lymphoma with recurrent genetic abnormalities t(9:22)(q34;q11.2); BCR-ABL1 t(v;11q23); MLL rearranged t(12;21)(p13;q22); TEL-AML1 (ETV6-RUNX1) Hyperdiploidy (chromosomes >50 but <66) Hypodiploidy (chromosomes<45) t(5;14)(q31;q32)(il3-igh) t(1;19)(q23;p13.3); E2A-PBX1(TCF3-PBX1) B lymphoblastic leukemia/lymphoma, NOS
Prognosis of B-ALL, NOS B-ALL has a good prognosis in children, but it is less favorable in adults. In children, the overall complete remission rate is >95% and in adults 60 85%. Approximately 80% of children with B-ALL appear to be cured, while this figure is less than 50% for adults Borowitz MJ and Chang JKC, The WHO classification of tumours of haematopoietic and lymphoid tissues IARC, 2008
Gene expression profiling of ALL in Children Ph Like Den Boer et al. Lancet Oncology 2009
Definition of BCR ABL1 like ALL Do not have the BCR ABL1 fusion protein or t(9;22)(q34;q11.2) yet have a gene-expression profile similar to that of patients with BCR ABL1 ALL Negative for most recurrent genetic abnormalities MLL-rearrangement, ETV6-RUNX1, E2A-rearrangement, Hyperdiploidy (?)
Prognotic significance of Ph like ALL German Cohort (n=145) Dutch group (n=92) Den Boer et al. Lancet Oncology 2009
Ph-like ALL, inferior EFS and OS in children, adolescent and young adults Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
Frequency of BCR ABL1 like ALL Study cohort: 264 of 1725, 15.3% Children, standard risk 1-9 years, and WBC <50K (n=330): 10% Children, high risk 10-15 years, and WBC 50K (n=853): 13% Adolescents (n=374) 16-20 years, 21% Young adults 21-39 years (n=168), 27% Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
Ph-like ALL in adults/elderly Herold T, et al. Ph-like acute lymphoblastic leukemia in older adults. N Engl J Med. 2014 Dec 4;371(23):2235
Ph-like B-ALL, significance goes beyond prognosis Ph-like B-ALL is characterized by the presence of recurrent kinase alterations - Genomic alterations activating kinase signaling were identified in 91% of patients with Ph-like ALL Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
Sub-classification of Ph-like ALL by Recurrent Kinase Alterations
The breakdown of genetic lesions in Ph-like ALL by age group Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
Potential Target kinase inhibitor therapy
Identification of Ph-like ALL cases and actionable kinase alterations Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
Screening for Ph-like ALL Molecular Lesions Relapse/refractory ALL, screening for Ph-like ALL CRLF2 by Flow-cytometry Positive for CRLF2 Negative for CRLF2 JAK2 (JAK2R683) or JAK1 Mutations by NGS Fusions - ABL1, ABL2, JAK2, EPOR, PDGFRB, NTRK3, TYK2, CSF1R
Phase II Clinical Trial Personalized Medicine in Patients with ALL (continued) Design: Age 10 yrs Relapsed/ refractory B-cell ALL Ph-like ALL CRLF2 overexpression JAK mutations/fusions EPOR fusions SH2B3 deletion IL7R mutation Ruxolitinib Plus Chemotherapy N=40 ABL1, ABL2, PDGFRB fusions Dasatinib Plus Chemotherapy N=40
Back to our patient CD19 BV 421 V450-A 10 5 10 4 10 3 10 2-10 2 99.9% 0.1% 0.0% 0.0% -10 2 10 3 10 4 10 5 PE-A CD19 BV 421 V450-A 5 0.2% 99.8% 10 10 4 10 3 10 2-10 2 0.0% 0.0% -10 2 10 3 10 4 10 5 CRLF2 PE-A Count 234 176 117 59 0-10 2 10 2 10 3 10 4 10 5 CRLF2 PE-A
CRLF2 rearrangement in 94% interphases
Metaphase FISH showed a cryptic t(y;14), IgH@CRLF2
Next generation sequencing JAK2 mutation positive NM_004972.3(JAK2):c.2047A>G p.r683g Exon 16 SNV Missense ASXL1 NM_015338.5(ASXL1):c.3149T>C p.m1050t Exon 12 SNV Missense
Common mutations seen in ph-like ALL by NGS Inherited GATA3, rs3824662 variant, SNP Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15
CRLF2+ B-ALL in adults, MDACC experience 21 de novo B ALL cases and 34 relapsed/persistent B ALL cases The frequency of CRLF2 expression among de novo B-ALL, NOS, and relapsed/persistent B-ALL, NOS, was 23% and 23%, respectively CRLF2 FISH performed in 10 CRLF+ cases, all positive; 8 had metaphase FISH done: 7 with IgH- CRLF2 only 1 deletion of Y (P2RY8-CRLF2) 5 of these cases tested for JAK2 by whole exon sequencing, 3/5 were positive Konoplev et al: USCAP 2015 Abstract Notification (#1442)
Post induction, MRD positive 0.05% B-ALL cells CD19 BV 421 V450-A 10 5 10 4 10 3 10 2-10 2-10 2 10 3 10 4 10 5 CD10 PE-Cy7-A CD58 PE-A 10 5 10 4 10 3 10 2-10 2-10 2 10 3 10 4 10 5 CD38 APC-A CD19 BV 421 V450-A 10 5 10 4 10 3 10 2-10 2-10 2 10 3 10 4 10 5 CRLF2 PE-A
Summary Ph-like B-ALL comprises a significant subset of B-ALL, particularly in B-ALL NOS, and B-ALL with a hypodiploidy, occasionally in B-ALL with a hyperdiploidy Ph-like B-ALL is characterized by recurrent kinase alterations, potentially for kinase inhibitor therapy; Ph-like ALL can be detected with an algorithm composed of flow cytometry, FISH, molecular testing (NGS and fusion transcript) B-ALL has an inferior outcome, but a lot remains unknown in elderly adults
Practical points about Ph-like ALL: Screening for targetable kinase alterations is the most critical! B-ALL does not have characteristic morphological features; CRLF2 is an easy flow cytometry marker for implementation Not all CRLF2+ B ALL are Ph-like; Screening JAK2 mutation; A good marker for MRD in our experience A FISH panel for B-ALL: ABL1, ABL2, JAK2, EPOR, PDGFRB, NTRK3, TYK2, CSF1R is feasible
References Mullighan CG, Su X, Zhang J, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med 2009; 360: 470-80. Den Boer ML, van Slegtenhorst M, De Menezes RX, et al. A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. Lancet Oncol 2009; 10: 125-34. Roberts KG, Li Y, Payne-Turner D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014 Sep 11;371(11):1005-15. Perez-AndreuV, Inherited GATA3 variants are associated with Ph-like childhood acute lymphoblastic leukemia and risk of relapse. Nat Genet. 2013 Dec;45(12):1494-8. Perez-AndreuV, Blood. A genome-wide association study of susceptibility to acute lymphoblastic leukemia in adolescents and young adults.2015 Jan 22;125(4):680-6. Harvey RC, Kang H, Roberts KG, et al. Development and Validation Of a Highly Sensitive and Specific Gene Expression Classifier To Prospectively Screen and Identify B-Precursor Acute Lymphoblastic Leukemia (ALL) Patients With a Philadelphia Chromosome-Like ( Phlike or BCR-ABL1-Like ) Signature For Therapeutic Targeting and Clinical Intervention. Blood 2013;122:826.
Ph-like ALL: MDACC Data Fraction progression free 1.0 0.8 0.6 0.4 0.2 0.0 0 AugBFM Ph-like p=0.001 Progression Free Survival 1 2 3 4 5 6 7 8 Years Ph-like median age 24 yo (18-38) Augm BFM 23 yo (18-39)
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Outcome analyses for IKZF1 alteration
Microarray gene expression profiling Roberts KG N Engl J Med. 2014 Sep 11;371(11):1005-15