Current Status of Precision Hematology

- From the pathologists’ viewpoint

Young-Uk Cho Department of Laboratory Medicine,

University of Ulsan, College of Medicine and Asan Medical Center, Seoul, Korea

ICKSH 2019

There is no conflict of interest.

Contents

• Introduction• Accurate diagnosis• Evidence-based diagnosis

– Risk stratification– Therapeutic implication

• Germline predisposition• Minimal residual disease• Summary and conclusion

INTRODUCTION

https://www.cpgr.org.za/precision-medicine-in-south-africa-a-cost-benefit-analysis-framework/

Pathologic diagnosis: Revised WHO 2016 classification

Evidence-based diagnosis: Risk stratification: Therapeutic implication (target therapy)

Germline predisposition

Minimal residual disease

ACCURATE DIAGNOSIS

Revised 2016 WHO classification of myeloid neoplasms and acute leukemia

• Myeloproliferative neoplasms• Mastocytosis• Myeloid/lymphoid neoplasms with eosinophilia and

rearrangement of PDGFRA, PDGFRB, or FGFR1, or with PCM1-JAK2

• Myelodysplastic/myeloproliferative neoplasms• Myelodysplastic syndromes• Myeloid neoplasms with germline predisposition• Acute myeloid leukemia• Blastic plasmacytoid dendritic cell neoplasm• Acute leukemia of ambiguous lineage• B-lymphoblastic leukemia/lymphoma• T-lymphoblastic leukemia/lymphoma

Blood 2016;127:2391-405.

Major changes: from WHO 2008 to 2016 classification system

Disease Diagnostic tool New finding

CML, accelerated phase

Genetics ≥2 mutations in BCR-ABL1 during TKI therapy

CNL Genetics CSF3R mutation

PV CBC Hb >16.5 g/dL or Hct >49% (♂) Hb >16.0 g/dL or Hct >48% (♀)

ET and PMF Genetics CALR mutation

Eosinophilia Cytogenetics PCM1-JAK2 rearrangement

JMML Genetics PTPN11, KRAS, NRAS, NF1, CBL mutations

MDS Genetics SF3B1 mutation

AML or MDS Cytomorphology Blast ≥20% of all cells in BM

AML Genetics RUNX1 mutation, BCR-ABL1

B-LL Genetics BCR-ABL1-like

B-LL Cytogenetics iAMP21

T-LL Flow cytometry Early T-cell precursor lymphoblastic leukemia

Blood 2016;127:2391-405.

The diagnosis is supported by the presence of SETBP1 and/or ETNK1mutations.

In the appropriate clinical context, mutations in genes oftenassociated with CMML (ex, TET2, SRSF2, ASXL1, and SETBP1)support the diagnosis.

54/F

CNL vs atypical CML ?AML with mutated RUNX1 vs AML with myelodysplasia-related changes ?

Personal data

NeutrophiliaNeutrophil precursors <10%Hypercellular marrowMyelodysplasia (+), but not significant

Mod Pathol 2018;31:429-441.

74/M

JAK2 V617F (60%)KRAS (33%)TET2 (48%)

58/M

MPL (44%)ASXL1 (43%)TET2 (48%)TET2 (42%)SRSF2 (46%)NRAS (25%)

Myeloid neoplasms with features intermediate between primarymyelofibrosis and chronic myelomonocytic leukemia

Haematologica 2015;100:1117-30.

AML with

• NPM1 mutation

• Biallelic CEBPA mutation

• RUNX1 mutation

• History of MDS or MDS/MPN

• MDS-related cytogenetic abnormality

• Multilineage dysplasia

AML with recurrent genetic abnormalities

AML with myelodysplasia-related changes

PP-031 (Reclassifying Acute Myeloid Leukemia According to the Revised 2016 WHO Classification in a Large Patient Group)

?

Diagnostic modality for Ph-like ALL

Blood 2017;130:2064-2072.

Schema of activated kinase signaling inPh-like ALL

Current Ph-like ALL genetic testing algorithmused by the Children’s Oncology Group

From a practical standpoint, it is difficult to identify these leukemias withoutcomplex laboratory analysis, and it is also difficult to screen cases of B-ALL todetermine which cases would need such analysis. - Revised WHO classification p.208

Blood 2017;130:2064-2072.

Semin Hematol 2018;55:235-241.

EVIDENCE-BASED DIAGNOSIS

Blood 2017;129:424-447

ELN(European LeukemiaNet) Risk Stratification by Genetics in Non-APL AML

Blood 2018;132:187-196.

N=445 (CBF AML)Clonal interference: the coexistence clones sharing a commonancestor and harboring independent lesions targeting the samepathway (in this study, the presence of ≥2 signaling clones in a singlepatient sample, eg, KRASG13D and NRASG12S)

28%

https://www.nccn.org/professionals/physician_gls/pdf/mds.pdf

Mayo Clin Proc 2018;93:1363-1374.

N=685 (Mayo 357, NTUH 328)WHO-defined primary MDS

Mayo alliance prognostic modelRisk factor Point

Genetic

Monosomal karyotype (MK) 4

non-MK other than single/double 5q- 1

RUNX1 mutation 1

ASXL1 mutation 1

absence of SF3B1 mutation 1

Clinical

age >70 years 2

severe anemia1 2

platelet count <75×109/L 1

bone marrow blasts ≥10% 11Hb level of <8 g/dL for women & <9 g/dL for men

4-tiered model• High > 6 points• Int-2 5-6 points• Int-1 3-4 points• Low 0-2 points

Survival data on 357 Mayo Clinicpatients with primary MDS stratified bythe new Mayo alliance prognosticmodel for MDS.

Survival data on 328 National TaiwanUniversity Hospital patients withprimary MDS stratified by the newMayo alliance prognostic model forMDS.

Mayo Clin Proc 2018;93:1363-1374.

Survival data on 357 Mayo Clinic patients with primary MDS stratified byeither the new Mayo alliance prognostic model for MDS or the IPSS-Rprognostic models.

Mayo Clin Proc 2018;93:1363-1374.

https://www.nccn.org/professionals/physician_gls/pdf/mpn.pdf

HMR mutations: ASXL1, SRSF2, EZH2, IDH1, IDH2

J Clin Oncol 2018;36:310-318.

MIPSS70: validation training

MIPSS70-Plus: validation training

Clonal hemopoiesis and therapy-related myeloid neoplasms. (A) Cumulativeincidence of therapy-related myeloid neoplasms in patients with or without clonalhemopoiesis in the case and control cohorts. Vertical tick marks represent censoredpatients (B) Variant allele frequencies of mutations detected as clonal hemopoiesisbetween cases who developed therapy-related myeloid neoplasms and controls who didnot.

30%

7%

Case Control

CH+ 10 17

CH- 4 37

Lancet Oncol 2017;18:100-11.

Cumulative incidence of therapy-related myeloid neoplasms in patients with or without clonal hemopoiesis in the external cohort

Lancet Oncol 2017;18:100-11.

Lymphoma treated with CHOP (n=74)

29%

0%

Genomically defined targeted therapiesDisease Target Therapy

APL PML-RARA ATRA, Arsenic

CML, ALL BCR-ABL1 TKIs

AML, ETP-ALL FLT3 Midostaurin, Quizartinib, Gilteritinib, Crenolanib

IDH2 Enasidenib

IDH1 Ivosidenib

AML, Mastocytosis KIT Dasatinib

MPN CSF3R Ruxolitinib

AML, MDS, MDS/MPN Splice gene H3B-8800

AML KM2TA-PTD DOT1L inhibitor

AML, MDS MEK Trametinib

Cohesin complex gene

Poly ADP ribose polymerase inhibitor

Ph-like ALL ABL1-class fusions Dasatinib

JAK-STAT pathways Ruxolitinib

FLT3 FLT3 inhibitor

NTRK3 Crizotinib

N Engl J Med 2016;374:2209-2211.

1540 patients in three prospective trials Driver mutations in 111 cancer genes + Cytogenetic data + Clinical data

GERMLINE PREDISPOSITION

Blood 2016;127:2391-405.

Cancer Cell 2015;27:658-70.

Germline and somatic mutations ofthree families with history of MDSand leukemia

BiallelicAutosomal dominantLong latency (median, 62 years-old)Leukopenia Hypocellular BM normal karyotype

Germline and somatic DDX41 mutations in hematological malignancies.

Int J Hematol 2017;106:163-174.

CaucasianAsian

Leukemia 2017;31:1020-1022.

The patient and the donor had an identical DDX41 germlinemutation, while the patient had an additional DDX41 somaticmutation at a higher allele frequency at the time of MDS diagnosiscompared with that in the healthy donor.

49/M

MDS-EB-2

Allogeneic BMT from his HLA-identical sibling

7 months later,MDS-EB-2 relapseComplete donor chimerism

Development into AML Donor cell leukemia

Case no.

Sex Age Diagnosis Germline?VAF 40-60%

SomaticVAF <40%

Karyotype

1 M 76 AML, relapse p.A500fs (-) 45,X,-Y[2]/46,XY[28]

2 F 59 AML, relapse p.E3K (-) 46,XX[20]

3 M 57 AML p.Y33C (-) 46,XY[20]

4 F 66 AML, relapse p.D139G (-) 46,XX[20]

5 M 20 APL, relapse p.K187R (-) 46,Y,t(X;1)(p10;p10),t(15;17)(q24;q21)[17]/46,XY[3]

6 F 47 AML, refractory (-) p.D336E 46,XX,t(3;13)(q27;q14)[8]/46,XX[9])

7 F 62 AML, refractory (-) p.R525H 46,XX[8]//46,XY[32]

8 M 79 AML p.A488T (-) 46,XY,add(2)(p13),der(2)add(2)(p13)add(2)(q37)[11]/46,idem,inv(7)(q22q36)[10]/46,XY[4]

Summary of AML cases with DDX41 mutations in Asan Medical Center

Jan. 2018 ~ Dec. 2018N = 115Frequency: 7.0% (8/115)No patients with biallelic variants

Case no.

Sex Age Diagnosis Germline?VAF 40-60%

SomaticVAF <40%

Karyotype

1 M 76 MDS-MLD p.V152G p.T227M 46,XY[20]

2 M 58 MDS-EB-2 p.Y259C p.R525H 46,XY[20]

3 M 76 MDS-EB-2 p.V152G p.R525H 46,XY[20]

4 M 71 MDS-EB-2 p.Y259C p.R525H 46,XY,+1,der(1;7)(q10;p10)[5]/46,XY,dup(1)(q21q32[1]/46,XY[14]

5 F 77 MDS-EB-2 (-) p.A321S 46,XX[20]

6 M 60 MDS-EB-2 p.E7* p.G228C 46,XY[20]

7 M 78 MDS-EB-2 p.V152G p.T227M 45,X,-Y[17]/46,XY[3]

8 M 61 MDS-EB-1 p.Y259C p.T227M 46,XY[20]

9 M 71 MDS-EB-1 p.Y259C p.R525H 46,XY,del(7)(q22q31)[16]/46,XY[14]

10 M 64 MDS-EB-1 p.Y259C p.R525H 46,XY[10]

11 M 79 MDS-EB-1 p.L328R p.G530S 46,XY[20]

12 M 62 MDS-MLD p.V152G p.T227M 46,XY[20]

Jan. 2018 ~ Dec. 2018N = 68Frequency: 17.6% (12/68)

Summary of MDS cases with DDX41 mutations in Asan Medical Center

Recurrent germline variants: p.Y259C (0.1% in Korean) & p.V152G (0.045% in Korean)

Recurrent somatic variants: p.R525H & p.T227M

Normal karyotype, Advanced disease, Male predominance

MINIMAL RESIDUAL DISEASE

Blood Adv 2018;2:1356-1366.

AML (n=430)Targeted NGS (54 genes)

Persistence of mutations: 51.4%RAS pathway genes: cleared after induction

VAF during CR: 0.02 – 47%VAF >2.5% : often DTA mutations

N Engl J Med 2018;378:1189-1199.

The presence of residual disease that specifically included coexisting non-DTA mutations represented a predictor of impending relapse.

The detection of persistent non-DTA mutations at any allele frequency was strongly associated with an increased relapse risk, reduced RFS, and reduced OS.

Persistent non-DTA mutations during CR: 28.4% of combined cohort (430 patients)

N Engl J Med 2018;378:1189-1199.

SUMMARY AND CONCLUSION

• Revised WHO 2016 classification– New genetic markers More straightforward

diagnosis of hematologic malignancies – But, still diagnostic difficulty, equivocalness or overlap

• Evidence-based diagnosis– Risk stratification system incorporating mutation

information. ex, ELN, MIPSS70, Mayo alliance model etc.

– Candidate for target therapy. ex, IDH2 R172• Germline predisposition

– Clinically relevant to recognize hematologic malignancies with germline predisposition

• Minimal residual disease– Targeted NGS-based detection of MRD– Refining post-remission risk stratification

In conclusion, hematopathologists should integrate molecular genetic test results into the diagnosis of hematologic malignancies and translate them for the treating physicians in terms of precision medicine.

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