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Genome-wide sequencing enables genetic distinction of MDS/MPN subtypes

Aug 18, 2020

Based on the World Health Organization (WHO), myelodysplastic/myeloproliferative neoplasms (MDS/MPN) are a group of myeloid neoplasms with clinical and pathological characteristics that overlap with MPN and MDS. The group includes the following conditions in adult patients: chronic myelomonocytic leukemia (CMML), atypical chronic myeloid leukemia (aCML), MDS/MPN-unclassifiable (MDS/MPN-U), and MDS/MPN with ring sideroblasts and thrombocytosis (MDS/MPN-RS-T). 1Despite the fact that a high proportion of MDS/MPN cases harbour myeloid-related somatic mutations, these are still not considered under the current diagnostic work-up. 2To further investigate the mutational landscape between the various MDS/MPN subtypes, and thus, to enable their diagnostic genetic distinction, Laura Palomo et al. published an extensive genome-wide sequencing study in Blood. 2We hereby provide a summary of the published study results.  

Study design

  • All patients underwent cytomorphological as well as conventional chromosome banding analysis (CBA)
  • Whole genome sequencing was performed in 349 patients and whole exome sequencing in the remaining 18 patients, and data were analysed with the Illumina’s BaseSpace Sequence Hub
  • Variant allele frequency estimations were used to estimate clonal and subclonal variant associations 

Patient characteristics

  • A total of 367 patients with MDS/MPN diagnosis based on the WHO classification 1with the following subtypes:
    • CMML (n = 119)
    • aCML (n = 71)
    • MDS/MPN-RS-T (n = 71)
    • MDS/MPN-U (n = 106)
  • Chromosomal abnormalities:
    • Abnormal karyotype as detected by CBA was observed in 29% of patients, with the most common chromosomal abnormalities being: +8 (12%), −7/del(7q) (5%), and −Y (3%)
    • They were not very common in patients with the MDS/MPN-RS-T and CMML subtypes, but were quite common in patients with the MDS/MPN-U and aCML subtypes ( Table 1)
  • The key patient baseline characteristics per disease subgroup are shown below in Table 1

Table 1 . Key patient baseline characteristics 2

aCML, atypical chronic myeloid leukemia; BM, bone marrow; CI, confidence interval; CMML, chronic myelomonocytic leukemia; Hb, hemoglobin; MDS/MPN, myelodysplastic/myeloproliferative neoplasms; MDS/MPN-RS-T, MDS/MPN with ring sideroblasts and thrombocytosis; MDS/MPN-U, MDS/MPN-unclassifiable; NR, not reached; OS, overall survival; WBC, white blood cells

Characteristic

CMML

(n = 119)

aCML

(n = 71)

MDS/MPN-RS-T

(n = 71)

MDS/MPN-U

(n = 106)

Male patients, %

66

70

38

63

Median age (range), years

77 (50–89)

74 (50–92)

74 (22–93)

75 (32–91)

BM blasts, %

< 5%

≥ 5%

 

68

32

 

76

24

 

96

4

 

72

28

Median BM ring sideroplasts (range)

0 (0–18)

0 (0–14)

66 (18–97)

0 (0–84)

Blood counts, median

Hb, g/dL

WBC count, × 10 9

Platelets, × 10 9

Neutrophils, × 10 9

Monocytes, × 10 9

Blasts, %

 

11.8

16.1

119.0

8.2

4.0

0.0

 

10.1

44.8

102.0

28.5

0.8

2.0

 

9.4

6.6

564.0

4.0

0.2

0.0

 

9.4

27.3

121.0

18.2

0.7

1.0

Karyotype, %

Available

Normal

Altered

Complex

 

100

83

17

0

 

97

58

42

4

 

97

90

10

0

 

96

53

47

12

Patient outcomes

Cases with follow-up, %

Median follow-up (range), months

Leukemic transformation, %

Median OS (95% CI), months

 

83

39 (2–112)

18

74 (48–101)

 

79

12 (3–98)

9

16 (12–20)

 

73

48 (2–163)

 9

NR

 

69

21 (2–182)

10

80 (NR)

Results

Thirty genes were found to be recurrently mutated in ≥ 3% of patients with all of them having been previously associated in myeloid neoplasms. The most frequently detected ones are shown below in Table 2 

Table 2 . Most common genes recurrently mutated in ≥ 3% of MDS/MPN patients 2

aCML, atypical chronic myeloid leukemia; CMML, chronic myelomonocytic leukemia; MDS/MPN, myelodysplastic/myeloproliferative neoplasms; MDS/MPN-RS-T, MDS/MPN with ring sideroblasts and thrombocytosis

Gene

Frequency, %

MDS/MPN subtype positively associated with the genetic mutation

ASXL1

51

aCML

TET2

45

CMML

SRSF2

35

CMML

SF3B1

24

MDS/MPN-RS-T

JAK2

19

MDS/MPN-RS-T

EZH2

17

RUNX1

17

SETBP1

15

aCML

NRAS

13

CBL

13

KRAS

10

CMML

  • The authors then assessed the existence of genotype-phenotype associations and potential correlations between MDS/MPN subtypes and molecular events. The strongest subtype-mutation associations identified are shown in Table 2
  • The MDS/MPN-U subtype was strongly associated with the less common TP53and U2AF1mutations
  • Epigenetic regulators and splicing factors had significantly higher variant allele fractions (VAFs) when compared with transcription factors or signalling genes, and were identified as primary driver mutations
    • The SF3B1mutation was detected as a primary hit in 21% of patients, and in 12% of cases was considered as a single founder event
    • Mutations in the epigenetic regulators DNMT3A, TET2, ASXL1(DTA genes) were identified in the ancestral clone in 67% of patients
  • The mutational profile and clonal architecture varied amongst MDS/MPN subtypes with specific mutation combinations and clonal architectures correlating to different MDS/MPN subtypes. All the correlations are shown below in Table 3. In general, the MDS/MPN-RS-T subtype was the least heterogenous molecular profile while the MDS/MPN-U subtype displayed the highest genetic heterogeneity  

Table 3 . Mutational and clonal profile of different MDS/MPN subtypes 2

aCML, atypical chronic myeloid leukemia; CMML, chronic myelomonocytic leukemia; MDS/MPN, myelodysplastic/myeloproliferative neoplasms; MDS/MPN-RS-T, MDS/MPN with ring sideroblasts and thrombocytosis; MDS/MPN-U, MDS/MPN-unclassifiable

MDS/MPN subtype

Mutational profile

Clonal architecture

CMML

(n = 119)

TET2(71%) mutations: biallelic TET2(46%) or TET2- SRSF2combination (45%)

Mainly in ancestral clone

SRSF2(55%)

Mainly as founder mutation

ASXL1(49%)

Mainly as founder mutation

CBL, NRAS, KRASor JAK2

Mainly in secondary clones

aCML

(n = 71)

ASXL1(92%)

Usually in ancestral clone

SETBP1(38%) equally codominant or secondary to ASXL1

No SETBP1and secondary ASXL1mutations detected in ancestral clones

CSF3Ror EZH2

In secondary clones

MDS/MPN-RS-T

(n = 71)

 

 

SF3B1(97%)

Mainly in ancestral clones

JAK2(37%)

Mainly in secondary clones

TET2(23%)

Either in ancestral or secondary clones

DNMT3A(18%)

Always as founder mutation

ASXL1(11%)

Either in ancestral or secondary clones

MDS/MPN-U

(n = 106)

TP53(13%)

  • The authors further performed a principal component analysis to further identify prognostic mutation combinations that could help with the differential diagnosis of the various MDS/MPN subtypes. The results of this analysis showed that
    • CMML was significantly represented by the TET2mutation combination
    • aCML was significantly represented by combinations between ASXL1, EZH2,and SETBP1
    • SRSF2mutations were linked to CMML when combined with TET2mutations, but with aCML when found together with SETBP1mutations
    • RUNX1mutations were linked to CMML when combined with SRSF2, but with aCML when co-mutated with EZH2
    • MDS/MPN-RS-T was significantly represented by SF3B1together with JAK2or DNMT3Amutation combinations
  • 74% of patients with previously diagnosed MDS/MPN-U could be re-classified based on their mutational profile:
    • The ’CMML-like’ (17%), ‘aCML-like’ (33%), or ‘MDS/MPN-RS-T-like’ (11%) had mutations and outcomes similar to the respective subtype they resembled
    • There were two additional categories, the ‘TP53’ subtype in 13% of the patients harbouring TP53mutations which correlated with a bad outcome, and the ‘Other’ subtype (26%) which could not be further characterized
  • The presence of cytogenetic abnormalities was significantly linked to a lower overall survival in all MDS/MPN subtypes, except for patients with aCML
    • ASXL1was significantly and consistently linked to unfavourable patient outcomes for all MDS/MPN subtypes except for aCML 

Conclusion

The results of this study provide insights and suggest the use of molecular markers for the potential differential diagnosis of MDS/MPN subtypes. For all subtypes, specific genetic clusters were identified that can help in their clinical identification. Additionally, almost 75% of the clinically highly heterogenous MDS/MPN-U subtype could be associated with other MDS/MPN subtypes or a prognostically adverse ’TP53’ subtype based on their molecular signature. Despite the lack of paired germline controls in this study, the results did show that different genetic mutations could be used to characterize most of the MDS/MPN subtypes. Furthermore, co-occurring additional mutations were associated with different outcomes.  These results pave the way for the consideration of the mutational profiles in the current clinical work-up of patients with MDS/MPN.

  1. Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood.2016;127(20):2391-405. DOI: 10.1182/blood-2016-03-643544
  2. Palomo L, Meggendorfer M, Hutter S, et al. Molecular landscape and clonal architecture of adult myelodysplastic/myeloproliferative neoplasms Blood. 2020. DOI: 10.1182/blood.2019004229