CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS E. Fabiani 1 , - - PowerPoint PPT Presentation

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clonal evolution in therapy related neoplasms
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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS E. Fabiani 1 , - - PowerPoint PPT Presentation

Nov 29, 2022 335 likes •534 views

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS E. Fabiani 1 , G. Falconi 1 , L. Fianchi 2 , M. Criscuolo 2 , T. O9one 1 , L. Cicconi 1 , S. Hohaus 2 , S.

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SLIDE 1
  • E. ¡Fabiani ¡1, ¡G. ¡Falconi ¡1, ¡L. ¡Fianchi2, ¡M. ¡Criscuolo2, ¡T. ¡O9one1, ¡L. ¡Cicconi1, ¡ ¡
  • S. ¡Hohaus2, ¡S. ¡Sica2, ¡M. ¡Postorino1, ¡A. ¡Neri3, ¡M. ¡LioneB3, ¡ ¡
  • G. ¡Leone2, ¡F. ¡Lo-­‑Coco1 ¡and ¡MT. ¡Voso1 ¡

1Department ¡of ¡Biomedicine ¡and ¡Preven3on, ¡Universita’ ¡Tor ¡Vergata, ¡ ¡Rome, ¡Italy, ¡

¡

2Department ¡of ¡Hematology, ¡Universita’ ¡CaBolica ¡Sacro ¡Cuore, ¡Rome, ¡Italy ¡

¡

3Department ¡of ¡Clinical ¡Sciences ¡and ¡Community ¡Health, ¡Università ¡degli ¡studi ¡di ¡Milano, ¡Italy ¡ ¡

CLONAL ¡EVOLUTION ¡IN ¡THERAPY-­‑RELATED ¡NEOPLASMS ¡

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Italian ¡Registry ¡on ¡Secondary ¡Leukemias. ¡Fianchi ¡et ¡al., ¡Am ¡J ¡Hematol ¡2015 ¡

Therapy-related myeloid neoplasms are characterized by high incidence of complex karyotypes, frequent abnormalities of chromosome 7 and/or 5 High prevalence of the t(4;11)(q21;q23) translocation have been commonly reported in t-ALL.

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Voso ¡et ¡al., ¡Leukemia ¡2013 ¡and ¡Fabiani ¡et ¡al., ¡Haematologica ¡2014. ¡ OK ¡et ¡al., ¡Leuk ¡Res ¡2015. ¡Muta3on ¡hotspots ¡of ¡53 ¡genes ¡

= ¡ ≠ ¡

TP53 ¡

Prevalence of Somatic Mutations in t-MN

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Patient Characteristics

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Mutational screening of common somatic mutations and other gene alterations in therapy-related leukemia patients Sanger Sequencing Next Generation Sequencing IDH1 R132 IDH2 R140/R172 DNMT3A R882 ASXL1 SF3B1 ex 13-16 SRSF2 P95 U2AF1 S34 SETBP1 SKI Domain N-RAS K-RAS Validation & quantification

  • f the mutated clone

TP53 Epigenetic enzymes Spliceosome machinery Pyrosequencing Q-RT-Polymerase chain reaction t(4;11)(q21;q23) KMT2A/AFF1

  • 1. Methods
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SLIDE 6

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Mutations identified in the t-MN sample were then tracked backwards in samples collected during follow-up of the primary tumor, using high sensitivity techniques High-throughput Next Generation Sequencing ² Specific homemade designed primers were linked to specific flags ² Average coverage was >120000x for all corresponding specific amplicon ² Variant allele frequencies in % (alternative allele count/total depth x100)

  • 2. Methods
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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

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IDH1 R132 IDH2 R172 IDH2 R140 DNMT3A R882 U2AF1 SF3B1 13-16 SRSF2 SETBP1 N-RAS K-RAS ASXL1

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Screening of genetic changes in therapy-related neoplasms ² We identified 8 mutations (IDH1 R132H, SRSF2 P95H, SF3B1 K700E, SETBP1 G870R, TP53 Y220C, ASXL1 Y591*, ASXL1 S689* and ASXL1 R693*) in 7 of 13 t-MN patients ² UPN 9 carried two mutations (IDH1 R132H and SRSF2 P95H) ² UPN 14, a t-ALL patient, was KMT2A-AFF1-positive

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Quantification of the identified variants at the time of t-MN diagnosis ² Pyrosequencing analyses, specifically designed to quantify the mutations confirmed the data obtained from Sanger sequencing in all cases. ² Mutations identified in epigenetic regulators, spliceosome enzymes and SETBP1 were detectable at a variant allele frequency (VAF) of 20 to 42% at the time of t-MN diagnosis ² TP53 mutation was detectable at a lower rate (6,75%) ¡ ¡ ² UPN9 carried two mutations (IDH1 R132H and SRSF2 P95H), at a similar VAF (38% and 35%, respectively) suggesting that the two mutations were present in the same leukemic clone. ² Quantitative evaluation of the KMT2A-AFF1 transcript in UPN 14 revealed strong positivity for the chimeric transcript at the time of t-ALL diagnosis (3500 copies /104 ABL)

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Disease markers and clonal evolution

Ultra-deep NGS reveals at least two different patterns of clonal evolution Somatic mutations characterizing the t-MN clone were not detectable at primary cancer diagnosis and appeared after cytotoxic treatment Somatic mutations were detectable at primary cancer diagnosis, prior to any cytotoxic treatment First ¡scenario ¡ Second ¡scenario ¡

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SLIDE 10
  • 1. ¡First ¡scenario ¡

Somatic mutations characterizing the t-MN clone were not detectable at primary cancer diagnosis and appeared after cytotoxic treatment

MICMA/PB-SCT RTX

Variant allele frequency (%)

AML-12 Trial 0.0 35.0 AML DG BC DG (53 mos) t-MN DG (83 mos) CTH + RT

D) UPN6: SF3B1 K700E

40 35 30 25 20 15 10 5 25 20 15 10 5

0.0

Variant allele frequency (%)

B-ALL DG GMALL 05/93 t-MN DG (32 mos) 0.0 20.0 CR (23 mos)

E) UPN13: SETBP1 G870R

25 20 15 10 5

F) UPN6: SF3B1 K700E G) UPN13: SETBP1 G870R

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Fabiani et al., submitted

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Somatic mutations characterizing the t-MN clone were not detectable at primary cancer diagnosis and appeared after cytotoxic treatment CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Fabiani et al., submitted

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NHL DG

A) UPN4: ASXL1 R693*

30.0 13.0 CHOP/MICMA/ HD-CTX MICMA/PB-SCT 0.0 0.0 0.0 0.0

35 30 25 20 15 10 5

Variant allele frequency (%)

(21 mos) (30 mos) (43 mos) t-MN DG (113 mos) (120 mos) Fludarabin CTX RTX RTX

  • 2. ¡First ¡scenario ¡
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SLIDE 12

Somatic mutations characterizing the t-MN clone were not detectable at primary cancer diagnosis and appeared after cytotoxic treatment CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Fabiani et al., submitted

B) UPN3: ASXL1 S689*

45 40 35 30 25 20 15 10 5

Variant allele frequency (%)

NHL DG 0.0 (3 mos) (9 mos) (14 mos) 0.0 0.0 0.0 CHOP R-MICMA PB-SCT (20 mos) (23 mos) (49 mos) (78 mos) t-MN DG (86 mos) 29.0 19.0 34.0 46.0 35.0 R-Vel-dex Lenalidomide

  • 3. ¡First ¡scenario ¡
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SLIDE 13

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Genomic alteration characterizing the t-ALL clone was not detectable at primary cancer diagnosis and appeared after cytotoxic treatment

Fabiani et al., submitted

APL DG CR (11 mos) CR (13 mos) CR (15 mos) t-ALL DG (18 mos) Allo-SCT (24 mos) (31 mos) 58 962 3522 4390

Copies/104 ABL

AIDA 2000 (induction, consolidation & manteinance) (21 mos) Clofarabine Endoxan

C) UPN14: KMT2A/AFF1

(20 mos) Vincristine Daunorubicin L-Asparaginase

5000 4000 3000 2000 1000

  • 4. ¡First ¡scenario ¡
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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

  • 1. Second scenario

Somatic mutations were detectable at primary cancer diagnosis, prior to any cytotoxic treatment

APL DG CR (14 mos) CR APL (20 mos) t-MN DG (30 mos)

Variant allele frequency (%)

AIDA 2000

A) UPN2: TP53 Y220C

7.0 6.0 5.0 4.0 3.0 2.0 1.0

6.00 2.03 2.01 0.10

Fabiani et al., submitted

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SLIDE 15

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS Somatic mutations were detectable at primary cancer diagnosis, prior to any cytotoxic treatment

Fabiani et al., submitted

Variant allele frequency (%)

45 40 35 30 25 20 15 10 5

0.3 7.0 40.0 42.0

B) UPN1: ASXL1 Y591*

NHL DG (31 mos) (36 mos) t-MN DG (83 mos) Pro MACE Cytabom/RT

  • 2. Second scenario
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SLIDE 16

Somatic mutations were detectable at primary cancer diagnosis, prior to any cytotoxic treatment CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

0.0 0.0 35.0 38.0 35.0

Variant allele frequency (%)

NHL DG Chlorambucil/Rituximab/RT Follow-up (1 mos) t-MN DG (100 mos)

IDH1 R132H SRSF2 P95H C) UPN9

40 35 30 25 20 15 10 5

Fabiani et al., submitted

  • 3. Second scenario
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SLIDE 17

Conclusions

CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

² Secondary leukemogenesis is a heterogeneous process ² Somatic mutations in critical genes may be induced by the cytotoxic treatment (4/13 of studied patients) ² The t(4;11)(q21;q23) translocation was induced by the cytotoxic treatment ² Somatic mutations in critical genes may precede and favor leukemic development (3/13 of studied patients)

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CLONAL EVOLUTION IN THERAPY-RELATED NEOPLASMS

Giulia Falconi Tiziana Ottone Laura Cicconi Massimiliano Postorino Maria Teresa Voso Francesco Lo Coco Marianna Criscuolo Luana Fianchi Stefan Hohaus Simona Sica Giuseppe Leone Marta Lionetti Antonino Neri