Targetable kinase gene fusions in high-risk B-ALL

A study from the Children's Oncology Group

Shalini C. Reshmi, Richard C. Harvey, Kathryn G. Roberts, Eileen Stonerock, Amy Smith, Heather Jenkins, I. Ming Chen, Marc Valentine, Yu Liu, Yongjin Li, Ying Shao, John Easton, Debbie Payne-Turner, Zhaohui Gu, Thai Hoa Tran, Jonathan V. Nguyen, Meenakshi Devidas, Yunfeng Dai, Nyla A. Heerema, Andrew J. Carroll & 15 others Elizabeth A. Raetz, Michael J Borowitz, Brent L. Wood, Anne L. Angiolillo, Michael J. Burke, Wanda L. Salzer, Patrick A. Zweidler-McKay, Karen R. Rabin, William L. Carroll, Jinghui Zhang, Mignon L. Loh, Charles G. Mullighan, Cheryl L. Willman, Julie M. Gastier-Foster, Stephen P. Hunger

Research output: Contribution to journalArticle

Abstract

Philadelphiachromosome-like(Ph-like) acutelymphoblasticleukemia(ALL) isahigh-risk subtype characterized by genomic alterations that activate cytokine receptor and kinase signaling. We examined the frequency and spectrum of targetable genetic lesions in a retrospective cohort of 1389 consecutively diagnosed patients with childhood B-lineage ALL with high-risk clinical features and/or elevated minimal residual diseaseatthe end of remission induction therapy. The Ph-like gene expression profile was identified in 341 of 1389 patients, 57 of whom were excluded from additional analyses because of the presence of BCR-ABL1 (n = 46) or ETV6-RUNX1 (n = 11). Among the remaining 284 patients (20.4%), overexpression and rearrangement of CRLF2 (IGH-CRLF2 or P2RY8-CRLF2) were identified in 124 (43.7%), with concomitant genomic alterations activating the JAK-STAT pathway (JAK1, JAK2, IL7R) identified in 63 patients (50.8% of those with CRLF2 rearrangement). Among the remaining patients, using reverse transcriptase polymerase chain reaction or transcriptome sequencing, we identified targetable ABL-class fusions (ABL1, ABL2, CSF1R, and PDGFRB) in 14.1%, EPOR rearrangements or JAK2 fusions in 8.8%, alterations activating other JAK-STAT signaling genes (IL7R, SH2B3, JAK1) in 6.3% or other kinases (FLT3, NTRK3, LYN) in 4.6%, and mutations involving the Ras pathway (KRAS, NRAS, NF1, PTPN11) in 6% of those with Ph-like ALL. We identified 8 new rearrangement partners for 4 kinase genes previously reported to be rearranged in Ph-like ALL. The current findings provide support for the precision-medicine testing and treatment approach for Ph-like ALL implemented in Children's Oncology Group ALL trials.

Original languageEnglish (US)
Pages (from-to)3352-3361
Number of pages10
JournalBlood
Volume129
Issue number25
DOIs
StatePublished - Jun 22 2017

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Oncology
Gene Fusion
Phosphotransferases
Fusion reactions
Genes
Platelet-Derived Growth Factor beta Receptor
Cytokine Receptors
Transcriptome
Polymerase chain reaction
RNA-Directed DNA Polymerase
Gene expression
Medicine
Remission Induction
Precision Medicine
Reverse Transcriptase Polymerase Chain Reaction
Testing
Mutation
Therapeutics

ASJC Scopus subject areas

  • Immunology
  • Biochemistry
  • Hematology
  • Cell Biology

Cite this

Reshmi, S. C., Harvey, R. C., Roberts, K. G., Stonerock, E., Smith, A., Jenkins, H., ... Hunger, S. P. (2017). Targetable kinase gene fusions in high-risk B-ALL: A study from the Children's Oncology Group. Blood, 129(25), 3352-3361. https://doi.org/10.1182/blood-2016-12-758979

Targetable kinase gene fusions in high-risk B-ALL : A study from the Children's Oncology Group. / Reshmi, Shalini C.; Harvey, Richard C.; Roberts, Kathryn G.; Stonerock, Eileen; Smith, Amy; Jenkins, Heather; Chen, I. Ming; Valentine, Marc; Liu, Yu; Li, Yongjin; Shao, Ying; Easton, John; Payne-Turner, Debbie; Gu, Zhaohui; Tran, Thai Hoa; Nguyen, Jonathan V.; Devidas, Meenakshi; Dai, Yunfeng; Heerema, Nyla A.; Carroll, Andrew J.; Raetz, Elizabeth A.; Borowitz, Michael J; Wood, Brent L.; Angiolillo, Anne L.; Burke, Michael J.; Salzer, Wanda L.; Zweidler-McKay, Patrick A.; Rabin, Karen R.; Carroll, William L.; Zhang, Jinghui; Loh, Mignon L.; Mullighan, Charles G.; Willman, Cheryl L.; Gastier-Foster, Julie M.; Hunger, Stephen P.

In: Blood, Vol. 129, No. 25, 22.06.2017, p. 3352-3361.

Research output: Contribution to journalArticle

Reshmi, SC, Harvey, RC, Roberts, KG, Stonerock, E, Smith, A, Jenkins, H, Chen, IM, Valentine, M, Liu, Y, Li, Y, Shao, Y, Easton, J, Payne-Turner, D, Gu, Z, Tran, TH, Nguyen, JV, Devidas, M, Dai, Y, Heerema, NA, Carroll, AJ, Raetz, EA, Borowitz, MJ, Wood, BL, Angiolillo, AL, Burke, MJ, Salzer, WL, Zweidler-McKay, PA, Rabin, KR, Carroll, WL, Zhang, J, Loh, ML, Mullighan, CG, Willman, CL, Gastier-Foster, JM & Hunger, SP 2017, 'Targetable kinase gene fusions in high-risk B-ALL: A study from the Children's Oncology Group', Blood, vol. 129, no. 25, pp. 3352-3361. https://doi.org/10.1182/blood-2016-12-758979
Reshmi SC, Harvey RC, Roberts KG, Stonerock E, Smith A, Jenkins H et al. Targetable kinase gene fusions in high-risk B-ALL: A study from the Children's Oncology Group. Blood. 2017 Jun 22;129(25):3352-3361. https://doi.org/10.1182/blood-2016-12-758979
Reshmi, Shalini C. ; Harvey, Richard C. ; Roberts, Kathryn G. ; Stonerock, Eileen ; Smith, Amy ; Jenkins, Heather ; Chen, I. Ming ; Valentine, Marc ; Liu, Yu ; Li, Yongjin ; Shao, Ying ; Easton, John ; Payne-Turner, Debbie ; Gu, Zhaohui ; Tran, Thai Hoa ; Nguyen, Jonathan V. ; Devidas, Meenakshi ; Dai, Yunfeng ; Heerema, Nyla A. ; Carroll, Andrew J. ; Raetz, Elizabeth A. ; Borowitz, Michael J ; Wood, Brent L. ; Angiolillo, Anne L. ; Burke, Michael J. ; Salzer, Wanda L. ; Zweidler-McKay, Patrick A. ; Rabin, Karen R. ; Carroll, William L. ; Zhang, Jinghui ; Loh, Mignon L. ; Mullighan, Charles G. ; Willman, Cheryl L. ; Gastier-Foster, Julie M. ; Hunger, Stephen P. / Targetable kinase gene fusions in high-risk B-ALL : A study from the Children's Oncology Group. In: Blood. 2017 ; Vol. 129, No. 25. pp. 3352-3361.
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abstract = "Philadelphiachromosome-like(Ph-like) acutelymphoblasticleukemia(ALL) isahigh-risk subtype characterized by genomic alterations that activate cytokine receptor and kinase signaling. We examined the frequency and spectrum of targetable genetic lesions in a retrospective cohort of 1389 consecutively diagnosed patients with childhood B-lineage ALL with high-risk clinical features and/or elevated minimal residual diseaseatthe end of remission induction therapy. The Ph-like gene expression profile was identified in 341 of 1389 patients, 57 of whom were excluded from additional analyses because of the presence of BCR-ABL1 (n = 46) or ETV6-RUNX1 (n = 11). Among the remaining 284 patients (20.4{\%}), overexpression and rearrangement of CRLF2 (IGH-CRLF2 or P2RY8-CRLF2) were identified in 124 (43.7{\%}), with concomitant genomic alterations activating the JAK-STAT pathway (JAK1, JAK2, IL7R) identified in 63 patients (50.8{\%} of those with CRLF2 rearrangement). Among the remaining patients, using reverse transcriptase polymerase chain reaction or transcriptome sequencing, we identified targetable ABL-class fusions (ABL1, ABL2, CSF1R, and PDGFRB) in 14.1{\%}, EPOR rearrangements or JAK2 fusions in 8.8{\%}, alterations activating other JAK-STAT signaling genes (IL7R, SH2B3, JAK1) in 6.3{\%} or other kinases (FLT3, NTRK3, LYN) in 4.6{\%}, and mutations involving the Ras pathway (KRAS, NRAS, NF1, PTPN11) in 6{\%} of those with Ph-like ALL. We identified 8 new rearrangement partners for 4 kinase genes previously reported to be rearranged in Ph-like ALL. The current findings provide support for the precision-medicine testing and treatment approach for Ph-like ALL implemented in Children's Oncology Group ALL trials.",
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T1 - Targetable kinase gene fusions in high-risk B-ALL

T2 - A study from the Children's Oncology Group

AU - Reshmi, Shalini C.

AU - Harvey, Richard C.

AU - Roberts, Kathryn G.

AU - Stonerock, Eileen

AU - Smith, Amy

AU - Jenkins, Heather

AU - Chen, I. Ming

AU - Valentine, Marc

AU - Liu, Yu

AU - Li, Yongjin

AU - Shao, Ying

AU - Easton, John

AU - Payne-Turner, Debbie

AU - Gu, Zhaohui

AU - Tran, Thai Hoa

AU - Nguyen, Jonathan V.

AU - Devidas, Meenakshi

AU - Dai, Yunfeng

AU - Heerema, Nyla A.

AU - Carroll, Andrew J.

AU - Raetz, Elizabeth A.

AU - Borowitz, Michael J

AU - Wood, Brent L.

AU - Angiolillo, Anne L.

AU - Burke, Michael J.

AU - Salzer, Wanda L.

AU - Zweidler-McKay, Patrick A.

AU - Rabin, Karen R.

AU - Carroll, William L.

AU - Zhang, Jinghui

AU - Loh, Mignon L.

AU - Mullighan, Charles G.

AU - Willman, Cheryl L.

AU - Gastier-Foster, Julie M.

AU - Hunger, Stephen P.

PY - 2017/6/22

Y1 - 2017/6/22

N2 - Philadelphiachromosome-like(Ph-like) acutelymphoblasticleukemia(ALL) isahigh-risk subtype characterized by genomic alterations that activate cytokine receptor and kinase signaling. We examined the frequency and spectrum of targetable genetic lesions in a retrospective cohort of 1389 consecutively diagnosed patients with childhood B-lineage ALL with high-risk clinical features and/or elevated minimal residual diseaseatthe end of remission induction therapy. The Ph-like gene expression profile was identified in 341 of 1389 patients, 57 of whom were excluded from additional analyses because of the presence of BCR-ABL1 (n = 46) or ETV6-RUNX1 (n = 11). Among the remaining 284 patients (20.4%), overexpression and rearrangement of CRLF2 (IGH-CRLF2 or P2RY8-CRLF2) were identified in 124 (43.7%), with concomitant genomic alterations activating the JAK-STAT pathway (JAK1, JAK2, IL7R) identified in 63 patients (50.8% of those with CRLF2 rearrangement). Among the remaining patients, using reverse transcriptase polymerase chain reaction or transcriptome sequencing, we identified targetable ABL-class fusions (ABL1, ABL2, CSF1R, and PDGFRB) in 14.1%, EPOR rearrangements or JAK2 fusions in 8.8%, alterations activating other JAK-STAT signaling genes (IL7R, SH2B3, JAK1) in 6.3% or other kinases (FLT3, NTRK3, LYN) in 4.6%, and mutations involving the Ras pathway (KRAS, NRAS, NF1, PTPN11) in 6% of those with Ph-like ALL. We identified 8 new rearrangement partners for 4 kinase genes previously reported to be rearranged in Ph-like ALL. The current findings provide support for the precision-medicine testing and treatment approach for Ph-like ALL implemented in Children's Oncology Group ALL trials.

AB - Philadelphiachromosome-like(Ph-like) acutelymphoblasticleukemia(ALL) isahigh-risk subtype characterized by genomic alterations that activate cytokine receptor and kinase signaling. We examined the frequency and spectrum of targetable genetic lesions in a retrospective cohort of 1389 consecutively diagnosed patients with childhood B-lineage ALL with high-risk clinical features and/or elevated minimal residual diseaseatthe end of remission induction therapy. The Ph-like gene expression profile was identified in 341 of 1389 patients, 57 of whom were excluded from additional analyses because of the presence of BCR-ABL1 (n = 46) or ETV6-RUNX1 (n = 11). Among the remaining 284 patients (20.4%), overexpression and rearrangement of CRLF2 (IGH-CRLF2 or P2RY8-CRLF2) were identified in 124 (43.7%), with concomitant genomic alterations activating the JAK-STAT pathway (JAK1, JAK2, IL7R) identified in 63 patients (50.8% of those with CRLF2 rearrangement). Among the remaining patients, using reverse transcriptase polymerase chain reaction or transcriptome sequencing, we identified targetable ABL-class fusions (ABL1, ABL2, CSF1R, and PDGFRB) in 14.1%, EPOR rearrangements or JAK2 fusions in 8.8%, alterations activating other JAK-STAT signaling genes (IL7R, SH2B3, JAK1) in 6.3% or other kinases (FLT3, NTRK3, LYN) in 4.6%, and mutations involving the Ras pathway (KRAS, NRAS, NF1, PTPN11) in 6% of those with Ph-like ALL. We identified 8 new rearrangement partners for 4 kinase genes previously reported to be rearranged in Ph-like ALL. The current findings provide support for the precision-medicine testing and treatment approach for Ph-like ALL implemented in Children's Oncology Group ALL trials.

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