Identification and Characterization of Genetic Subtypes in High-Risk B-Precursor Acute Lymphoblastic Leukemia with Functional Analysis of Novel Genetic Lesions

  • Shih, Lee-Yung (PI)
  • Chen, Leslie Y. (CoPI)
  • Huang, Ying Jung (CoPI)
  • Kuo, Ming Chung (CoPI)

Project: National Science and Technology CouncilNational Science and Technology Council Academic Grants

Project Details

Abstract

Background: Acute lymphoblastic leukemia (ALL) is the most common cancer in children with steadily improved cure rate over time. However, adult ALL patients had a much inferior outcome compared with children. Over the past decade, there has been increasing evidence of better outcomes for young adults treated with pediatric regimens compared to adult regimens. Monitoring of minimal residual disease (MRD) is now widely applied in risk-adapted therapy and has been demonstrated as the most powerful prognostic indicator in childhood ALL in the major childhood ALL treatment groups in the United States and Europe. Up to now, there are no MRD-based protocols for adult ALL in Taiwan. To improve treatment outcome of young adult patients, we will use the pediatric MRD-directed TPOG-ALL 2013 protocol to treat young adults with ALL and then further apply to adults. In addition, a diverse array of genetic alterations were recently identified in childhood ALL by using genome-wide approaches, especially, the Ph-like subgroup which is defined as gene expression profile similar to Ph-positive ALL but BCR-ABL1 negative. Of critical importance, Ph-like ALL confers a very poor outcome and harbors many novel subtypes of genetic aberrations, most of which could serve as potential therapeutic targets. The clinical and prognostic relevance of these genetic aberrations in adult Ph-like ALL remains to be explored and thus more works are required for adult patients. In this study, we will apply various approaches for early identification of this high-risk group of ALL patients who might benefit from alternative therapy and/or potential targeted therapy. Aim: Our specific aims are: (1) to identify and characterize each genetic subtype of Ph-like ALL subgroup in adult B-ALL (older than 39 years) and high-risk pediatric/young adult B-ALL with high MRD levels; (2) to search novel fusion genes and novel gene mutations by high throughput technology in high-risk B-ALL patients who have no known fusion genes detected or no detectable target gene mutations; (3) to study the in vitro biological functions and drug responsiveness of new SH2B3 mutants, novel gene mutations and/or novel fusion gene(s) identified in this project; (4) to correlate the genetic alterations and their co-existing genetic lesions with clinical features and outcomes in high risk B-ALL. Materials and methods: We will use the low density microarray cards with 15 targeted genes to identify the Ph-like ALL in adults and in high-risk children/young adults based on the MRD levels during induction therapy according to TPOG-ALL 2013 protocol. For those high-risk B-ALL with CRLF2 over-expression, RT-PCR will be used to detect P2RY8-CRLF2 fusion and FISH will be used for the detection of IGH-CRLF2 translocation. For those without CRLF2 rearrangements, we will further use multiplex RT-PCR assays to detect recurrent known tyrosine kinase or cytokine receptor fusion genes, and next generation sequencing techniques to identify the gene mutations involved in JAK/STAT signaling. For those Ph-like ALL without detectable recurrent known kinase-activating lesions, we will further use whole transcriptome sequencing (RNAseq) to search novel fusion genes and use whole exome sequencing to identify potential novel gene mutations. The identified novel fusion genes or gene mutations and/or new SH2B3 mutants will be transformed into mouse cell lines for analysis of cell proliferation and survival, and phosphorylation of downstream signal molecules by Western blotting and/or phospho flow cytometry. Drug sensitivities of transformed cells will also be assessed using different inhibitors. Finally, we will correlate all the genetic alterations with clinico-hematologic features and treatment outcomes of the patients. Significance: Identification of high-risk Ph-like ALL subgroup and characterization of each genetic subtype of B-ALL in adults and high-risk children/young adults along with integration of specific targeted inhibitors in the future treatment will improve the treatment outcomes and increase the cure rate for high-risk B-ALL patients.

Project IDs

Project ID:PC10601-0359
External Project ID:MOST104-2314-B182-032-MY3
StatusFinished
Effective start/end date01/08/1731/07/18

Keywords

  • Minimal residual disease
  • Ph-like ALL
  • CRLF2 rearrangement
  • Kinase fusion gene

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