Program: Oral and Poster Abstracts
Type: Oral
Session: 618. Acute Lymphoblastic Leukemia: Biology, Cytogenetics and Molecular Markers in Diagnosis and Prognosis: New Genomic Discoveries in Acute Lymphoblastic Leukemia
We identified 4657 non-synonymous clonal and subclonal somatic mutations (3926 single nucleotide variants (SNV) and 731 insertion-deletion mutations; indels) in 3030 genes, with a mean of 17.6 per case (range 1-50). 176 potential driver genes were identified statistical analysis or by known pathogenic role in cancer. These included NOTCH1 (n=194, 73%), FBXW7 (n=64, 24%), PHF6 (n=50, 19%), PTEN (n=37, 14%), USP7 (n=32, 12%), DNM2 (n=29, 11%) and BCL11B (n=27, 10%). New mutations in T-ALL included CCND3 (n=15, 6%), MYB (n=13, 5%), CTCF (n=13, 5%), MED12 (n=7, 3%), USP9X (n=7, 3%), SMARCA4 (n=7, 3%) and CREBBP (n=6, 2%). In addition to MYB amplification, we identified missense mutations and in-frame protein insertions at the N-terminus of MYB, with a hotspot at codon 14 in a region of six acidic residues in an otherwise hydrophilic N-terminal tail. These mutations resulted in a disordered region that is predicted to affect nuclear localization. The MYB mutations detected were enriched in non-ETP cases (n=13; 8 non-ETP, 1 near-ETP, 4 unknown). Other genes enriched in non-ETP cases included RPL10, CNOT3, MYCN and DDX3X. MED12 mutations were more common in ETP ALL.
Sub-clonal mutations (mutant allele fraction of less than 30%) were identified in 111 of 176 driver genes in 198 (75%) cases including NOTCH1 (n=94), FBXW7 (n=29) and PTEN (n=17) indicating that sub-clonal evolution is a hallmark of T-ALL. In addition, multiple mutations in individual genes were commonly observed in single cases. For example, up to 3 different somatic NOTCH1 mutations were detected in each of 9 patients, with 2 different NOTCH1 mutations in 49 cases.
Integration of sequence mutations with copy number aberration data showed the following pathways to be most frequently mutated: cell cycle/tumor suppression (N=225; CDKN2A/B (n=206), CDKN1B (n=35), RB1 (n=28)); NOTCH1/FBXW7 (n=212), PI3K-AKT (n=130), JAK-STAT (n=99) and Ras (n=51). Mutations in the PI3K-AKT, JAK-STAT and Ras signaling pathways were mutually exclusive. We identified a high frequency of mutations in transcriptional regulators in 222 cases, including 108 cases with mutations in a core regulatory complex comprising TAL1 (n=51), MYB (n=45) RUNX1 (n=18) and GATA3 (n=13). In 90 of these 108 cases (83%), only a single mutation was present in any of the four genes, consistent with a central role of this complex in leukemogenesis. Epigenetic alterations were identified in 178 cases, including PHF6 (n=63), SMARCA4 (n=23), KDM6A (n=22) and EZH2 (n=18), and new deletions and mutations in KMT2A (MLL; n=11).
Interim analysis of transcriptome sequencing data of 126 T-ALL cases detected fusions in 61 (48%) samples, which could be separated into two categories. One weres in-frame fusions resulting in a chimeric protein. The most frequent included MLLT10 fusions (PICALM-MLLT10 (n=3), DDX3X-MLLT10 (n=2) and NAP1L1-MLLT10 (n=1)), KMT2A fusions (KMT2A-MLLT1 (n=4), MLLT6-KMT2A (n=1) and MKT2A-MLLT4 (n=1)), as well as internal tandem duplication mutations involving FLT3 (n=6; 3 ETP, 1 near-ETP, 1 non-ETP, 1 unknown) and NOTCH1 (n=2). We also identified novel fusions including ETV6-CTNNB1 and STMN1-SPI1 (n=1 each). The other category contains rearrangement-driven aberrant expression, including rearrangements in TLX1 (n=11), TLX3 (n=4), TAL1 (n=2), and TAL2 (n=3). Moreover, we found a novel TAL2 transcript in all the 3 cases with TAL2 rearrangement, hijacking a new exon 6kb upstream of the canonical TAL2 transcription start site and extending approximate 3.5kb downstream.
These findings provide the first comprehensive landscape of genomic alterations in T-ALL and have provided new insights into the genes and pathways mutated in this disease, their interaction, and the nature of clonal heterogeneity in T-ALL.
Disclosures: Hunger: Spectrum Pharmaceuticals: Consultancy ; Jazz Pharmaceuticals: Consultancy ; Sigma Tau: Consultancy ; Merck: Equity Ownership . Mullighan: Cancer Science Institute: Membership on an entity’s Board of Directors or advisory committees ; Amgen: Honoraria , Speakers Bureau ; Incyte: Consultancy , Honoraria ; Loxo Oncology: Research Funding .
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