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LBA-4 Integrated Genomic Analysis Identifies UBTF Tandem Duplications As a Subtype-Defining Lesion in Pediatric Acute Myeloid Leukemia

Program: General Sessions
Session: Late-Breaking Abstracts Session
Hematology Disease Topics & Pathways:
AML, Acute Myeloid Malignancies, Genomics, Epidemiology, Bioinformatics, Health Outcomes Research, Clinical Research, Diseases, Pediatric, Computational Biology, Biological Processes, Myeloid Malignancies, Genomic Profiling, Pathogenesis, Technology and Procedures, Study Population
Tuesday, December 14, 2021, 9:00 AM-10:30 AM

Masayuki Umeda, MD1*, Jing Ma, PhD1*, Benjamin J. Huang, MD2*, Kohei Hagiwara, MD3*, Tamara Westover, BS1*, Sherif Abdelhamed, PhD1, Juan Martin Barajas, PhD1, Melvin Edward Thomas III, PhD1*, Michael P Walsh, PhD1*, Guangchun Song1*, Liqing Tian, Ph.D3*, Yanling Liu, PhD3*, Xiaolong Chen, PhD3*, Pandurang Kolekar, Ph.D3*, Quang Tran, PhD3*, Scott Foy, PhD3*, Jamie L. Maciaszek, PhD1*, Andrew B Kleist, MD, PhD4*, Amanda R. Leonti, MS5*, Bensheng Ju, PhD3*, John Easton, PhD3*, Huiyun Wu, PhD6*, Virginia Valentine7*, Marc Valentine, BA7*, Yen-Chun Liu1*, Rhonda E. Ries, MA5*, Jenny L. Smith, MSc, MEd5*, Evan Parganas1*, Ilaria Iacobucci, PhD1, Ryan Hiltenbrand, MS1*, Jonathan Miller, MD, PhD8, Jason Myers9*, Evadnie Rampersaud, PhD9*, Delaram Rahbarinia, MSc3*, Michael Rusch, BS3*, Gang Wu, PhD9*, Hiroto Inaba, MD, PhD8, Yi-Cheng Wang, MS10*, Todd A. Alonzo, PhD11*, James R. Downing, MD1, Charles G. Mullighan, MBBS, MD1, Stanley B Pounds, PhD6*, M. Madan Babu, PhD12*, Jinghui Zhang, PhD3*, Jeffrey E. Rubnitz, MD8, Soheil Meshinchi, M.D., Ph.D.5, Xiaotu Ma, PhD3* and Jeffery M. Klco, MD, PhD1

1Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
2UCSF, San Francisco, CA
3Department of Computational Biology, St. Jude Children's Research Hospital, Memphis, TN
4Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI
5Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
6Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN
7Cytogenetics, St. Jude Children's Research Hospital, Memphis, TN
8Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
9Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN
10Children's Oncology Group, Monrovia, CA
11Department of Preventive Medicine, University of Southern California, Monrovia, CA
12Department of Structural Biology and the Center for Data Driven Discovery, St. Jude Children’s Research Hospital, Memphis, TN

Children with acute myeloid leukemia (AML) have a dismal prognosis due to a high relapse rate; however, the molecular basis leading to relapsed pediatric AML has not yet been fully characterized. To define the spectrum of alterations common at relapse, we performed integrated profiling of 136 relapsed pediatric AML cases with RNA sequencing (RNA-seq), whole-genome sequencing, and target-capture sequencing. In addition to well-characterized fusion oncoproteins, such as those involving KMT2A (n=36, 26.5%) or NUP98 (n=18, 13.2%), we also identified somatic mutations in UBTF (upstream binding transcription factor) in 12 of 136 cases (8.8%) of this relapsed cohort.

Somatic alterations of the UBTF gene, which encodes a nucleolar protein that is a component of the RNA Pol I pre-initiation complex to ribosomal DNA promoters, have rarely been observed in AML. In our cohort, all alterations can be described as heterozygous in-frame exon 13 tandem duplications (UBTF-TD), either at the 3' end of exon 13 of UBTF or of the entire exon 13 (Fig. A). As we noticed limited detection in our pipeline as a result of complex secondary indels alongside the duplications, we established a soft-clipped read-based screening method to detect UBTF-TD more efficiently. Applying the screening to RNA-seq data of 417 additional pediatric AMLs from previous studies and our clinical service, we identified 15 additional UBTF-TDs, many of which have not been previously reported. At the amino acid level, UBTF-TDs caused amino acid insertions of variable sizes (15-181 amino acids), duplicating a portion of high mobility group domain 4 (HMG4), which includes short leucine-rich sequences.

UBTF-TD AMLs commonly occurred in early adolescence (median age: 12.6, range: 2.4-19.6), and 19 of the total 27 cases had either normal karyotype (n=12) or trisomy 8 (n=7). UBTF-TD is mutually exclusive from other recurrent fusion oncoproteins, such as NUP98 and KMT2A rearrangements (Fig. B), but frequently occurred with FLT3-ITD (44.4%) or WT1 mutations (40.7%). The median variant allele fraction (VAF) of the UBTF-TD was 48.0% (range: 9.7-66.7%). In four cases with data at multiple disease time points, the identical UBTF-TDs were present at high allele fractions at all time points, suggesting that UBTF-TD is a clonal alteration. tSNE analysis of the transcriptome dataset showed that UBTF-TD AMLs share a similar expression pattern with NPM1 mutant and NUP98-NSD1 AML subtypes, including NKX2-3 and HOXB cluster genes (Fig. C). Altogether, these findings suggest that UBTF-TD is a unique subtype of pediatric AML.

To address the impact of UBTF-TD expression in primary hematopoietic cells, we introduced UBTF-TD and UBTF wildtype expression vectors into cord blood CD34+ cells via lentiviral transduction. UBTF-TD expression promotes colony-forming activity and cell growth, yielding cells with a persistent blast-like morphology (Fig. D). Further, transcriptional profiling of these cells demonstrated expression of HOXB genes and NKX2-3, similar to UBTF-TD AMLs in patients, indicating that UBTF-TD is sufficient to induce the leukemic phenotype.

To investigate the prevalence of UBTF-TDs in larger de novo AML cohorts, we applied the above UBTF-TD screening method to the available de novo AML cohorts of TCGA (n=151, adult), BeatAML (n=220, pediatric and adult), and AAML1031 (n=1035, pediatric). We identified UBTF-TDs in 4.3% (45/1035) of the pediatric AAML1031 cohort, while the alteration is less common (0.9%: 3/329, p=0.002) in the adult AML cohorts (Fig. E). In the AAML1031 cohort, UBTF-TDs remain mutually exclusive with known molecular subtypes of AML and commonly occur with FLT3-ITD (66.7%) and WT1 (40.0%) mutations and either normal karyotype or trisomy 8. The presence of UBTF-TDs in the AAML1031 cohort is associated with a poor outcome (Fig. F, median overall survival, 2.3 years) and MRD positivity; multivariate analysis revealed that UBTF-TD and WT1 are independent risk factors for overall survival within FLT3-ITD+ AMLs.

In conclusion, we demonstrate UBTF-TD defines a unique subtype of AMLs that previously lacked a clear oncogenic driver. While independent of subtype-defining oncogenic fusions, UBTF-TD AMLs are associated with FLT3-ITD and WT1 mutations, adolescent age, and poor outcomes. These alterations have been under-recognized by standard bioinformatic approaches yet will be critical for future risk-stratification of pediatric AML.

Disclosures: Iacobucci: Amgen: Honoraria; Mission Bio: Honoraria. Miller: Johnson & Johnson's Janssen: Current Employment. Mullighan: Pfizer: Research Funding; Illumina: Membership on an entity's Board of Directors or advisory committees; AbbVie: Research Funding; Amgen: Current equity holder in publicly-traded company.