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4302 The XPO1-FOXC1-HOX Functional Axis Opens New Therapeutic Avenues to Treat DEK-NUP214 AML Patients

Program: Oral and Poster Abstracts
Session: 617. Acute Myeloid Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Poster III
Hematology Disease Topics & Pathways:
Research, Fundamental Science, Biological therapies, Acute Myeloid Malignancies, AML, Translational Research, genomics, Diseases, Myeloid Malignancies, Biological Processes, molecular biology
Monday, December 11, 2023, 6:00 PM-8:00 PM

Fadimana Kaya, MSc, BSc1*, Findlay Bewicke-Copley, PhD, MSc, BSc2*, Pedro Casado Izquierdo, PhD3*, Jiexin Zheng, MBBS, MA, MRCP4*, Juho Jalmari Miettinen, PhD5*, Naeem Khan, PhD6*, Szilvia Krizsán7*, Joseph J Saad, MSc8*, Vincent-Philippe Lavallée9*, Alexis Nolin-Lapalme10*, Josée Hébert, MD11*, Janet Matthews12*, Marianne Grantham13*, Doriana Di Bella14*, Krister Wennerberg, PhD15*, Alun Parsons16*, John G. Gribben, MD, DSc17, James D. Cavenagh, MD18, Sylvie D Freeman19, Csaba Bödör, PhD7*, Guy Sauvageau, MD/PhD20, Caroline A. Heckman, PhD21, Jun Wang22*, Jean-Baptiste Cazier23*, David Taussig, PhD, MRCP, FRCPath24, Dominique Bonnet, PhD25, Pedro R Cutillas, PhD22, Kevin Rouault-Pierre, PhD26*, Jude Fitzgibbon, PhD27* and Ana Rio-Machin, PhD22*

1Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, ENG, United Kingdom
2Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
3Centre for Genomics and Computational Biology, Barts Cancer Institute, London, ENG, GBR
4Centre for Genomics and Computationa Biology, Barts Cancer Institute, London, GBR
5Institute for Molecular Medicine Finland (FIMM), Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
6Institute of Immunology and Immunotherapy, Birmingham, ENG, GBR
7HCEMM-SU Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
8Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
9Centre Hospitalier Universitaire Sainte-Justine Research Center, Montreal, QC, CAN
10Institute for Research in Immunology and Cancer, Montreal, Canada
11Institut de recherche en Immunologie et Cancer, Université de Montréal, Montreal, QC, Canada
13Barts Health NHS Trust, LONDON, GBR
14Barts Cancer Institute, Queen Mary University of London, London, GBR
15Biotech Research & Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
16HiLIFE – Helsinki Institute of Life Science, Institute for Molecular Medicine Finland – FIMM, Helsinki, Finland
17Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
18Department of Haematology, St. Bartholomew's Hospital, London, GBR
19University of Birmingham, Cheltenham, United Kingdom
20University of Montreal, Montreal, QC, CAN
21Institute for Molecular Medicine Finland, Institute For Molecular Medicine Finland FIMM, Helsinki, Finland
22Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
23Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
24The Royal Marsden Hospital and Institute of Cancer Research, London, United Kingdom
25The Francis Crick Institute, London, GBR
26Centre for Haemato-Oncology, Barts Cancer Institute, London, United Kingdom
27AstraZeneca, Waltham, MA

Introduction: t(6;9)(p23;q34.1)/DEK-NUP214 patients represent a discrete group of younger AML patients recognised as a separate disease entity in the World Health Organization classification of myeloid neoplasms. They typically display a dismal prognosis, higher relapse rate and a striking co-occurrence with FLT3-ITD mutations in > 70% of cases. DEK is a nuclear factor that has been attributed multifunctional roles, including gene regulation, while its fusion partner, NUP214, plays a pivotal role in nuclear export by interacting with transport receptors such as XPO1. However, the precise mechanism by which DEK-NUP214 drives leukaemia remains unclear.

Aims: Application of a multi-omics profiling to understand the oncogenic mechanisms underlying DEK-NUP214 fusion protein and identify potential therapeutical vulnerabilities.

Methods: A comprehensive multi-omics screening (whole genome sequencing, targeted sequencing, transcriptomics, (phosphor)proteomics, mass cytometry (CyTOF) and in vitro drug screening) was conducted on 57 untreated primary AML samples from cytogenetically poor-risk AML, including four cases with t(6;9) translocation (complex karyotype (n=20), -7/del(7) (n=15), KMT2A rearrangements (not including t(9;11)) (n=12), t(6;9) (n=4) and other poor-risk karyotypes (inv(3), -5/del(5), t(3;12)/+8 or -17/del(17)) (n=6)). The t(6;9)/DEK-NUP214 cell line FKH-1, was utilised as a model for in vitro experiments and compared with other AML cell lines (OCI-AML3, KASUMI-1, THP-1, P31-FUJ, MV4-11 and K562). In vitro drug treatments were conducted in the cell lines and patient samples using Cell-Titer&Glo, and transcriptional changes were evaluated using qPCR and RNA-seq. To examine the function of selected target genes of DEK-NUP214, we used lentiviral shRNA system followed by cell cycle, apoptosis, differentiation, and cell proliferation assays.

Results: An integrative RNA-seq analysis of our cohort and a separate series of 691 AML cases that included three additional t(6;9) cases (Leucegene, https://leucegene.ca/) revealed 128 genes significantly upregulated and 74 downregulated in t(6;9) patients compared to other AML samples. The overexpressed genes included some known leukaemia mediators (FOXC1, HOXA and HOXB genes), the genes previously reported in t(6;9) patients (EYA3, SESN1 and PRDM2) and novel genes with roles in haematopoiesis or cancer cell survival that showed the most significant differences (NFIX and GGT5). The significant overexpression of these genes was also confirmed in the t(6;9) FKH-1 cell line. In vitro drug screening of 527 licenced or investigational drugs allowed us to identify the compounds that were most effective and selective for t(6;9) patients in comparison with other AML cytogenetic groups. The two XPO1 inhibitors (Selinexor and Eltanexor) included in our drug panel were within the four top-ranked compounds. Of note, qPCR and RNA-seq analyses in the cell lines and primary patient samples showed that inhibition of XPO1 resulted in significant downregulation of the expression of FOXC1, NFIX, EYA3, HOXA and HOXB genes, highlighting a functional axis linking these target genes, XPO1 and the fusion. In line with this finding, silencing of FOXC1 in the FKH-1 cells led to an increase in apoptosis, lower cell proliferation and reduced clonogenic capacity, accompanied by a concomitant downregulation of HOXA and HOXB genes. Collectively, these findings support a key role of FOXC1 in DEK-NUP214-driven AML.

Conclusion: This study offers valuable insights into the molecular and pathological mechanisms underlying t(6;9)-AML, revealing a functional interaction between DEK-NUP214, XPO1 and FOXC1, and providing evidence to consider XPO1 inhibition as a potential new avenue to treat these patients.

Disclosures: Zheng: Astellas: Honoraria. Hébert: BMS: Research Funding. Gribben: Janssen Pharmaceuticals, Inc: Consultancy, Research Funding, Speakers Bureau; AstraZeneca: Consultancy, Research Funding; AbbVie: Consultancy, Speakers Bureau; Kite, A Gilead Company: Consultancy, Speakers Bureau; Novartis: Consultancy; Bristol Myers Squibb: Speakers Bureau. Freeman: BMS: Research Funding; JAZZ: Research Funding, Speakers Bureau; MPAACT: Membership on an entity's Board of Directors or advisory committees; NOVARTIS: Membership on an entity's Board of Directors or advisory committees, Speakers Bureau. Sauvageau: BMS: Research Funding; ExCellThera: Current Employment, Current equity holder in private company, Honoraria, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding. Heckman: Kronos Bio: Research Funding; Novartis: Research Funding; Zentalis Pharmaceuticals: Research Funding; Autolus: Consultancy; Oncopeptides: Research Funding; WNTResearch: Research Funding; Amgen: Honoraria. Taussig: Ellipses Pharma: Consultancy. Fitzgibbon: Astra Zeneca: Current Employment, Other: may own stock or stock options.

*signifies non-member of ASH