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945 Transcriptional and Genomic Characterization of Measurable Residual Disease (MRD) Cells in Acute Myeloid Leukemia (AML)

Program: Oral and Poster Abstracts
Type: Oral
Session: 617. Acute Myeloid Leukemias: Biomarkers, Molecular Markers and Minimal Residual Disease in Diagnosis and Prognosis: Minimal Residual Disease Detection in AML and Single Cell Investigations
Hematology Disease Topics & Pathways:
Research, clinical trials, Acute Myeloid Malignancies, AML, Translational Research, Clinical Research, genomics, Diseases, Myeloid Malignancies, Biological Processes, Minimal Residual Disease
Monday, December 12, 2022: 5:00 PM

Catia Patricia Simoes, MD1*, Sara Villar2*, Beñat Ariceta, BSc3*, Juan-José Garcés, PhD4, Leire Burgos5*, Diego Alignani, PhD5*, Sarvide Sarai6*, David Martinez-Cuadron7*, Juan Miguel Bergua Burgués8*, Susana Vives, PhD9*, Lorenzo Algarra10*, Mar Tormo11, Pilar Martinez Sanchez, MD12*, Josefina Serrano13*, Pilar Herrera14*, Fernando Ramos15*, Olga Salamero16*, Esperanza Lavilla17*, Cristina Gil18*, Jose Luiz Lopez Lorenzo, MD19*, María Belén Vidriales, MD20*, María Carmen Chillón Santos, PhD21*, Jorge Labrador22*, José F. Falantes23*, Maria Jose Sayas24*, Rosa Ayala25*, Joaquín Martínez-López, MD, PhD26*, Ana Alfonso-Pierola, MD, PhD27*, María José Calasanz, PhD5*, Felipe Prosper, MD28*, Jesús San-Miguel, MD, PhD29, Miguel A. Sanz, MD30, Pau Montesinos, PhD, MD31* and Bruno Paiva32*

1Clinica Universidad De Navarra, Centro De Investigacion Medica Aplicada (CIMA),, Pamplona, Spain
2Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada (CIMA), IDISNA, C-CUN, CIBER-ONC, Pamplona, Pamplona, Spain
3Hematological Diseases Laboratory, Clínica Universidad de Navarra, Centro de Investigación Médica Aplicada (CIMA), IDISNA, C-CUN, CIBER-ONC, Pamplona, Pamplona, Spain
4Centro de Investigación Médica Aplicada, University of Navarra, Clínica Universidad De Navarra - Centro De Investigación Médica Aplicada, Pamplona, Spain
5Centro de Investigación Médica Aplicada, University of Navarra, Pamplona, Spain
6Centro de Investigación Médica Aplicada, University of Navarra, Clínica Universidad de Navarra, Pamplona, Spain
7Hospital Universitario La Fe, Valencia, Valencia, Spain
8Hospital San Pedro de Alcántara, Cáceres, Spain
9ICO-Hospital Germans Trias i Pujol, Badalona, Spain
10Hospital Universitario General de Albacete, Albacete, Spain
11Hospital Clínico Universitario de Valencia, Valencia, Spain
12Hematology Department, Hospital Universitario 12 de Octubre, CNIO, Complutense University, Madrid, Spain
13IMIBIC, Cordoba, Spain
14Hospital Universitario Ramón y Cajal, Madrid, Spain
15Department of Hematology, Hospital Universitario De LeóN and Instituto De Biomedicina (IBIOMED), Un, Leon, Spain
16Hospital Universitario Vall d'Hebrón, Barcelona, Barcelona, Spain
17Hospital Universitario Lucus Augusti, Lugo, Spain
18Hematology Department, Hospital General Universitario de Alicante, Alicante, Spain
19Fundación Jiménez Díaz, Madrid, Madrid, Spain
20Instituto de Investigación Biomédica de Salamanca, Hospital Universitario de Salamanca, Salamanca, Spain
21Hematology Dept., Hospital Universitario de Salamanca, Spain, Salamanca, Spain
22Hospital Universitario de Burgos, Burgos, Burgos, Spain
23Hospital Universitario Virgen del Rocío, Sevilla, Spain
24Hospital Universitario Dr. Peset, Valencia, Spain
25Haematological Malignancies Clinical Research Unit, Hospital 12 de Octubre Universidad Complutense, CNIO, CIBERONC, Madrid, Spain
26Hematology Department, Hospital Universitario 12 de Octubre, Madrid, Spain
27Department of Oncology-Hematology, Centro de Investigación Médica Aplicada (CIMA), Navarra university-IDISNA. Centro de Investigación Biomédica en Red de Cáncer, CIBERONC. Clínica Universidad de Navarra, Pamplona, Spain
28Department of Oncology-Hematology, Centro de Investigación Médica Aplicada (CIMA), Navarra university-IDISNA. Centro de Investigación Biomédica en Red de Cáncer, CIBERONC. Clínica Universidad de Navarra, Pamplona, Navarra, Spain
29Clínica Universidad de Navarra, CIMA, CIBERONC, IDISNA, Pamplona, Spain
30Hematology Department, Hospital Universitari i Politècnic La Fe, Valencia, Spain
31Hospital Politecnico Universitario La Fe, Valencia, Spain, Spain
32Clinica Universidad de Navarra, Centro de Investigacion Medica Aplicada (CIMA), Instituto de Investigacion Sanitaria de Navarra (IDISNA), CIBER-ONC number CB16/12/00369, Pamplona, Spain

Background: Failure to achieve complete response (CR) and undetectable MRD is associated with inferior survival in AML. However, there is virtually no data on the molecular traits of treatment resistant cells to understand the mechanisms of MRD resistance. This would be particularly relevant in elderly AML, for which outcomes remain dismal despite increasing CR rates with novel combinations.

Aim: Uncover mechanisms of MRD resistance in elderly AML by comparing the transcriptional and genomic profile of patient-matched leukemic cells at diagnosis and after treatment with semi-intensive chemotherapy or hypomethylating agents.

Methods: 285 AML patients with a median age of 75 were included in the phase 3 PETHEMA-FLUGAZA trial and were randomized to receive induction and consolidation with fludarabine and cytarabine (FLUGA) vs 5-azacitidine (AZA). After consolidation, patients continued with the same treatment if MRD ≥ 0.01% or stopped if MRD < 0.01%. MRD was assessed using multidimensional flow cytometry, and highly-purified MRD cells were isolated according to patient-specific aberrant phenotypes using FACS. Leukemic blasts and T cells (germline control) were also sorted at diagnosis.

A 3’ end RNAseq method optimized for generating libraries from low-input starting material (MARSeq) was used. RNAseq was performed at diagnosis in 220 patients, and in paired diagnostic-MRD leukemic cells from 22 patients. Whole-exome sequencing (WES) was performed using molecular barcoding in paired diagnostic-MRD leukemic cells from 14 patients.

Results: After induction, 35 patients were in partial remission (PR), 51 attained CR/CRi but persistent MRD (CR/MRD+), and 13 achieved CR/CRi and undetectable MRD (CR/MRD-). There were no differences in median overall survival (OS) between patients in PR vs CR/MRD+ (median of 21 vs 20 months, p = .603), and both were numerically inferior to that observed in CR/MRD- patients (median of 27 months, p = .097).

There was only one gene (PIEZO2) differentially expressed between leukemic cells at diagnosis vs after treatment in patients achieving PR (n = 10). By contrast, there were 117 differentially expressed genes between leukemic cells at diagnosis vs after treatment in CR/MRD+ patients (n = 12). To confirm that gene deregulation was intrinsically associated with treatment resistance, the prognostic value of gene (over or under) expression in accordance with the differential observed between diagnostic and MRD leukemic cells, was subsequently analyzed in the 220 patients with RNAseq data at diagnosis. Over expression of 3 genes (IGFBP2, LINC00475 and PLEKHG3) and under expression of 12 genes (eg, CASC15, KDM7A and MEX3B) among the 117 identified above, was significantly associated with inferior OS. Interestingly, none of the genes was prognostic in the BeatAML cohort, suggesting that the transcriptome of MRD resistance may be specific of treatment.

A total of 6,054 mutations were detected after WES of matched leukemic cells at diagnosis and after treatment, in 14 patients achieving CR/MRD+. Amongst these, 4,708 (78%) were detected at both time points, 354 (6%) were present at diagnosis while absent in MRD blasts, and 992 (16%) emerged during MRD resistance (p ≤ 0.008). There were no differences between treatment arms in the number of shared and private mutations in diagnostic vs MRD cells. Amongst the 1,346 mutations that either became undetectable or present at MRD, recurrence (ie, ≥ 3 patients) was observed in 47 genes. Acquired mutations in AVP and UBXN11 were observed in MRD cells from 6 of the 14 patients.

Conclusions: This study showed that elderly AML patients treated with semi-intensive chemotherapy or hypomethylating agents, have dire survival regardless of achieving PR vs CR/MRD+. However, RNAseq analyses of resistant cells uncovered that whereas PR is characterized by primary resistance and transcriptionally stability from diagnosis, CR/MRD+ is associated with the emergence of molecular traits of acquired resistance. These findings could help explaining why additional treatment with the same schema is unable to overcome the poor prognosis of persistent MRD in elderly AML patients achieving CR/CRi. First-ever simultaneous RNAseq and WES of patient-matched diagnostic and MRD blasts, suggests that a few deregulated genes and recurrent mutations with limited or previously unknown role in AML pathobiology, are associated with MRD resistance and inferior OS.

Disclosures: Bergua Burgués: Incyte: Research Funding; Pfizer: Research Funding; Astellas: Research Funding; Celgene: Research Funding. Ramos: BMS: Consultancy, Honoraria, Membership on an entity's Board of Directors or advisory committees; Janssen: Honoraria; Novartis: Honoraria; Abbvie: Honoraria; Pfizer: Honoraria; Astellas: Consultancy, Honoraria; Sandoz: Honoraria; Jazz: Honoraria. San-Miguel: Abbvie, Amgen, BMS, Celgene, GSK, Haemalogix, Janssen-Cilag, Karyopharm, MSD, Novartis, Takeda, Regeneron, Roche, Sanofi, and SecuraBio: Consultancy, Other: Advisory Board. Montesinos: TAKEDA: Consultancy, Membership on an entity's Board of Directors or advisory committees, Other: Research grant, Research Funding; NERVIANO: Consultancy; BEIGENE: Consultancy; ASTELLAS: Consultancy, Speakers Bureau; JAZZPHARMA: Consultancy, Research Funding, Speakers Bureau; NOVARTIS: Consultancy, Research Funding, Speakers Bureau; OTSUKA: Consultancy; RYVU: Consultancy; KURA ONCOLOGY: Consultancy; ABBVIE: Consultancy, Research Funding, Speakers Bureau; BMS: Consultancy, Research Funding, Speakers Bureau; PFIZER: Consultancy, Research Funding, Speakers Bureau; INCYTE: Consultancy, Speakers Bureau; GILEAD: Consultancy, Speakers Bureau; MENARINI/STEMLINE: Consultancy, Research Funding. Paiva: Takeda: Honoraria, Research Funding; Adaptive: Honoraria; GSK: Honoraria, Research Funding; EngMab: Research Funding; Sanofi: Consultancy, Honoraria, Research Funding; Janssen: Consultancy, Honoraria; Bristol-Myers Squibb: Consultancy, Honoraria, Research Funding; Roche Glycart AG: Honoraria, Research Funding; Amgen: Honoraria; Gliead: Honoraria; Oncopeptides: Honoraria.

*signifies non-member of ASH