Prognostic impact of variant allele frequency in intensively treated patients with NPM1-mutated AML: a PETHEMA study
Abstract
NPM1-mutated acute myeloid leukemia (AML) is genetically well-defined, but clinical outcomes remain heterogeneous, suggesting that quantitative clonal features may refine current risk stratification. We analyzed 688 intensively treated NPM1-mutated AML integrating variant allele frequency (VAF), mutation order, and clonal architecture inferred by PyClone and ClonEvol. Co-mutations were present in 97% of patients (median = 3 per case), dominated by DNMT3A (49%), FLT3-ITD (46%), TET2 (22%), and IDH2 (20%). Prognostic modelling of NPM1 VAF identified an optimal cut-off of 31.44%, defining NPM1high and NPM1low groups. NPM1low correlated with splicing-related alterations and independently predicted inferior overall (HR = 1.46; p = 0.037) and relapse-free survival (HR = 1.40; p = 0.036). Gene-specific VAF analyses revealed divergent effects across partners, high DNMT3A, FLT3-OTHER, KRAS, and PTPN11 burdens were adverse, whereas high IDH2 VAF was protective. Combined models showed that patients with NPM1high and favorable co-mutation VAFs had the best outcomes, while dual unfavorable burdens conferred the poorest survival. Mutation ordering inferred from VAFs positioned NPM1 after epigenetic and splicing lesions but before signaling and transcription-factor mutations. Non-canonical orders, such as early FLT3-OTHER/TKD or WT1 prior to NPM1, significantly stratified outcomes. Clonal reconstruction revealed predominantly linear evolutionary trajectories (84.3%), with increased mutational burden and clonal diversity associating with inferior survival. Notably, intra-clonal co-localization of NPM1 with IDH1 or TET2 was associated with improved outcomes, whereas co-localization with WT1 predicted dismal prognosis. These results demonstrate that quantitative and structural dimensions of clonality refine the biological and prognostic landscape of NPM1-mutated AML beyond mutational status alone.
Article Details
Authors (48)
José Vicente Gil
Accredited Research Group on Hematology, Instituto de Investigación Sanitaria la Fe, 46026 Valencia, Spain, Valencia, Spain
Claudia Sargas
Rosa Ayala
HOSPITAL 12 DE OCTUBRE, MADRID, Spain
Norma C. Gutierrez
Hospital Universitario de Salamanca. IBSAL. Centro de Investigación del Cáncer, Salamanca, Spain
José Antonio Pérez-Simón
María Teresa Gómez-Casares
Hospital Universitario Doctor Negrín, Las Palmas de Gran Canaria, Las Palmas de Gran Canarias, Spain
María José Larrayoz
Navarra University Clinic, PAMPLONA, Spain
Esther Prados de la Torre
University of Cordoba (UCO), Maimonides Institute for Biomedical Research of Cordoba (IMIBIC), Hematology Unit, Reina Sofia University Hospital, Córdoba, Spain
Isabel Cano-Ferri
Hospital Universitari i Politècnic La Fe, Valencia, Spain
Irene Navarro
Hematology Department, Hospital Universitari i Politècnic, La Fe, Valencia, València, Spain
Cristina Gil
Hospital Alicante, alicante, Spain
Teresa Bernal del Castillo
Hospital Universitario Central de Asturias–Instituto Universitario del Principado de Asturias–Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
Eduardo Rodríguez-Arbolí
Department of Hematology, Hospital Universitario Virgen del Rocío, Instituto de Biomedicina de Sevilla (IBiS/CSIC), University of Seville, Seville, Spain
Esther Pérez Santaolalla
Hospital Universitario de Donostia, Donostia, Spain
Rafael Colmenares
Hospital Universitario 12 De Octubre, Madrid, Spain
Mar Tormo
Hospital Clinico Universitary. INCLIVA Research Institute, Valencia 46010, Spain
Juan Miguel Bergua Burgues
Hospital San Pedro de Alcántara. Cáceres, Caceres, Spain
María-Luz Amigo
Hospital Morales Meseguer, Murcia, Spain
Carlos Rodríguez-Medina
Hospital Universitario de Gran Canaria Dr. Negrín, Las Palmas De Gran Canaria, Spain
Josefina Serrano
University Hospital Reina Sofia. IMIBIC. UCO, Cordoba, Spain
Ana Oliva
Hospital Virgen de la Candelaria, Tenerife, Spain
Juan Manuel Alonso-Domínguez
Princess Margaret Cancer Centre, Toronto, Ma, Canada
Víctor Noriega
Complejo Hospitalario Universitario A Coruña, A Coruña, Spain
Jesús-Lorenzo Algarra
Hospital General de Albacete, Albacete, Spain
Mayte T Olave
Hospital Clínico Lozano Blesa. Zaragoza, ZARAGOZA, Spain
Maria Jose García Perez
Hospital Universitario Torrecárdenas, Almeria, Spain
María del Carmen Couto
University Hospital Virgen de Valme, Sevilla, Spain
Agata Almela-Gallego
Leon University Hospital, Leon, Spain
María García-Fortes
Hospital Universitario Virgen de la Victoria, Málaga, Spain
Dolores Dolores Madrigal-Toscano
Virgen Macarena University Hospital, Seville, Spain
Lourdes Hermosín
Servicio Hematología, Hospital de Jerez, Jerez de la Frontera, Jerez de la Frontera, Cadiz, Spain
Mercedes Colorado
Hospital Universitario Marqués de Valdecilla, Santander, Spain
Raimundo García-Boyero
Hospital General Universitario de Castellón, Castellón, Spain
Francisco Ibañez-Alis
Valencia General Hospital, Valencia, Spain
María Solé-Rodríguez
Department of Haematology of Hospital Juan Ramón Jiménez, Huelva, Huelva, Spain
Carmen Martinez Chamorro
Hospital Universitario Quironsalud Madrid and Universidad Europea de Madrid, Pozuelo de Alarcon, Spain
Maria C. Mateos
Complejo Hospitalario de Navarra, Pamplona, Spain
María del Carmen García Garay
Hospital Clínico Universitario Virgen de la Arrixaca, Murcia, Spain
Antonio Solana-Altabella
Hospital Universitari i Politècnic La Fe; Dep. of Pharmacy, University of Valencia, Valencia, Spain
Beatriz Martín-Herreros
Instituto de Investigación Sanitaria La Fe, València, Spain
Joaquín Martínez-López
Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Hospital 12 de Octubre, Complutense University of Madrid, Centro Nacional de Investigaciones Oncológicas, Madrid Institute of Cancer, Madrid
M. Carmen Chillon
Hospital Universitario de Salamanca, IBSAL, CIBER-ONC number CB16/12/00233 y Centro de Investigacion del Cancer de Salamanca-IBMCC (USAL-CSIC), Salamanca, Salamanca, Spain
Elena Soria
Virgen del Rocio University Hospital, Institute of Biomedicine of Seville (IBIS/CSIC), University of Seville, Seville, Spain
Cristina Bilbao-Sieyro
Hospital Universitario de Gran Canaria Dr. Negrín, Instituto de Investigación Sanitaria de Canarias (IISC), Las Palmas De Gran Canaria, Spain
Maria J José Calasanz
UNIVERSITY OF NAVARRA, Pamplona, Spain
Joaquin Sánchez-García
Hospital Universitario Reina Sofía, Córdoba, Spain
Eva Barragan
Pau Montesinos
Hospital Universitari i Politecnic La Fe, Valencia, Spain