Clinico-genomic profiling and clonal dynamic modeling of TP53-aberrant myelodysplastic syndrome and acute myeloid leukemia

References

• The Cancer Genome Atlas (TCGA). Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013; 368:2059–2074.
   PubMed Web of Science ®Google Scholar
• Welch JS, Petti AA, Miller CA, et al. TP53 and decitabine in acute myeloid leukemia and myelodysplastic syndromes. N Engl J Med. 2016;375(21):2023–2036.
   PubMed Web of Science ®Google Scholar
• Tyner JW, Tognon CE, Bottomly D, et al. Functional genomic landscape of acute myeloid leukaemia. Nature. 2018;562(7728):526–531.
   PubMed Web of Science ®Google Scholar
• Bowen D, Groves MJ, Burnett AK, et al. TP53 gene mutation is frequent in patients with acute myeloid leukemia and complex karyotype, and is associated with very poor prognosis. Leukemia. 2009;23(1):203–206.
   PubMed Web of Science ®Google Scholar
• Seifert H, Mohr B, Thiede C, et al. The prognostic impact of 17p (p53) deletion in 2272 adults with acute myeloid leukemia. Leukemia. 2009;23(4):656–663.
   PubMed Web of Science ®Google Scholar
• Middeke JM, Herold S, Rücker-Braun E, et al. TP53 mutation in patients with high-risk acute myeloid leukaemia treated with allogeneic haematopoietic stem cell transplantation. Br J Haematol. 2016;172(6):914–922.
   PubMed Web of Science ®Google Scholar
• Bernard E, Nannya Y, Hasserjian RP, et al. Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes. Nat Med. 2020;26(10):1549–1556.
   PubMed Web of Science ®Google Scholar
• Byrd JC, Mrózek K, Dodge RK, et al. Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from cancer and leukemia group B (CALGB 8461). Blood. 2002;100(13):4325–4336.
   PubMed Web of Science ®Google Scholar
• Schoch C, Kern W, Kohlmann A, et al. Acute myeloid leukemia with a complex aberrant karyotype is a distinct biological entity characterized by genomic imbalances and a specific gene expression profile. Genes Chromosomes Cancer. 2005;43(3):227–238.
   PubMed Web of Science ®Google Scholar
• Haase D, Stevenson KE, Neuberg D, et al. TP53 mutation status divides myelodysplastic syndromes with complex karyotypes into distinct prognostic subgroups. Leukemia. 2019;33(7):1747–1758.
   PubMed Web of Science ®Google Scholar
• Lindsley RC, Saber W, Mar BG, et al. Prognostic mutations in myelodysplastic syndrome after stem-cell Transplantation. N Engl J Med. 2017;376(6):536–547.
   PubMed Web of Science ®Google Scholar
• Bagger FO, Sasivarevic D, Sohi SH, et al. BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis. Nucleic Acids Res. 2016;44(D1):D917–D924.
   PubMed Web of Science ®Google Scholar
• Gerstung M, Papaemmanuil E, Martincorena I, et al. Precision oncology for acute myeloid leukemia using a knowledge bank approach. Nat Genet. 2017;49(3):332–340.
   PubMed Web of Science ®Google Scholar
• Cerami E, Gao J, Dogrusoz U, et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2012;2(5):401–404.
   PubMed Web of Science ®Google Scholar
• Futreal AP, Coin L, Marshall M, et al. A census of human cancer genes. Nat Rev Cancer. 2004;4(3):177–183.
   PubMed Web of Science ®Google Scholar
• Tate JG, Bamford S, Jubb HC, et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Res. 2019;47(D1):D941–D947.
   PubMed Web of Science ®Google Scholar
• Ashburner M, Ball CA, Blake JA, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25(1):25–29.
   PubMed Web of Science ®Google Scholar
• The Gene Ontology Consortium. The gene ontology resource: 20 years and still going strong. Nucleic Acids Res. 2019; 47:D330–D338.
   PubMed Web of Science ®Google Scholar
• Mi H, Muruganujan A, Ebert D, et al. PANTHER version 14: More genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools. Nucleic Acids Res. 2019;47(D1):D419–D426.
   PubMed Web of Science ®Google Scholar
• O'Leary NA, Wright MW, Brister JR, et al. Reference sequence (RefSeq) database at NCBI: CURRENT status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44(D1):D733–D745.
   PubMed Web of Science ®Google Scholar
• Gu Z, Gu L, Eils R, et al. Circlize Implements and enhances circular visualization in R. Bioinformatics. 2014;30(19):2811–2812.
   PubMed Web of Science ®Google Scholar
• Ediriwickrema A, Aleshin A, Reiter JG, et al. Single-cell mutational profiling enhances the clinical evaluation of AML MRD. Blood Adv. 2020;4(5):943–952.
   PubMed Web of Science ®Google Scholar
• Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391–2405.
   PubMed Web of Science ®Google Scholar
• Rucker FG, Schlenk RF, Bullinger L, et al. TP53 alterations in acute myeloid leukemia with complex karyotype correlate with specific copy number alterations, monosomal karyotype, and dismal outcome. Blood. 2012;119(9):2114–2121.
   PubMed Web of Science ®Google Scholar
• Joerger AC, Ang HC, Fersht AR. Structural basis for understanding oncogenic p53 mutations and designing rescue drugs. Proc Natl Acad Sci USA. 2006;103(41):15056–15061.
   PubMed Web of Science ®Google Scholar
• May P, May E. Twenty years of p53 research: structural and functional aspects of the p53 protein. Oncogene. 1999;18(53):7621–7636.
   PubMed Web of Science ®Google Scholar
• Dohner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424–447.
   PubMed Web of Science ®Google Scholar
• Russo A, Migliavacca M, Zanna I, et al. p53 mutations in L3-loop zinc-binding domain, DNA-ploidy, and S phase fraction are independent prognostic indicators in colorectal cancer: a prospective study with a five-year follow-up. Cancer Epidemiol Biomarkers Prev. 2002;11(11):1322–1331.
   PubMed Web of Science ®Google Scholar
• Hourigan CS, Dillon LW, Gui G, et al. Impact of conditioning intensity of allogeneic transplantation for acute myeloid leukemia with genomic evidence of residual disease. J Clin Oncol. 2020;38(12):1273–1283.
   PubMed Web of Science ®Google Scholar
• Jaiswal S, Fontanillas P, Flannick J, et al. Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med. 2014;371(26):2488–2498.
   PubMed Web of Science ®Google Scholar
• Mazumdar C, Shen Y, Xavy S, et al. Leukemia-associated cohesin mutants dominantly enforce stem cell programs and impair human hematopoietic progenitor differentiation. Cell Stem Cell. 2015;17(6):675–688.
   PubMed Web of Science ®Google Scholar
• Demir S, Boldrin E, Sun Q, et al. Therapeutic targeting of mutant p53 in pediatric acute lymphoblastic leukemia. Haematologica. 2020;105(1):170–181.
   PubMed Web of Science ®Google Scholar
• Montesinos P, Beckermann BM, Catalani O, et al. MIRROS: a randomized, placebo-controlled, phase III trial of cytarabine ± idasanutlin in relapsed or refractory acute myeloid leukemia. Future Oncol. 2020;16(13):807–815.
   PubMed Web of Science ®Google Scholar
• Maslah N, Salomao N, Drevon L, et al. Synergistic effects of PRIMA-1Met (APR-246) and 5-azacitidine in TP53-mutated myelodysplastic syndromes and acute myeloid leukemia. Haematologica. 2020;105(6):1539–1551.
   PubMed Web of Science ®Google Scholar
• Sallman DA, DeZern AE, Garcia-Manero G, et al. Eprenetapopt (APR-246) and azacitidine in TP53-mutant myelodysplastic syndromes. J Clin Oncol. 2021;39(14):1584–1594.
   PubMed Web of Science ®Google Scholar