TP53 copy number and protein expression inform mutation status across risk categories in acute myeloid leukemia

Abstract

Mutant TP53 is an adverse risk factor in acute myeloid leukemia (AML), but large-scale integrated genomic-proteomic analyses of p53 alterations in AML patients remain limited. We analyzed TP53 mutational status, copy number (CN), and protein expression data in AML (N=528) and provide a compilation of mutation sites and types across disease subgroups among treated and untreated patients. Our analysis shows differential hotspots in subsets of AML and uncovered novel pathogenic variants involving TP53 splice sites. In addition, we identified TP53 CN loss in 70.2% of TP53-mutated AML, which had more deleterious TP53 mutations and copy neutral loss of heterozygosity in 5/32 (15.6%) AML patients who had intact TP53 CN. Importantly, we demonstrate that mutant p53 protein expression patterns by immunohistochemistry evaluated using digital image-assisted analysis provide a robust readout that integrates TP53 mutation and allelic states in patients with AML (sensitivity=94.49%, specificity=90.48%). Protein expression of p53 by immunohistochemistry informed mutation status irrespective of TP53 CN status. Genomic analysis of co-mutations in TP53-mutant AML showed a muted landscape that encompassed primarily mutations in genes involved in epigenetic regulation (DNMT3A and TET2), RAS/MAPK signaling (NF1, KRAS/NRAS, PTPN11), and RNA splicing (SRSF2). In summary, our data provides a rationale to refine risk stratification of AML patients on the basis of integrated molecular and protein-level TP53 analyses.

Correlation of p53 immunohistochemistry with TP53 mutational status and overall survival in newly diagnosed acute myeloid leukaemia

“…Therefore, we considered a higher threshold of ≥7% staining as optimal despite lower sensitivity. In agreement with our findings, a recent study also identified a threshold of ~7% strong p53 staining to predict AML TP53‐ mutational status 12 . This study and ours demonstrate that a higher threshold of p53 staining appears to be necessary to accurately predict mutational status in AML compared to studies predominately evaluating MDS, where a threshold of ~1% strong staining correlates with the presence of a TP53 mutation 5,11 .…”

“…In theory, high VAF should also correlate with both accumulated mutated p53 protein as well as copy number status, and others have found that a VAF >40% is associated with adverse prognosis in AML and could be indicative of copy number loss. 11,12 However, we found no association between VAF and OS and no association between VAF and percent p53 positive cells. Although mutated TP53 results in protein accumulation, different mutations may result in different levels of stability and may not impact accumulation equally.…”

The 5th edition of the World Health Organization Classification of Haematolymphoid Tumours: Myeloid and Histiocytic/Dendritic Neoplasms

“…This "multi-hit" mutational status results in a neoplastic clone that lacks any residual wild-type p53 protein. Clinical detection of biallelic TP53 alterations is based on sequencing analysis (covering at least exons 4 to 11) [29,32], often coupled with a technique to detect copy number status, usually fluorescence in situ hybridization with a probe set specific for the TP53 locus on 17p13.1 and/or array techniques (e.g., comparative genomic hybridization or single nucleotide polymorphism arrays) [33]. Loss of genetic material at the TP53 locus may also be inferred by next-generation sequencing [29].…”

“…32 Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany. 33 Departments of Pathology and Oncology, Fudan University, Shanghai, China. 34 Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.…”

Pure erythroid leukemia is characterized by biallelic <i>TP53</i> inactivation and abnormal p53 expression patterns in <i>de novo</i> and secondary cases

“…Mutations frequently seen in other myeloid neoplasms are less common in PEL, indicating that biallelic loss of TP53 function is a feature of PEL and may play a critical role in the development of PEL. Of note, biallelic TP53 alteration is not specific to PEL and can be seen in other myeloid neoplasms, such as AML 8 and therapy-related MDS. 9 Thus, TP53 mutations alone may not be sufficient to block the differentiation of erythroid lineage and drive pronormoblast proliferation, a pathognomonic feature of PEL.…”