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Background  Expression of the  NPM1  gene, encoding nucleophosmin, is upregulated in cancers. Although more than ten  NPM1  transcripts are known, the reports were usually limited to one predominant transcript. In leukemia, the  NPM1  expression has not been widely studied so far. In acute myeloid leukemia (AML), the mutational status of the gene seems to play a pivotal role in carcinogenesis. Therefore, the aim of the study was to quantify alternative  NPM1  transcripts in two types of acute leukemia, AML and ALL (acute lymphoblastic leukemia).    Methods  Using droplet digital PCR, we analyzed the levels of three protein-coding  NPM1  transcripts in 66 samples collected from AML and ALL patients and 16 control samples. Using RNA-seq, we detected 8 additional  NPM1  transcripts, including non-coding splice variants with retained introns. For data analysis, Welch two sample t-test, Pearson’s correlation and Kaplan–Meier analysis were applied.    Results  The levels of the particular  NPM1  transcripts were significantly different but highly correlated with each other in both leukemia and control samples. Transcript  NPM1.1 , encoding the longest protein (294 aa), had the highest level of accumulation and was one of the most abundant transcripts in the cell. Comparing to  NPM1.1,  the levels of the  NPM1.2  and  NPM1.3  transcripts, encoding a 265-aa and 259-aa proteins, were 30 and 3 times lower, respectively. All three  NPM1  transcripts were proportionally upregulated in both types of leukemia compared to control samples. In AML, the levels of  NPM1  transcripts decreased in complete remission and increased again with relapse of the disease. Low levels of  NPM1.1  and  NPM1.3  were associated with better prognosis. The contribution of non-coding transcripts to the total level of  NPM1  gene seemed to be marginal, except for one short 5-end transcript accumulated at high levels in AML and control cells. Aberrant proportions of particular  NPM1  splice variants could be linked to abnormal expression of genes encoding alternative splicing factors.    Conclusions  The levels of the studied  NPM1  transcripts were different but highly correlated with each other. Their upregulation in AML and ALL, decrease after therapy and association with patient outcome suggests the involvement of elevated  NPM1  expression in the acute leukemia pathogenesis.    Electronic supplementary material  The online version of this article (10.1186/s12967-018-1608-2) contains supplementary material, which is available to authorized users.

NPM1 alternative transcripts are upregulated in acute myeloid and lymphoblastic leukemia and their expression level affects patient outcome