SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia

Abstract

T-cell prolymphocytic leukemia (T-PLL) is an aggressive malignancy with a median survival of the patients of less than two years. Besides characteristic chromosomal translocations, frequent mutations affect the ATM gene, JAK/STAT pathway members, and epigenetic regulators. We here performed a targeted mutation analysis for 40 genes selected from a RNA sequencing of 10 T-PLL in a collection of 28 T-PLL, and an exome analysis of five further cases. Nonsynonymous mutations were identified in 30 of the 40 genes, 18 being recurrently mutated. We identified recurrently mutated genes previously unknown to be mutated in T-PLL, which are SAMHD1, HERC1, HERC2, PRDM2, PARP10, PTPRC, and FOXP1. SAMHD1 regulates cellular deoxynucleotide levels and acts as a potential tumor suppressor in other leukemias. We observed destructive mutations in 18% of cases as well as deletions in two further cases. Taken together, we identified additional genes involved in JAK/STAT signaling (PTPRC), epigenetic regulation (PRDM2), or DNA damage repair (SAMHD1, PARP10, HERC1, and HERC2) as being recurrently mutated in T-PLL. Thus, our study considerably extends the picture of pathways involved in molecular pathogenesis of T-PLL and identifies the tumor suppressor gene SAMHD1 with ~20% of T-PLL affected by destructive lesions likely as major player in T-PLL pathogenesis.

Fig. 1. Distribution of mutated genes in the T-PLL cohort analyzed by targeted capture sequencing and WES

Mutated genes are indicated as black fields for the 33 T-PLL that carried at least one mutated gene. * indicate the five cases for which results are generated by WES. Not listed are 10 genes without any mutations, which are BCL11B, CBL, CUX1, ETV6, JAK1, MTOR, RUNX1, SUZ12, VOPP1, and ZRSR2

Fig. 2. Variant allele frequencies of 18 mutated genes carrying at least two mutations

Variant allele frequencies below 20% are not considered. Depicted are all mutations per gene. Bars indicate mean and S.D.

Fig. 3. Pattern and distribution of mutations in SAMHD1

Depicted are all mutations. The missense mutation in brackets was also observed in hematopoietic non-tumor cells of a female patient carrying two SAMHD1 mutations. The scale indicates the numbering of the amino acids. SAM sterile alpha motif, HDc Histidine (H)-Aspartate (D) containing

Fig. 4. SAMHD1 mRNA and protein expression in T-PLL

a mRNA expression levels (−ΔCT values) for SAMHD1 of T-PLL with mutated or deleted SAMHD1 (affected) compared to T-PLL with wild-type SAMHD1 (unaffected). Samples with mutated or deleted SAMHD1 have a lower SAMHD1 mRNA expression. GAPDH was used as internal reference. Bars indicate mean and S.D. b. Protein expression levels of 12 T-PLL samples. Samples with mutated SAMHD1 or losses show lower SAMHD1 protein expression compared to WT samples. β-actin served as loading control. mut mutated, WT wild type, UPD uniparental disomy, ACTB Actin beta

Fig. 5. Lack of toxic effects of cytarabine on T-PLL cells

IC₅₀ values for cytarabine of 12 T-PLL samples separated into SAMHD1 affected (n = 4) and SAMHD1 unaffected (n = 7) cases. Bars indicate mean and S.D.

Fig. 6. dATP levels of T-PLL and healthy donor samples

Display of dATP levels from dNTP measurement from 2 × 10⁶ cells. Samples 1–4: T-PLL with SAMHD1 mutations. Samples 5–7: T-PLL with wild-type SAMHD1. Samples 8–10: healthy donor-derived CD3⁺ T cells. In samples 5–10 the dNTP levels were not detectable