Somatic PTPRT and ANGPT2 Mutations in Large Granulocyte Leukemia

T-cell large granular lymphocyte (T-LGL) leukemia is a rare, clonal disease characterized by the expansion of mature CD3+CD8+ cytotoxic T-cells. It is often associated with autoimmune disorders and immune-mediated cytopenias. Our recent findings suggest that up to 40% of T-LGL patients harbor mutations in the STAT3 gene (Koskela et al, NEJM, 2012). In the remaining T-LGL patients, the pathogenetic mutations are not known.

To identify additional somatic mutations, we chose two STAT3 mutation negative T-LGL leukemia patients for exome sequencing. CD8+ T-cells were used as test cells and matched CD4+ T-cells as control. The exome was captured with the Nimblegen SeqCap EZ Exome Library v2.0 and the sequencing was performed with the Illumina HiSeq2000 sequencing platform. Candidate somatic mutations were identified with a bioinformatics pipeline consisting of BWA for sequence alignment, Samtools for alignment filtering and Varscan for somatic mutation calling.

Index patient 1 was diagnosed with T-LGL leukemia at the age of 70 and a TCR repertoire assay revealed one minor T- cell clone in the leukemic sample (Vβ7.1: 28 %). Exome sequencing revealed 10 nonsynonymous nucleotide variants with p-values lower than 0.01, of which the tumor suppressor gene Protein tyrosine phosphatase (PTP) receptor T (PTPRT) had a variant frequency of 14%. PTPRT has previously been found to reverse Tyr⁷⁰⁵ phosphorylation on STAT3, a modification associated with STAT3 deactivation. In this novel mutation, a highly conserved hydrophobic valine residue is converted into methionine (V995M). The mutation occurs in the cytoplasmic part of the protein, within the tyrosine-protein phosphatase 1 domain. The PTPRT V995M mutation may thereby affect STAT3 activity by reducing dephosphorylation of Tyr⁷⁰⁵, thus increasing the expression of STAT3 target genes.

Index patient 2 was a 40 year-old male with untreated T-LGL leukemia. A TCR repertoire assay showed one predominant T-cell clone in the leukemic T-cells (Vβ13.2: 70%). Exome sequencing revealed 8 nonsynonymous nucleotide variants with p-values lower than 0.01. The missense mutation K436E in Angiopoietin-2 (ANGPT2), presenting with the lowest somatic p-value (1,06⁻⁰⁹) and highest variant frequency (34%), was the most relevant candidate involved in the pathogenesis of leukemia. The mutation occurs on the surface of ANGPT2 within the well-conserved fibrinogen C-terminal domain. This domain binds the receptor TIE2 and the change in the polarity induced by K436E mutation is likely to affect the binding of TIE2 by ANGPT2. Overexpression of ANGPT2 has previously been shown to confer an adverse prognostic factor in other forms of leukemia. While these mutations appear biologically relevant and exciting, we have not yet seen them in other LGL patients screened so far (n=80).

Somatic mutations in the PTPRT and ANGPT2 genes may represent rare genetic causes for T-LGL leukemia. Screening for these mutations in a larger cohort of patients is warranted. The mutation in the PTPRT gene is particularly exciting as it may directly impact the STAT3 pathway, which is a common pathogenetic event in T-LGL leukemia. Inactivating mutations of the PTPRT gene may have the same functional consequence as activating mutations of STAT3 in LGL patients.

Koskela:Novartis: Honoraria; BMS: Honoraria; Janssen-Cilag: Honoraria. Kallioniemi:TEKES-FiDiPro: Research Funding. Porkka:Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria, Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding. Mustjoki:Bristol-Myers Squibb: Honoraria, Research Funding; Novartis: Honoraria.