First case of AML with rare chromosome translocations: a case report of twins

Leukemia is different from solid tumor by harboring genetic rearrangements that predict prognosis and guide treatment strategy. PML-RARA, RUNX1-RUNX1T1, and KMT2A-rearrangement are common genetic rearrangements that drive the development of acute myeloid leukemia (AML). By contrast, rare genetic rearrangements may also contribute to leukemogenesis but are less summarized. Here we reported rare fusion genes ZNF717-ZNF37A, ZNF273-DGKA, and ZDHHC2-TTTY15 in a 47-year-old AML-M4 patient with FLT3 internal tandem duplication (ITD) discovered by whole genome sequencing (WGS) using the patient’s healthy sibling as a sequencing control. This is, to our knowledge, the first case of AML with fusion gene ZNF717-ZNF37A, ZNF273-DGKA, and ZDHHC2-TTTY15.

Thanks to the development of next generation sequencing, variations with low population frequency are able to be identified. The identification of susceptible or driver genes are also accelerated by twin or family study. Here we reported rare fusion genes ZNF717-ZNF37A, ZNF273-DGKA, and ZDHHC2-TTTY15 in AML with FLT3/ITD by a twin study.
The patient presented to hospital second time at 24 July, 2015. Routine blood test showed leukocyte count of 18. 70× 10 9 /L, Hb of 69 g/L, platelet count of 30 × 10 9 /L. Bone marrow aspiration showed primitive and immature cells made up 79% of the bone marrow cells. IEA (Idarubicin +Etoposide+Aza-C) regimen was administrated but bone marrow depression occurred. Bone marrow aspiration showed active myeloproliferative activity and primitive and immature cells made up 92% of the bone marrow cells.
The patient left hospital.
The patient presented to hospital third time at 17 August, 2015. Routine blood test showed leukocyte count of 61.46× 10 9 /L, Hb of 62 g/L, platelet count of 101 × 10 9 /L. Homoharringtonine+Etoposide were administrated. The patient left the hospital at 19 October, 2015.
The patient presented to hospital fourth time at 1 November, 2015. Routine blood test showed leukocyte count of 145.72× 10 9 /L, Hb of 71 g/L, platelet count of 15 × 10 9 /L. The patient deteriorated rapidly and passed away.

Whole genome sequencing
Peripheral blood mononuclear cells (PBMCs) from the patient T3 (leukocyte count of 145.72× 10 9 /L) and healthy sibling T4 were collected and genome DNA were isolated for WGS. Paired end 150 bp (PE150) sequencing on Illumina HiSeq X was performed at the Core Genomic Facility of Beijing Annoroad Genomics. All data were aligned to hg19 with BWA, arranged with samtools, marked with Picard, locally aligned with GATK. The coverage rate at 30× is 89.82%.
Single nucleotide polymorphism (SNP) was annotated using ANNOVAR. A total 3,033,876 SNPs were shared between T3 and T4. T4 had 317,907 unique SNPs while T3 had 301,334 unique SNPs.

Discussion and conclusions
Here, we reported the first case of AML-M4 in a 47 years old man bearing ZNF717-ZNF37A, ZNF273-DGKA, and ZDHHC2-TTTY15 fusions detected by WGS analysis.
ZNF273 was reported by the database (http://donglab. ecnu.edu.cn/databases/FusionCancer/) to be fused with TPRKB in two cases, one in melanoma and another in prostate cancer.
DGKA, the gene encoding diacylglycerol kinase alpha (DGKα) which is a negative regulator of oncogene Ras [7], has attracted much interests from cancer researchers recently due to its involvement in multiple signaling pathways. DGKα inhibition compromises cancer cell viability, impairs angiogenesis, and notably boost T cell activation and enhance cancer immunotherapies [8]. DGKA was reported to form fusions with ASB8 in prostate cancer and RAB5B in uterine carcinosarcoma by TCGA database. DGKA was also reported to be fused with STARD4 in 4 Burkitt's lymphoma cases and with CD74 in one lung cancer from Dong lab's database.
DGKA may play a role in leukemogenesis. DGKα was absent in non-differentiated human promyelocytic leukemia cell line HL-60 cells, but was robustly upregulated during differentiation. By contrast, the other DGK isoforms (δ, ε, γ, ζ) existed in undifferentiated HL-60 cells but were remarkably decreased throughout differentiation [9]. DGKα was also reported to be abundant in the nuclei of human erythroleukemia cell line K562, and to be involved in cell cycle progression of K562 cells [10]. The information implicates that DGKα may be involved in the differentiation and cell cycle progression of leukemia cells.
The fusion between ZNF273 and DGKα may result in the production of a new protein with changed localization that may in turn influence how the kinase activity of DGKα exerts. The fusion between ZNF273 and DGKα led to the replacement of N-terminal domain of DGKα by the whole Zn finger domain of ZNF273 (Fig. 2). Deletion of the N-terminal domain of DGKα was reported to confer no effect on enzyme activity but result in constitutive localization of DGKα at the plasma membrane in intact T cells [11]. ZNF273-DGKα fusion may lead to dysregulated signaling pathway in leukemia cells.
ZDHHC2, a palmitoyl acyltransferase [12], has been reported by multiple groups to be involved in gastric adenocarcinoma [13], hepatocellular carcinoma [14]. ZDHHC2 was reported to be fused with LTBP1 in two breast cancer cases, with PPP2R2A in one ovarian cancer, with FGD6 in one sarcoma case from TCGA database.  TTTY15 fusions have been reported in prostate cancer [3]. TTTY15-USP9Y fusion has been found in multiple cases of hepatocellular cancer, lung cancer, melanoma, prostate cancer, implicating a potential driver function of TTTY15-USP9Y fusion in carcinogenesis.