Integration of a bacterial gene sequence into a chronic eosinophilic leukemia patient's genome as part of a fusion gene linker

Abstract

Analysis of databases from the human genome project (HGP), the 1000 Genomes Project (1KGP), and The Cancer Genome Atlas (TCGA) revealed bacterial DNA integration into the human somatic genome, particularly in tumor tissues. Fusion genes have also been associated with tumorigenesis and 34 PDGFR fusion genes are linked to hematological malignancies. Here, we determined that a 17-bp homologous sequence in Marinobacter sp. Hb8, Rhodococcus fascians D188, Rhodococcus sp. PBTS2, Micrococcus luteus strain trpE16 and M. luteus NCTC 2665 integrates into the genome of a chronic eosinophilic leukemia patient as part of the linker for the novel CDK5RAP2-PDGFRα fusion gene. The resulting fusion protein that has CDK5RAP2's self-activating domain and PDGFRa's tyrosine kinase domain but lacks PDGFRa's membrane-binding and ligand-dependent activation properties may act together with the integrated bacterial sequence to readily phosphorylate downstream targets, amplify proliferation signals and promote leukemic cancer progression.

Keywords: Cdk5rap2; Leukemia; PDGFRα.

Fig. 1

Insertion of the 18-bp sequence into the CDK5RAP2-PDGFRα fusion gene. a. Schematic diagram showing the structures of full-length CDK5RAP2, full-length-PDGFRα, and CDK5RAP2-PDGFRα fusion protein with its junction structure between CDK5RAP2 and PDGFRα. The N-terminal (aa 1 to 494) of CDK5RAP2 (exons 1–13), containing the coiled-coil domains (dark gray boxes), fuses with the C-terminal (aa 581 to 1089) of PDGFRα (exons 12–22), containing the tyrosine kinase domain, resulting in the 1016 aa CDK5RAP2-PDGFRα fusion protein. The 40-bp junction is composed of a 22-bp PDGFRα inverted intron 9 (aa 494–501, light gray box) and an 18-bp from an unknown source (aa 501–508). b. NCBI BLAST Search revealed that the18-bp is 100% identical to a sequence in Marinobacter sp. Hb8 complete genome (CP017715.1). Of the 18-bp, 17-bp (2–18) is 100% identical to a sequence in Rhodococcus fascians D188 complete genome (CP015235.1), Rhodococcus sp. PBTS2 complete genome (CP015220.1), Micrococcus luteus strain trpE16 genome (CP007437.1) and Micrococcus luteus NCTC 2665 complete genome (CP001628.1). The “a” (gray) is likely added during the fusion event, which together with “aa” in the inverted intron 9 sequence encodes K that does not exist in PDGFRα. c. Sequence alignment of intron 10 from PDGFRα [GenBank Accesssion # NP_006206.4] with AluSz6 retrotransposon [Accession # DF0000052]. AluSz6 was found using Dfam 2.0 database. Sequences were aligned by CLUSTAL OMEGA 1.2.2 Multiple Sequence Alignment software. Nucleotide numbers are indicated on either side. Asterisks denote identical sequences between hPDGFRα and AluSz6. Broken lines represent missing nucleotide sequences in AluSz6