A Single Gene-Mediated Perturbation of the Human Genome Leads to Malignant Transformation in a Murine Transgenic Model

We hypothesized that induction or activation of a gene that directly affects DNA integrity can provide a tool for ongoing genomic changes in a cell and may eventually lead to oncogenesis. In the human genome, apurinic/apyrimidinic (AP) sites are created by number of external and internal factors including exposure to chemicals, UV radiation, DNA damaging agents, reactive oxygen species (ROS), DNA glycosylases and/or spontaneous hydrolysis by other mechanisms. AP sites are pre-mutagenic lesions that can also affect normal DNA replication. An evolutionarily conserved mechanism "base excision repair (BER)" has been established to identify and repair such sites. As part of BER, AP nucleases cleave the phosphodiester backbone at 5' to the AP site, prior to its repair. Although APEX 1 and 2 are the nucleases required for this repair, their hyperactivity has been connected with increased DNA breaks. We have previously observed that over expression of either APEX 1 or APEX 2 leads to malignant transformation with number of genomic changes including copy number alterations, single nucleotide variants (SNVs) and structural changes.

In this study, we investigated if transgenic overexpression of APEX2 in B cells in mice will cause tumorogenesis. We specifically overexpressed APEX2 in B cells by generating Tg,CD19Cre^+/-,APEX2^+/- mouse lines and used Tg,CD19Cre^+/- mouse (siblings of trail group) as control. The expression of APEX2 was detected by immunohistochemical (IHC) staining, which confirmed specific expression of APEX2 in lymph nodes. We next evaluated impact of APEX2 expression on B cell genome. We isolated B220⁺ B cells from spleen of 8 weeks old mice, and identified both increased single strand break (SSB) and double strand breaks (DSB). After 45 weeks of age and at variable times thereafter, 40% (23/58) of Tg,CD19Cre^+/-,APEX2^+/- mice showed enlargement of the lymph nodes and spleen. Histology showed effacement of normal tissue architecture by a nodular or diffuse population of atypical lymphoid cells in interfollicular areas. A distinct pattern of B220⁺BCL6⁺CD5^- B-cell lymphomas were identified after IHC staining, which resemble human diffuse large B-cell lymphoma (DLBCL). To investigate the changes at genomic level, we performed whole genome sequencing of tumor tissues from 3 mice as well as heart tissues (with lowest APEX2 expression) from the same mice to be used as controls. From single nucleotide varients (SNVs) calling, we observed average of 24,388 SNVs in the tumor with acquisition of new copy number changes and significant number of structural variants including average of 43 translocations, 51 deletions, 21 duplications and 24 inversion. Indel frequency was variable with average of 348. We observed mutational hotspots on chr6, chr12 and chr16. Variant allele frequency (VAF) data shows clonality of chr11 related mutations. We observed most frequent T>G, and then T>C mutations in all 3 samples. Interestingly, the mutational signature analysis showed signature 17 accounting for an average of 60% of mutations followed by signature 9. According to the mutational signature profile of different diseases, both signature 9 and 17 are observed in human B cell lymphoma.

To understand the genesis of the malignant transformation, we scarified Tg,CD19Cre^+/-,APEX2^+/- mice and control Tg,CD19Cre^+/- mouse at 25 weeks after birth to see the pre-malignant changes in lymphoid organs. We observed enlarged and increased follicle numbers in lymph nodes and in spleen in Tg,CD19Cre^+/-,APEX2^+/- mice compared to control. A single cell sequencing is underway to detect clonal changes at an early stage.

Our results demonstrate a single DNA-repair related gene responsible for inducing genomic instability with malignant transformation providing a model to study oncogenesis as well as possible preventative measures.