Lakhani, Asad A (March 2023) The Role of Recurrently Observed Aneuploidy in Tumorigenesis. PhD thesis, Cold Spring Harbor Laboratory.
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Abstract
Nearly 90% of human tumors exhibit aneuploidy, an alteration in the copy number of whole chromosomes or chromosomal arms. Despite a century since the preliminary observation of aneuploidy in cancer, the exact mechanisms by which chromosomal variability contributes to tumorigenesis remain unclear. The simultaneous alteration in the dosage of hundreds of genes on the aneuploid chromosome means that identifying dosage-sensitive driver genes is difficult. This is further complicated by the technical challenge of inducing targeted chromosomal arm gain or loss, and of distinguishing the phenotypic effects of the aneuploid chromosome from effects of genomic instability. To navigate these challenges, we developed a suite of tools called ReDACT: Restoring Disomy in Aneuploid cells using CRISPR Targeting. These chromosomal engineering techniques enable the elimination of specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies across diverse cancer backgrounds. We engineered loss of trisomy 1q in models of ovarian (A2780) and gastric cancer (AGS), as well as mammary epithelial cells (MCF10A); loss of trisomy 8q in colorectal cancer cells (HCT116, RKO); and loss of trisomies 1q, 7p and 8q in melanoma (A2058) cells. While loss of the aneuploid chromosome only had a mild effect on cellular proliferation, the aneuploidy-loss populations formed both fewer and smaller colonies under conditions of anchorage-independent growth in soft agar assays – a key hallmark of cancer. This effect was more severe for loss of 1q than for loss of 7p or 8q aneuploidy. A2780 and A2058 cells disomic for chromosome 1q failed to form tumors following subcutaneous xenografts in nude mice. However, we observed 1q regain in both in vitro proliferation assays and following xenografts, indicating an evolutionary pressure to re-establish aneuploidy dosage. Furthermore, 1q loss impaired malignant transformation of MCF10A cells: 1q trisomic cells transduced with HRASG12V formed tumors, whereas 1q disomic cells did not. Strikingly, HCT116 cells disomic for chromosome 8q showed a greater deficit in colony formation compared to loss of the oncogenic KRASG13D and CTNNB1pS45del alleles. Similarly, RKO 8q-loss clones also exhibited a greater deficit in colony formation compared to loss of the two BRAFV600E alleles. In fact, we observed chr12 gain in HCT116 8q disomy xenografts, which served to amplify KRASG13D and compensate for 8q loss. These results collectively highlight the importance of aneuploid chromosomes towards cancer phenotypes. To identify dosage-sensitive genes present on chromosome 1q that may be driving 1q aneuploidy, we transcriptionally downregulated several candidates in parental, 1q trisomic cells, and identified the genes whose inhibition resulted in a proliferative defect. Of these, overexpression of MDM4 and MCL1 in 1q disomic cells resulted in a partial rescue of the colony-deficit phenotype. Our results suggest MDM4 and MCL1 act in a dosage-sensitive manner to downregulate TP53 pathway activity and inhibit apoptosis respectively, thereby partially accounting for the oncogenic benefits of a 1q trisomy. Furthermore, we identify targeting of UCK2, a gene involved in the pyrimidine salvage pathway, as a therapeutic vulnerability in 1q aneuploid cells. Overall, we demonstrate that specific aneuploidies play essential roles in tumorigenesis, raising the possibility that targeting these “aneuploidy addictions” could represent a novel approach for cancer treatment.
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