Collateral Lethality: A new therapeutic strategy in oncology

Abstract

Genomic deletion of tumor suppressor genes (TSG) is a rite of passage for virtually all human cancers. The synthetic lethal paradigm has provided a framework for the development of molecular targeted therapeutics that are functionally linked to the loss of specific TSG functions. In the course of genomic events that delete TSGs, a large number of genes with no apparent direct role in tumor promotion also sustain deletion as a result of chromosomal proximity to the target TSG. In this perspective, we review the novel concept of "collateral lethality", which has served to identify cancer-specific therapeutic vulnerabilities resulting from co-deletion of passenger genes neighboring TSG. The large number of collaterally deleted genes, playing diverse functions in cell homeostasis, offers a rich repertoire of pharmacologically targetable vulnerabilities presenting novel opportunities for the development of personalized anti-neoplastic therapies.

Figure 1. Collateral Deletion of Metabolic Genes Neighboring a Major Tumor Suppressor Locus

Genomic deletions inactivate tumor suppressor genes but may also collaterally delete chromosomal neighbors, if their deletion does not unduly compromise cell viability. Each row starting with the designator “TCGA-“ represents copy number data from a primary tumor from the TCGA in the 1p36 region, with segments in light blue representing regions of heterozygous deletion and dark blue, homozygous deletion. Homozygous deletions (dark blue) target tumor suppressor genes, such as mir34A [85], ERBB Receptor Feedback Inhibitor 1 (ERRFI1) [86], Tumor Necrosis Factor Receptor Superfamily, Member 9 (TNFRSF9) [46], Kinesin Family Member 1B (KIF1B) [87], Calmodulin Binding Transcription Activator 1 (CAMTA1) [88] and probably others [88] [89]. In addition, neighboring genes, such as the metabolic housekeeping enzymes Enolase 1 (ENO1), Nicotinamide Nucleotide Adenylyltransferase 1 (NMNAT1), 6-phosphogluconate dehydrogenase (PGD), can be co-deleted by virtue of chromosomal proximity to the aforementioned tumor suppressor genes.

Figure 2. Pharmacological Vulnerability Exposed by Homozygous Deletions in Essential-Redundant Paralogues

Homozygous deletions targeting tumor suppressor genes sometimes contain passenger genes that carry out a cell essential function but whose deletion is tolerated because of redundant action of a paralogue. In such cases, it may be possible to selectively target cancer cells by using small-molecule inhibitors targeting the non-deleted redundant paralogue. Proof-of-principle of this concept was demonstrated in glioma cells harboring deletion of Enolase 1 (ENO1), resulting in dramatic sensitization to ablation of Enolase 2 (ENO2) [50].

Figure 3. Redundant Biochemical Pathways-based collateral lethality

Two (or greater) biochemical pathways can lead to the same essential cellular process. Passenger homozygous deletions can affect one of those pathways while leaving the other intact, thus having no detrimental effect on cancer cell viability but causing the remaining pathway to become essential. Using selective inhibitors against key enzymes of the non-deleted pathway could lead to tumor specific cell death while leaving normal tissues unharmed. While this concept is yet to be proved experimentally in cancer, it is strongly support by model organism data [59]. An example is the production of ribose-5-phosphate as a backbone for nucleic acid synthesis, which can be obtained from either the oxidative or non-oxidative pathways of the pentose phosphate shunt (see Figure 4). 1p36 deleted tumors often harbor deletions in 6-phosphogluconate dehydrogenase (PGD), which is part of the oxidative pathway. These cancers are expected to be highly sensitive to inhibition of the non-oxidative pathway.

Figure 4. Deletion of PGD renders cells reliant on the non-oxidative Pentose Phosphate Shunt for Nucleotide Biosynthesis

Nucleotide biosynthesis for DNA and RNA requires Ribose-5-phosphate, which can be derived from either Glucose-6-phosphate through the oxidative arm of the pentose phosphate shunt or the glycolytic intermediates, fructose-6-phosphate and glyceraldehyde-3-phosphate, through the non-oxidative arm. Genetic data in yeast indicate that both the non-oxidative and oxidative arms are on their own, dispensable for cell viability. However, yeast do not tolerate simultaneous inactivation of both arms of the pathway, such as the combined loss of 6-phosphogluconate dehydrogenase (PGD) with either transketolase (TKT), transaldolase (TALD) or Ribulose Isomerase/Epimerase (RPI/ RPE), shown in Red. Given that no alternative pathways of Ribose-5-phosphate synthesis are known, it is very likely that cancer cells with 1p36 deletion encompassing PGD (Figure 1) would be entirely dependent on the non-oxidative arm of the pentose phosphate shunt, and as such, highly sensitive to inhibition of either TKT, TALD, RPI or RPE.

Figure 5. Heterozygous passenger deletions as targets for collateral lethality

Panel A. “Drug-induced haploinsufficency” refers to sensitization that a heterozygous deletion causes to a specific inhibitor of the deleted gene, provided this gene exerts an essential function, its inhibition exhibits threshold toxicity and its expression is proportional to genomic copy number. As such a 50% deficiency means much less inhibitor is required to reach toxic threshold and consequently, cells harboring such deletions are sensitized to such an inhibitor. Drug-induced haploinsufficiency has been studied for decades in the context of model organisms but its application to cancer therapy is just beginning to be realized. Panel B: Genetic variation occurs in about 1 in 300 nucleotides in the human genome [75]. This variation is present in different alleles of the same gene, causing alterations that have neither significant phenotypic nor functional effects. Antisense oligonucleotide (ASO) technology can be used to target essential genes that are heterozygously deleted in cancers. These oligonucleotides are able to target polymorphisms that only differ by as little as one pair from each other, thereby inactivating one allele while leaving the other intact. In the figure above, an essential gene is encoded by alleles A and a. Tumor cells contain a heterozygous deletion in allele A. By introducing an antisense-oligonucleotide (ASO) directed against allele a (green), it is possible to cause selective death in cancer cells while leaving normal tissues intact.