Targeting the absence: Homozygous DNA deletions as immutable signposts for cancer therapy

Abstract

Many cancers harbor homozygous DNA deletions (HDs). In contrast to other attributes of cancer cells, their HDs are immutable features that cannot change during tumor progression or therapy. I describe an approach, termed deletion-specific targeting (DST), that employs HDs (not their effects on RNA/protein circuits, but deletions themselves) as the targets of cancer therapy. The DST strategy brings together both existing and new methodologies, including the ubiquitin fusion technique, the split-ubiquitin assay, zincfinger DNA-recognizing proteins and split restriction nucleases. The DST strategy also employs a feedback mechanism that receives input from a circuit operating as a Boolean OR gate and involves the activation of split nucleases, which destroy DST vector in normal (nontarget) cells. The logic of DST makes possible an incremental and essentially unlimited increase in the selectivity of therapy. If DST strategy can be implemented in a clinical setting, it may prove to be curative and substantially free of side effects.split nucleases ͉ split ubiquitin ͉ zinc fingers A major obstacle to drug-based therapies of human diseases that are both efficacious and substantially free of side effects is the massive interconnectedness and redundancy of molecular circuits in living cells. In the case of cancer, the problem is exacerbated by genomic instability of many, possibly most, cancers. This property increases heterogeneity of malignant cells in the course of tumor progression or anticancer treatment and is one reason for the failure of most drug-based cancer therapies (1, 2). A few relatively rare cancers, such as testicular carcinoma, Wilm's kidney tumor, and some leukemias in children, can often be cured through chemotherapy but require cytotoxic treatments of a kind that cause severe side effects and are themselves carcinogenic (3, 4). Several recent advances, including the use of antiangiogenic compounds and inhibitors of specific kinases, hold the promise of efficacious, curative therapies (5-7). Nevertheless, major human cancers are still incurable once they have metastasized.In the present work, I suggest an approach to cancer therapy that involves homozygous deletions (HDs). Recent studies have demonstrated that many human cancers, including major ones, contain a significant number of scattered homozygous deletions (8-21). A salient property of an HD that involves DNA sequences not present elsewhere in the genome is that HD cannot revert. For this and other reasons, HDs may prove to be a particularly appropriate target for therapy. The difficulty here is that HD is an ''absence,'' and therefore it cannot be a conventional molecular target. Nevertheless, an HD-specific anticancer regimen is feasible through a strategy described below (Figs. 1-3).This strategy, termed deletion-specific targeting (DST), employs homozygous deletions as ''negative'' targets of cancer therapy. The DST strategy is implemented through molecular circuits that combine both existing and new methodologies. One of the methods is the ...

Discovery of Cellular Regulation by Protein Degradation

“…The DST strategy also employs a new feedback mechanism that receives input from a circuit operating as a Boolean OR gate and involves the activation of split nucleases, which destroy the DST vector in normal (non-target) cells. The logic of DST makes possible an incremental and essentially unlimited increase in the selectivity of treatment (158).…”

“…The difficulty here is that an HD is an "absence," and therefore it cannot be a conventional molecular target. Nevertheless, an HDspecific regimen is feasible, on paper so far (158). This strategy, termed deletion-specific targeting (DST), employs HDs (not their effects on RNA/protein circuits, but deletions themselves) as the targets of cancer therapy.…”

“…Can small compounds, with their inherently low informational content, ever enable a definitive cure of cancer that is free of collateral damage? The notion that underlies (and motivated) the DST strategy (158) is that a curative, side effect-free treatment may require polymer-scale, multitarget, Boolean-type circuits, i.e. that simpler (smaller) drugs may ultimately not suffice, particularly in regard to side effects.…”

“…In 2007, I proposed a new approach to cancer therapy that involves homozygous DNA deletions (158). Such deletions are present in many (possibly most) cancers and differ from any other attribute of a cancer cell by the fact that a homozygous deletion (HD) cannot revert.…”

Method of Detecting and Targeting Mutations in Cancer

“…Recently a conceptual paper was published [16] describing a technique for targeting DNA in non-tumor cells. However, key components of that method (such as split nucleases) do not currently exist so that the approach cannot be implemented at this time, and DNA methylation and compaction in non-tumor cells may limit the method's applicability should it become possible to test it.…”