Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy

Veronica Rendo,Tobias Sjöblom,Ivaylo Stoimenov,Peter Nygren,Per Artursson,Elin Sjöberg,Lars Johansson,Adrian Ng,Richard Svensson,Ian Cheong,André Mateus,Anna-Lena Gustavsson,Casey OʼBrien,Marios Giannakis

doi:10.1038/s41467-020-15111-4

Abstract

Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. To find exploitable targets, we map prevalent genetic polymorphisms to protein structures and identify 45 nsSNVs (non-synonymous small nucleotide variations) near the catalytic sites of 17 enzymes frequently lost in cancer. For proof of concept, we select the gastrointestinal drug metabolic enzyme NAT2 at 8p22, which is frequently lost in colorectal cancers and has a common variant with 10-fold reduced activity. Small molecule screening results in a cytotoxic kinase inhibitor that impairs growth of cells with slow NAT2 and decreases the growth of tumors with slow NAT2 by half as compared to those with wild-type NAT2. Most of the patient-derived CRC cells expressing slow NAT2 also show sensitivity to 6-(4-aminophenyl)-N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes.

Highlights

Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells
From the putative target proteins identified, we selected N-acetyltransferase 2 (NAT2) because of its (a) known role in drug metabolism, (b) non-redundant and well defined substrate specificity, (c) gastrointestinal tract (GI) restricted expression, (d) location on a chromosome arm frequently lost during transition from colorectal adenoma to carcinoma[24], (e) 10-fold activity difference between the gene products encoded by the wild-type and a common variant allele, and (f) clinically relevant substrates as ~10 commonly used drugs are subject to NAT2 metabolism, among them the cytotoxic drug amonafide[25], where rapid acetylators have ~4.5-fold higher plasma ratio of N-acetyl-amonafide to amonafide than slow acetylators leading to increased systemic toxicity[26]
Loss of NAT2, a non-essential enzyme involved in drug metabolism, in colorectal cancers emerged as an attractive target conceptually different from synthetic lethality (ENO2, PRMT5, ME3) or targeting genes essential for cell survival (POLR2A, RPA70, or PSMC2)

Summary

Introduction

Cancer chemotherapy targeting frequent loss of heterozygosity events is an attractive concept, since tumor cells may lack enzymatic activities present in normal constitutional cells. Most of the patient-derived CRC cells expressing slow NAT2 show sensitivity to 6-(4-aminophenyl)N-(3,4,5-trimethoxyphenyl)pyrazin-2-amine (APA) treatment. These findings indicate that the therapeutic index of anti-cancer drugs can be altered by bystander mutations affecting drug metabolic genes. Targeting of the loss of heterozygosity (LOH) events occurring as cancer genomes inactivate tumor suppressor genes has been achieved by allele-specific inhibition, where variants of essential genes such as the 70-kDa subunit of replication protein A (RPA70) near TP53 are silenced using antisense oligonucleotides[16]. We here demonstrate that a recurring loss of heterozygosity event affecting a drug metabolic activity (NAT2) can increase the sensitivity to a low molecular weight cytotoxic compound

Methods

Results

Conclusion