The 'Pushmi-Pullyu' of DNA REPAIR: Clinical Synthetic Lethality

Abstract

Maintenance of genomic integrity is critical for adaptive survival in the face of endogenous and exogenous environmental stress. The loss of stability and fidelity in the genome caused by cancer and cancer treatment provides therapeutic opportunities to leverage the critical balance between DNA injury and repair. Blocking repair and pushing damaged DNA through the cell cycle using therapeutic inhibitors exemplify the 'pushmi-pullyu' effect of disrupted DNA repair. DNA repair inhibitors (DNARi) can be separated into five biofunctional categories: sensors, mediators, transducers, effectors, and collaborators that recognize DNA damage, propagate injury DNA messages, regulate cell cycle checkpoints, and alter the microenvironment. The result is cancer therapeutics that takes advantage of clinical synthetic lethality, resulting in selective tumor cell kill. Here, we review recent considerations related to DNA repair and new DNARi agents and organize those findings to address future directions and clinical opportunities.

Keywords: DNA damage repair; DNA damage response; genomic instability; homologous recombination defects; mutational burden; synthetic lethality.

Figure I. Bio-functional Classification of DNA Repair Inhibitors

The drugs used to block DNA repair can be categorized by their functions in maintaining genomic fidelity. Sensors recognize DNA damage and create flags to signal injury presence. They secondarily participate in recruitment of proteins to mediate activation of the DNA repair pathways. Mediators are multifunctional and exert their effects in more than one phase of the cell cycle progression mediated by the cell cycle checkpoints. Signal transducers are enzymes, such as polymerases, kinases, and phosphatases, that control the activity of the cell cycle checkpoints after DNA damage and/or effect physical change on the DNA, such as exonuclease or ligase functions. Effectors block the progression through the cell cycle under normal conditions, to allow for DNA repair. Dysregulation of such effectors with rapid movement through the cell cycle may lead to accumulation and propagation of deleterious mutations and subsequent damage resulting in genomic instability. The collaborators may be important in modulating the immune and oxygen-regulated cellular microenvironment such as to either augment injury, activate immune response to neoantigens, or provide reactive oxygen species. Abbreviations: PARP1/2, poly(ADP-ribose) polymerase 1/2; RAD1/9/17, RAD1 checkpoint DNA exonuclease, RAD9 checkpoint clamp component, RAD17 checkpoint clamp loader component; BRCA1, BRCA1, DNA repair associated; TP53BP1, tumor protein p53 binding protein 1; MRN complex, MRE11-RAD50-NBS1 complex; ATM, ATM serine/threonine kinase inhibitor; ATR, ATR serine/threonine kinase inhibitor; RAD51, RAD51 recombinase; H2AX, H2A histone family member X; CHEK1/2, checkpoint kinase 1/2; WEE1, WEE1 G2 checkpoint kinase

Figure 1. Hypoxia-Regulated DNA Repair

During DNA replication, translation and transcription, as well as during epigenetic and post-translational modification, DNA is repaired using a number of pathways including HR, MMR, NER, BER, NHEJ, and TLS. DNA repair protein expression is sensitive to and modulated by hypoxia and oxia. In hypoxic conditions, DNA repair pathway protein expression is decreased in many instances, and NER, BER and NHEJ proteins involved in the DNA damage response are increased. The primary point of action for specific agents and inhibitors are indicated by repair pathways, damage response, and as a function of the stage of DNA replication and modification. During replication and repair, the hypoxic microenvironment may predispose to a loss of function phenotype. Abbreviations: HR, homologous recombination; MMR, mismatch repair; NER, nucleotide excision repair; BER, base excision repair; NHEJ, non-homologous end joining; TLS, translesion synthesis; RAD51, RAD51 recombinase; BRCA2, BRCA2, DNA repair associated; RAD51B/C, RAD51 paralogs B and C; XRCC3, X-ray repair cross complementing 3; RAD52, RAD52 homolog DNA repair protein; MLH1, mutL homolog 1; PMS1, postmeiotic segregation increased 1; MSH6, mutS homolog 6; RAD23B, RAD23 homolog B; APE1, apurinic/apyrimidinic endonuclease 1; OGG1, 8-oxoguanine DNA glycosylase; MYH, mutY DNA glycosylase; NEIL2, nei like DNA glycosylase 2; NUDT1, nudix hydrolase 1; XRCC6, X-ray repair cross complementing 6; XRCC5, XRCC5, X-ray repair cross complementing 5; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; FANCD2, fanconi anemia complementation group D2; NBN, nibrin; ERCC1, excision repair cross-complementation group 1; XPA, xeroderma pigmentosum, complementation group A; XPC, xeroderma pigmentosum, complementation group C; POLI, DNA polymerase iota; i, inhibitor; ATRi, ataxia telangiectasia and Rad3-related kinase inhibitor ; ATMi, ataxia telangiectasia mutated kinase inhibitor ATM serine/threonine kinase inhibitor; DNA-PKi, DNA-dependent protein kinase inhibitor; POLE, DNA polymerase epsilon; ARID1a, AT-rich interaction domain 1A; EZH2i, enhancer of zeste homolog 2 inhibitor; PARPi, poly(ADP-ribose) polymerase inhibitor; CHEK1/2i, checkpoint kinase 1/2 inhibitor; chemo, chemotherapy; RT, radiotherapy; HDACi, histone deacetylase inhibitor

Figure 2. Effect of DNA Damage Repair Inhibitors on Cell Cycle Progression

TP53 is a sensor that guards the integrity of the genome by altering progression through the cell cycle at the G1/S, S, and G2/M checkpoints. Progression through the cell cycle is tightly regulated by cyclins and cyclin-dependent kinases. Blockade of cell cycle checkpoints propagates DNA damage by permitting the replication of unrepaired DNA and increasing mutational burden. All these events lead to genomic instability and enhanced susceptibility to DNA repair inhibitors, such as those listed on the figure. Abbreviations: i, inhibitor; DNARi, DNA repair inhibition; CHEK1, checkpoint kinase 1 inhibitor; CHEK1/2i, checkpoint kinases 1/2; WEE1, WEE1 G2 checkpoint kinase; MYT1, myelin transcription factor 1; CDK1/2, cyclin dependent kinases 1/2; CDK4/6/9, cyclin dependent kinases 4/6/9; ATR, ataxia telangiectasia and Rad3-related kinase; DNA-PKCS, DNA-dependent protein kinase catalytic subunit; MDM2, MDM2 proto-oncogene; TP53, tumor protein p53.

Figure 3. Targets of Opportunity in DNA Damage Response (DDR) and Homologous Recombination Deficiency (HRD)

Endogenous and Exogenous DNA abnormalities and injury result in the DNA damage response and DNA repair, and lead to cell cycle arrest. Arrest of the cell cycle may result in apoptosis or mitotic catastrophe. These events provide targets of opportunity for the treatment of genomically unstable cancer through the inhibition of DNA repair (DNAR) and cell cycle (CC) progression. DNA repair inhibitors (DNARi) block enzymes and proteins critical for DNA replication and repair including PARPi, CDK4i, Wee1i, CHEK1/2i, ATMi, ATRi and DNA-PKcsi. Abbreviations: DNAR, DNA repair; i, inhibitor; DNARi, DNA repair inhibitor; PARP, poly(ADP-ribose) polymerase; PARPi, poly(ADP-ribose) polymerase inhibitor; ATR, ATR serine/threonine kinase; ATM, ATM serine/threonine kinase; DNA-PKcs, DNA-dependent protein kinase catalytic subunit; CCi, cell cycle; CHEK, checkpoint kinase; CHEK1/2i, checkpoint kinase 1/2 inhibitor; ATMi, ATM serine/threonine kinase inhibitor; ATRi, ATR serine/threonine kinase inhibitor ; DNA-PKcsi, DNA-dependent protein kinase catalytic subunit inhibitor; WEE1, WEE1 G2 checkpoint kinase; WEE1i, WEE1 G2 checkpoint kinase inhibitor; CDK4/6, cyclin dependent kinase 4/6; CDK4/6i, cyclin dependent kinase 4/6 inhibitor; SWI/SNF, switching defective/sucrose nonfermenting; ARID1a, AT-rich interaction domain 1A; SMARC, SWI/SNF related, matrix associated, actin dependent regulator of chromatin; MYC-BETi, MYC and bromodomain and extra-terminal inhibitor; DDR, DNA Damage Response; p53^mut, tumor protein 53 mutated; CCND, cyclin D; CCNE, cyclin E

Figure 4. Endogenous and Exogenous Modulators of Clinical Synthetic Lethality

A circos plot cartoon is used to describe the relationship between endogenous and exogenous inducers or modulators of DNA damage. This DNA damage may collaborate with DNA repair inhibition to create a clinical synthetic lethal event. Endogenous effectors include genomic instability, somatic/germline mutations, cell cycle defects and oncogenic drivers; whereas, exogenous effectors include the events within the cancer cell microenvironment, immune- or tumor/vascular/stromal-mediated DNA injury, and exogenous processes such as ambient or therapeutic radiation and chemotherapeutics. Abbreviations: TOP1/2i, topoisomerase 1/2 inhibitor; i, inhibitor