Hereditary Breast and Ovarian Cancer Driven by BRCA1/BRCA2 Variants: Chromosomal Instability Pathways, Integrative Omics-Based Stratification, Synthetic Lethality Approaches, and Evolving Therapeutic Paradigms

Hereditary breast and ovarian cancer (HBOC) represent one of the most extensively studied inherited cancer predisposition syndromes, accounting for a substantial proportion of early-onset and familial breast and ovarian cancers worldwide. Breast cancer remains the most frequently diagnosed malignancy among women globally, while ovarian cancer, although less common, is associated with disproportionately high mortality due to late-stage diagnosis (Sung et al., 2021). Approximately 5–10% of breast cancers and 10–15% of ovarian cancers are hereditary in nature, with germline pathogenic variants in BRCA1 and BRCA2 constituting the predominant genetic drivers of HBOC (Narod & Foulkes, 2004; Kuchenbaecker et al., 2017). Carriers of deleterious BRCA1/BRCA2 variants face a markedly elevated lifetime risk of developing breast and ovarian cancers, often at younger ages and with more aggressive clinical behavior, underscoring the profound clinical significance of this syndrome.

The discovery of BRCA1 in 1994 and BRCA2 in 1995 marked a paradigm shift in cancer genetics and molecular oncology (Miki et al., 1994; Wooster et al., 1995). These tumor suppressor genes encode large, multifunctional proteins that play central roles in the maintenance of genomic stability, particularly through the homologous recombination (HR) DNA repair pathway. BRCA1 is involved in DNA damage sensing, cell cycle checkpoint control, and repair pathway choice, whereas BRCA2 primarily facilitates RAD51-mediated strand invasion during double-strand break repair (Roy et al., 2012; Venkitaraman, 2014). Loss of BRCA1 or BRCA2 function results in defective high-fidelity DNA repair, driving genomic instability and tumorigenesis. Beyond their canonical roles in DNA repair, BRCA proteins are also implicated in replication fork protection, chromatin remodeling, transcriptional regulation, and centrosome duplication, highlighting their broad biological relevance in safeguarding chromosomal integrity.

BRCA alterations can occur in both germline and somatic contexts, with distinct clinical and therapeutic implications. Germline BRCA1/ BRCA2 mutations are inherited and confer cancer susceptibility across multiple tissues, necessitating genetic counseling, familial risk assessment, and preventive strategies such as enhanced surveillance or risk-reducing surgery (Petrucelli et al., 2016). In contrast, somatic BRCA mutations arise exclusively within tumor cells and are not transmitted to offspring; nevertheless, they can phenocopy germline BRCA deficiency at the molecular level, particularly with respect to homologous recombination deficiency (HRD) (Meric-Bernstam et al., 2021). Importantly, both germline and somatic BRCA alterations predict sensitivity to DNA-damaging agents and targeted therapies such as poly(ADP-ribose) polymerase (PARP) inhibitors, reinforcing the need for comprehensive BRCA testing strategies in clinical oncology.

Tumors harboring BRCA1 or BRCA2 loss exhibit a characteristic set of molecular and phenotypic features collectively referred to as the hallmarks of BRCA-deficient tumors. These include profound chromosomal instability (CIN), accumulation of DNA double-strand breaks, replication stress, aneuploidy, and reliance on error-prone DNA repair pathways such as non-homologous end joining (Lord & Ashworth, 2016). BRCA1-deficient breast cancers frequently display a basal-like or triple-negative phenotype, while BRCA2-associated tumors more often resemble sporadic hormone receptor–positive cancers, reflecting divergent biological consequences of BRCA loss (Turner et al., 2004; Nolan et al., 2012). At the genomic level, BRCA-deficient tumors demonstrate distinct mutational signatures, large-scale state transitions, and genomic scars that can be quantitatively captured through HRD scores, providing valuable biomarkers for therapeutic stratification (Alexandrov et al., 2013).

The growing recognition of molecular heterogeneity within BRCA-driven cancers has highlighted the limitations of single-gene testing and uniform treatment approaches. This has fueled the adoption of integrative genomics and precision oncology strategies, which combine genomics, epigenomics, transcriptomics, proteomics, and metabolomics to achieve a more refined classification of tumors and to identify actionable vulnerabilities (Berger & Mardis, 2018). Multi-omics profiling enables the detection of “BRCAness” phenotypes in tumors lacking canonical BRCA mutations, expands the pool of patients who may benefit from synthetic lethality–based therapies, and facilitates the prediction of therapeutic response and resistance mechanisms (Lord et al., 2019). In parallel, advances in computational biology and artificial intelligence are accelerating the translation of complex omics data into clinically meaningful decision-making tools.

This review aims to provide an integrated and up-to-date synthesis of current knowledge on BRCA1/BRCA2-driven hereditary breast and ovarian cancer, with a particular focus on (i) the molecular mechanisms linking BRCA dysfunction to chromosomal instability, (ii) the application of integrative omics approaches for tumor stratification and biomarker discovery, (iii) the principles and expanding landscape of synthetic lethality–based therapeutic strategies, and (iv) evolving clinical paradigms aimed at overcoming therapeutic resistance. By bridging fundamental biology with translational and clinical insights, this review seeks to highlight emerging opportunities and remaining challenges in the precision management of BRCA-associated cancers.

2. GENETIC ARCHITECTURE OF BRCA1 AND BRCA2

2.1 Gene Structure and Functional Domains

BRCA1 and BRCA2 are large tumor suppressor genes that encode multifunctional proteins essential for the maintenance of genomic integrity. The BRCA1 gene, located on chromosome 17q21, encodes a protein of 1,863 amino acids characterized by two highly conserved functional domains. The N-terminal RING (Really Interesting New Gene) domain mediates heterodimerization with BARD1, conferring E3 ubiquitin ligase activity critical for DNA damage signaling and protein turnover. The C-terminal BRCT (BRCA1 C-Terminal) tandem repeats function as phospho-protein binding modules that orchestrate DNA damage response (DDR) signaling, cell-cycle checkpoint control, and repair pathway choice (Roy et al., 2012; Huen et al., 2010).

In contrast, BRCA2, located on chromosome 13q13.1, encodes a 3,418-amino-acid protein primarily dedicated to homologous recombination repair. The central region of BRCA2 contains eight BRC repeats, which directly bind and regulate RAD51 recombinase, facilitating nucleoprotein filament formation at sites of double-strand breaks. The C-terminal DNA-binding domain (DBD), comprising oligonucleotide/oligosaccharide-binding folds and a helical domain, anchors BRCA2 to single- and double-stranded DNA, ensuring accurate strand invasion and repair fidelity (Venkitaraman, 2014). Functional disruption of these domains underlies the DNA repair deficiency observed in BRCA-mutant tumors.

2.2 Spectrum of BRCA Variants

Pathogenic alterations in BRCA1 and BRCA2 encompass a wide mutational spectrum, including frameshift and nonsense mutations, splice-site alterations, missense variants affecting critical domains, and large genomic rearrangements (LGRs) such as exon deletions or duplications. Clinically, BRCA variants are classified as pathogenic, likely pathogenic, variants of uncertain significance (VUS), likely benign, or benign, according to standardized guidelines (Richards et al., 2015). While pathogenic and likely pathogenic variants have well-established clinical implications, VUS remain a major challenge in genetic counseling due to limited functional or epidemiological evidence.

Distinct founder mutations have been identified in specific populations, reflecting historical and geographic genetic bottlenecks. For example, the BRCA1 mutations 185delAG and 5382insC, and the BRCA2 mutation 6174delT, are prevalent among Ashkenazi Jewish populations, whereas other recurrent mutations are observed in Icelandic, Dutch, French-Canadian, and South Asian cohorts (Rebbeck et al., 2018). Additionally, LGRs contribute significantly to BRCA mutation burden in certain populations and may be underdetected by sequencing-only approaches, emphasizing the need for comprehensive testing strategies (Sluiter & van Rensburg, 2011).

2.3 Penetrance and Cancer Risk Modulation

The penetrance of BRCA1 and BRCA2 mutations is high but variable, influenced by gene-specific effects, modifying loci, hormonal factors, and epigenetic regulation. BRCA1 mutation carriers exhibit a higher lifetime risk of breast cancer (≈65–80%) and ovarian cancer (≈35–45%), with tumors often presenting at an earlier age and displaying a basal-like or triple-negative phenotype. In contrast, BRCA2 mutation carriers have a comparable breast cancer risk (≈60–75%) but a lower ovarian cancer risk (≈10–20%), and tumors more frequently resemble sporadic, hormone receptor–positive cancers (Kuchenbaecker et al., 2017).

Cancer risk is further modulated by genetic modifiers, including common low-penetrance alleles identified through genome-wide association studies (GWAS), as well as variants in DNA repair genes such as PALB2, ATM, and CHEK2 (Antoniou et al., 2014). Epigenetic mechanisms, including BRCA1 promoter hypermethylation and chromatin remodeling, can phenocopy genetic loss and contribute to interindividual variability in cancer risk and therapeutic response (Esteller et al., 2000). These multilayered influences underscore the complexity of risk prediction in BRCA mutation carriers and the necessity for integrative risk models.

Table 1. Key Genetic and Functional Features of BRCA1 and BRCA2

Figure 1: From BRCA Genetic Variants to Cancer Risk

BRCA1 and BRCA2 function as central guardians of genome stability by coordinating multiple layers of the DNA damage response (DDR). Through their roles in homologous recombination repair (HRR), replication fork protection, and cell-cycle regulation, these proteins prevent the accumulation of chromosomal aberrations that drive tumorigenesis. Loss of BRCA function disrupts these tightly regulated processes, resulting in chromosomal instability, replication stress, and malignant transformation.

3.1 Homologous Recombination Repair (HRR)

Role in Double-Strand Break Repair

Homologous recombination repair represents the most accurate pathway for the resolution of DNA double-strand breaks (DSBs), particularly during the S and G2 phases of the cell cycle when a sister chromatid is available as a repair template. BRCA1 acts early in HRR by promoting DNA end resection through the recruitment of CtIP and the MRN (MRE11–RAD50–NBS1) complex, thereby facilitating the generation of 3′ single-stranded DNA overhangs required for homology search (Huen et al., 2010). In contrast, BRCA2 operates downstream by directly mediating the loading of RAD51 onto resected DNA, a step essential for strand invasion and error-free repair (Venkitaraman, 2014).

Deficiency in either BRCA1 or BRCA2 shifts DSB repair toward error-prone pathways such as non-homologous end joining (NHEJ), leading to deletions, translocations, and chromosomal rearrangements that contribute to oncogenic transformation (Lord & Ashworth, 2016).

Interaction with RAD51, PALB2, ATM/ATR

The tumor suppressor functions of BRCA proteins are mediated through extensive protein–protein interaction networks. PALB2 (Partner and Localizer of BRCA2) serves as a molecular bridge between BRCA1 and BRCA2, anchoring BRCA2 to sites of DNA damage and stabilizing RAD51 nucleoprotein filaments (Xia et al., 2006). BRCA1 and BRCA2 also intersect with upstream DNA damage sensors, including ATM and ATR kinases, which phosphorylate multiple DDR components to activate cell-cycle checkpoints and coordinate repair pathway choice (Roy et al., 2012). Disruption of these interactions compromises HRR efficiency and amplifies chromosomal instability.

3.2 Replication Fork Protection

Fork Stabilization Mechanisms

Beyond DSB repair, BRCA1 and BRCA2 play critical roles in protecting stalled replication forks from pathological degradation. Under conditions of replication stress, BRCA proteins stabilize nascent DNA strands by preventing excessive nuclease-mediated resection, particularly by MRE11. BRCA2, in cooperation with RAD51, coats stalled replication forks, shielding them from collapse and preserving replication competence (Schlacher et al., 2011). BRCA1 contributes to fork remodeling and restart through its interactions with FANCD2 and other fork-associated proteins.

Consequences of Fork Collapse

In BRCA-deficient cells, failure to protect stalled replication forks leads to fork collapse, DSB formation, and reliance on alternative, error-prone repair mechanisms. This process generates extensive chromosomal aberrations, including copy number variations and chromatid breaks, which fuel genomic heterogeneity and therapy resistance (Quinet et al., 2017). Replication fork instability is now recognized as a key driver of chromosomal instability in BRCA-mutant tumors and a major determinant of sensitivity to DNA-damaging agents and PARP inhibitors.

3.3 Maintenance of Genomic Integrity

Cell Cycle Checkpoint Regulation

BRCA1 exerts a pivotal role in enforcing cell-cycle checkpoints in response to DNA damage. Through interactions with ATM/ATR and checkpoint kinases CHK1 and CHK2, BRCA1 contributes to G1/S and G2/M arrest, allowing sufficient time for DNA repair before cell division (Cortez et al., 1999). Loss of BRCA1-mediated checkpoint control permits the propagation of damaged DNA into daughter cells, exacerbating genomic instability and tumor progression.

Centrosome Duplication Control

In addition to DNA repair and checkpoint functions, BRCA1 regulates centrosome duplication, ensuring proper mitotic spindle formation and chromosomal segregation. BRCA1 ubiquitin ligase activity, mediated through its RING domain, limits centrosome amplification. BRCA1 deficiency leads to supernumerary centrosomes, multipolar spindles, and aneuploidy—hallmark features of chromosomal instability observed in BRCA-mutant cancers (Starita et al., 2004).

Table 2. Roles of BRCA1 and BRCA2 in DNA Damage Response and Chromosomal Stability

Chromosomal instability (CIN) is a defining biological feature of BRCA1/BRCA2-deficient tumors and represents a direct consequence of impaired DNA damage repair, defective replication stress responses, and aberrant mitotic control. CIN encompasses both numerical chromosomal alterations (aneuploidy) and structural chromosomal aberrations, driving tumor heterogeneity, disease progression, and therapeutic resistance.

4.1 Mechanistic Basis of CIN

Aneuploidy and Structural Chromosomal Aberrations

Loss of BRCA1 or BRCA2 function leads to defective homologous recombination repair, forcing cells to rely on error-prone DNA repair pathways such as non-homologous end joining and microhomology-mediated end joining. This results in chromosomal translocations, deletions, duplications, and complex rearrangements, collectively referred to as structural chromosomal aberrations (Lord & Ashworth, 2016). Persistent DNA damage and faulty chromosome segregation further promote aneuploidy, a hallmark of BRCA-deficient tumors that correlates with aggressive clinical behavior and poor prognosis (Sansregret et al., 2018).

Telomere Dysfunction

BRCA proteins contribute to telomere integrity by facilitating proper replication and protection of telomeric DNA. BRCA1, in particular, regulates telomere length and structure through interactions with shelterin complex components. In BRCA-deficient cells, telomere shortening, telomere fragility, and end-to-end chromosomal fusions are frequently observed, leading to breakage–fusion–bridge cycles that perpetuate chromosomal instability (McPherson et al., 2006). Telomere dysfunction thus acts as a continuous source of genomic rearrangements in BRCA-mutant tumors.

Mitotic Spindle Defects

BRCA1 plays a critical role in centrosome duplication control and mitotic spindle assembly. Its loss results in centrosome amplification, multipolar spindle formation, and erroneous kinetochore–microtubule attachments. These mitotic abnormalities cause unequal chromosome segregation during cell division, further exacerbating aneuploidy and CIN (Stolz et al., 2010). Although BRCA2 is less directly involved in spindle regulation, its role in preserving DNA integrity indirectly ensures proper mitotic progression.

4.2 CIN-Driven Tumor Evolution

Genomic Heterogeneity

CIN generates extensive intra-tumoral and inter-tumoral heterogeneity by continuously reshaping the cancer genome. In BRCA-deficient tumors, ongoing chromosomal missegregation and structural alterations create genetically diverse subclones with distinct growth advantages, metastatic potential, and immune evasion strategies (Bakhoum & Cantley, 2018). This heterogeneity complicates disease classification and poses major challenges to durable therapeutic responses.

Clonal Selection and Therapy Resistance

Under therapeutic pressure, CIN accelerates clonal evolution, enabling the emergence of resistant subpopulations. For instance, secondary BRCA reversion mutations, restoration of replication fork protection, or activation of compensatory DNA repair pathways can arise through CIN-driven genomic remodeling, ultimately conferring resistance to platinum-based chemotherapy and PARP inhibitors (Lord et al., 2019). Thus, CIN not only drives tumor initiation but also shapes treatment outcomes in BRCA-mutated cancers.

4.3 CIN as a Therapeutic Vulnerability

Replication Stress Exploitation

Paradoxically, the same genomic instability that fuels tumor evolution also creates exploitable vulnerabilities. BRCA-deficient tumors experience chronic replication stress, characterized by stalled replication forks and excessive DNA damage. Therapeutic strategies that further exacerbate replication stress—such as inhibition of ATR, CHK1, or WEE1—can overwhelm residual repair capacity, leading to catastrophic genomic collapse and selective tumor cell death (Pilie et al., 2019).

CIN Biomarkers for Treatment Stratification

Quantitative measures of CIN, including aneuploidy scores, large-scale state transitions (LSTs), telomeric allelic imbalance (TAI), and composite homologous recombination deficiency (HRD) scores, have emerged as predictive biomarkers for response to DNA-damaging agents and PARP inhibitors (Telli et al., 2016). Integration of CIN metrics with multi-omics data enables refined patient stratification and supports the rational design of personalized therapeutic regimens.

Table 3. Key Chromosomal Instability Mechanisms and Therapeutic Implications in BRCA-Deficient Tumors

Figure 2: CIN Pathways and Therapeutic Opportunities in BRCA-Deficient Tumors

5. INTEGRATIVE OMICS-BASED STRATIFICATION OF BRCA-DRIVEN CANCERS

The molecular heterogeneity of BRCA1/BRCA2-driven cancers extends beyond single-gene alterations and necessitates a comprehensive, multi-dimensional analytical framework. Integrative omics-based stratification combines genomic, epigenomic, transcriptomic, proteomic, and metabolomic data to capture the complex biological states of tumors, refine risk prediction, and guide precision therapeutic interventions. This approach has been instrumental in identifying homologous recombination–deficient (HRD) phenotypes, predicting response to DNA-damaging agents, and uncovering resistance mechanisms.

5.1 Genomics and Epigenomics

Whole-Genome and Exome Sequencing

Whole-genome sequencing (WGS) and whole-exome sequencing (WES) have become foundational tools for identifying germline and somatic BRCA1/BRCA2 mutations, co-occurring DNA repair gene alterations, and complex structural variants. WGS, in particular, enables the detection of large-scale rearrangements, mutational signatures, and copy number alterations that characterize BRCA-deficient tumors (Nik-Zainal et al., 2016). These genomic features provide a more nuanced assessment of homologous recombination proficiency than BRCA mutation status alone.

BRCA Promoter Methylation

Epigenetic silencing of BRCA1 through promoter hypermethylation represents a non-mutational mechanism of homologous recombination deficiency, particularly in sporadic breast and ovarian cancers. Tumors with BRCA1 promoter methylation often phenocopy germline BRCA1-mutant cancers in terms of genomic instability and sensitivity to platinum agents and PARP inhibitors (Esteller et al., 2000; Turner et al., 2007). Incorporation of methylation profiling into diagnostic pipelines therefore expands the population eligible for HRD-targeted therapies.

HRD (Homologous Recombination Deficiency) Scores

Composite HRD scores, derived from measures such as loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LSTs), quantify the extent of genomic scarring caused by defective HR repair. These scores have demonstrated predictive value for response to platinum-based chemotherapy and PARP inhibitors across multiple tumor types, independent of BRCA mutation status (Telli et al., 2016; Marquard et al., 2015).

5.2 Transcriptomics and Proteomics

BRCA-Associated Expression Signatures

Transcriptomic profiling has revealed distinct BRCA-associated gene expression signatures, reflecting disrupted DNA repair, replication stress, and cell-cycle control. BRCA1-deficient tumors often exhibit basal-like transcriptional programs, whereas BRCA2-deficient cancers display greater overlap with luminal subtypes (Parker et al., 2009). These expression patterns aid in tumor classification and may predict sensitivity to specific therapeutic regimens.

Immune-Related Gene Expression Patterns

BRCA-driven tumors frequently demonstrate elevated expression of immune-related genes, including interferon-stimulated genes and immune checkpoint molecules such as PD-L1. This immunogenic phenotype is thought to arise from increased tumor mutational burden and cytosolic DNA accumulation, leading to activation of the cGAS–STING pathway (Pantelidou et al., 2019). Proteomic analyses further complement transcriptomic data by capturing post-translational modifications and signaling pathway activation states relevant to therapy response.

5.3 Metabolomics and Tumor Microenvironment

Metabolic Reprogramming in BRCA-Mutant Tumors

Metabolomic studies have uncovered metabolic adaptations in BRCA-deficient tumors, including altered nucleotide biosynthesis, redox imbalance, and increased reliance on glycolysis and glutamine metabolism. These metabolic shifts support survival under chronic replication stress and may create novel therapeutic vulnerabilities (Kim et al., 2019).

Stromal and Immune Cell Interactions

The tumor microenvironment (TME) plays a crucial role in shaping disease progression and treatment response. BRCA-mutant tumors often exhibit increased infiltration of tumor-infiltrating lymphocytes (TILs) and dynamic interactions with stromal components, including cancer-associated fibroblasts. Integrating spatial transcriptomics and proteomics with metabolomic data provides insight into how tumor–stroma crosstalk influences immune evasion and therapeutic resistance (Binnewies et al., 2018).

5.4 Multi-Omics Integration and AI-Driven Classification

Systems Biology Approaches

Systems biology frameworks integrate diverse omics layers to construct network models of BRCA-driven tumor biology. These models capture pathway interdependencies, identify key regulatory nodes, and enable the functional interpretation of complex datasets beyond single-gene analyses (Kristensen et al., 2014).

Predictive Biomarkers for Therapy Response

Artificial intelligence (AI) and machine learning algorithms are increasingly applied to multi-omics datasets to develop predictive biomarkers for therapy response and resistance. Integrative models combining HRD scores, gene expression profiles, immune signatures, and clinical variables have shown promise in stratifying patients for PARP inhibitors, platinum chemotherapy, and combination therapies involving immune checkpoint blockade (Kather et al., 2020). Such approaches represent a critical step toward fully personalized oncology in BRCA-driven cancers.

Table 4. Omics Platforms and Their Clinical Utility in BRCA-Driven Cancer Stratification

Figure 3: Flowchart of Integrative Omics-Based Stratification Framework

6. SYNTHETIC LETHALITY IN BRCA-DEFICIENT CANCERS

The concept of synthetic lethality has emerged as a cornerstone of precision oncology in BRCA1/BRCA2-deficient cancers. By exploiting the unique DNA repair dependencies created by homologous recombination deficiency (HRD), synthetic lethal strategies enable selective eradication of tumor cells while sparing normal tissues. The clinical success of poly(ADP-ribose) polymerase (PARP) inhibitors has validated this approach and catalyzed the development of next-generation synthetic lethal therapies targeting replication stress and DNA damage response (DDR) pathways.

6.1 Concept and Biological Basis of Synthetic Lethality

DNA Repair Pathway Dependencies

Synthetic lethality arises when the simultaneous impairment of two genes or pathways results in cell death, whereas loss of either alone is compatible with survival. In BRCA-deficient tumors, inactivation of homologous recombination repair creates a profound dependency on backup DNA repair pathways, including base excision repair, single-strand break repair, and replication stress response pathways (Lord & Ashworth, 2017). These compensatory mechanisms become essential for maintaining minimal genomic integrity in the absence of functional BRCA1 or BRCA2.

Selective Tumor Cell Killing

The therapeutic appeal of synthetic lethality lies in its ability to achieve tumor-selective cytotoxicity. Normal cells, which retain functional BRCA-mediated HR repair, tolerate inhibition of compensatory pathways. In contrast, BRCA-deficient cancer cells accumulate irreparable DNA damage upon disruption of these pathways, leading to replication catastrophe and apoptosis (Kaelin, 2005). This differential vulnerability underpins the favorable therapeutic index observed with synthetic lethal agents in BRCA-mutant cancers.

6.2 PARP Inhibitors as Prototypical Synthetic Lethal Agents

Mechanism of Action

PARP enzymes, particularly PARP1, play a critical role in the detection and repair of single-strand DNA breaks (SSBs). PARP inhibitors (PARPi) block catalytic PARP activity, preventing efficient SSB repair and leading to the conversion of SSBs into double-strand breaks during DNA replication. In BRCA-proficient cells, these lesions are repaired by homologous recombination; however, in BRCA-deficient cells, the inability to repair DSBs results in lethal genomic instability (Bryant et al., 2005; Farmer et al., 2005).

PARP Trapping and DNA Repair Collapse

Beyond catalytic inhibition, PARP inhibitors induce PARP trapping, a process in which PARP1 becomes immobilized on DNA at sites of damage, physically obstructing replication fork progression. PARP trapping potency varies among agents, with talazoparib demonstrating particularly strong trapping activity (Murai et al., 2012). Trapped PARP–DNA complexes exacerbate replication stress, promote fork collapse, and drive widespread chromosomal fragmentation, culminating in synthetic lethal cell death in BRCA-mutant tumors.

6.3 Beyond PARP: Emerging Synthetic Lethal Targets

ATR, CHK1, and WEE1 Inhibitors

Given the chronic replication stress experienced by BRCA-deficient tumors, key regulators of the replication stress response have emerged as attractive synthetic lethal targets. ATR kinase senses stalled replication forks and coordinates cell-cycle arrest and DNA repair. Inhibition of ATR or its downstream effectors CHK1 and WEE1 abrogates S and G2/M checkpoints, forcing cells with damaged DNA into premature mitosis and inducing mitotic catastrophe (Pilie et al., 2019). Early-phase clinical trials suggest enhanced efficacy of these agents in HRD-positive tumors, either as monotherapies or in combination with PARP inhibitors.

POLθ and DNA-PK Inhibition

BRCA-deficient cells rely heavily on alternative, error-prone DNA repair pathways such as microhomology-mediated end joining (MMEJ), which is orchestrated by DNA polymerase theta (POLθ). Genetic or pharmacological inhibition of POLθ selectively kills HR-deficient cells, positioning POLθ as a promising synthetic lethal target (Ceccaldi et al., 2015). Similarly, inhibition of DNA-dependent protein kinase (DNA-PK) disrupts non-homologous end joining, further limiting DNA repair capacity and enhancing genomic instability in BRCA-mutant cancers.

Targeting Replication Stress Pathways

Additional strategies focus on amplifying replication stress through inhibition of proteins involved in fork stabilization, origin firing control, and nucleotide metabolism. Targeting these pathways can push BRCA-deficient cells beyond their tolerable threshold of genomic instability, offering opportunities for combination therapies designed to overcome resistance to PARP inhibitors (O’Connor, 2015).

Table 5. Synthetic Lethal Targets and Therapeutic Strategies in BRCA-Deficient Cancers