The enrichment of Fanconi anemia/homologous recombination pathway aberrations in ATM/ATR-mutated NSCLC was accompanied by unique molecular features and poor prognosis

Normal cells are persistently exposed to exogenous and endogenous challenges that induce DNA damage, and DNA damage response (DDR) pathways help maintain the integrity of the genome and prevent neoplasia, as DDR is closely associated with cell cycle arrest, DNA repair, and apoptotic machinery [1]. As a result, genomic instability caused by DDR deficits is one of the key hallmarks of cancer, given that DDR is critical for both tumorigenesis and cancer treatment [2]. Ataxia telangiectasia mutated protein (ATM) and Ataxia telangiectasia and Rad3 related protein (ATR), which belong to the phosphatidylinositol 3-kinase-related kinase (PIKK) family, are two of the major regulators of DDR [3]. Indeed, more than 4000 cancer-associated ATM/ATR mutations were identified in various types of cancer, including lung cancer, breast cancer, colorectal cancer, pancreatic cancer, prostate cancer, and endometrial cancer, although the function and cancer implications of most of these ATM/ATR mutations were largely unknown [4]. Therefore, it is clinically important to characterize pathogenic ATM/ATR mutations, which would in turn help infer the involvement of other variants of uncertain significance of these two PIKK genes in cancer.

Previous studies have found the close interplay among different DDR pathways, and the deficiency in one DDR factor leads to heavy dependence on other DDR components in order to maintain viability during DNA damage [5]. This provides a promising strategy to target cancer. Besides the well-known poly(ADP-ribose) polymerase (PARP) inhibitors to target BRCA1/2-deficient cancers [6], preclinical studies have shown that defects in ATM, BRCA1/2, and TP53 confer sensitivity to ATR inhibition in tumor cells [7‐10]. Thereby, multiple different ATM and ATR inhibitors have been developed, many of which are currently under clinical investigation [11, 12]. For example, Berzosertib is a highly potent and first-in-class ATR inhibitor that has demonstrated promising results during phases I and/or II clinical trials against non-small cell lung cancer (NSCLC) [13], small cell lung cancer [14], triple-negative breast cancer [15], high-grade serous ovarian cancer [16], and advanced solid tumors [17, 18]. Several other ATR inhibitors (e.g., Ceralasertib, M4344, and Elimusertib) and ATM inhibitors (e.g., AZD0156, AZD1390, KU60019, M3541, and M4076) are also being actively studied [19‐25]. As a result, it is imperative to identify a subset of patients who may benefit from these newly developed ATM/ATR inhibitor drugs.

In the current study, we retrospectively investigated 191 NSCLC patients with pathogenic or likely pathogenic ATM/ATR mutations using large-panel next-generation sequencing (NGS), and the result was then compared with that of 308 NSCLC patients without any types of ATM/ATR variants to elucidate the PIKK aberration-associated clinical and genomic features. Our conclusions were then further validated using an external cohort of 2727 NSCLC patients (48 with pathogenic/likely pathogenic ATM/ATR mutations and 2679 without any ATM/ATR variations) from publicly available NGS databases. We aimed to demonstrate the unique molecular patterns associated with ATM/ATR alterations in NSCLC and stratify patients for targeted therapy.

The DDR pathways are promising targets for anti-cancer therapy, and various DDR-related genes are currently under clinical development, such as PARP, ATM, ATR, DNA-PK, CHK1, CHK2, and WEE1 [37]. Our study focused on the pathogenic mutations of ATM and ATR, as both genes are from the PIKK family that is critically involved in DNA damage repair in normal cells as well as tumor cells. Intriguingly, we found that NSCLC patients with either of these two PIKK gene alterations were significantly associated with higher TMB and MSI, but not chromosomal instabilities. This result is consistent with the cellular function of ATM/ATR, given that ATM primarily regulates the DNA double-strand breaks response while ATR is mainly activated by extensive single-strand DNA structures that result from stalled DNA replication forks [38]. Two major categories of signaling pathways were enriched in patients with ATM/ATR mutations, including proliferation-related and DNA repair-related pathways. In particular, ATM/ATR-mutated patients have a profound enrichment of FA and HR pathway aberrations, and these NSCLC patients had more mutational burdens, higher MSI, and worse prognosis. To the best of our knowledge, this is the largest study that analyzes the molecular and clinical implications of pathogenic ATM/ATR mutations in NSCLC.

DDR-related PIKK genes are commonly mutated in cancer [39]. Waskiewicz et al. reported 2551 ATM mutations and 1,394 ATR mutations from 46,588 tumor samples [4]. Notably, most of these mutations were variants of uncertain significance (VUS), and only a few of them were located at the kinase active site. As a result, it would be difficult to infer the clinical characteristics and implications of loss-of-function mutations of ATM/ATR in cancer patients. We, thereby, focused on the pathogenic and likely pathogenic ATM/ATR mutations, most of which were frameshift and nonsense changes that disrupted critical domains of these proteins. The unique genetic profiles and features that were associated with known pathogenic ATM/ATR mutations could then be used to predict the function of ATM/ATR VUS in future studies. Additionally, we found that ATM/ATR pathogenic mutations were frequently accompanied by FA/HR mutations in NSCLC patients, which is not observed in the non-ATM/ATR counterparts. This might imply a potential tumorigenesis process driven by detrimental DDR alterations in NSCLC. That is, the acquisition of one copy of ATM/ATR pathogenic mutation in pre-cancerous cells might not be sufficient to drive NSCLC tumor formation, and it also requires aberrations in FA/HR to disrupt the DDR pathways, thus further elevating the mutational rate and increasing the chance to introduce other crucial oncogenic mutations (Additional file 1: Fig S9). Consistent with this speculation, we observed that patients with both ATM/ATR and FA/HR mutations had the highest level of TMB and MSI, and they were also likely to harbor mutations in various proliferation-related pathways. Therefore, it is possible that the concurrent FA/HR aberrations and ATM/ATR mutations help fine-tune the DDR machinery to introduce enough mutations to drive tumorigenesis/tumor progression while keeping certain levels of genomic integrity to maintain tumor cell survival.

It has been shown that ATM and ATR regulate partially overlapped but nonredundant downstream pathways during DNA repair [40], and defects in one PIKK protein might be compensated by the other to maintain the survival of cancer cells [12]. For example, loss of ATM in tumors makes tumors more rely on ATR-mediated intra-S and G2/M checkpoints [41], and inhibition of ATR could selectively kill cancer cells with ATM deficiency [7]. Although most of the NSCLC patients in our cohort harbored only one pathogenic ATM/ATR mutation, the additional FA/HR mutations could further weaken the DDR pathways, making them vulnerable to further DDR inhibition. Multiple previous pre-clinical and clinical studies have investigated the use of specific DDR inhibitors to target tumors with some DDR mutations/deficiencies. In a phase 1b clinical trial, Plummer et al. explored the effects of berzosertib in advanced NSCLC with different DDR mutational statuses [13]. Intriguingly, they found that TMB levels, rather than the mutation of a single DDR gene, were better associated with the response to berzosertib, and patients with high TMB tended to have an improved objective response rate. Furthermore, Schram et al. conducted a phase 2b trial to treat patients with BRCA1/2- or ATM-altered advanced solid tumors using avelumab (an anti-PD-L1 monoclonal antibody) plus talazoparib (a PARP inhibitor) [42]. Although the trial did not meet the prespecified objective response rate, they found that the drug response rate in TMB-high patients was higher than in TMB-low patients. We discovered that ATM/ATR-mutated, FA/HR-altered patients had significantly higher TMB/MSI and poor prognosis. The FA pathway could repair DNA interstrand crosslinks [43], whereas the HR pathway is well known to regulate DNA double-strand break repair [44]. Cai’s group found that knockout of both ATM and genes in the FA pathway inhibited end resection and induced toxic levels of non-homologous DNA end joining, and FA-deficient tumors were sensitive to ATM inhibitors [45]. The dual DDR mutations in ATM/ATR-mutated, FA/HR-altered tumors were likely to make them susceptible to further DDR inhibition while high TMB/MSI are predictive markers for better response to immune checkpoint inhibitors (ICIs) [46]. Therefore, this sub-cohort of NSCLC might benefit from DDR inhibitor and/or immunotherapy treatments.

There were several limitations of our study. Firstly, as the clinical outcome of most of the patients were not available, we cannot perform further prognostic analyses. Secondly, although DNA-PK is another major DDR-related PIKK, we were not able to recruit enough NSCLC patients with pathogenic DNA-PK mutations. Therefore, future studies are necessary to investigate whether DNA-PK mutations would have similar clinical impacts on NSCLC patients when compared with those with ATM/ATR mutations. Further, the interaction between ATM/ATR and FA/HR mutations at cellular levels are unclear and may contribute to clinical outcomes; thus, mechanistic explorations are needed in future studies. Moreover, we acknowledge the potential contribution of tumor heterogeneity to our findings; however, the targeted NGS and RNA-seq used in this study are bulk sequencing methods, which have limited ability to differentiate cell subpopulations in tumor tissues. Future studies using other advanced sequencing technologies, such as single-cell DNA/RNA sequencing, hold great promise for revealing the contribution of tumor heterogeneity to the observations made in our study. Lastly, due to the limited time and resources of this project, there is no experimental or functional validation of the results using NSCLC cell lines; however, we believe this work has achieved its intended objective of uncovering the clinical relevance and molecular landscape of ATM/ATR mutations in NSCLC using largescale real-world patient genomics datasets, presenting a strong foundation for subsequent mechanistic investigations.

In conclusion, we performed comprehensive genomic analysis to investigate the molecular and clinical significance of ATM/ATR pathogenic mutations in NSCLC, and we found ATM/ATR-mutated patients have a unique mutational profile and a specific enrichment of FA/HR aberrations, which might result in elevated nucleotide-level changes and poor prognosis. Our results proposed a novel DDR-driven tumorigenesis/progression model for NSCLC, and their reliance on aberrant DDR pathways implies the potential use of DDR inhibitors and/or immunotherapy to treat this subset of NSCLC patients.