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Germline mutations in high penetrance genes are associated with worse clinical outcomes in patients with non–small cell lung cancer

Open AccessPublished:September 20, 2022DOI:https://doi.org/10.1016/j.xjon.2022.09.001

      Abstract

      Objective

      To determine the frequency of pathogenic mutations in high-penetrance genes (HPGs) in patients with non–small cell lung cancer (NSCLC) and identify whether such mutations are associated with clinicopathologic outcomes.

      Methods

      Patients with NSCLC who had consented to participate in a linked clinical database and biorepository underwent germline DNA sequencing using a next-generation sequencing panel that included cancer-associated HPGs and cancer risk–associated single nucleotide polymorphisms (SNPs). These data were linked to the clinical database to assess for associations between germline variants and clinical phenotype using Fisher's exact test and multivariable logistic and Cox regression.

      Results

      We analyzed 151 patients, among whom 33% carried any pathogenic HPG mutation and 23% had a genetic risk score (GRS) >1.5. Among the patients without any pathogenic mutation, 31% were at cancer stage II or higher, compared with 55% of those with 2 types of HPG mutations (P = .0293); 40% of patients with both types of HPG mutations had cancer recurrence, compared with 21% of patients without both types (P = .0644). In multivariable analysis, the presence of 2 types of HPG mutations was associated with higher cancer stage (odds ratio [OR], 3.32; P = .0228), increased recurrence of primary tumor (OR, 2.93; P = .0527), shorter time to recurrence (hazard ratio [HR], 3.03; P = .0119), and decreased cancer-specific (HR, 3.53; P = .0039) and overall survival (HR, 2.44; P = .0114).

      Conclusions

      The presence of mutations in HPGs is associated with higher cancer stage, increased risk of recurrence, and worse cancer-specific and overall survival in patients with NSCLC. Further large studies are needed to better delineate the role of HPGs in cancer recurrence and the potential benefit of adjuvant treatment in patients harboring such mutations.

      Video Abstract

      (mp4, (27.19 MB)

      Narrated presentation of the visual abstract.

      Figure thumbnail fx1

      Key Words

      Abbreviations and Acronyms:

      GRS (genetic risk score), HPG (high-penetrance gene), HR (hazard ratio), HGS (next-generation sequencing), NSCLC (non–small cell lung cancer), OR (odds ratio), OS (overall survival), SNP (single nucleotide polymorphism)
      Figure thumbnail fx2
      Cancer-specific survival stratified by type of pathogenic HPG mutations. Shaded areas represent Hall–Wellner 95% confidence bands.
      Carrier status for pathogenic germline mutations in high-penetrance genes in a non–small cell lung cancer population was associated with more advanced stage and worse clinical outcomes.
      Knowledge regarding the impact of germline mutations in non–small cell lung cancer is limited. This study suggests that germline pathogenic mutations in high-penetrance genes are associated with a more aggressive cancer phenotype. Future work combining germline genetic risk stratification along with somatic tumor changes may further improve our ability to treat patients with lung cancer.
      Advancements in our understanding of the somatic mutations in non–small cell lung cancer (NSCLC) has led to the development of targeted molecular therapy and immunotherapy, with practice-changing results.
      • Rosell R.
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      Erlotinib versus standard chemotherapy as first-line treatment for European patients with advanced EGFR mutation-positive non–small-cell lung cancer (EURTAC): a multicentre, open-label, randomised phase 3 trial.
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      Durvalumab after chemoradiotherapy in stage III non–small-cell lung cancer.
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      Neoadjuvant nivolumab plus chemotherapy in resectable lung cancer.
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      Osimertinib in resected EGFR-mutated non–small-cell lung cancer.
      The role of the patient's underlying genetic makeup also may have a significant impact on cancer development and outcomes, but this historically has received less attention than somatic driver mutations. The heritability of lung cancer was estimated at 18% in twin studies.
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      Familial risk and heritability of cancer among twins in Nordic countries.
      Population-based studies also have implicated family history as a significant risk factor for lung cancer.
      • Cannon-Albright L.A.
      • Carr S.R.
      • Akerley W.
      Population-based relative risks for lung cancer based on complete family history of lung cancer.
      Many questions regarding tumor biology cannot be answered based on somatic mutations alone: Why do some heavy smokers develop lung cancer while others do not? Why do some patients present with widely metastatic disease and others with a small primary tumor and a single metastasis? Why do cancers that are seemingly similar biologically have radically different outcomes in different patients?
      Across a variety of cancers, pathogenic germline mutations in high-penetrance genes (HPGs) have been implicated in both an increased risk of developing cancer and the development of more aggressive cancers. Our group has published work showing how a targeted inherited cancer panel including HPGs and using single nucleotide polymorphisms (SNPs) to generate a polygenic genetic risk score (GRS) not only can help identify patients at increased risk of developing prostate cancer, but also is associated with worse clinical outcomes.
      • Shi Z.
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      • et al.
      Performance of three inherited risk measures for predicting prostate cancer incidence and mortality: a population-based prospective analysis.
      ,
      • Xu J.
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      • Isaacs W.B.
      • Helfand B.T.
      Inherited risk assessment of prostate cancer: it takes three to do it right.
      Although research on germline mutations among lung cancer patients is in its early stages, recent evidence suggests that a considerably high proportion of lung cancer patients have germline pathogenic mutations in HPGs.
      • Liu M.
      • Liu X.
      • Suo P.
      • Gong Y.
      • Qu B.
      • Peng X.
      • et al.
      The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility.
      • Lu C.
      • Xie M.
      • Wendl M.C.
      • Wang J.
      • McLellan M.D.
      • Leiserson M.D.
      • et al.
      Patterns and functional implications of rare germline variants across 12 cancer types.
      • Parry E.M.
      • Gable D.L.
      • Stanley S.E.
      • Khalil S.E.
      • Antonescu V.
      • Florea L.
      • et al.
      Germline mutations in DNA repair genes in lung adenocarcinoma.
      • Tian P.
      • Cheng X.
      • Zhao Z.
      • Zhang Y.
      • Bao C.
      • Wang Y.
      • et al.
      Spectrum of pathogenic germline mutations in Chinese lung cancer patients through next-generation sequencing.
      Genes that have been associated with lung cancer include ATM, BRCA1, DIS3, ERCC2, FANCG, MRE11A, PALB2, PIK3C2G, and XRCC2 in lung adenocarcinoma, and BRCA2, BRIP1, DIS3, FANCA, FANCC, MAP3K15, and PARP3 and lung squamous cell carcinoma.
      • Schrader K.A.
      • Cheng D.T.
      • Joseph V.
      • Prasad M.
      • Walsh M.
      • Zehir A.
      • et al.
      Germline variants in targeted tumor sequencing using matched normal DNA.
      In this study, we used a prospectively collected linked clinical database and biorepository along with next-generation sequencing (NGS) of DNA to analyze the prevalence of pathogenic mutations in HPGs and overall GRS in patients with NSCLC. We also assessed for any association between pathogenic mutations and clinicopathologic outcomes, including cancer stage, histologic grade, cancer recurrence, and overall survival (OS) and cancer-specific survival. It was our hypothesis that an increased prevalence of pathogenic HPG mutations and elevated GRS would be associated with worse clinical outcomes.

      Methods

      Study Population

      The study cohort comprised patients with either primary lung adenocarcinoma or squamous cell carcinoma, diagnosed between March 1, 2013, and November 1, 2017, who had consented to participate in a prospectively collected linked clinical database and biorepository and had either a blood or tissue sample from which DNA could be extracted. Patients had to be age ≥18 years at the time of diagnosis. This study was approved by the NorthShore University HealthSystem Institutional Review Board (IRB EH18-162, March 20, 2018).

      Data Collection

      Clinicopathologic data, including age, sex, age at diagnosis, smoking history, clinical and pathologic stage, vital status, recurrence, and type of therapy, were obtained from a prospectively collected clinical database along with the electronic medical record and the institutional cancer registry.

      Genetic Analysis

      Germline DNA was sequenced using a targeted NGS panel targeting 355 HPGs and 23 SNPs associated with lung cancer risk (Online Data Supplement). HPGs are genes in which rare disruptive or protein-truncating variants confer a high risk of disease. The probes for capturing exon regions in these genes were manufactured by Roche NimbleGen. The SeqCap EZ Library SR User's Guide (Roche) was followed for library preparation and capture of targeted sequences. Paired-end sequencing of 2 × 150 bp was performed on an Illumina NextSeq500 sequencer. The median coverage for the samples was at 300×.
      Candidate HPGs evaluated in this study include those involved in DNA repair and/or cancer-related genes. Selection of DNA repair genes was based on the catalog of 178 human DNA repair genes, including genes involved in base excision repair, nucleotide excision repair, mismatch repair, homologous recombination, and nonhomologous end joining.
      • Lange S.S.
      • Takata K.
      • Wood R.D.
      DNA polymerases and cancer.
      Cancer-related genes were selected based on our review of published articles on susceptibility genes in all major types of cancer, including lung cancer.
      • Stoffel E.M.
      Screening in GI cancers: the role of genetics.
      ,
      • Rahman N.
      Realizing the promise of cancer predisposition genes.
      Cancer-related genes have a very broad range of functions, including those ubiquitously expressed, and participate in such fundamental processes as cell cycle regulation.

      Bioinformatics Analysis

      Paired-end reads were aligned to the GRCh37 version of the human genome using Burrows–Wheeler Aligner v0.7 to generate BAM files.
      • Li H.
      • Durbin R.
      Fast and accurate short read alignment with Burrows-Wheeler transform.
      After sorting the BAM files using samtools, polymerase chain reaction duplicates were marked using Picard, and realignment around putative gaps was performed using the Genome Analysis Toolkit v3.2-2. Variant calling was performed with the Genome Analysis Toolkit Haplotype caller. ANNOVAR (http://annovar.openbioinformatics.org/en/latest) and snpEff were used for annotating variants and for retrieving information on variants in the population-based studies, such as the 1000 Genomes Project (www.1000genomes.org), NHLBI-ESP 6500 exomes, ExAC (http://exac.broadinstitute.org/), and gnomAD (http://gnomad.broadinstitute.org/), and clinical databases, such as the Human Gene Mutation Database
      • Stenson P.D.
      • Ball E.V.
      • Mort M.
      • Phillips A.D.
      • Shiel J.A.
      • Thomas N.S.
      • et al.
      Human gene mutation database (HGMD): 2003 update.
      and ClinVar.
      • Landrum M.J.
      • Lee J.M.
      • Riley G.R.
      • Jang W.
      • Rubinstein W.S.
      • Church D.M.
      • et al.
      ClinVar: public archive of relationships among sequence variation and human phenotype.
      The pathogenicity of variants was defined based on American College of Medical Genetics and Genomics criteria.
      • Green R.C.
      • Berg J.S.
      • Grody W.W.
      • Kalia S.S.
      • Korf B.R.
      • Martin C.L.
      • et al.
      ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.
      Specifically, pathogenic and likely pathogenic mutations are defined as (1) all protein-truncating mutations unless their allele frequency is ≥5% in any racial group in population databases or is reported as benign or likely benign in ClinVar, and (2) nonsynonymous changes if their allele frequency is <5% and reported as pathogenic and likely pathogenic mutations in ClinVar.

      GRS

      GRS, a population-standardized polygenic risk score (PMID: 31037745), was calculated based on 23 lung cancer risk–associated SNPs identified from previous genome-wide associated studies as
      GRS=i=1nORigiWi


      Wi = fi2ORi2+2fi(1-fi)ORi+(1-fi)2


      where gi is the genotype of SNP i in an individual (0, 1, or 2 risk alleles), ORi is the odds ratio (OR) of SNP i estimated from external studies, and fi is the risk allele frequency of SNP i based on gnomAD (non-Finnish European population). The GRS value can be interpreted as relative risk to the general population.

      Statistical Analysis

      The genomic data were linked to the corresponding clinical database. Because consent for the biorepository and clinical database was granted prior to the revised common rule outlining broad consent, the genetic data and the clinical data were kept separate and were linked only by an “honest broker,” which kept the investigators blinded to the link between genetic data and any protected health information.
      With the blinded, linked data, we assessed for associations between germline mutations and clinical phenotype, including pathologic stage, tumor grade, and disease recurrence, using Fisher's exact test. Recurrence rate was defined as any recurrence of the primary tumor. Time to recurrence was measured from the last day of definitive treatment to the documented first recurrence. OS and cancer-specific survival were measured from the date of diagnosis. No adjustments for multiple comparisons were made because of the small sample size with too few mutations and clinical events for adequate power. Univariate analyses of time to recurrence, OS, and cancer-specific survival were performed using the Kaplan–Meier method and log-rank test. Estimated 5-year survival rates were reported. Multivariable logistic regression and Cox regression were used to assess factors associated with clinical outcomes. OR was reported for logistic regression, and hazard ratio (HR) was reported for Cox regression. All statistical analyses were performed using SAS 9.4 (SAS Institute) with 2-tailed tests and a significance level of P < .05.

      Results

      Demographics

      We analyzed 151 patients with NSCLC for whom both genetic material and clinicopathologic data were available. Demographic and clinicopathologic data for the entire cohort are presented in Table 1. The majority of patients were at pathologic stage I (n = 96; 64%) with only 7 patients (4.6%) at pathologic stage IV. Twenty-seven patients (18%) were never smokers, and only 13 (9%) were current smokers. Thirty-eight patients (26%) had a family history of lung cancer, and 92 patients (65%) had a family history of other cancers. Most cancers were adenocarcinomas (n = 109; 72%). Thirty-five patients (35%) had documented recurrence of their primary cancer.
      Table 1Patient characteristics
      CharacteristicValue
      Total patients151
      Age, y, mean ± SD69 ± 9
      Female sex, n (%)91 (60.3)
      Race, n (%)
       Caucasian135 (89.4)
       African American4 (2.6)
       Asian8 (5.3)
       Other4 (2.6)
      Smoking status, n (%)
       Never smoker27 (17.9)
       Former smoker111 (73.5)
       Current smoker13 (8.6)
      Pack-y smoked, median (IQR) (missing, n = 38)30 (21-50)
      Previous history of lung cancer, n (%)7 (4.6)
      Family history of lung cancer, n (%) (missing, n = 4)38 (25.9)
      Family history of other cancer, n (%) (missing, n = 9)92 (64.8)
      Topology, n (%) (missing, n = 3)
       Upper lobe83 (56.1)
       Middle lobe10 (6.8)
       Lower lobe55 (37.2)
      Histology, n (%)
       Adenocarcinoma109 (72.2)
       Squamous cell carcinoma42 (27.8)
      Laterality, n (%)
       Left61 (40.4)
       Right90 (59.6)
      Surgery type, n (%)
       None7 (4.6)
       Wedge20 (13.2)
       Segmentectomy12 (7.9)
       Lobectomy112 (74.2)
      Complications, n (%) (missing, n = 10)46 (32.6)
      Lymph node dissection, n (%) (missing, n = 4)141 (95.9)
      Lymph nodes examined, n, median (IQR)13 (8-18)
      Lymph nodes positive, n, median (range) (missing, n = 9)0 (0-7)
      Surgical resection, n (%) (missing, n = 23)
       R0127 (99.2)
       R11 (0.8)
       R20
      AJCC pathologic staging, n (%)
       pT stage
      pT05 (3.3)
      pT181 (53.6)
      pT246 (30.5)
      pT3-T419 (12.6)
       pN stage
      pN0119 (78.8)
      pN115 (9.9)
      pN216 (10.6)
      pN31 (0.7)
       pM stage
      pM0147 (97.4)
      pM14 (2.6)
      Pathologic stage group, n (%)
       I96 (63.6)
       II31 (20.5)
       III17 (11.3)
       IV7 (4.6)
      Lymphovascular invasion, n (%) (missing, n = 19)23 (17.4)
      Tumor grade, n (%) (missing, n = 16)
       Well differentiated44 (32.6)
       Moderately/moderately to poorly differentiated50 (37.0)
       Poorly differentiated41 (30.4)
      Chemotherapy, n (%)49 (32.5)
      SD, Standard deviation; IQR, interquartile range; AJCC, American Joint Committee on Cancer.

      Genetic Analysis

      We identified 50 patients (33%) who were carriers of any pathogenic mutation of HPGs, with 34 patients (23%) carrying a pathogenic mutation in a cancer-related gene, 38 (25%) harboring a pathogenic mutation in a DNA repair gene (25%), and 22 (15%) harboring a pathogenic mutation in a gene involved in both DNA repair and cancer-related functions (Table 2). The most common mutations were a GBA, MUTYH, or POLQ mutation in 4 patients (3%) and either a CHEK2 or GJB2 mutation in 3 patients (2%). The mean GRS was 1.2; 34 patients (23%) had a GRS >1.5 and 16 (11%) had a GRS >2.0.
      Table 2Frequency of cancer-related and DNA repair genes
      Cancer-related genesDNA repair genes, n (%)
      NoncarrierCarrierTotal
      Noncarrier101 (66.9)16 (10.6)117 (77.5)
      Carrier12 (8.0)22 (14.6)34 (22.5)
      Total113 (74.8)38 (25.2)151 (100)

      Clinicopathologic Outcomes

      Both carrier status of a pathogenic HPG mutation and elevated GRS were associated with a higher pathologic stage, with the strength of the association varying based on the degree of genetic mutation (Figure 1, A). Among the patients with no pathogenic HPG mutation, 31% (31 of 101) presented at stage II or higher and 11% (11 of 101) were at stage III or higher. Among patients with a pathogenic mutation in either a cancer-related gene or a DNA repair gene but not both, 43% (12 of 28) were at stage II or higher and 21% (6 of 28) were at stage III or higher, a rate not statistically different from those without any mutations (P = .3069). For patients who were carriers for both a cancer-related gene and a DNA repair gene pathogenic mutation, there was a significant clinical and statistical difference compared to patients without any mutation, with 55% (12 of 22) presenting at stage II or higher and 32% (7 of 22) presenting at stage III or higher (P = .0293). When combined with an elevated GRS, the presence of any pathogenic HPG mutation showed the largest difference compared to those without any mutation (P = .0147). Although only 11 patients had both an HPG mutation and a GRS >1.5, 8 of them (73%) were at stage II or higher and 4 (36%) were at stage III or higher. GRS alone was not associated with later stage at presentation. There was not significant association between HPGs or GRS and histologic grade.
      Figure thumbnail gr1
      Figure 1Pathologic stage (A) and recurrence of primary tumor (B) stratified by high-penetrance gene (HPG) mutation and genetic risk score (GRS). HPG, High-penetrance gene; GRS, genetic risk score.
      We also looked at recurrence of the primary tumor and found a higher overall rate of recurrence in patients with a pathogenic HPG mutation compared with patients without an HPG mutation, with the degree of statistical significance varying according to the type of HPG mutation. Recurrence data were available for the entire cohort. Nine patients where never disease-free and were excluded from the analysis. The clinical association was strongest in patients with pathogenic mutations in both a DNA repair gene and a cancer-related gene, as 8 out of the 20 patients (40%) harboring such mutations experienced recurrence, compared with only 20 of 97 patients (21%) without any pathogenic mutation, although the statistical association fell just below the preset threshold of significance (P = .0644) (Figure 1, B). Patients who were carriers of a pathogenic HPG mutation in either a cancer-related gene or a DNA repair gene had only a slightly higher rate of primary tumor recurrence compared with patients who were not carriers of any pathogenic HPG mutation (28% [7 of 25] vs 21%; P = .4279). Unlike stage at presentation, the combination of a pathogenic HPG mutation and elevated GRS did not have a meaningful clinical or statistical difference with respect to overall recurrence (P = .6783).
      In addition to overall recurrence rate, we measured time to recurrence, OS, and cancer-specific survival (Figure 2). Among patients without any pathogenic HPG mutation, 80% were free of recurrence at 5 years, compared with only 69% of patients harboring a pathogenic mutation in either a cancer-related gene or a DNA repair gene but not both and only 55% of patients harboring pathogenic mutations in both a cancer-related gene and a DNA repair gene (P = .0330 both vs none) (Figure 2, A). The 5-year OS rate for patients without any pathogenic mutation was 75%, compared with 68% for patients with only one type of mutation and 51% for those harboring mutations in both a cancer-related gene and a DNA repair gene (P = .0063 both vs none) (Figure 2, B). The 5-year cancer-specific survival rate for patients without any pathogenic mutation was 86%, compared with 77% for patients with only one type of mutation and 65% for patients with mutations in both a cancer-related gene and a DNA repair gene (P = .0020 both vs none) (Figure 2, C).
      Figure thumbnail gr2
      Figure 2Kaplan-Meier curves of time to recurrence (A), overall survival (B), and cancer-specific survival (C) stratified by type of high-penetrance gene (HPG) mutation. Shaded areas represent Hall–Wellner 95% confidence bands. HPG, High-penetrance gene.
      Multivariable logistic and Cox regression analysis was performed on all clinical and genetic variables to assess for association with increased tumor grade, increased pathologic stage at presentation, recurrence of primary tumor, OS, and cancer-specific survival (Tables 3 and 4). None of the genetic variables were associated with increased tumor grade, although patients with squamous cell cancer were much more likely to have moderate to poor tumor grade (HR, 5.53; P = .0032). Harboring a mutation in both a DNA repair gene and a cancer-related gene was most strongly associated with presentation at higher stage (OR, 3.32; P = .0228), shorter time to recurrence (HR, 3.03; P = .0119), worse OS (HR, 2.44; P = .0114), and worse cancer-specific survival (HR, 5.53; P = .0039) compared with a lack of pathogenic mutation. We also found evidence of an association with any recurrence of the primary tumor (OR, 2.93; P = .053), although with a weaker statistical significance than the other clinical outcomes. Patients harboring only a mutation in either a DNA repair gene or a cancer-related gene did not show any statistically significant differences compared with those without any pathogenic mutation. GRS was not associated with any measured pathologic or clinical outcomes.
      Table 3Multivariable logistic regression analysis
      VariablesModerate to poor tumor gradePathologic stage II-IVRecurrence of primary tumor
      OR (95% CI)P valueOR (95% CI)P valueOR (95% CI)P value
      Female vs male1.06 (0.43-2.59).89800.57 (0.27-1.20).13850.81 (0.35-1.89).6248
      Current or former smoker, yes vs no1.26 (0.48-3.33).64071.05 (0.37-3.03).92591.93 (0.53-7.07).3230
      Histology, squamous cell vs adenocarcinoma62.59 (3.99-982.72).00321.44 (0.61-3.40).40801.07 (0.43-2.70).8845
      Lymphovascular invasion, yes vs no1.73 (0.55-5.46).35085.93 (2.14-16.46).00061.78 (0.60-5.35).3016
      Pathogenic HPG mutation
       Cancer-related or DNA repair vs none1.21 (0.41-3.54).73041.80 (0.68-4.76).23611.06 (0.34-3.33).9198
       Cancer-related and DNA repair genes vs none0.87 (0.22-3.48).83863.32 (1.18-9.31).02282.93 (0.99-8.68).0527
      Significant P values are in bold type. OR, Odds ratio; CI, confidence interval; HPG, high-penetrance gene.
      Table 4Multivariable Cox regression analysis
      VariablesTime to recurrenceOverall survivalCancer-specific survival
      HR (95% CI)P valueHR (95% CI)P valueHR (95% CI)P value
      Female vs male0.79 (0.40-1.56).49380.64 (0.37-1.10).10620.70 (0.34-1.45).3366
      Current or former smoker, yes vs no1.82 (0.61-5.41).28182.55 (0.82-7.94).10741.40 (0.42-4.68).5825
      Histology, squamous cell vs adenocarcinoma1.26 (0.61-2.63).53651.80 (1.02-3.18).04331.79 (0.83-3.84).1375
      Lymphovascular invasion, yes vs no1.83 (0.71-4.76).21381.93 (0.95-3.90).06902.37 (0.90-6.23).0802
      Pathogenic HPG mutation
       Cancer-related or DNA repair vs none0.85 (0.34-2.13).72301.87 (0.95-3.68).07062.01 (0.82-4.93).1257
       Cancer-related and DNA repair genes vs none3.03 (1.28-7.20).01192.44 (1.22-4.86).01143.53 (1.50-8.34).0039
      Significant P values are in bold type. HR, Hazard ratio; CI, confidence interval; HPG, high-penetrance gene.

      Discussion

      In this study of 151 patients with NSCLC, we found that more than 30% of the patients harbored a pathogenic mutation in an HPG, and nearly 25% had a GRS >1.5. We also identified an association between the presence of HPG pathogenic mutations and a more aggressive clinical phenotype. Patients who were carriers for pathogenic HPG mutations were more likely to present at a higher pathologic stage, had an increased likelihood of cancer recurrence and shorter time to recurrence, and had decreased OS and cancer-specific survival, with the strongest clinical and statistical associations seen in patients harboring pathogenic mutations across both cancer-related genes and DNA repair genes. Although GRS by itself was not associated with a more aggressive cancer phenotype, those patients who had both an HPG mutation and an elevated GRS were much more likely to present at a more advanced pathologic stage (Figure 3 and Video 1).
      Figure thumbnail gr3
      Figure 3Graphical abstract summarizing the background, methods, major findings, and implications of this study. HPG, High-penetrance gene; GRS, genetic risk score.
      There are relatively few published studies on germline HPG mutations and NSCLC, and many of them had either small patient samples or used relatively small gene panels. One exception is a large study from China that looked at 1764 patients using a 381-gene NGS panel and found pathogenic or likely pathogenic mutations in 3.8% of the patients and in 25 different genes, the majority of which are involved in DNA repair pathways.
      • Tian P.
      • Cheng X.
      • Zhao Z.
      • Zhang Y.
      • Bao C.
      • Wang Y.
      • et al.
      Spectrum of pathogenic germline mutations in Chinese lung cancer patients through next-generation sequencing.
      A separate study of 1026 patients that used a much smaller 58-gene panel found pathogenic or likely pathogenic mutations in 4.7% of the patients.
      • Liu M.
      • Liu X.
      • Suo P.
      • Gong Y.
      • Qu B.
      • Peng X.
      • et al.
      The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility.
      Although neither of these studies looked at outcomes, the second study did look at family history. Patients with pathogenic or likely pathogenic mutations were more likely than patients without such mutations to have a first-degree relative who also had lung cancer. Compared with the general population, patients with lung cancer were nearly 18 times more likely to have a pathogenic or likely pathogenic mutation.
      These findings suggest that these mutations are associated with an increased risk of developing lung cancer. The most common mutations were in BRCA2, CHECK2, and ATM. In our study, we found a significantly higher proportion of patients—33%—who harbored an HPG mutation. Whether this is due to differences in the panels is unclear, although the larger study used a 381-gene panel, so that is unlikely to be the sole reason. Our population was mostly Caucasian, compared with an East Asian population in the Chinese studies, and further validation across more varied and larger populations will be necessary. CHECK2 was also among the higher-frequency mutations in our study, but still represented only 2% of the total patients and 6% of patients with an HPG mutation.
      Even fewer studies have examined the clinical impact of germline mutations in lung cancer. Reckamp and colleagues
      • Reckamp K.L.
      • Behrendt C.E.
      • Slavin T.P.
      • Gray S.W.
      • Castillo D.K.
      • Koczywas M.
      • et al.
      Germline mutations and age at onset of lung adenocarcinoma.
      published a study in 2021 that looked a subset of mutations, specifically TP53/EGFR, BRCA2, Fanconi anemia (FA) genes, and non-FA DNA repair genes, in 187 patients with NSCLC. They found a similar proportion of patients with pathologic variants as we found in our study (26.7% vs 33%) and an earlier age of cancer onset depending on the gene mutation. The greatest impact was in patients with a BRCA2 mutation, in whom cancer was diagnosed a median of 12.2 years earlier than in patients without this mutation. TP53, EGFR, and FA genes all showed associations with earlier age of onset, whereas non-FA DNA repair genes were not associated with age of onset. A separate study of 12 different cancers and >4000 patients found that pathogenic germline mutations were associated with early age of onset across multiple cancers.
      • Lu C.
      • Xie M.
      • Wendl M.C.
      • Wang J.
      • McLellan M.D.
      • Leiserson M.D.
      • et al.
      Patterns and functional implications of rare germline variants across 12 cancer types.
      In that study, lung cancer patients with a BRCA1 or BRCA2 mutation presented at a median age of 63 years, compared with 66 years for patients who did not carry a pathogenic mutation.
      • Lu C.
      • Xie M.
      • Wendl M.C.
      • Wang J.
      • McLellan M.D.
      • Leiserson M.D.
      • et al.
      Patterns and functional implications of rare germline variants across 12 cancer types.
      An analysis of 119 patients with NSCLC looked the relationship between repair gene (ERCC1, XP, and XRCC1) and glutathione S-transferase gene (GSTP1, GSTT1, and GSTM1) SNPs and clinical outcomes, including response to response to platinum-based chemotherapy, treatment toxicity, and OS.
      • Kalikaki A.
      • Kanaki M.
      • Vassalou H.
      • Souglakos J.
      • Voutsina A.
      • Georgoulias V.
      • et al.
      DNA repair gene polymorphisms predict favorable clinical outcome in advanced non–small-cell lung cancer.
      In that study, SNPs within ERCC1 were associated with improved treatment response and better OS (9.8 months vs 14.1 months), whereas the combination of ERCC1 and XRCC1 polymorphisms was identified as a prognostic factor for improved OS in a Cox multivariable analysis.
      • Kalikaki A.
      • Kanaki M.
      • Vassalou H.
      • Souglakos J.
      • Voutsina A.
      • Georgoulias V.
      • et al.
      DNA repair gene polymorphisms predict favorable clinical outcome in advanced non–small-cell lung cancer.
      The clinical implications of our findings are unclear. As highlighted, this is a burgeoning field, and although the data presented here are intriguing, this study is merely a starting point for further research into the complex interplay between patients' genetic risk and cancer outcomes. The outcomes on which we focused—stage at presentation, cancer recurrence, and OS and cancer-specific survival—are complex and lie at the intersection of numerous competing factors, including underlying patient genetics, epigenetic and environmental factors, tumor-specific factors, and social determinants of health. In the study reported by Lu and colleagues,
      • Lu C.
      • Xie M.
      • Wendl M.C.
      • Wang J.
      • McLellan M.D.
      • Leiserson M.D.
      • et al.
      Patterns and functional implications of rare germline variants across 12 cancer types.
      germline mutations in BRCA1 and BRCA2 were associated with a greater frequency of somatic mutations across multiple cancers. This is especially relevant in light of several recently reported studies using serum biomarkers and tumor molecular profiling to identify patients at increased risk of cancer recurrence. Seder and colleagues
      • Seder C.W.
      • Arndt A.T.
      • Jordano L.
      • Basu S.
      • Fhied C.L.
      • Sayidine S.
      • et al.
      Serum biomarkers may prognosticate recurrence in node-negative, non–small cell lung cancers less than 4 centimeters.
      used a panel of 47 biomarkers to accurately identify patients with early-stage cancer <4 cm who were at risk of recurrence with a negative predictive value of 83% and overall accuracy of 78%. A now commercially available product (DetermaRx; Oncocyte) uses a 14-gene panel (of tumor somatic mutations) and has been shown to very accurately predict recurrence and to guide adjuvant chemotherapy use in patients with stage I-IIA NSCLC.
      • Woodard G.A.
      • Kratz J.R.
      • Haro G.
      • Gubens M.A.
      • Blakely C.M.
      • Jones K.D.
      • et al.
      Molecular risk stratification is independent of EGFR mutation status in identifying early-stage non–squamous non–small cell lung cancer patients at risk for recurrence and likely to benefit from adjuvant chemotherapy.
      ,
      • Kratz J.R.
      • Haro G.J.
      • Cook N.R.
      • He J.
      • Van Den Eeden S.K.
      • Woodard G.A.
      • et al.
      Incorporation of a molecular prognostic classifier improves conventional non–small cell lung cancer staging.
      In future studies, we hope to study the interaction between somatic predictors of recurrence with a patient's underlying genetic risk. This may allow us to better stratify which patients are at risk for recurrence and poor outcomes and which patients may respond best to the ever-increasing number of available therapies, and could serve as the next level of advancement in treating patients with lung cancer.

      Study Limitations

      Our study has several limitations. First, our population was relatively small, consisting of only 151 patients, the majority of whom were stage I, which may preclude generalization to the broader lung cancer population. Second, the overall frequency of pathogenic mutations and clinical events was small, and thus our results may be underpowered to show a statistically significant impact, especially in patients with only a single class of gene mutation. The mutation frequency in specific genes was even lower, leaving us unable to draw any specific conclusions with respect to specific mutations and clinicopathologic outcomes. Third, the targeted NGS panel was developed based on studies published before 2017, and as such, several newly reported lung cancer risk-associated SNPs were not analyzed, including the recent genome-wide associated study of Gabriel and colleagues.
      • Gabriel A.A.
      • Atkins J.R.
      • Penha R.C.
      • Smith-Byrne K.
      • Gaborieau V.
      • Voegele C.
      • et al.
      Genetic analysis of lung cancer and the germline impact on somatic mutation burden.

      Conclusions

      Our study is one of the first in a North American population to apply a large gene panel to patients with NSCLC. Unlike previous studies that correlated results with specific mutations, our study has demonstrated that genome-wide identification of pathogenic HPG mutations is associated with worse outcomes, most significantly in patients with mutations in multiple oncogenic pathways. Further studies, including larger studies and studies considering somatic variables, will help further define the role of genetic testing in the treatment of NSCLC (Video Abstract).

      Webcast

      You can watch a Webcast of this AATS meeting presentation by going to: https://www.aats.org/resources/1588.
      Figure thumbnail fx3

      Conflict of Interest Statement

      The authors reported no conflicts of interest.
      The Journal policy requires editors and reviewers to disclose conflicts of interest and to decline handling or reviewing manuscripts for which they may have a conflict of interest. The editors and reviewers of this article have no conflicts of interest.

      Supplementary Data

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