Whole-Exome Sequencing Identifies Somatic Mutations Associated With Lung Cancer Metastasis to the Brain

DOI: https://doi.org/10.21203/rs.3.rs-74758/v1


Background: Lung cancer is the most aggressive cancer which representing one-quarter of all cancer-related deaths, and metastatic spread accounts for >70% of these deaths, especially brain metastasis. Metastasis associated mutations are important biomarkers for metastasis prediction and outcome improvement.  

Methods: In this study, we applied whole-exome sequencing to identify potential metastasis related mutation in 12 paired lung cancer and brain metastasis samples.

Results: We identified 1,702 SNVs and 6,131 mutation events in 1,220 genes. Furthermore, we identified several lung cancer metastases associated genes (KMT2C, AHNAK2). A mean of 3.1 driver gene mutation events per tumor with the dN/dS of 2.13 indicating a significant enrichment for cancer driver gene mutations. Mutation spectrum analysis found lung-brain metastasis samples have more similar Ti/Tv(transition/transversion) profile with brain cancer in which C>T transitions are more frequently while lung cancer has more C>A transversion. We also found the most important tumor onset and metastasis pathways such as chronic myeloid leukemia, ErbB signaling pathway and glioma pathway. Finally, we identified a significant survival associated mutation gene ERF in both TCGA (P=0.01) and our dataset (P=0.012). Conclusion: In summary, we conducted a pairwise lung-brain metastasis based exome-wide sequencing and identified some novel metastasis related mutations which provided potential biomarkers for prognosis and targeted therapeutics. 


Lung cancer(LC) is the leading cause of cancer death in both men and women, accounting for one-quarter of all cancer deaths(1). The five-year survival rate has failed to improve significantly over the last 30 years and remains a mere 19%, due to recurrence and metastasis. Metastasis accounts for about 90% of cancer-related deaths and is the inevitable outcome of most human tumors. The most common site of lung cancer metastasis the brain, and about 50% of all lung cancers develop into brain metastasis (BM) during the process of the disease (2, 3). It has been reported that the rate of brain metastasis from lung cancer has recently increased, placing a great burden on public health services.

‘Seed-and-soil’ hypothesis, which is the most widely accepted hypothesis for the formation of metastasis, denotes that the growth of metastatic cancer cells depends on the intrinsic abilities of the cancer cells themselves (‘seeds’) and the target organ microenvironment (‘soil’)(4). The cancer cell population has multiple, genetically heterogeneous subpopulations(5). Metastasis is a Darwinian natural selection process in which cancer cells(seeds) with distinct metastatic traits that enable them to obtain metastatic advantage are selected from a genetically- and epigenetically-heterogeneous tumor cell subpopulations (6, 7). The advantageous lung cancer cells(‘seeds’) proliferate in brain(‘soil’) that provide a congenial ground and form metastatic brain tumors, whose genetic landscape is reshaped(8).

A large number of studies has attempted to predict high rate for BM in lung cancer, and it has been found that the factors include young age (<60 years) (9, 10), non-squamous cell carcinoma (10, 11) and the presence of clinical bulky mediastinal lymph nodes (≥ 2 cm)(9) are associated with a high BM rate. However, other studies reported conflicting results (12, 13). Many candidate metastasis genes also have been found to be involved in metastasis through changes in gene expression levels(14). The expression levels of E-cadherin, N- cadherin, KIFC1, and FALZ may be used to identify patients at high risk of lung-brain metastasis (15, 16). However, the molecular basis of metastatic gene expression remains largely unknown, and the genetic profiles of brain metastases from Lung cancer might give us a closely insight into tumour initial, dissemination and local progression (14).

To reveal the molecular mechanisms and the genetic alterations involved in metastasis from lung tumors to the brain, we carried out whole-exome sequencing (WES) of the primary tumors and the corresponding brain metastases from 12 patients with metastatic non-small-cell lung carcinoma. Our study can be instrumental for the identification of new genetic targets which may provide new therapeutic strategies for the design of drug intervention to improve the severity of the disease.

Materials And Methods

Patients and specimens

The pairwise lung-brain tumor samples and adjacent histologically normal tissue samples from 12 patients were collected in Sun Yat-sen memorial hospital from 2010 to 2015. The Ethics Committee at Sun Yat-sen memorial hospital approved the utilization of samples, and all patients signed the informed consent form. 12 paired samples were subjected to HE staining, then isolated the normal cells from the tumor cells through histopathological examination. The normal cells were regard as matched normal controls. The total amount of DNA extracted from the archived formalin-fixed paraffin-embedded (FFPE) samples of tumor tissue was up to standard and qualified.

Next-generation Sequencing, Variant Calling And Annotation

The genomic DNAs were exacted and sonicated to an average size of 200 bp. The targeted DNA fragments were captured pulldown and exon-wide libraries were created using the Roche SeqCap EZ Exome V3 and TruePrep DNA Library Prep Kit V2 for Illumina (#TD501, Vazyme, Nanjing, China), and paired-end sequence data were generated using Illumina HiSeq machines. The sequence data were aligned to the human reference genome (NCBI build 37) using BWA and sorted and removed PCR duplication using GATK (17). Somatic mutation calling was performed using Mutect1, Mutect2 (17) and VarDict (18). Somatic mutations existing in at least two of the results of the three software were selected as high confident mutations and be involved in the further bioinformatics and bio-statistical analysis. Copy number variants (CNVs) from whole-exome sequencing data were detected by CNVKIT(19). The dN/dS ratios of each domain were calculated via The DiversiTools according to Xia described(20). The GISTIC2.0 was used to identify regions of the genome that are significantly amplified or deleted across a set of samples(21). Somatic variants were annotated by Ensembl Variant Effect Predictor (22). Transition (Ti) and transversion (Tv) ratio were applied to measure the selection in cancer genomes and to show mutation characteristics between different cancer types.

Spectrum, Signatures Of Somatic Mutations And Subclonal Architecture Inference

Non-negative matrix factorization and model-selection were applied to delineate mutational processes underlying genome-wide SNVs and to identify the major mutational signatures(23). In the cohort, one sample was considered as a strong association with one mutational signature if the proportion of the contribution > 20% with MutationalPatterns (version 1.10) (24) and deconstructSigs (25). The sub-clonal architecture of tumors was inferred by sciClone (26) and clonevol(27).

Survival Analysis, Enrichment Analysis And Other Related Statistics

Pathway analysis was based on DAVID bioinformatics(28), and webgestalt (29) with significant Benjamini adjusted p-value (p < 0.05). The co-mutation profile was prepared with R package ComplexHeatmap (30). Cox regression was applied for survival analysis between mutation and overall survival time and the K-M plot were used to show the difference between the survival time among different groups. TCGA mutation and survival data were downloaded from the GDC database (https://portal.gdc.cancer.gov/exploration). In the validation study to ERF, we download the expression and survival data of ERF mutation and expression from TCGA project, Cox-regression was conducted to binary gene expression data dichotomized by median expression level for TCGA dataset. Since our research subjects in a small sample size, all the clinical related statistical analysis is considered to be significant when p < 0.05 without multiple correction test.


Landscape of somatic mutations in primary lung cancer and brain metastasis

We collected and quantified DNA from the original 12 non-small cell lung cancer (NSCLC) patient FFPE samples and the matched brain metastasis samples. The average coverage depth for the tumor cells and normal cells were 194 × and 120×. Detailed clinicopathological information is summarized in Supplementary Table 1. We identified 1,702 SNVs and 6,131 mutation events in 1,220 genes from 12 paired lung cancer (LC) and brain metastasis (BM), including LC most frequently driver gene mutations such as TP53, EGFR, BRCA1, BRCA2, and BRAF. We identified a mean of 3.1 driver gene mutation events per tumor with the dN/dS of 2.13 which is slightly higher than non-metastasis lung cancer samples in The Cancer Genome Atlas (TCGA), indicating a significant enrichment for the cancer driver gene mutations. We did not find any difference of the dN/dS ratio between primary tumor (dN/dS = 2.20), brain metastasis tumor (dN/dS = 2.06) and shared mutations between lung cancer and brain (dN/dS = 2.25).

We found that more somatic mutations in BM lesions (median 71, range 23–180) than in LC lesions (median 48.5, range 13–187), while the difference was not statistically significant (p = 0.069, Student's t test) (Supplementary Fig. 1B). High correlation between TMB( tumor mutation burden) of LC and TMB of BM were confirmed by Pearson coefficient 0.65 (p = 0.02) (Supplementary Fig. 1C,1D), indicating the TMB of BM can be estimated by that of primary lung cancer when brain tissue is not available, so as to screen patients who will most likely benefit from PD-L1 immunotherapy. 18.2% (0.5–35.9%) of all SNVs were shared between LC and BM, clearly suggesting a common ancestral truncal clone with 30.0% (9.3–60.8%) LC-specific and 51.8% (19.9–79.7%) BM-specific, respectively (Fig. 1B). Although metastases had more private SNVs than the primary tumor, they were not enriched for the pan-cancer driver genes (31)(Fig. 1C). It suggested that few additional private genomic driver genes were required for metastasis when the primary cancer is already advanced.

We identified several lung cancer metastases associated genes (KMT2C, AHNAK2, PDE4DIP, ANKRD36C, and BAGE2), and the mutations of these genes showed distribution diversity among the LC and BM samples (Fig. 1A and 1D). KMT2C mutations were found in 25% samples in LC, however, the mutation frequency in BM was up to 50%, indicating the positive selection of KMT2C mutations during metastasis. AHNAK2 have significant enrichment in LC according to TCGA dataset with mutation ratio of 18.8% in lung cancer while 9.98% in Pan-cancer (p = 7.2 × 10− 9, Chi-square test). However, mutation frequency of AHNAK2 in our dataset is as high as 26.9% which is 1.43 times of LC population in TCGA dataset (p = 0.02, Chi-square test). We also observed all EGFR mutations were shared between LC and BM, suggesting that EGFR mutations are drivers and likely to be an early event before BM.

In order to provide more landscape for the mutations identified in our study, we conducted a pathway analysis to the most frequently mutation genes (mutation frequency > 5%) (Supplementary table2). We found the most important tumor pathways were chronic myeloid leukemia (p = 0.002), ErbB signaling pathway (p = 0.0014) and glioma pathway(p = 0.05). Keyword enrichment indicates important metabolic abnormal for the lung-metastasis cancers including EGF-like domain and tyrosine-specific phosphatase (Supplementary table3).

Copy Number Variations

To further explore BM-related molecular events, genomic copy number variations (CNV) were analyzed: 8q21.2, 6p22.1, 12p13.33, 5q35.3 were the most common chromosome deleted regions in both LC and BM, and 8q24.13 were the most commonly regions with gain copy numbers in both LC and BM (Supplementary Fig. 2A). Loss of 6p22.1, which harbors HLA-A, HLA-G and HLA-H, was most frequent in both LC and BM of patient 9 and in BM of patient 11 (Supplementary Fig. 2B). Interestingly, these samples also had high TMB (Supplementary Fig. 1C). This may be due to the loss of HLA function associated with higher overall mutation burden and a larger fraction of HLA-binding neoantigens(32). The recurrent deletion of HLA was detected as the early events, indicating the important role of the immune system in LCBM, and these patients may benefit from immunotherapy.

The differences include gains of chromosomes 7q35 and loss of 7q22.1, 7q36.3, which were more frequent in metastasis samples, and gains of chromosomes 11q13.2 and losses of 7q11.23, 2q13 which were less frequent. Most recurrent CNV regions were shared in LC and BM samples, indicating that CNVs are early molecular events in tumorigenesis and metastasis.

Spectrum And Signatures

To determine the relationships between the mutational spectra and tumor organ sites, we analyzed the spectra of LC, BM from our study and primary lung adenocarcinoma (LUAD), lung squamous cell carcinoma (LUSC), low grade glioma (LGG), glioblastoma multiforme (GBM) from TCGA dataset. C > T was the most common base substitutions in our LC and BM samples, which was much closer to primary brain cancer (LGG and GBM) but significantly different from primary lung cancer (LUAD and LUSC) which has higher C > A transversion (Fig. 2A). These evidences consistent with our hypothesis that the mutations identified in our study have higher probability to be associated with brain metastasis. The mutational spectrum of LC and BM samples from the same individuals are more similar to each other than that from different patients, implying that different mutational processes were involved during the development of metastasis between the different patients (Fig. 2B).

We further analyzed mutational signatures in BM and LC and signatures 1, 3 and 4, which have been linked to aging, BRCA1/2 mutations and smoking, respectively, were identified as dominant in either BM or LC samples (33) (Fig. 2C). There was no significant difference between the signature levels of LC and BM tissues(Wilcoxon rank sum test, p༞0.05), indicating the change of mutational signatures happened before metastasis and may not lead to their great difference between the two groups.

Clonal Evolution During The Development Of Lcbm

Phylogenetic trees give clear overviews of the order of mutation events, allowing the track of emergence and movement of clones from LC to BM (Fig. 3). Phylogenetic trees of the 9 patients showed that mutations on the trunk were probably earlier genetic alteration events, followed by those on the branch mutations occurred later during tumorigenesis and BM development. Clonal evolution analyses revealed that LC tumors and BM tumors had the same evolutionary process in three patients (P02, P07 and P10), LC tumors harbor a cluster of LC-private clones in other three patients (P05 and P08) and BM tumors harbor clones that are nonexistent in matched LC tumors in other three patients (P06, P13 and P15), indicating the mutations on BM-private clones may contribute to metastatic progression.

Overall Survival By Genotype

In order to identify independent prediction factor for outcomes, we conducted survival analysis to several potential factors. Patients with the aberrations of 18 genes in LC (Supplementary Fig. 3) and 15 genes in BM (Supplementary Fig. 4) had significantly worse OS than those without these aberrations (p < 0.05). Of these genes, we identified a significant survival associated mutation gene ERF which was confirmed by both TCGA (p = 0.01) (Fig. 4A) and our dataset (p = 0.012) (Fig. 4C). What’s more, in order to show the prognostic roles of ERF, we also found high expression of ERF genes in TCGA is a significant risk factors for the overall survival time (HR = 1.46, p < 1.2 × 10− 22, Fig. 4B). Taken together, our findings reveal an important role for ERF in prognostic prediction of lung cancer.

Multivariate analysis demonstrated gender (p = 2.02 × 10− 119), smoking status (p = 1.21 × 10− 269), metastatic tumor size (p = 0), and the ratio of shared mutations in lung and brain cancers(p = 0.019) were significant associate with overall survival time while no significant association were found in drinking status (p = 0.996), the number of metastatic tumors (p = 0.746), the mutation numbers of primary tumor (p = 0.840) or metastatic tumor (p = 0.248) (Fig. 4D).


The metastatic cascade involves multiple steps, including invasion, entry into the circulation from the primary tumor, systemic dissemination, arrest and extravasation in secondary organs, settlement into latency, reactivation, outgrowth, and potential seeding of tertiary metastasis (34). Genetic and epigenetic changes accumulating among primary tumor cells and metastases may contribute to these multiple steps of metastatic cascade (35, 36). Hence, it is necessary to collect a well-defined cohort of matched primary tumors and BM to perform comparative deep sequencing analyses to acquire some biomarkers of metastasis. However, most patients with brain metastasis of lung cancer (LCBM), which were in the late stage at diagnosis, typically are treated with palliative approaches such as chemotherapy, targeted therapy and whole-brain radiotherapy instead of neurosurgical resection. Thus rarely have researchers have the opportunity to investigate matched primary-metastatic tumors in the mutation status of analyzed genes between tumor sites on a large-scare(37).

In this study, we collected 12 paired lung cancer and brain metastasis samples fortunately and identified some genes associated with LCBM. KMT2C (lysine-specific methyltransferase 2C, also known as MLL3), which belongs to mixed-lineage leukemia (MLL) family of histone methyltransferases, was the most commonly mutated gene in our samples. Recent studies have revealed frequent mutations of KMT2C in several epithelia and myeloid cells, and it was identified as a putative tumor suppressor (38, 39). Metastatic spread has been proposed that circulating tumor cell (CTC) populations in the blood of carcinoma patients contain cells with the clonal capacity to initiate metastatic growth in distant organs, thus having similarity with the hematologic tumor. KMT2C originally identified as oncogenic fusions in leukemia (40), and the most enriched pathway is chronic myeloid leukemia in our study. Hashim et al. reported that the Keap1-Nrf2-ARE pathway is mutated in NSCLC patients that metastasised to the brain and in CTC according to WGS(41). Recent reports demonstrated that metastatic brain tumors of NSCLC and lung adenocarcinoma patients frequently carried EGFR mutations than those who without(42, 43). Our results further emphasized the association between the brain metastasis of lung cancer and leukemia. AHNAK2(AHNAK nucleoprotein 2) is a prognostic marker and an oncogenic protein for clear cell renal cell carcinoma and hypoxic upregulation of AHNAK2 support EMT (epithelial-mesenchymal transition) and cancer cell stemness (44). Cancer cells acquire characteristics of self-renewal, motility, and invasiveness, traits that facilitate metastatic dissemination during EMT(45). That is, the driver gene mutation of AHNAK2 may promote metastatic colonization of the lung to brain by supporting EMT.

Our finding depicted that chronic myeloid leukemia and ErbB signaling pathway were mutated in the majority of LCBM patients supports our hypothesis that mutations in these pathways may indeed provide a survival advantage to these cells and help them reach distant sites. Of note, Glioma pathways have also been identified. Ti/Tv profile showed our mutation profile is much closer to brain cancer mutation profile since brain cancer has high C > T transitions are more frequently while lung cancer has a higher frequency of C > A transversion. These evidences highly indicate that brain tumor-related events are involved in the process of LCBM.

Multivariate analysis demonstrated the high ratio of shared mutations were associated with better prognosis(46, 47). This implies the patients might have a preferable prognosis when the tendency of metastatic cancer mutation was more inclined to primary cancer, that is the BM sample might not have evolved from the primary cancer but rather they had a shared antecedent. Limited inter-tumor heterogeneity between LC and BM within the same patients results in effective postoperative chemotherapy and radiotherapy in this situation.

Overall, we revealed the genomic difference between metastatic and primary tissues, and identified several genes associated with LCBM. While further molecular biology studies to validate the role of identified candidates and a larger-scare LCBM samples would be required to confirm our findings, this study provides a preliminary evidence of the genetic evolution of LC metastases and further gives us an advantage to reveal the therapeutic vulnerabilities of LC metastatic tumor.



whole- exome sequencing; LC:lung cancer; BM:brain metastasis; LCBM:Brain metastasis of lung cancer; Ti/Tv:transition/transversion; FFPE:formalin-fixed paraffin-embedded; HE staining:hematoxylin-eosin staining ; NSCLC:non-small cell lung cancer; CNV:copy number variations; LUAD:lung adenocarcinoma; LUSC:lung squamous cell carcinoma; LGG:low grade glioma; GBM:glioblastoma multiforme; CTC:circulating tumor cell; EMT:epithelial-mesenchymal transition;



This work was sponsored by Shanghai Tongshu Biotechnology Co., Ltd

Authors’ contributions

Yuefei Deng and Pengcheng Li designed the study and devised the experiments. Zhiwei Zhou and Yutao Huang provided tumor samples and clinical information. Zhenghao Liu, Meiguang Zheng and Bingxi Lei dealt with the data analysis and prepared the main manuscript. Zhenghao Liu, Wenpeng Li and Qinbiao Chen edited figures and searched literature. All authors contributed to the discussions and manuscript preparation.



Availability of data and materials

All the sequencing data was deposited in the NCBI database under the BioProject accession code SRP182103 and PRJNA515561

Ethics approval and consent to participate

This study protocol was approved by the Ethics Committee of Sun Yat-sen memorial hospital and Tongji Medical college.

Consent for publication

Not applicable.

Competing interests

The authors declare no conflict of interest.


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