Sample collection and patient characteristics
Of the 1746 NSCLC cases, RET rearrangements were identified in 25 cases (1.43 %) with locally advanced or metastatic NSCLC, of which 20 (80%) were female. The 25 patients have mean age of 53.5 ranging from 27 to 78. NGS testing was performed on their 25 pairs of FFPE tumor tissue and PBL samples. In addition, we performed cfDNA NGS testing on 17 of them to check their RET gene status in cfDNA sample. All the samples passed the histology quality control (HQC) and yielded sufficient DNA for NGS.
Identification of RET rearrangements using targeted sequencing
In this study, we designed probes to cover the intron 6 ,7,8,9,10, 11 of RET as well as introns of some well-known RET fusion partners to identify RET rearrangement of the DNA from patients’ FFPE samples. We identified RET rearrangements and analyzed the corresponding breakpoints for these patients. The statistical summary of the rearrangement events was presented in Table 1 and in Fig. 1. The breakpoint distribution in RET was shown in Fig. 2. The results showed that 14 out of 25 patients had an KIF5B-RET fusion, with KIF5B exon15-RET exon12, KIF5B exon23-RET exon12, and KIF5B exon24-RET exon11 detected in 14, 3, and 1 patient respectively. It also detected one novel RET fusion partner PLCE1 and 4 intergenic-breakpoint fusions.
Table 1
Fusion Type
|
Counts
|
percent(%)
|
KIF5B-exon15-RET-exon12
|
14
|
56
|
CCDC6-exon1-RET-exon12
|
3
|
12
|
KIF5B-exon23-RET-exon12
|
1
|
4
|
KIF5B-exon24-RET-exon11
|
1
|
4
|
PLCE1-exon20-RET-exon11
|
1
|
4
|
RET-exon11-CCDC6-exon3
|
1
|
4
|
Other
|
4
|
16
|
Mutational profiles of RET fusion-positive NSCLC patients
Genomic alterations were detected in 24 (n = 24/25, 96%) samples with a total of 113 alterations including nonsynonymous mutations and splicing mutations. The top 20 alterations were listed in Figure 3A. The mutation landscapes of RET fusion-positive NSCLC patients were highly heterogeneous. The median TMB was 2.4 mut/Mb with a range between 0 to 8.4 mut/Mb, which is similar to the TMB value of TCGA NSCLC cohort[35].
Besides, a heatmap was created to illustrate the somatic mutations detected in the tumor tissues of the patients (Figure 3A). TP53 was the top altered (n = 10, 42%), followed by SETD2 (n = 4, 17%), CSMD3 (n = 3, 12%), and PTEN (n = 3, 12%). Other genomic alterations with low frequencies were ATM (n = 2, 6%), CACNA1C (n = 2, 8%), CIC (n = 2, 8%), CTCF (n = 2, 8%), DOT1L (n = 2, 8%), FANCA (n = 2, 8%), FANCG (n = 2, 8%),LRP1B (n = 2, 8%), MAP2K4 (n = 2, 8%), NOTCH1(n = 2, 8%), PRKCI (n = 2, 8%), PTPRT (n = 2, 8%) , RB1 (n = 2, 8%), SMAD4 (n = 2, 8%), and SUZ12 (n = 2, 8%). Alterations in DICER1 were identified in one sample (n = 1, 4%). Moreover, the results were compared with the MSK-IMPACT study [32], from which we extracted 30 RET fusion positive cases that yielded 81 mutations. Overall, the results of our study and MSK-IMPACT research were highly consistent, both of which showed that TP53 and SETD2 were the most frequently altered genes (Fig. 3B).
Then the mutational signatures were further studied. It was observed that C>T transition happened most frequently, followed by C>G transversions (Fig. 4). This pattern is consistent with COSMIC signature 84 according to website(https://cancer.sanger.ac.uk/signatures/sbs/sbs84/) that had been found in some cancer samples.
Different driver gene mutations demonstrated inter-tumor heterogeneity. TP53 mutations in exon 4-8 were observed, and the TP53 mutation sites on the peptide sequence were elaborately portrayed in a lollipop plot. (Fig. 5).
Copy number aberrations of RET fusion-positive NSCLC patients
Somatic copy number alterations were detected in 11 (n = 11/25, 44%) samples. A total of 22 alterations were discovered, including gain and loss (Fig. 6). CDK4 were the most commonly amplified gene (n = 3/11, 27%). Loss of copy number was observed in FGFR3 with highest frequency (n = 4/11, 36%).
PD-L1 expression and Microsatellite Instability (MSI) status of RET fusion-positive NSCLC patients
High (≥ 50%), intermediate (1–49%), and negative (< 1%) PD-L1 expression was observed in 0/14 (0%), 8/14 (57%), and 6/14(43%) cases, respectively.
MSI status were evaluated in 20 cases. They were all microsatellite stable (MSS).
Concordance in tumor DNA(tDNA) and plasma DNA(ctDNA) sample pairs of RET fusion-positive NSCLC patients
A total of 17 tDNA and ctDNA sample pairs were analyzed. 9 patients are found to have the same breakpoint of RET fusions in both tDNA and ctDNA samples, indicating 52.9% RET fusion could be detected in ctDNA. A total of 111 mutations (snv and indel) were identified, including 90 in tDNA and 64 in plasma ctDNA, and 43 concordant mutations in both tDNA and plasma ctDNA. Seven sample pairs (7/17, 41.2%) had concordant mutations in both tDNA and plasma ctDNA, and the average variant frequency in these plasma ctDNA samples was 8.17%.