General clinical and mutational characteristics in Chinese lung adenocarcinoma patients
As shown in Table 1, a total of 248 Chinese lung adenocarcinoma patients were identified and included in this study. According to the results of PD-L1 expression essay, these patients were divided into three group, PD-L1 negative group with a TPS < 1% (n = 124, 50%), PD-L1 intermediate group with a TPS 1%-49% (n = 93, 38%), and PD-L1high group with a TPS ≥ 50% (n = 38, 12%) (Table 1).
Table 1
Clinical characteristics of patients by PD-L1 expression groups
|
PD-L1 < 1%
|
PD-L1 1%-49%
|
PD-L1 ≥ 50%
|
P
|
N = 248
|
124 (50%)
|
93 (38%)
|
31 (12%)
|
|
Gender (n)
|
|
|
|
|
Male (134)
|
65 (52%)
|
49 (53%)
|
19 (61%)
|
0.66
|
Female (117)
|
59 (48%)
|
44 (47%)
|
12 (39%)
|
|
Age at diagnosis (years)
|
|
|
|
|
Median (range)
|
58 (23 ~ 84)
|
58 (27 ~ 80)
|
60 (32 ~ 73)
|
0.86
|
TMB (Mut/Mb)
|
|
|
|
|
Median (IQR)
|
4.0 (2.01 ~ 5.36)
|
3.4 (2.68 ~ 6.70)
|
6.0 (4.02 ~ 14.41)
|
< 0.001
|
TNB (Neo/Mb)
|
|
|
|
|
Median (IQR)
|
1.3 (0.67 ~ 2.68)
|
1.3 (0.67 ~ 3.35)
|
2.7 (1.34 ~ 4.02)
|
0.09
|
HLA LOH
|
|
|
|
|
Negative
|
98 (79%)
|
77 (83%)
|
21 (68%)
|
0.16
|
Positive
|
26 (21%)
|
16 (17%)
|
10 (32%)
|
|
TMB, tumor mutation burden; Mut/Mb, mutations per megabase; TNB, tumor neoantigen burden; Neo/Mb, neoantigens per megabase; HLA, human leukocyte antigen; LOH, loss of heterogeneity; IQR, interquartile range. |
P values < 0.05 are indicated in bold and italics. |
The median age and gender proportion was very similar among the three group, implying that PD-L1 expression level was not affected by either age or gender. The median TMB in PD-L1 high group was significantly higher than the median values both in the PD-L1 intermediate group and PD-L1 negative group [median (interquartile range) 6.0 mut/Mb (4.02 ~ 14.41) versus 3.4 mut/Mb (2.68 ~ 6.70) versus 4.0 mut/Mb (7 2.01 ~ 5.36), respectively; P < 0.001] (Table 1). Compared with PD-L1 negative group, the median TNB in PD-L1 high group was obviously higher than the median value in the PD-L1 negative group [median (interquartile range) 2.7 neo/Mb (1.34 ~ 4.02) versus 1.3 neo /Mb (0.67 ~ 2.68), respectively; P < 0.05], despite in PD-L1 intermediate group [median (interquartile range) 2.7 neo/Mb (1.34 ~ 4.02) versus 1.3 neo /Mb (0.67 ~ 3.35); P > 0.1]. However, the CIN or HLA LOH was not associated with any of the three PD-L1 groups (P > 0.1).
Significant genomic mutations and signaling pathways associated with PD-L1 expression in Chinese lung adenocarcinoma patients
The 25 most frequently genomic alternations with a frequency more than 15%, such as high oncogenic amplifications or mutations and deep deletions in tumor suppressors, were listed in Fig. 1. These included EGFR and TP53 in PD-L1 negative group and PD-L1 intermediate group, EGFR, TP53, KRAS, ERBB2, ZFHX4, ZNF521, PRKDC, NF1 and SETD2 in PD-L1 high group. Among the three PD-L1 groups, there were significant enrichments of gene mutation in TP53 (74.2% versus 54.8% versus 42.7%, P < 0.01) and KMT2D (12.9% versus 4.3% versus 0.8%, P < 0.01) in these 248 Chinese lung adenocarcinoma patients. In contrast to the PD-L1 negative group or PD-L1 intermediate group, patients in PD-L1 high group were obviously enriched with genomic mutations in PRKDC (22.6% versus 3.2% versus 4%, P < 0.01), SETD2 (16.1% versus 3.2% versus 3.2%, P < 0.05) and TET1 (12.9% versus 4.3% versus 0.8%, P < 0.05). Slight changes of PD-L1 expression were presented in BRAF mutations of PD-L1 intermediate group to PD-L1 negative group (10.8% versus 3.2%, P < 0.05), or KRAS mutations of PD-L1 high group to PD-L1 intermediate group (25.8% versus 8.6%, P < 0.05). No dramatic fluctuations were observed in PD-L1 expression of EGFR mutant patients.
Key signaling pathways related with PD-L1 expression in Chinese lung adenocarcinoma patients
Next, we also performed further analyses in oncogenomic pathways in this study (Fig. 2). Tumors with alterations involved with the DNA damage response (DDR) signaling pathway in PD-L1 negative group was less frequently than PD-L1 high group (54.84% versus 87.1%, P < 0.001) or PD-L1 intermediate group (54.84% versus 70.94%, P < 0.05), due to the significant gene mutations in check point factor (CPF), mismatch repair (MMR), and nonhomologous end-joining (NHEJ) (See supplementary Figure S1). In PD-L1 high group, alternations in TP53 pathway were more frequently than PD-L1 negative group (80.65% versus 51.61%, P < 0.01) and PD-L1 intermediate group (80.65% versus 59.14%, P < 0.05). Besides, percentages of mutated pathways were significantly different in PD-L1 high group to PD-L1 negative group, including cell cycle signaling pathway (38.71% versus 15.32%, P < 0.01) and NOTCH signaling pathway (32.26% versus 13.71%, P < 0.05). After comparing the copy number variations (CNVs) in PD-L1 high and PD-L1 negative groups, amplification of TRRAP, H3F3B, KMD5A and CCNE1 and deletions of FAT1 and B2M were enriched in PD-L1 high group. On the contrast, amplifications of CREBBP, MAPK1, MDM2, EGFR, TERT and ETV1 and deletions of FANCA, SMARCA4, STK11, DNMT3A, SMARCB1, NF2 and RB1 were enriched in PD-L1 negative groups.
Major immune signatures linked to PD-L1 expression in lung adenocarcinoma patients from TCGA database
Based on TCGA-LUAD database, we primarily characterized immune signatures in lung adenocarcinoma patients among different PD-L1 expression groups in Fig. 3A-F and found that most of patients in high PD-L1 group were determined as high-grade immune subtypes (C2-C4). Compared with PD-L1 negative group, higher levels of IFN-gamma, CD8 + T cells, NK cells, NK CD56 dim cells, Th1 cells, Th2 cells (P < 0.0001) and lower percentage of NK CD56 bright cells and Th17 cells (P < 0.05) was observed in PD-L1 high group, suggesting high PD-L1 expression level can be a prognostic marker for the clinical response to of immune cells during anti-cancer immunotherapy.
Potential therapeutic response correlated to SETD2 mutation from immunotherapy cohort
As shown in Fig. 3G-J, the prognostic value of SETD2 mutation was slight positive with overall survival from MSKCC cohort (HR 1.92 [95%CI 0.90–4.10], P = 0.085), but not progression-free survival among the patients from Rizvi cohort (HR 1.35 [95%CI 0.70–2.57], P = 0.37). Furthermore, the percentage of IFN-gamma (P < 0.01) was significantly higher in SETD2 mutant group than in wild-type subgroup, despite no significant difference of CD8 + T-cells.