| Literature DB >> 35356154 |
Hongge Liang1,2, Yan Xu1, Minjiang Chen1, Jing Zhao1, Wei Zhong1, Xiaoyan Liu1, Xiaoxing Gao1, Shanqing Li3, Ji Li4, Chao Guo3, He Jia5, Mengzhao Wang1.
Abstract
Purpose: Immune checkpoint inhibitors (ICIs) have recently emerged as an important option for treating patients with advanced non-small cell lung cancer (NSCLC). Neoantigens are important biomarkers and potential immunotherapy targets that play important roles in the prognosis and treatment of patients with NSCLC. This study aimed to evaluate and characterize the relationships between somatic mutations and potential neoantigens in specimens from patients who underwent surgical treatment for NSCLC. Patients andEntities:
Keywords: genetic mutation characteristics; neoantigens; non-small cell lung cancer; tumor neoantigen burden; whole exome sequencing
Mesh:
Substances:
Year: 2022 PMID: 35356154 PMCID: PMC8959482 DOI: 10.3389/fimmu.2021.749461
Source DB: PubMed Journal: Front Immunol ISSN: 1664-3224 Impact factor: 7.561
Figure 1Flow chart of candidate neoantigen design. 1) Quality control and statistical analysis were performed on original tumor and normal FASTQ data. 2)Bwa was used to compare FASTQ data to human reference genome HG19. Samblaster was used to mark duplication on reads. 3)SamTools was used to convert the Sam file into BAM file and build index. 4)GATK Mutect2 was used to call and filter somatic mutation, and then obtain mutation information. 5)The original FASTQ information was used for HLA typing using Optitype. 6) Netmhcpan4 was used to predict peptide affinity according to HLA type. 7) The expression data of lung cancer patients in TCGA were downloaded, and the mean values of expression data of lung adenocarcinoma and lung squamous cell carcinoma patients were calculated respectively. 8) Neoantigen was scored according to the sequencing data, mutation frequency, expression of HLA, expression of transcript, expression of immune-related gene to obtain the final neoantigen results.
Figure 2Gene disturbance map. The X-axis represents the sample type, and “xiehe28” is our 28 samples, and the other samples are tumors in TCGA database. The Y-axis represents log 10 (mutations per sample). The red line in the figure represents the mean value. Note, SKCM, skin cutaneous melanoma. LUSC, lung squamous cell carcinoma. LUAD, lung adenocarcinoma. BLCA, bladder cancer; ESCA, esophageal cancer; HNSC, head and neck squamous cell carcinoma; STAD, stomach adenocarcinoma; DLBC, Diffuse large B-cell lymphoma; UCEC, Uterine corpus endometrial carcinoma; COAD, colon adenocarcinoma; OV, Ovarian cancer; LIHC, liver hepatocellular carcinoma; CESC, cervical squamous cell carcinoma; READ, rectal adenocarcinoma; KIPP, Kidney renal papillary cell carcinoma; KIRC, kidney renal clear cell carcinoma; UCS, uterine carcinosarcoma; BRCA, breast cancer; GBM, glioblastoma; SARC, sarcoma; CHOL, cholangiocarcinoma; MESO, mesothelioma; PAAD, pancreatic adenocarcinoma; ACC, adrenocortical carcinoma; LGG, lower grade glioma; PRAD, Prostate adenocarcinoma; KICH, kidney chromophobe; TGCT, tenosynovial giant cell tumor; THYM, thymoma; LAML, acute myeloid leukemia; UVM, uveal melanoma; THCA, thyroid carcinoma; PCPG, pheochromocytoma and paraganglioma.
Clinicopathological characteristics of 28 patients.
| No. | Gender | Age | Smoking history (pack years) | Pathology | TNM stage | Clinical stage | Tumor size | Tumor history |
|---|---|---|---|---|---|---|---|---|
|
| Male | 38 | No | A | T1bN0M0 | Ia2 | 14mm | No |
|
| Male | 61 | 20 | A | T1bN0M0 | Ia2 | 23mm | No |
|
| Male | 59 | No | A | T1aN0M0 | Ia1 | 10mm | No |
|
| Male | 58 | 30 | A | T1aN0M0 | Ia1 | 8mm | No |
|
| Female | 70 | No | A | T1bN0M0 | Ia2 | 20mm | No |
|
| Female | 76 | No | A | T1bN0M0 | Ia2 | 20mm | Yes |
|
| Male | 56 | 30 | A | T1bN1M0 | IIb | 20mm | No |
|
| Male | 70 | 10 | A | T2aN0M0 | Ib | 40mm | No |
|
| Male | 59 | No | A | T1cN0M0 | Ia3 | 25mm | No |
|
| Male | 47 | 30 | A | T2bN2M0 | IIIa | 20mm | No |
|
| Female | 52 | No | A | T1aN0M0 | Ia1 | 10mm | No |
|
| Female | 41 | 2 | A | T3N2M0 | IIIb | 20mm | No |
|
| Female | 60 | No | A | T1cN0M0 | Ia3 | 18mm | No |
|
| Female | 68 | No | A | T1bN0M0 | Ia2 | 15mm | No |
|
| Male | 73 | No | A | T1cN0M0 | Ia3 | 30mm | Yes |
|
| Female | 60 | No | A | T1bN0M0 | Ia2 | 13mm | No |
|
| Female | 54 | 3 | A | T1cN0M0 | Ia3 | 27mm | Yes |
|
| Female | 71 | No | A | T1bN0M0 | Ia2 | 15mm | No |
|
| Female | 58 | No | A | T3N0M0 | IIb | 60mm | No |
|
| Female | 63 | No | A | T1bN0M0 | Ia2 | 20mm | No |
|
| Male | 49 | 30 | S | T2aN1M0 | IIb | 32mm | No |
|
| Male | 61 | 40 | A | T1bN0M0 | Ia2 | 15mm | Yes |
|
| Male | 61 | 35 | A | T2bN1M0 | IIb | 40mm | No |
|
| Male | 56 | 30 | A | T2bN2M0 | IIIa | 28mm | No |
|
| Male | 63 | 40 | A | T2aN0M0 | Ib | 36mm | Yes |
|
| Male | 64 | 50 | S | T1cN1M0 | IIb | 30mm | No |
|
| Male | 64 | 3 | S | T2bN1M0 | IIb | 60mm | Yes |
|
| Male | 64 | 40 | LCNEC | T2aN0M0 | Ib | 40mm | No |
A, adenocarcinoma; S, squamous carcinoma; LCNEC, large-cell-neuroendocrine carcinoma.
Figure 3Neoepitope and neoantigen maps of the patients included in our study.
Figure 4Spectral heat map of common gene mutations. (A) all mutations; (B) neoantigen-associated mutations. Spectrum heat map of common gene mutations in patients. (C) with high tumor neoantigen burden; (D) with low tumor neoantigen burden.
Spearman correlation analysis of candidate neoantigens.
| Neoantigens | N | Correlation coefficient | P-value |
|---|---|---|---|
| nonsynonymous mutation | 28 | 0664 | <0.001 |
| Frame shift indel | 28 | 0.755 | <0.001 |
| In frame indel | 28 | 0.071 | 0.718 |
| Missense mutation | 28 | 0.603 | 0.001 |
| Nonsense mutation | 28 | 0.501 | 0.007 |
| Nonstop mutation | 28 | 0.211 | 0.282 |
| Splice site | 28 | 0.546 | 0.003 |
| A>T/T>A mutation frequency | 28 | 0.279 | 0.151 |
| A>C/C>A mutation frequency | 28 | 0.641 | <0.001 |
| A>G/G>A mutation frequency | 28 | -0.690 | <0.001 |
| T>C/C>T mutation frequency | 28 | -0.535 | 0.003 |
| T>G/G>T mutation frequency | 28 | 0.388 | 0.041 |
| C>G/G>C mutation frequency | 28 | 0.418 | 0.027 |
Multiple linear regression of candidate neoantigens.
| Variants | Unstandardized coefficients | Unstandardized coefficients Beta | t-value | P-value | 95.0% confidence interval of B | ||
|---|---|---|---|---|---|---|---|
| B | Standard error | Lower limit | Higher limit | ||||
| (Constant) | -2.811 | 10.84 | -0.259 | 0.798 | -25.235 | 19.614 | |
| Frameshift indel | 1.612 | 1.139 | 0.154 | 1.415 | 0.17 | -0.744 | 3.968 |
| Missense mutation | 0.5 | 0.115 | 0.674 | 4.342 | 0 | 0.262 | 0.739 |
| Nonsense mutation | 0.782 | 1.418 | 0.08 | 0.552 | 0.587 | -2.152 | 3.716 |
| Splice site | 16.209 | 12.101 | 0.104 | 1.339 | 0.194 | -8.825 | 41.243 |
Figure 5Gene heat map of different numbers of neoantigens in 28 patients.