An EGFR L858R mutation identified in 1862 Chinese NSCLC patients can be a promising neoantigen vaccine therapeutic strategy.

Background: This study aimed to develop a vaccine that targets mutation-derived neoantigen in Chinese non-small-cell lung cancer (NSCLC). Methods: A cohort of 1862 Chinese NSCLC patients who underwent targeted sequencing with a 1021-gene panel was investigated. HLA typing was done using OptiType v1.0 and neoantigens were predicted by netMHCpan v4.0. HLA LOH was inferred using the lohhla algorithm and TMB were quantified by counting the total number of non-synonymous ones based on our panel data. CIBERSORT was utilized to estimate the TME in different EGFR mutant subtype by using TCGA data. Results: HLA-A*11:01(42.59%) was the top one allele and HLA-A*33:03(12.94%) ranked 12th. EGFR L858R (22.61%) was the most prevalent gene variant. The binding affinity (IC50 MT = 22.9 nM) and shared frequency (2.93%) of EGFR L858R in combination with HLA-A*33:03 were optimal. In a subsequent further analysis on immunological features of EGFR mutant subtypes, 63.1% HLA loss of heterozygosity LOH (HLA LOH) and 0.37% (7 of 1862) B2M aberrations were found in our population, both had no significant association with EGFR mutant subtypes suggesting that the process of antigen presentation involved HLA LOH and B2M mechanisms in EGFR L858R is working. Tumor mutation burden (TMB) was investigated by utilizing our panel and showed that EGFR L858R had the lowest TMB compared with other EGFR mutant subtypes. In addition, analysis of 22 immune cell types from The Cancer Genome Atlas (TCGA) data showed EGFR L858R was correlated with low level of CD8 T cells, activated CD4 memory T cells and elevated level of macrophage M2 suggesting an inhibited tumor microenvironment (TME). Conclusion: Our study identified that EGFR L858R neoantigen had the potential to generate cancer vaccines in NSCLC patients with HLA A*33:03. The neoantigen-based vaccines may become an effective salvage regimen for EGFR L858R subgroup after targeted therapy or immune checkpoint inhibitors (ICIs) failure.

Association of Tumor Protein p53 and Ataxia-Telangiectasia Mutated Comutation With Response to Immune Checkpoint Inhibitors and Mortality in Patients With Non-Small Cell Lung Cancer.

Importance: Immune checkpoint inhibitors (ICIs) can elicit durable antitumor responses in patients with non-small cell lung cancer (NSCLC), but only 20% to 25% of patients respond to treatment. As important genes in the DNA damage response pathway, comutation in the tumor protein p53 (TP53) and ataxia-telangiectasia mutated (ATM) genes may be associated with genomic instability and hypermutation. However, the prevalence of TP53 and ATM comutation and its association with response to ICIs are not fully understood. Objective: To examine the prevalence of the TP53 and ATM comutation, the potential mechanism, and its association with response to ICIs among patients with NSCLC. Design, Setting, and Participants: This multiple-cohort study included patients with NSCLC from the Geneplus Institute, the Cancer Genome Atlas (TCGA), and the Memorial Sloan Kettering Cancer Center (MSKCC) databases and from the POPLAR and OAK randomized controlled trials. Samples in the Geneplus cohort were collected and analyzed from April 30, 2015, through February 28, 2019. Data from TCGA, the MSKCC, and the POPLAR and OAK cohorts were obtained on January 1, 2019, and analyzed from January 1 to April 10, 2019. Next-generation sequencing assays were performed on tumor samples by the Geneplus Institute. Genomic, transcriptomic, and clinical data were obtained from TCGA and MSKCC databases. Exposures: Comprehensive genetic profiling was performed to determine the prevalence of TP53 and ATM comutation and its association with prognosis and response to ICIs. Main Outcomes and Measures: The main outcomes were TP53 and ATM comutation frequency, overall survival (OS), progression-free survival, gene set enrichment analysis, and immune profile in NSCLC. Results: Patients with NSCLC analyzed in this study included 2020 patients in the Geneplus cohort (mean [SD] age, 59.5 [10.5] years; 1168 [57.8%] men), 1031 patients in TCGA cohort (mean [SD] age, 66.2 [9.5] years; 579 [56.2%] men), 1527 patients in the MSKCC cohort (662 [43.4%] men), 350 patients in the MSKCC cohort who were treated with ICIs (mean [SD] age, 61.4 [13.8] years; 170 [48.6%] men), and 853 patients in the POPLAR and OAK cohort (mean [SD] age, 63.0 [9.1] years; 527 [61.8%] men). Sites of TP53 and ATM comutation were found scattered throughout the genes, and no significant difference was observed in the frequency of TP53 and ATM comutation within the histologic subtypes and driver genes. In 5 independent cohorts of patients with NSCLC, TP53 and ATM comutation was associated with a significantly higher tumor mutation burden compared with the sole mutation and with no mutation (TCGA, MSKCC, Geneplus, and POPLAR and OAK cohort). Among patients treated with ICIs in the MSKCC cohort, TP53 and ATM comutation was associated with better OS than a single mutation and no mutation among patients with any cancer (median OS: TP53 and ATM comutation, not reached; TP53 mutation alone, 14.0 months; ATM mutation alone, 40.0 months; no mutation, 22.0 months; P = .001; NSCLC median OS: TP53 and ATM comutation, not reached; TP53 mutation alone, 11.0 months; ATM mutation alone, 16.0 months; no mutation, 14.0 months; P = .24). Similar results were found in the POPLAR and OAK cohort in which the disease control benefit rate, progression-free survival, and OS were all greater in patients with the TP53 and ATM comutation compared with the other 3 groups (median progression-free survival: TP53 and ATM comutation, 10.4 months; TP53 mutation, 1.6 months; ATM mutation, 3.5 months; no mutation, 2.8 months; P = .01; median OS: TP53 and ATM comutation, 22.1 months; TP53 mutation, 8.3 months; ATM mutation, 15.8 months; no mutation, 15.3 months; P = .002). Conclusions and Relevance: This study's findings suggest that the TP53 and ATM comutation occurs in a subgroup of patients with NSCLC and is associated with an increased tumor mutation burden and response to ICIs. This suggests that TP53 and ATM comutation may have implications as a biomarker for guiding ICI treatment.

PPARG rs3856806 C>T Polymorphism Increased the Risk of Colorectal Cancer: A Case-Control Study in Eastern Chinese Han Population.

Purpose: Functional variants in the peroxisome proliferator-activated receptor gamma (PPARG) and PPARG co-activator 1 (PPARGC1) family (e.g., PPARGC1A and PPARGC1B) genes were predicted to confer susceptibility to colorectal cancer (CRC). The aim of the present study was to explore the relationship between PPARG, PPARGC1A, PPARGC1B polymorphism and the risk of CRC. Patients and methods: We conducted a case-control study with 1,003 CRC cases and 1,303 controls. We selected the PPARG rs3856806 C>T, PPARGC1A rs2970847 C>T, rs8192678 C>T, rs3736265 G>A and PPARGC1B rs7732671 G>C and rs17572019 G>A SNPs to assess the relationship between PPARG, PPARGC1A, PPARGC1B their variants and risk of CRC. Results: We found that the PPARG rs3856806 C>T polymorphism increased the risk of CRC (TT vs. CC: adjusted OR, 1.59, 95% CI 1.08-2.35, P = 0.020; TT/CT vs. CC: adjusted OR, 1.26; 95% CI 1.06-1.49; P = 0.009 and TT vs. CC/CT: adjusted OR, 1.54; 95% CI 1.05-2.26; P = 0.028), even after a Bonferroni correction test. The stratified analysis revealed that the PPARG rs3856806 C>T polymorphism also increased the risk of CRC, especially in male, ≥61 years old, never smoking, never drinking, BMI ≥ 24 kg/m2, colon cancer and rectum cancer subgroups. Conclusion: Our findings highlight that the PPARG rs3856806 C>T polymorphism may increase the risk of CRC. In the future larger sample size case-control studies with a detailed functional assessment are needed to further determine the relationship of the PPARG rs3856806 C>T polymorphism with CRC risk.

SNHG8 is identified as a key regulator of epstein-barr virus(EBV)-associated gastric cancer by an integrative analysis of lncRNA and mRNA expression.

The Epstein-Barr virus (EBV) is associated with a variety of cancers, including gastric cancer, which has one of the highest mortality rates of all human cancers. Long non-coding RNAs (lncRNAs) have been suggested to have important causal roles in gastric cancer. However, the interaction between lncRNAs and EBV has not yet been studied. To this end, we sequenced 11,311 lncRNAs and 144,826 protein-coding transcripts from four types of tissue: one non-EBV-infected gastric carcinoma (EBVnGC) and its adjacent normal tissue, and one EBV-associated gastric carcinoma (EBVaGC) and its adjacent normal tissue. Five lncRNAs showed EBVaGC-specific expression; of those, one (SNHG8) was validated using real-time PCR in an independent cohort with 88 paired gastric cancer and adjacent tissue samples. To explore the functions of SNHG8, we identified its mRNA targets on the lncRNA-mRNA co-expression network of the Illumina Body Map, which contains the RNA sequencing data of mRNAs and lncRNAs from 16 normal human tissues. SNHG8 lncRNA was found to affect several gastric cancer-specific pathways and target genes of EBV. Our results reveal the intertwined tumorigenesis mechanisms of lncRNA and EBV and identify SNHG8 as a highly possible candidate biomarker and drug target of gastric cancer.

Associations of THBS2 and THBS4 polymorphisms to gastric cancer in a Southeast Chinese population.

Thrombospondin-2 (THBS2) and Thrombospondin-4 (THBS4) play an important role in cancer development and progression. However, genetic evidence for their roles in gastric cancer (GC) is lacking. The aim of this study was to explore the association of THBS2/THBS4 polymorphisms with risk and clinicopathological features of GC in a Southeast Chinese population. Eight tagging SNPs in THBS2 and THBS4 were genotyped in 761 GC cases and 739 controls from Chinese case-control sets using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. THBS2/THBS4 mRNA expression was studied in 82 human GC tumors and in mouse stomach tissues by real-time PCR. We found that both THBS2 and THBS4 were abundantly expressed in mouse stomach. THBS4 mRNA expression in human stomach was associated with tumor size (P = 0.002) and tumor-node-metastasis (TNM) (P = 0.010), and THBS2 mRNA expression was associated with the TNM (P = 0.010). Patients with the rs77878919^AG genotype were more prone to developing diffuse-type GC. THBS4 SNPs (rs77878919 and rs7736549) had a modest cumulative effect on the risk of poor prognosis (TNM), with that risk in the highest trend for patients carrying both these unfavorable genotypes. In addition, individuals carrying the THBS4 rs10474606 variant homozygous AA had a modest reduced GC risk. We conclude that THBS2/THBS4 may be functional in playing important role in GC, which was supported by the evidence of the mRNA overexpression in GC and the modest associations of THBS2/THBS4 polymorphisms to GC. These findings might be useful for risk assessment and prognosis prediction of GC.

Clinicopathologic features of 112 cases with mantle cell lymphoma.

OBJECTIVE: This study aims to explore the clinicopathologic features of 112 patients with mantle cell lymphoma (MCL). METHODS: Data from 112 MCL cases were collected, and immunohistochemical assay was conducted. Fluorescence in situ hybridization (FISH) detected a break in the CCND1 gene. The t-test was used in the statistical analysis. RESULTS: All tumor cells in the 112 cases expressed B cell-related antigen, including 1 blastoid subtype and 1 polymorphic subtype. Among all cases, 106 expressed CD5 and 104 expressed cyclin D1. A break in the CCND1 gene was not found in 3 cases with CD5-MCL. IgH/CCND1 polyploid was observed in 2 classic cases. CONCLUSION: MCL is a type of special immunophenotypic B-cell lymphoma. The prognoses of blastoid and polymorphic subtypes are poor. Special subtypes should be classified during diagnosis.

Diagnostic validity of human papillomavirus E6/E7 mRNA test in cervical cytological samples.

Human papillomavirus (HPV) DNA tests tend to show high sensitivity, but poor specificity in detecting high-grade cervical lesions. This study aimed to explore the clinical performance of QuantiVirus(®) HPV E6/E7 mRNA in identifying ≥Grade 2 cervical intraepithelial neoplasia. Thin-prep(®) liquid based cytology test (LBC) samples were collected from October 2009 to October 2011 from women who underwent outpatient hospital-based gynecological screening. LBC samples were processed for E6/E7 mRNA detection and HPV DNA detection. Of 335 patients, 135 (40.3%) were HPV E6/E7 mRNA positive for high-risk HPV subtypes. The positivity rate of HPV E6/E7 mRNA increased with the severity of cytological and histological evaluation. An optimal cut-off value of ≥567copies/ml was determined using receiver operating characteristic (ROC) curve, and positive predictive value and negative predictive value of cut-off value (≥567copies/ml) were higher than those of E6/E7 mRNA positivity only, but not significant. QuantiVirus(®) HPV E6/E7 mRNA testing may be a valuable tool in triage for identifying ≥Grade 2 cervical intraepithelial neoplasia. A high specificity and a low positivity rate of E6/E7mRNA testing as a triage test in HPV DNA-positive women can be translated into a low referral for colposcopy. Studies composed of large population-based samples of women and with rigorous disease ascertainment, are needed to establish the optimal cut-off point based on ROC curve analysis.

[Effect of PC cell-derived growth factor RNA interference on biological behavior of esophageal squamous carcinoma cells].

OBJECTIVE: To investigate the effect of PC cell-derived growth factor (PCDGF) RNA interference on esophageal squamous carcinoma cells Eca-109 in vitro. METHODS: The PCDGF-shRNA expression vector was transfected into the Eca-109 cells by liposome. After transfection, the mRNA and protein expressions of PCDGF were detected by RT-PCR and Western-blot respectively. Cell Counting Kit-8 (CCK-8) assay and Boyden chamber method were performed to measure the cell proliferation and invasion ability respectively. RESULTS: The expression levels of PCDGF mRNA and protein were both decreased in Eca-109 cells transfected with PCDGF-shRNA expression vector (transfection group). Twenty-four, 48 and 72 h after transfection, the cells proliferation in the transfection group was inhibited, and the inhibition rate was 20.4%, 21.1% and 20.9% respectively. The cell proliferation activity in the transfection group was significantly lower than that in the non-transfection group, liposome group and negative vector group (all P<0.05). The number of cell migration in the non-transfection group,negative vector group, liposome group and transfection group was 118.8±12.0, 100.8±9.0, 114.3±4.7, and 53.5±16.3 respectively. The differences were statistically significant between the transfection group and the other 3 groups (all P<0.05). CONCLUSIONS: PCDGF RNA interference can inhibit the proliferation and invasion abilities of esophageal squamous carcinoma cells in vitro. PCDGF gene may be the new target of gene therapy.

KRAS mutation and NF-κB activation indicates tolerance of chemotherapy and poor prognosis in colorectal cancer.

BACKGROUND: Evidence shows a strong relationship between KRAS mutations and the NF-κB signaling pathway. In colorectal cancer, however, the study of this subject has been very limited and results are inconsistent. AIMS: To examine the relationship between KRAS mutations and NF-κB activation and their effect on chemotherapy response and survival of colorectal cancer patients. MATERIALS AND METHODS: NF-κB activation was analyzed by immunohistochemistry in 167 primary colorectal cancer specimens in which the KRAS mutation status was confirmed. Clinical and pathologic data were extracted from the medical records and reviewed. RESULTS: Of 167 tumors screened, 63 (37.7 %) had NF-κB activation, 59 (35.3 %) had KRAS mutations, and 30 (18.0 %) had both NF-κB activation and KRAS mutations. The frequency of NF-κB activation in tumors with KRAS mutations was significantly higher than in tumors with wild type KRAS; 50.8 versus 30.6 %, P = 0.012. Patients with both KRAS mutations and NF-κB activation had a lower objective response to first-line chemotherapy than patients with other tumors, 23.8 versus 49.4 % (P = 0.035). Compared to patients with both KRAS mutations and NF-κB activation, overall survival of patients in other groups was significantly higher; median overall survival was 28.4 months (95 % CI 21.0-35.8) versus 46.3 months (95 % CI 39.4-53.2), hazard ratio 0.259 (95 % CI 0.125-0.538), P = 0.005. CONCLUSIONS: NF-κB activation was associated with KRAS mutation, and both KRAS mutation and NF-κB activation were indicative of high tolerance of chemotherapy and poor prognosis for colorectal cancer patients. Tumors with KRAS mutations and NF-κB activation may be a unique subtype of colorectal cancer.

[Association of polymorphism in matrix metalloproteinase-2 and tissue inhibitor of metalloproteinase-2 with genetic susceptibility of gastric cancer].

OBJECTIVE: This study was to explore the correlations between genetic variants in MMP2-1306C/T, TIMP2 2379C/T, TIMP2 303G/A and the genetic susceptibility to gastric carcinoma (GC) in Fujian province, China. METHODS: A case-control study was conducted. Polymorphisms of MMP2-1306C/T, TIMP2 2379C/T, TIMP2 303G/A in 479 gastric carcinoma patients and 469 cancer-free controls, frequency-matched by age and sex, were determined by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). Multivariate logistic regression analysis was used to evaluate the correlations between the polymorphisms with the susceptibility to gastric cancer. Tests for an interaction between the MMP2-1306C/T and TIMP2 2379C/T or TIMP2 303G/A were performed using the likelihood ratio test. RESULTS: The frequencies of GG, AG, AA of TIMP2 303G/A in gastric cancer group were 55.9% (267/478), 38.7% (185/478) and 5.4% (26/478); and those in control group were 53.1% (243/458), 36.9% (169/458) and 10.0% (46/458), which showed a significant difference between the patient and control groups (χ(2) = 7.0, P = 0.03). As compared with AA genotype, patients with GG + AG had a significantly higher risk of the cancer with OR of 1.94 (95%CI: 1.2 - 3.2). The frequencies of GG + AG and AA of TIMP2 303G/A in the muscle group were 87.5% (70/80), 12.5% (10/80), however, those in the serosa and beyond group were 96.0% (382/398), 4.0% (16/398), respectively, which showed a significant difference between the patient in muscle group and the serosa and beyond group (χ(2) = 9.32, P = 0.002). As compared with AA genotype, patients with GG + AG had a significantly higher risk in tumor invasion with OR of 3.4 (95%CI: 1.5 - 7.8). The frequencies of CC + CT, TT of TIMP2 2379C/T in the lymphoma node non-metastasis group were 93.4% (113/121), and 6.6% (8/121), but those in the lymphoma node metastasis group were 98.6% (349/354) and 1.4% (5/354), respectively, which showed a significant difference between the patient in the lymphoma node non-metastasis group and in the lymphoma node metastasis group in genotype distributions of TIMP2 2379C/T) χ(2) = 9.16, P = 0.002). As compared with TT genotype, patients with CC + CT had a significantly higher risk in lymph node metastasis with OR of 4.9 (95%CI: 1.6 - 15.3). MMP2-1306C/T genotype was not associated with tumor size, tissue differentiation, invasion, TNM nor lymph node metastasis of gastric carcinoma (χ(2)(tumor size) = 0.05, P = 0.98; χ(2)(depth of invasion) = 1.87, P = 0.39; χ(2)(histological type) = 0.55, P = 0.76; χ(2)(LN metastasis) = 0.44, P = 0.80; χ(2)(TNM) = 2.6, P = 0.28). There was no significant interaction between the polymorphisms of the two genes observed (χ(2) values were 0.98 and 0.80, P values were 0.81 and 0.85). CONCLUSION: Polymorphism of TIMP2 is significantly related with occurrence and development of GC and maybe acts as a new biomarker of GC in prognosis.

[Significance of the expression of lymphocytes and cytokines infiltrating in HCC].

AIM: To reveal the classification of lymphocytes and expression of cytokines infiltrating in HCC, and investigate the significance of changes of immune microenvironment in HCC. METHODS: 76 tumor and non-tumor tissues of HCC were collected to detect the amount of immune cells in the tissues by FCM and immunohistochemistry (IHC). Th1/Th2 cytokines in tissues were detected by Cytometric bead array (CBA), and TGF-1, VEGF detected by ELISA. RESULTS: There were more CD3(+); T cells, CD4(+); Th cells, Treg cells, and CD45RO(+); memory T cells in tumors than in non-tumor tissues. On the contrary there were less CD8(+); CTLs in tumors. There was negative correlation between Treg and Th or CTL cells. CD69, which is the early activating factor, expressed less on CD3(+); T cells and NK cells in tumors than non-tumor tissues. Whereas HLA-DR, which is the late activating factor, expressed more on CD3(+); T cells in tumors than non-tumor tissues. More IL-10, TGF-1 and VEGF were secreted in tumors than non-tumor tissues. CONCLUSION: Along with the decrease of effective immune cells and increase of suppressor immune cells and cytokines, the lymphocytes infiltrating in the tumor were immune incompitence, which contributed to the tumorigenesis.

[Correlation of polymorphism of Nme1-1465 T>C and TGFß1-509 T>C with genetic susceptibility of gastric carcinoma].

OBJECTIVE: To explore the correlation of functional genetic variants in Nme1-509 C>T and TGFß1-1465 T>C genes to the genetic susceptibility of gastric carcinoma in Fujian province, China. METHODS: A case-control study was conducted in a population in Fujian province. The polymorphism of TGFß1-509 C>T (rs1800469), Nme1-1465 T>C (rs16949649) in 273 gastric carcinoma patients and 277 cancer-free controls, frequency-matched by age and sex, were analysed by using Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF-MS). Adjusted odds ratios (OR) and 95% confidence evaluation intervals (95%CI) measured by multivariate Logistic regression analysis were adopted in studying the correlation of the gene polymorphism with the susceptibility of gastric cancer. RESULTS: After the adjustment using Logistic regression or the potential confounding effects of gender and age, as compared with TT+CT genotype gastric carcinoma patients, the homozygous Nme1-1465CC genotype carriers had a significantly higher risk in lymph node metastasis, with the OR of 2.5 (95%CI 0.08-2.10; P=0.029). There was no association obtained between TGFß1-509 T>C genotype with the tumor size, cell differentiation, tumor invasion and lymph node metastasis in gastric carcinoma. In the intestinal type gastric carcinoma group, when compared with the wild homozygous Nme1 TT* TGFß1 CC, Nme1 TC* TGFß1 TC, Nme1 TC* TGFß1 TT and Nme1 CC* TGFß1 TC genotype carriers, there was a significantly decrease of risk in gastric carcinogenesis of 0.42 fold (95%CI 0.54-0.94, P=0.022), 0.32 fold (95%CI 0.42-0.97, P=0.013) and 0.26 fold (95%CI 0.42-0.97, P=0.008), respectively. CONCLUSIONS: There is a significant relationship between polymorphism of Nme1-1465 T>C and the prognosis of carcinoma of stomach. It also demonstrates that coexistence of Nme1-1465 T>C and TGFß1-509 T>C genes may provide a synergistic effect of increasing the susceptibility of gastric carcinogenesis.