Chinese Cancer Research Articles

Immunogenicity of Del19 EGFR mutations in Chinese patients affected by lung adenocarcinoma

BackgroundMutant peptides presented by cancer cells are superior vaccine candidates than self peptides. The efficacy of mutant K-Ras, P53 and EGFR (Epidermal Growth Factor Receptor) peptides have been tested as cancer vaccines in pancreatic, colorectal, and lung cancers. The immunogenicity of EGFR Del19 mutations, frequent in Chinese lung adenocarcinoma patients, remains unclear.ResultsWe predicted the HLA binding epitopes of Del19 mutations of EGFR in Chinese lung adenocarcinoma patients with NetMHC software. Enzyme-linked immunosorbent assay (ELISA) was performed to detect the EGFR-reactive IgG in lung cancer patients. Del19 mutations may be presented by multiple HLA Class I molecules, with delE746_A750 presented by 37.5% of Chinese population. For HLA Class II molecules, Del19 mutations of EGFR may be presented by multiple HLA-DRB1 molecules, with delE746_A750 presented by 58.1% of Chinese population. Serum reactivity to wild type EGFR protein was significantly higher in patients with Del19 EGFR mutations than those with EGFR L858R point mutation or with EGFR wild type genotype.ConclusionsThese findings suggest that Del19 mutations of EGFR, with an estimated frequency of 40% in Chinese lung adenocarcinoma patients, may serve as unique targets for immunotherapy in Chinese lung cancer patients.

Multicenter Observational Study of Chinese Non-Small Cell Lung Cancer (NSCLC) Patients With Rare Driver Gene Mutation

Multicenter Observational Study of Chinese Non-Small Cell Lung Cancer (NSCLC) Patients With Rare Driver Gene Mutation

Prevalence and prognosis significance of cardiovascular disease in cancer patients: a population-based study.

Background: Cardiovascular disease (CVD) is a heavy burden on cancer patients worldwide. This study aimed to evaluate the prevalence and influence of cardiovascular risk factors (CVRF) and CVD on the all-cause mortality among Chinese cancer patients.Results: Overall, 13.0% of all cancer patients had at least one type of CVRFs and 5.0% with CVDs. Patients with CVRF or CVD presented more frequently at later stages and received higher percentage of oncotherapy. During 1,782,527 person-years of follow-up, the all-cause mortality in cancer patients with CVDs and with CVRFs was higher compared with those without (182.6/1000, 109.5/1000 and 93.3/1000 person-years, respectively). Cox regression analysis showed that patients with heart failure (HR 1.79, 95% CI 1.61-1.99), myocardial infarction (HR 1.50, 95% CI 1.16-1.95), atrial fibrillation (HR 1.30, 95% CI 1.09-1.53), stroke (HR 1.21, 95% CI 1.11-1.32), hypertension (HR 1.10, 95% CI 1.04-1.16) and diabetes (HR 1.16, 95% CI 1.08-1.24) had increased all-cause mortality, whereas dyslipidemia patients had better prognosis (HR 0.73, 95% CI 0.64-0.83). Stratified by cancer type, the prognostic impact of specific CVRF or CVD varied.Methods: We consecutively recruited 710,170 cancer patients between Feb. 1995 and Jun. 2018. A stratified Cox proportional hazards model was used to analyze the effect of comorbidities on the overall survival of patients stratified by cancer type.Conclusions: Cancer patients are vulnerable to comorbidity related to heart and cerebral disease. The influence of comorbidities on prognosis is noticeable and specific both for the type of cancer and comorbidities.

Mutational analysis of BRCA1 and BRCA2 in northwest Chinese breast cancer patients

Background: BRCA1 and BRCA2 are the most well-known susceptibility genes in breast cancer, indicating high-risk breast cancer families and influencing both treatment options. However, data of BRCA mutation in Chinese breast cancer population was limited. Here we explored the BRCA1/2 mutation status and analyzed their clinicopathological relationships among breast cancer patients with high hereditary risk in northwest China. Methods: Breast cancer patients admitted to Xijing Hospital, between November 2015 and May 2016, with high hereditary risk were recruited. Fresh peripheral venous blood samples were collected for BRCA1/2 gene screening. Risk factors for BRCA1/2 mutations were studied via single-factor analysis and multivariable logistic analysis. Furthermore, we reviewed the literature and discussed the possible mechanism of the mutant genome types. Results: Eighty-two patients were enrolled in the study. Twenty (24.4%) of them were found with BRCA1/2 mutation, including 8 BRCA1 mutation and 13 BRCA2 mutation. BRCA1 and BRCA2 co-mutation was observed in only one case. The mutant genome types included pathogenic variant (4/82), potential pathogenic variant (4/82), beneficial mutations (8/82), and chemotherapy sensitivity-related mutations (5/82). Prognosis-related mutations were enriched in BRCA2 gene, while drug-sensitive related mutations were always observed in BRCA1 gene. Multiple logistic analysis showed that HER2 [odds ratio (OR) 4.58; 95% confidence interval (CI), 1.182–17.74; P=0.028) might be independent factor for BRCA1/2 mutation. Conclusions: The incidence and feature of BRCA1/2 mutation in our center was similar to that in other regions. HER2 expression was independent factor for BRCA1 and BRCA2 mutation. BRCA2 T/-, BRCA2 A/-, BRCA2 G/- and BRCA2 C/-mutation subtypes might be potential harmful mutations for Chinese breast cancer population.

MFOLFIRINOX as Adjuvent Chemotherapy in Treating Chinese Pancreatic Cancer Patients

mFOLFIRINOX as Adjuvent Chemotherapy in Treating Chinese Pancreatic Cancer Patients

Pharmacokinetics of pertuzumab administered concurrently with trastuzumab in Chinese patients with HER2-positive early breast cancer.

In the APHINITY study (NCT01358877, BIG 4-11/BO25126/TOC4939G), pertuzumab added to trastuzumab and chemotherapy significantly improved invasive disease-free survival as adjuvant treatment for patients with HER2-positive early breast cancer. The objective of this analysis was to assess the pharmacokinetics of pertuzumab in combination with trastuzumab in Chinese patients with early breast cancer. Samples for pertuzumab and trastuzumab pharmacokinetic analysis were taken from Chinese patients during cycle 1 of treatment and at steady-state in cycle 10. Noncompartmental analysis was used to estimate minimum and maximum serum concentrations (Cmax and Cmin), area under the concentration-time curve, clearance, and other pharmacokinetic parameters. In 15 patients, mean steady-state Cmax and Cmin pertuzumab serum concentrations (368 ± 177 μg/ml, and 122 ± 47 μg/ml, respectively) were numerically higher than observed previously in a pharmacokinetic analysis of the global population in APHINITY and in patients treated in the metastatic setting. The geometric mean ratio and corresponding 90% confidence interval for trastuzumab Cmax and Cmin in the presence (n = 15) or absence (n = 17) of pertuzumab were 104.6 (91.09-120) and 98.23 (84.58-114), respectively, indicating no apparent impact of pertuzumab on the pharmacokinetics of trastuzumab. Increases in pertuzumab Cmax and Cmin were not associated with an increase in adverse events. The APHINITY Chinese pharmacokinetic substudy analysis supports the dosing regimen for pertuzumab (840 mg loading dose followed by 420 mg maintenance doses every 3 weeks administered by intravenous infusion) in a Chinese HER2-positive early breast cancer patient population.

Self-Perceived Pain in Chinese Patients With Cancer.

BackgroundPain is one of the most burdensome and prevalent symptoms cancer patient report and it has severe negative impact on patient’s quality of life. The aim of this study is to estimate the prevalence of pain and to test the association between demographic, clinical, psychological factors, and self-assessed pain in Chinese cancer population.MethodsA total of 553 cancer patients were recruited in this cross-sectional study. Patient’s basic demographic data was collected by a study-designed information sheet, and patient’s pain, sleep disturbance and psychological distress were assessed by several validated measurements (MPQ-SF, AIS, FoP-Q-SF, PHQ-9, and GAD-7). Descriptive statistics and hierarchical multiple regression analyses were performed.ResultsOf the 553 patients, 411 (74.32%) patients reported that they experience some degree of pain. Fear of progression, anxiety, insomnia, and depressive symptoms were significantly associated with different subscales and the overall pain score in bivariate correlation matrix. Insomnia, depressive symptoms, and fear of cancer progression were significant independent factors of cancer pain on multivariate analyses.ConclusionPsychological factors play a great role in the relationship between objective pathophysiology and patient’s subjective experience of pain. It is important to evaluate each individual in detail with respect to psychological distress and pain severity when planning treatment and rehabilitation.

Epigenetic alterations are associated with tumor mutation burden in non-small cell lung cancer

BackgroundTo profile genomic and epigenomic of a naïve Chinese non-small cell lung cancer (NSCLC) cohort and investigate the association between tumor mutation burden (TMB) and DNA methylation (DNAm) to explore potential alternative/complimentary biomarkers for NSCLC immunotherapies.MethodsA total of 89 tumor tissues with matched normal tissues from Chinese NSCLC patients were collected and subjected to whole exome sequencing (WES). From comparison, each patient was evaluated for the TMB value and divided into high, medium and low TMB based on TMB tertile distribution and then relatively high and low TMB samples were selected and subjected to DNAm profiling.ResultsPatients in the low (n = 30), medium (n = 29), and high (n = 30) TMB tertiles had 1.1–2.5, 2.5–4.1, and 4.2–13.9 mutations/Mb, respectively. A statistical directly association between differential methylation probes (DMPs) and TMB level was observed in our cohort (r = 0.63, P value =0.0003) and this was confirmed by using TCGA NSCLC dataset (r = 0.43, P value =0.006). Relatively high TMB group (n = 16, 7.5–13.9 mutations/Mb) harbors more differential DMPs while less in relatively low TMB group (n = 13, 1.1–2.4 mutations/Mb). Eight hundred fifty-eight differential methylation regions (DMRs) were found in relatively high TMB group. In addition, 437 genes show DNAm aberrance status in high TMB patient group and 99 have been reported as its association with lung cancer.ConclusionTo our knowledge, this is the first report for direct link between the methylome alterations and TMB in NSCLCs. High TMB NSCLCs had more DNAm aberrance and copy number variations (CNVs). In addition, the TMB distribution of Chinese NSCLCs population is lower than that of TCGA.

Abstract 746: Genomic alteration of Chinese dMMR/MSI-H gastric cancer

Abstract Background: Gastric cancer is a high incidence malignancy often diagnosed at an advanced stage with limited therapeutic options and poor prognosis. A small fraction of gastric cancer with dMMR/MSI-H has extraordinary response to the immune checkpoint inhibitor treatment attributing to the immunogenicity generated by the elevated tumor mutation burden. At the meantime, the extensive genomic variants also cause profound impact on many other cancer related genes. Thus the understanding of dMMR/MSI-H gastric cancer genomic profiling is urgent for exploring clinical strategy to this cohort. Methods: Formalin Fixed Paraffin Embedded (FFPE) samples of 30 Chinese gastric cancer patients were collected for 450 gene panel based next-generation sequencing (NGS) assay. Genomic alterations including single base substitution, short and long insertions/deletions, copy number variations, gene fusions and rearrangement were assessed. Microsatellite instability (MSI) status and tumor mutational burden (TMB) were also calculated by NGS algorithm. Results: There were 15 males (50%) and 15 females (50%) diagnosed as gastric cancer with a median age of 67 years old. The TMB value of this cohort ranged from 29 to 118 muts/Mb, with the median value of 58 muts/Mb. The most frequent genomic alterations in Chinese MSI-H gastric cancer patients were revealed as KMT2D (50%), RNF43 (50%), CIC (50%), PIK3CA (50%), KMT2C (43%), ACVR2A (40%), TP53 (30%), ATM (33%), and ERBB3 (33%). Truncation has been found the most frequent gene alteration among these top mutations due to the deficiency of mismatch repair system caused reading frame shift. Epigenetic modifier genes with functions of chromatin remodeling and histone methylation have been found extensively mutated in MSI-H gastric cancer. Among eighteen (60%=18/30) patients carrying truncations in ARID1A whose coding protein participates in chromatin remodeling, seven of them possess loss-of-function biallelic truncations. Moderate frequency of mutation also occur at other genes in chromatin remodeling such as ARID1B (23%), PBRM1 (17%) and SMARCA4 (26%). About 77% patients in this cohort carry at least one truncation in genes belonging to the histone lysine methyltransferase 2 (KMT2) family such as KMT2A, KMT2C and KMT2D. Mutations of B2M gene which are commonly associated with resistance to immune checkpoint inhibitor have been found in 23% MSI-H gastric cancer. About 66% of the patients in this cohort carrying mutations in FBXW7, PIK3CA, PTEN, STK11 and TSC may benefit from the mTOR inhibitors. Conclusions: In general, dMMR/MSI-H gastric cancers possess elevated and dispersive TMB value. Epigenetic modifier genes involving in chromatin remodeling and histone methylation mutate frequently in MSI-H gastric cancer. About 66% of the patients in this cohort may benefit from the mTOR inhibitors. Citation Format: Jia Wei, Jian Wang, Xiangshan Fan, Yue Wang, Yao Fu, Kai Wang, Nandie Wu, Qin Liu, Yang Yang, Weifeng Wang, Baorui Liu. Genomic alteration of Chinese dMMR/MSI-H gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 746.

Abstract 3401: Genomic and transcriptome profile of 66 Chinese biliary tract cancer patient derived cell lines

Abstract Background: Biliary tract cancer (BTC) is an aggressive cancer with very poor prognosis. Currently there is no effective target therapy for BTC. To understand the genetic basis and look for potential drug targets of BTC, we sequenced the whole exome and transcriptome of 66 patient-derived primary cancer cells (PDC) from 23 unique patient samples. Methods: We cultured 66 patient derived cell lines (PDC) passage range from P10 to P15, from 23 BTC patients, with 1-9 PDC each patient. Both genomic DNA and total RNA were extracted from these cell lines, followed by WES and RNA sequencing on NovaSeq and HiSeq, respectively. Average sequencing coverage for WES is 139X and average data amount for RNA is 8.4Gbp. Variant calling was done by union set of Mutect and Pindel, with VAF cut-off 0.1 and filtered with a white variant list from COSMIC database. CNV was called from WES data by CNVKit with log2ratio cut-off 1.2. RNASeq data was mapped by STAR and fusion was calling by STAR-Fusion with at least 3 split reads. Results: A median of 57 non-silent mutations were identified in Chinese BTC which was about 2 folds (57 vs. 30) of that in TCGA cholangiocarcinoma. Ethnic differences were found between Chinese and western population. The top four genes with frequency in Chinese BTC higher than TCGA cholangiocarcinoma were TP53 (56.5% vs. 14.3%), EPPK1 (26.1% vs. 2.9%), FRAS1 (13.0% vs. 2.9%), and ZFHX3 (13.0% vs. 2.9%), while ANKRD36C (4.4% vs. 20.0%), PBRM1 (8.7% vs. 22.9%), and TCHH (4.4% vs. 17.1%) were the top three genes with frequency lower than TCGA cholangiocarcinoma. We also found two previously reported cholangiocarcinoma related genes, PEG3 and GNAS, both harbored mutations in 3 of 23 patients (8.7%) in our data. However, they were not reported in TCGA cholangiocarcinoma. A median of 158 CNVs (range: 5-299) in gene level were identified, and the top three frequently mutated CNVs genes were LILRA3, SIRPB1, and GSTT1. Copy number loss of CDKN2A were found in 7 of 23 patients. Totally, 234 unique fusions were identified with 2-17 fusions per patient (median: 8). Among these fusions 5 of them (C15orf57-CBX3, SCARB1-UBC, SAMD5-SASH1, NCOR2-UBC, and FTH1-EIF5A) were reported to be associated with cancers. There were also 19 fusions found in TCGA pan-cancer datasets. Conclusions: We built a comprehensive mutation landscape for Chinese BTC patients. Our results demonstrated ethnic differences between Chinese and TCGA Western cholangiocarcinoma patients. These PDC samples with profiled genetic information are good in vitro models for drug target discovery and validation for BTC patients. Citation Format: Feiling Feng, Qingbao Cheng, Bin Li, Liang Yang, Hua Dong, Bin Li, Dadong Zhang, Chang Xu, Xiaoya Xu, Yong Yu, Zishuo Chen, Zhizhen Li, Fugen Li, Zhiquan Qiu, Chen Liu, Xiaoqing Jiang. Genomic and transcriptome profile of 66 Chinese biliary tract cancer patient derived cell lines [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3401.

Abstract 1700: Alterations of DNA damage repair genes in Chinese primary liver cancer patients and its association with tumor mutation burden

Abstract Background: The genomic mutation features of primary liver cancer (PLC) varied from various pathology and etiology. Alterations in DNA damage repair (DDR) genes could induce genomic instability and accumulate tumor mutation burden (TMB), which was related to the efficacy of immune-checkpoint blockade treatment. However, the characteristics of DDR gene alterations and its association with TMB in PLC remain largely undefined. Method: We enrolled 357 Chinese PLC patients as training cohort and used the TCGA-LIHC data of 373 hepatocellular cancer patients as validation cohort. FFPE tumor tissues and matched blood samples were collected from these Chinese patients for next-generation-sequencing (NGS)-based 450 genes panel assay, which contains 35 DDR genes. All histological diagnoses were confirmed by independent pathologists. Correlation of the DDR pathway genes alterations with TMB was assessed by multiple linear regression model using R package “nlme”. The receiver operating characteristic (ROC) curve was applied to determine the diagnostic efficiency of DDR pathway genes for TMB high (which was defined as the top quantile) using R package “pROC”. Results: The training cohort of Chinese PLC patients included 282 males and 75 females with the mean age of 56.3 years old. The pathologic subtypes include 214 hepatocellular carcinoma (HCC), 122 intrahepatic cholangiocarcinoma (ICC) and 21 mixed hepato-cholangiocellular carcinoma (H-ChC). There are 25.8% (92/357) patients had at least one DDR gene alteration. The DDR mutation rate showed no significant differences among three subtypes of PLC (HCC vs ICC vs H-Chc: 22.9% (49/214) vs 30.3% (37/122) vs 28.6% (6/21), P=0.311). In addition, 16.3% (15/92) of the patients with DDR gene mutations have germline variations. The TMB in HCC patients was significantly higher than that in ICC patients but not in H-ChC patients (median TMB for HCC, ICC and H-ChC was 5.4, 3.1, and 3.9 Muts/Mb, Kruskal-Wallis test, P<0.001). Importantly, PLC patients with DDR gene mutations had significantly higher TMB compared to patients without DDR gene mutation (6.2 vs 3.9 Muts/Mb, P<0.001), which was further validated in TCGA-LIHC data (95 vs 64 mutations, P<0.001). The patients with germline DDR gene mutations had significant lower TMB compared with patients with somatic DDR gene mutations (3.1 vs 6.3 Muts/Mb, Wilcox test, P=0.041). We further defined 3 subtypes of DDR pathways (BER, FA and MMR) that significantly correlated with TMB in the training cohort, which exhibited diagnostic efficiency in distinguishing TMB-high or TMB-low PLC in TCGA-LIHC dataset (AUC: 0.67). Conclusion: DDR gene alterations were significantly positively associated with TMB in PLC. Mutations occurred in BER, FA or MMR pathways indicated higher TMB in PLC, which have the potential to serve as markers to predict the TMB level to guide the immune-checkpoint inhibitor therapy. Citation Format: Jianzhen Lin, Honglin Guo, Junping Shi, Xu Yang, Yan Jiang, Yi Bai, Junyu Long, Dongxu Wang, Jin Bian, Ming Yao, Kai Wang, Haitao Zhao. Alterations of DNA damage repair genes in Chinese primary liver cancer patients and its association with tumor mutation burden [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1700.

Abstract 4056: Correlation analysis between PD-L1 expression, TMB and clinical characteristics in Chinese non-small cell lung cancer

Abstract Background: Immunotherapy has played an increasingly important role in the treatment of non-small-cell lung cancer (NSCLC) and it was approved for the first-line treatment of advanced lung cancer. PD-L1 expression and TMB are two important immunotherapy biomarkers, however, the relationship between PD-L1 expression, TMB and clinical features is still unclear. Methods: A total of 205 Chinese NSCLC patients (pts) including 120 males and 85 females with a median age of 61.5 years (range 31-84) were enrolled. Tumor stage was evaluated according to the 8th edition of the AJCC/UICC TNM staging system for NSCLC. FFPE tumor and matched blood samples were collected for NGS based 450[[Unsupported Character - Codename ­]]gene panel assay. TMB was assessed by standard NGS algorithms. TMB data (median: 5.4 muts/Mb, range 0.8-68.9 muts/Mb) from 206 lesions were provided for analysis. 172, 16 and 18 lesions tissues were analyzed for PD[[Unsupported Character - Codename ­]]L1 expression by IHC with 22C3, 28-8 and ZR3 antibodies, respectively. Results: According to TNM staging system, pts were divided into stage I (44 pts), stage II (20 pts), stage III (40 pts) and stage IV (101 pts). The pathological types of pts are adenocarcinoma (69.4%), squamous cell carcinoma (18.4%) and other types (12.1%). 34.5% of lesions were positive for PD-L1 expression (TPS≥1%), including 25.7% PD-L1(TPS≥10%) and 16.5% PD-L1(TPS≥50%) respectively. Significant differences between males and females were observed in PD-L1 expression (TPS≥1%: 40.8% vs. 25.6%, p<0.05; TPS≥10%: 30.8% vs. 18.6%, p<0.05; TPS≥50%: 20.8% vs. 10.5%, p<0.05). In addition, males had higher TMB than females (median: 8.5 vs. 3 muts/MB, p<0.001). A higher percentage of males than females were identified with TMB≥10 muts/Mb (45.0% vs. 12.8%, p<0.001) and TMB≥20 muts/Mb (11.7% vs. 2.3%, p<0.05). The percentage of PD-L1 positive in advanced pts was higher than in stage I pts (TPS≥1%: 39.5% vs 19.6%, p<0.005; TPS≥10%: 30.7% vs 12.4%, p<0.005; TPS≥50%: 16.1% vs 5.2%, p<0.05). Squamous cell carcinoma had higher TMB than adenocarcinoma (median: 8.5 vs. 3.8 muts/MB, p<0.001). Squamous cell carcinoma had a higher percentage of TMB≥10 muts/Mb than adenocarcinoma (44.7% vs. 23.1%, p<0.01). A low correlation was observed between PD-L1 expression and TMB (p <0.001, r=0.2). Pts with PD-L1 TPS≥10% had higher TMB (median: 10 vs 3.8 muts/Mb, p<0.001) and pts with TMB≥10 muts/Mb had higher percentage of PD-L1 positive expression (50.8% vs 27.0%, p<0.001). Conclusion: In this study, we found the most commonly used two biomarkers for immune checkpoint inhibitors, PD-L1 expression and TMB, may be correlated with gender, stage and pathological type of NSCLC patients. There is also a weak correlation between these two biomarkers. Exploring the relationship between immune biomarkers and clinical features may better guide in screening more suitable patients for immune checkpoint blockade. Citation Format: Yang Yu, Xinglong Fan, Yucheng Wei, Zimin Liu, Zuping Lian, Hongxia Han, Ming Yao, Kai Wang. Correlation analysis between PD-L1 expression, TMB and clinical characteristics in Chinese non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4056.

Abstract 3423: HER2 amplification and microsatellite status distribution in Chinese gastric cancer patients

Abstract Background:Amplification and/or overexpression of human epidermal growth factor receptor-2 (HER2, also known as ERBB2) were present in 6.1-23.0% of gastric cancer. In breast cancer, amplification and overexpression of the HER2 are associated with poor prognosis. Meanwhile, MSI-H patients have an improved prognosis in gastric cancer. However, little is known about the association of these two indicators in gastric cancer. Method:260 tumor tissues and matched normal from gastric cancer patients were included in this study to reveal HER2 amplification and microsatellite status distribution of Chinese patients with gastric cancer using deep next generation sequencing (NGS) targeting 450 cancer genes. Microsatellite status (MSS or MSI-H) were evaluated according to NGS algorithms. Result:Male to female ratio was about 2:1 with a mean age of 60 years old. 241 tumors were primary tumors and 19 were metastases. MSI-H was detected in 16 samples (6.2%) and HER2 amplification was detected in 18 samples (6.9%), which were consistent with the previously reported incidences. The proportion of MSI-H in metastatic lesions was higher than that in primary lesions, but the difference was not statistically significant (10.5% vs. 5.8%, P=0.33). The detection of HER2 amplification in metastatic foci and primary tumors had a similar trend as that in MSI-H (15.8% for metastatic foci vs. 6.2% for primary tumors, P=0.13). Interestingly, our study revealed that HER2 amplification was mutually exclusive with MSI-H in both primary and metastatic lesions. MSI-H/HER2amp-, MSS/HER2amp+, and MSS/HER2amp- subgroups accounted for 5.8%, 6.2%, and 88% in primary cancers, while MSI-H/HER2amp-, MSS/HER2amp+ and MSS/HER2amp- subgroups accounted for 10.5%, 15.8% and 73.7% in metastasis, respectively. Conclusion:We analyzed the distribution of HER2 amplifications and microsatellite status in Chinese patients with gastric cancer. The detection rate of HER2 amplifications and MSI-H was consistent with previous reports. Interestingly, our data showed that both HER2 amplifications and MSI-H have higher detection rate in metastases than that in primary lesions, and the two biomarkers were mutual exclusive in our cohort. Citation Format: Jun Guo, Da Jiang, Wei Zhang, Ting Deng, Zhaojian Niu, Wenting Chen, Junping Shi, Shuirong Zhang, Lin Zhang. HER2 amplification and microsatellite status distribution in Chinese gastric cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3423.

Abstract 816: DNA methylation profiling from circulating tumor DNA for early diagnosis of non-small cell lung cancer

Abstract Introduction: Lung cancer found at an early stage carries much-improved prognosis. Unfortunately, there has been little success in developing blood-based diagnostic method. Profiling somatic mutations from ctDNA has shown great promise for cancer diagnosis, prognosis, and surveillance. Despite the substantial advances made in ctDNA detection techniques, the detection rate remains low for early stage disease. The role of aberrant DNA methylation in the process of tumorigenesis both at individual genes and a genome-wide scale has been well elucidated. It occurs very early in cancer development, thus capable of serving as a diagnostic biomarker. In this prospective study, we evaluated the potentiality of DNA methylation status obtained from ctDNA as an early diagnostic marker for NSCLC. Methods: Panel Design: Methylation data of tumor samples (12 types, n=4772), adjacent normal (8 types, n=411), and normal white blood cells (WBC, n=656) from TCGA and GSE were compared. Differentially methylated sites were extracted using modified wald-test with an adjusted p-value <0.05 and fold-change>2. Our panel covers 80,672 CpG sites, spanning 1.05Mb of human genome. We performed targeted bisulfite sequencing on plasma samples of 359 early stage Chinese NSCLC patients and 144 healthy individuals to interrogate their methylation statuses with an average sequencing depth of 1,000x. The Results: The training cohort consisted of 359 early stage Chinese lung cancer patients (266 stage IA, 25 stage IB, 43 stage II and 25 stage III) with a median age of 51 and 144 Chinese healthy individuals with a median age of 59. We constructed a diagnostic classification model using a support vector machine (SVM)-based machine learning classifier based on top 3,000 differentially methylated regions (DMRs) selected by random forest between tumor and normal plasma samples. Subsequently, 5-fold cross-validation with 100-time repeats were performed to gain a robust estimation of model performance, achieving a sensitivity of 79.4%, specificity of 95.4% and area under curve (AUC) of 95.2%. The model was subsequently validated in an independent cohort, consisting of 79 early stage Chinese NSCLC patients and 74 healthy individuals with comparable clinical characteristics as the patients in the training cohort. The model yielded a sensitivity of 77% and specificity of 90% in the validation cohort, suggesting its robustness. Conclusions: Overall, our findings demonstrated in a large clinical cohort the potential of profiling DNA methylation from ctDNA, which can effectively distinguish cancerous from healthy, for the purpose of diagnosis. This method has potential to serve as a supplementary or alternative approach in lung cancer early detection. The general concept can be further extended to other types of cancer diagnostics. Citation Format: Naixin Liang, Bingsi Li, Chenyang Wang, Tao Zheng, Jiayue Xu, Shuai Fang, Fujun Qiu, Jing Su, Lichen Zhang, Xin Lu, Miaomiao Song, Lingjian Yang, Han Han-Zhang, Xinru Mao, Hao Liu, Shanqing Li, Ke Ma, Zhihong Zhang. DNA methylation profiling from circulating tumor DNA for early diagnosis of non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 816.

Abstract 1703: New genetic variations discovered in KRAS wild-type cetuximab resistant Chinese colorectal cancer patients

Abstract The efficacy of Cetuximab therapy in colorectal cancer patients is limited by the development of therapeutic resistance. The currently known oncogenic ‘driver’ mutations do not fully explain the resistance mechanism of Cetuximab. Currently there are no reports of any studies that have explored new driver mutations in Cetuximab resistance by whole exome sequencing (WES). In this study, we performed WES to identify common genetic factors from twenty-two Cetuximab-sensitive and ten Cetuximab-resistant patients, aiming to discover characteristic genes associated with Cetuximab resistance. For Cetuximab-sensitive patients, the mutation frequency of MUC16, FCGBP, DMBT1 was found to be 100%, 90.91% and 86.36%, respectively. MUC16, PDE4DIP and TACC2 were altered in all 10 Cetuximab-resistant samples. We also discovered there are 151 significantly mutated genes (SMGs) in Cetuximab sensitive group and 37 in the resistant group. CYP4A11 was the most frequently mutated gene in Cetuximab-resistant patients. BCAS1, GOLGA6L1 and WNT16 were found to be the second group of frequently mutated genes which found in to occur at a frequency of 60% in resistant patients. After cosine similarity analysis with 30 known signatures, three mutational signatures (signature a, b and c) were found in all CRC tumors, similar to Signature 1, 5 and 6 in COSMIC, respectively. Gene ontology analysis was performed on SMGs and found twelve enriched GO terms. Four genes are enriched in six specific KEGG pathway groups, such as metabolism of xenobiotics by cytochrome P450, Steroid hormone biosynthesis, retinol metabolism and drug metabolism. In conclusion, we show that the establishment of a WES clinical study of Cetuximab resistance CRC with prospective follow-up of patients can help to identify candidate predictive biomarkers of response. Note: This abstract was not presented at the meeting. Citation Format: Changwen Jing, Ting Wang, Rong Ma, Haixia Cao, EnShun Xu, Zhuo Wang, Siwen Liu, Dan Chen, Junying Zhang, Yang Wu, Yuan Zhang, Ping Ding, Michael Y. Sha, Jianzhong Wu, Jifeng Feng. New genetic variations discovered in KRAS wild-type cetuximab resistant Chinese colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1703.

Germline DNA damage repair gene alterations in Chinese prostate patients: More than HRR and MMR.

e13041 Background: Prostate cancer is a worldwide most occurred malignancy in male population. Genetic aberrations of homologous recombination repair (HRR) pathway were proved to be associated with aggressive disease and poorer outcome but may also lead cancer cells more vulnerable to PARP inhibitors. Other than HRR, germline variants in mismatch repair (MMR), nucleotide excision repair (NER) were also identified. Thus, it is important to clarify the distribution of germline alterations of DDR pathways in Chinese prostate cancer patients. Methods: Sixty-five prostate cancer patients unselected for family history, stage of disease, or age at diagnosis were collected. DNA from peripheral blood was extracted. Whole-exon was captured and sequenced subsequently using MGI-SEQ 2000 platform. A total of 229 DDR genes were selected for further analysis. Germline variants were determined to be deleterious according to the ACMG 2015 guidelines. Results: Ten of 65 patients (15.38%) had 7 pathogenic/likely pathogenic germline variants involving 5 different genes: FANCD2 (n = 5), BRCA2 (n = 3), CHEK2 (n = 1), ATM (n = 1) and RECQL (n = 1). Nine patients (13.84%) carried variants predicated to be deleterious via in silico predicators. Taken together, deleterious/potential deleterious germline variants were categorized into 5 DDR pathways which were Fanconi Anemia (9.2%), HRR (9.2%), MMR (4.6%), BER (4.6%) and NER (1.5%). Patients with pathogenic/likely pathogenic germline variants had tendency to be early-onset (mean age [range] at diagnosis, 52[43-67] versus 64[37-80] years, P = 0.001). PSA level at initial diagnosis and self-reported family history did not have significant difference between deleterious mutation carriers and non-carriers (P = 0.396 for PSA level, P = 0.753 for family history). Moreover, metastasis and Gleason score were not associated with deleterious germline variants. Conclusions: Our data showed approximately 52% DDR mutation occurred in other DNA repair pathways besides HRR and MMR, which was a unique spectrum of germline variants in Chinese prostate cancer patients. This indicated distinct genetic etiology and potential therapeutic targets of prostate cancer in Chinese population. Moreover, early-onset in patients with deleterious germline variants is an important clinical character. Whole DDR pathway genes’ testing and counseling should be considered for application for young individuals.

Pathogenic germline mutation profile in Chinese lung cancers and related-driver mutation pattern.

e13003 Background: Many cancers could be driven by germline mutation exampled as BRCA1/2 in breast or ovarian cancer. However, the candidate predisposition variants for Chinese lung cancer are largely unknown. Methods: We reviewed 1797 Chinese lung cancer patients with paired tumor-normal samples sequenced by a 1021 gene panel. The annotation of germline variants within 95 selected susceptible genes was based on ACMG 2015 version guideline. Results: The frequency of patients identified with pathogenic or likely pathogenic (P/LP) germline variants were 5.95% (107 in 1797), which elevated to 10.1% (9 in 89) in patients younger than 40. Totally, 112 mutations from 35 genes were screened out. Recurrent pathogenic germline genes were BRCA2 (n = 14), FANCA (n = 9), RAD51D (n = 7), MUTYH (n = 7), ATM (n = 7) and TP53 (n = 5). The average age at diagnosis was numerically 2 years earlier in patients with P/LP (mean, 58.2 vs. 60.0, p = 0.22) than other patients without significance, but different genes contribute to discordant effects. Significantly early onset age was found in germline BRCA1/ 2 mutation (median, 52.5 versus 60.0 yrs in patients without P/LP, p = 0.0080) while later onset age was associated with germline PMS2 mutation (median, 74 versus 60.0 yrs, p = 0.0214 ). In terms of clinical actionable somatic mutation, the frequency of KRAS (15/89, 16.85% versus 121/1429, 8.47%, p = 0.012) and c-MET (6/89, 6.74% versus 31/1429, 2.17%, p = 0.018) in germline mutant patients were significantly higher, while TP53 (41/89, 46.07% versus 847/1429, 59.27%, p = 0.019) was apparently less mutated in P/LP lung cancer. As for frequency of EGFR, ALK, ROS-1, RET and BRAF, mutation frequency were not significantly different in lung cancer with germline mutation. Conclusions: Our study delineated the pathogenic germline mutation landscape in Chinese lung cancers for the first time. Predisposition genes demonstrated clinical actionable roles in onset age and therapeutic interventions. Further follow up may clarify the contribution of germline mutation to somatic mutation driven targeted therapy response and prognosis.

Correlation of HERVK with efficacy on anti-PD-1/PD-L1 therapy in a pilot metagenomics study on Chinese advanced lung cancer patients.

e14046 Background: Patient selection for PD-1 inhibitors in NSCLC is still based on imperfect screening biomarkers, including PD-L1 expression and tumor mutational burden(TMB).There are several reports show certain bacteria or virus infections are correlated with efficacy and prognosis on PD-1 inhibitors treatment. In order to explore more potential biomarkers for anti-PD-1 therapy, we investigate whether we can discover microorganisms in Chinese lung cancer patients and whether certain microorganism are correlated with efficacy or prognosis on anti-PD-1 therapy using metagenomics technology. Methods: In this study, 30 advanced lung cancer patient were enrolled, including 15 cases of adenocarcinoma, 12 cases of squamous carcinoma, 2 cases of Small cell lung cancer. 10 patients received PD-1/PD-L1 inhibitors as first-line therapy and other patients as second-line therapy. Among these 30 patients, 15 PR,1 CR, 10 PD, 4 SD according to RECIST 1.1. Plasma cell-free DNA (cfDNA) were collected from these patients prior to anti-PD-1 treatment and whole-genome sequencing of cfDNA at average coverage 5X was performed on Illumina NovaSeq in 2 ×150bp length model. A bioinformatics pipeline composed of 4 tools: BWA/Sambama/Kraken2/Bracken, was constructed to analyze the sequencing data. Non-human derived reads were extracted by sambama from the bam file that generated by BWA. Bacteria/Virus abundance in each sample was estimated through Bracken, followed by bac/vir database alignment in Kraken2. Results: In our pilot study, 4 patients were selected for metagenomics sequencing(1CR, 1PR, 2PD). Interestingly, over 100 different microbial sequence were detected in every patient. Compare microorganism in CR+PR patients to PD patients, Human endogenous retrovirus K (HERVK) were quite abundant in CR/PR patients but not in PD patients: 5.6 times more abundant in CR/PR patients comparing to PD patients. (HERVK abundance: CR:PR:PD = 1.20% : 0.32% : (0.17%, 0.10%)). HERVK is a family of human endogenous retroviruses associated with certain malignant tumors, studies have indicated that HERVK may trigger an antigen specific immune response for certain cancer patients. Conclusions: Metagenomics sequencing on plasma cfDNA could be a potential biomarker discovery approach to identify prognostic biomarkers for anti-PD-1 therapy. HERVK are correlated with efficacy on anti-PD-1 treatment in our pilot study, however more thorough investigation need to be conducted to confirm whether HERVK can be served as efficacy biomarkers for anti-PD-1.

Tumor copy number alteration (CNA) burden as a prognostic factor for overall survival in Chinese gastric cancers.

e15555 Background: Gastric cancer (GC) is associated with high morbidity and mortality rates in the world with poor prognosis and limited treatment options. The level of copy number alteration (CNA), termed CNA burden, is reported as a pan-cancer prognostic factor associated with recurrence and death. The current study aims to investigate association between CNA burden in primary tumor tissue and overall survival (OS) of Chinese patients with GC after surgical resection. Methods: The present study included 78 patients who had received surgical resection and adjuvant chemotherapy with poorly differentiated GC. The primary outcome was OS. Tumor specimens were obtained from surgery and submitted for next generation sequencing (NGS) with matched normal tissue samples. A 1408-gene panel was used to identify genome profiles. Data were analyzed using Cox proportional hazards models and Kaplan-Meier survival analysis. Results: The most frequently altered genes were TP53 (47%), PIK3CA (10%), PTEN (9%), NOTCH1 (8%) and RNF43 (6%), and copy numbers of TRPS1 (65%), COL1A2 (50%), CSMD3 (45%), ZFHX4 (45%), NAV3 (36%) varied most frequency in current cohort. Greater tumor CNA burden correlated with an increase in death from disease compared to a lower tumor CNA burden ( p= 0.0066). In addition, there were statistically significant differences in OS between different clinical staging ( p= 0.0011). Moreover, the Cox proportional hazard model showed that CNA burden was an independent prognosis factor in GC. Finally, we performed an independent signature that includes CNA burden and clinical staging to predict survival of GC. Conclusions: This study indicates that tumor CNA burden is an independent predictive survival biomarker for Chinese gastric cancers. CNA burden combined with clinical staging is a better predictor for postoperative survival prediction of gastric cancer.

Clinical outcomes of various resistance mechanisms of osimertinib in Chinese advanced non-small cell lung cancer patients.

e20530 Background: Increasing efforts have been invested in elucidating the resistance mechanisms to osimertinib. Major resistance mechanisms include but not limited to acquired EGFR mutations, predominantly C797, mutations in bypass pathways and small cell lung cancer (SCLC) transformation. However, no study has comprehensively investigated clinical outcomes of various mechanisms of resistance. Methods: 103 T790M positive advanced Chinese non-small cell lung cancer (NSCLC) patients who progressed on 1st generation EGFR-TKI were enrolled. Targeted sequencing, using a panel consisting of 168 lung cancer related genes, was performed on paired plasma samples collected prior to osimertinib and after the development of disease progression (PD) to profile mutation spectrum. 7 patients with no mutation detected at PD were excluded from analyses. Results: Major acquired mutations included 25% EGFR mutations, predominantly C797 and L792, 16% MET amplification, 8% TP53 mutations, 4% KRAS mutations, 4% RET fusions, 4% ERBB2 amplification and 6.25% RB1 mutations. Acquired RB1 mutation may indicate the possibility of SCLC transformation. Approximately, 30% of patients with no known resistance mechanisms at PD. In this cohort, we had 61 patients with 19 deletion and 35 patients with EGFR L858R prior to the initiation of osimertinib. We revealed patients with 19del acquired more mutations ( p= 0.014) and were more likely to acquire mutations in MAP/PI3Kpathway ( p= 0.04) and TP53 at PD ( p= 0.021). On the other hand, acquired ERBB2 amplifications were only detected in L858R-mutant patients ( p= 0.047). Furthermore, 36 patients preserved T790M and 60 patients lost T790M at PD. Our data revealed patients retaining T790M, often associated with activation of bypass signaling pathways or continued EGFR activation through tertiary mutations, had a longer progression-free survival (PFS) ( p= 0.047) and overall survival (OS) ( p= 0.04) comparing to patients with T790M loss, often with diverse and EGFR-independent mechanisms. We also show that patients with acquired C797S had significantly longer PFS ( p= 0.031), while patients with acquired MET amplifications had significantly shorter PFS ( p= 0.033). Conclusions: Collectively, we revealed differential clinical outcomes associated with various resistance mechanisms, representing an important step in advancing the understanding of resistance mechanisms of osimertinib.