GWAS follow-up study of esophageal squamous cell carcinoma identifies potential genetic loci associated with family history of upper gastrointestinal cancer.

Based on our initial genome-wide association study (GWAS) on esophageal squamous cell carcinoma (ESCC) in Han Chinese, we conducted a follow-up study to examine the single nucleotide polymorphisms (SNPs) associated with family history (FH) of upper gastrointestinal cancer (UGI) cancer in cases with ESCC. We evaluated the association between SNPs and FH of UGI cancer among ESCC cases in a stage-1 case-only analysis of the National Cancer Institute (NCI, 541 cases with FH and 1399 without FH) and Henan GWAS (493 cases with FH and 869 without FH) data (discovery phase). The top SNPs (or their surrogates) from discovery were advanced to a stage-2 evaluation in additional Henan subjects (2801 cases with FH and 3136 without FH, replication phase). A total of 19 SNPs were associated with FH of UGI cancer in ESCC cases with P < 10-5 in the stage-1 meta-analysis of NCI and Henan GWAS data. In stage-2, the association for rs79747906 (located at 18p11.31, P = 5.79 × 10-6 in discovery) was replicated (P = 0.006), with a pooled-OR of 1.59 (95%CI: 1.11-2.28). We identified potential genetic variants associated with FH of UGI cancer. Our findings may provide important insights into new low-penetrance susceptibility regions involved in the susceptibility of families with multiple UGI cancer cases.

Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China.

Little is known about the link between gastric microbiota and the epidemiology of gastric cancer. In order to determine the epidemiologic and clinical relevance of gastric microbiota, we used 16 S ribosomal RNA gene sequencing analysis to characterize the composition and structure of the gastric microbial community of 80 paired samples (non-malignant and matched tumor tissues) from gastric cardia adenocarcinoma (GCA) patients in Shanxi, China. We also used PICRUSt to predict microbial functional profiles. Compared to patients without family history of upper gastrointestinal (UGI) cancer in the non-malignant gastric tissue microbiota, patients with family history of UGI cancer had higher Helicobacter pylori (Hp) relative abundance (median: 0.83 vs. 0.38, p = 0.01) and lower alpha diversity (median observed species: 51 vs. 85, p = 0.01). Patients with higher (vs. lower) tumor grade had higher Hp relative abundance (0.73 vs. 0.18, p = 0.03), lower alpha diversity (observed species, 66 vs. 89, p = 0.01), altered beta diversity (weighted UniFrac, p = 0.002) and significant alterations in relative abundance of five KEGG functional modules in non-malignant gastric tissue microbiota. Patients without metastases had higher relative abundance of Lactobacillales than patients with metastases (0.05 vs. 0.01, p = 0.04) in non-malignant gastric tissue microbiota. These associations were observed in non-malignant tissues but not in tumor tissues. In conclusion, this study showed a link of gastric microbiota to a major gastric cancer risk factor and clinical features in GCA patients from Shanxi, China. Studies with both healthy controls and gastric cardia and noncardia cancer cases across different populations are needed to further examine the association between gastric cancer and the microbiota.

Germline Mutations in PALB2, BRCA1, and RAD51C, Which Regulate DNA Recombination Repair, in Patients With Gastric Cancer.

Up to 10% of cases of gastric cancer are familial, but so far, only mutations in CDH1 have been associated with gastric cancer risk. To identify genetic variants that affect risk for gastric cancer, we collected blood samples from 28 patients with hereditary diffuse gastric cancer (HDGC) not associated with mutations in CDH1 and performed whole-exome sequence analysis. We then analyzed sequences of candidate genes in 333 independent HDGC and non-HDGC cases. We identified 11 cases with mutations in PALB2, BRCA1, or RAD51C genes, which regulate homologous DNA recombination. We found these mutations in 2 of 31 patients with HDGC (6.5%) and 9 of 331 patients with sporadic gastric cancer (2.8%). Most of these mutations had been previously associated with other types of tumors and partially co-segregated with gastric cancer in our study. Tumors that developed in patients with these mutations had a mutation signature associated with somatic homologous recombination deficiency. Our findings indicate that defects in homologous recombination increase risk for gastric cancer.

Comparison of global gene expression of gastric cardia and noncardia cancers from a high-risk population in china.

OBJECTIVE: To profile RNA expression in gastric cancer by anatomic subsites as an initial step in identifying molecular subtypes and providing targets for early detection and therapy. METHODS: We performed transcriptome analysis using the Affymetrix GeneChip U133A in gastric cardia adenocarcinomas (n = 62) and gastric noncardia adenocarcinomas (n = 72) and their matched normal tissues from patients in Shanxi Province, and validated selected dysregulated genes with additional RNA studies. Expression of dysregulated genes was also related to survival of cases. RESULTS: Principal Component Analysis showed that samples clustered by tumor vs. normal, anatomic location, and histopathologic features. Paired t-tests of tumor/normal tissues identified 511 genes whose expression was dysregulated (P<4.7E-07 and at least two-fold difference in magnitude) in cardia or noncardia gastric cancers, including nearly one-half (n = 239, 47%) dysregulated in both cardia and noncardia, one-fourth dysregulated in cardia only (n = 128, 25%), and about one-fourth in noncardia only (n = 144, 28%). Additional RNA studies confirmed profiling results. Expression was associated with case survival for 20 genes in cardia and 36 genes in noncardia gastric cancers. CONCLUSIONS: The dysregulated genes identified here represent a comprehensive starting point for future efforts to understand etiologic heterogeneity, develop diagnostic biomarkers for early detection, and test molecularly-targeted therapies for gastric cancer.

[Studies on the risks of cardia neoplasm among immediate relatives of the patients in Shanxi province].

OBJECTIVE: To analyze the different risks of cardia neoplasms in the immediate relatives of the cardia cancer patients, through a case-control study. METHODS: A case-control study was adopted on 772 cases and 772 controls, and relative risk (RR) were measured to compare the results from paternal or matrilineal groups. RESULTS: (1) Risk of the 1st grade kinship to the male cardia-cancer-patient group was obviously higher than that of the control group with RR = 2.61 (95%CI: 1.44 - 4.73, P < 0.01). (2) The risks of both paternal (P < 0.05) and matrilineal (P < 0.05) in the male cardia-cancer-patients were obviously higher than that of the control groups while the risk of those male cardia-cancer-patients in the paternal was higher than that of the control group (P < 0.05), so as the case for female patients in the matrilineal group (P < 0.05). (3) Data from the 1st grade kinship of cardia-cancer-patient group showed that parents and siblings had a higher risk than the control group (P < 0.05). (4) No significant genetic differences were found between the paternal of either the cancer group or the control group (P > 0.05), but statistical difference was observed that the risk of someone being the matrilineal of the cancer group was higher than that of the control group (P < 0.05). CONCLUSION: The risks of cardia-cancer were higher in the 1st grade kinship, which including parents, brothers, sisters, maternal grandmother, mother, and maternal aunt. It was suggested that prevention programs should be focused on both earlier detection and treatment of the patients. New strategy for cancer prevention also need to be further developed.

[Study on the birth order of patients with esophagus cancer in Shanxi province].

OBJECTIVE: To explore the relationship between esophagus cancer patients and both environmental and genetic factors, through analyzing the data on birth orders from esophagus cancer patients of Shanxi province. METHODS: Both Greenwood and Haldane methods on birth order were used to study the 1101 cases with esophagus cancer from Shanxi province. All the patients had received surgery and were diagnosed, by pathological evidence. First certificates of the patients were confirmed through the standard genetic epidemiologic investigation. Birth order was investigated on probands of the 1101 cases with esophagus cancer and their 44 siblings. RESULTS: form the Greenwood method showed that there was a tendency for cases with esophagus cancer in birth orders First to Third. However, the Haldane method showed that the results were quite different between actual value and the average theory value of 6A (6A((actual value)) = 17 118, X ¯(6A(average theory value)) = 19 290, X = |6A-X ¯(6A)|/V(6A) = 7.63, X > 2) which suggested that the birth order had some effects on the occurrence of esophagus cancer. In addition, the actual value of 6A was lower than the theoretic average value, and the parents at younger productive age or baby at the first birth was easy to develop esophagus cancer. CONCLUSION: Esophagus cancer was related with the birth order, especially at early order, which was not consistent with the national reports on esophagus cancer. RESULTS: from this study suggested that there were certain effects of environmental risk factors on esophagus cancer patients.

Risk factors for esophageal and gastric cancers in Shanxi Province, China: a case-control study.

OBJECTIVE: Smoking and alcohol consumption explain little of the risk for upper-gastrointestinal (UGI) cancer in China, where over half of all cases in the world occur. METHODS: We evaluated questionnaire-based risk factors for UGI cancers in a case-control study from Shanxi Province, China, including 600 esophageal squamous cell carcinomas (ESCCs), 599 gastric cardia adenocarcinomas (GCAs), 316 gastric noncardia adenocarcinomas (GNCAs), and 1514 age- and gender-matched controls. RESULTS: Ever smoking and ever use of any alcohol were not associated with risk of UGI cancer; only modest associations were observed between ESCC risk and highest cumulative smoking exposure, as well as GNCA risk and beer drinking. While several associations were noted for socioeconomic and some dietary variables with one or two UGI cancers, the strongest and most consistent relations for all three individual UGI cancers were observed for consumption of scalding hot foods (risk increased 150-219% for daily vs. never users) and fresh vegetables and fruits (risk decreased 48-70% for vegetables and 46-68% for fruits, respectively, for high vs. low quartiles). CONCLUSION: This study confirms the minor role of tobacco and alcohol in UGI cancers in this region, and highlights thermal damage as a leading etiologic factor.

[A comparative study on the risks of esophagus-cancer patients among factors as blood relatives, paternal line, matriarchal and different sex].

OBJECTIVE: In order to provide new clues on the cause of esophagus-cancer through seeking for information among the relatives of esophagus-cancer-patients at high-risk, contrast analysis was carried out to compare the ORs between esophagus-cancer cases and the relatives of the patients. METHODS: Case-control study was adopted on 720 cases and 720 controls who were kin relatives of the patients. RESULTS: (1) Risk of the relatives to the esophagus-cancer-patient group (1.34% - 2.24%) was obviously higher than the control group (0.78% - 1.21%) (P < 0.01). In 1(st) grade relatives, the risk of parent's to the esophagus-cancer patients (6.11%) was obviously higher than the control group (2.97%) (P < 0.01). (2) According to the cascade analysis to the cases of both paternal and matriarchal, lines, results showed that the risks of both the paternal line (0.87% - 1.01%) and the matriarchal line (0.50% - 0.79%) in the group of esophagus-cancer cases were all obviously higher than the lines in the control groups (0.53% - 0.65%) and (0.38% - 0.47%). Data also showed that the risk among the male relatives of paternal line (eg: grandfathers', father's, uncles' etc.) in the group of cases was 2.68% while the matriarchal (eg: grandmother's, mother's, aunts' etc.) was 1.91%. Both figures were obviously higher than that in the control group (1.50% and 0.92%, P < 0.01). CONCLUSION: The risk factor of esophagus cancer of the next generation seemed higher if the father and his brothers or mother and her sisters having had esophagus-cancers.

[Studies on hereditary epidemiology of cardia cancer in Shanxi province.].

OBJECTIVE: Studies on cardia-cancer caused by hereditary factors. METHODS: Case-control method was adopted, with information including name, sex, date of birth, date of death of all the I, II, III relatives of the patients, diagnosis and the treatment collected. The hereditary probability of cardia cancer and the separation degree were calculated by Falconer and Li-Mentel-Gart. RESULTS: (1) Prevalence rates of cardia-cancer on relative I, relative II, relative III of cardia-cancer patients appeared to be 0.54%, 0.04%, and 0.05% respectively. Prevalence rates of upper-digestive-tract-cancer of relative I, relative II, relative III of cardia-cancer patients showed as: 2.50%, 0.36% and 0.13% respectively. Data showed that relative I > relative II > relative III and family cluster existed in both males and females. (2) Cardia-cancer hereditary probability of the relative I cardia-cancer probands was 11.71%, with males as 14.01% and females as 14.72%. The upper-digestive-tract-cancer hereditary probability of the relative I cardia-cancer probands was 13.87%, with males as 11.49% and females as 23.08%, both below 25%, indicating this was a low hereditary cancer. (3) The upper-digestive-tract-cancer separation of the blood compatriots of cardia-cancer patients was 0.0452, with males as 0.0441 and females as 0.0507, both below 0.25, indicating the nature of a multi-gene but not single-gene hereditary way. CONCLUSION: Hereditary factor is recognized as one of the high risk cardia cancer, but not the most risky factor causing the high morbidity of cardia cancer in Shanxi province.

Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China.

Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n = 30 cases) and Human U133A (n = 17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a high-frequency instability group (two-thirds of all cases with one or more instability category of > or =10%) and a low-frequency instability group (one-third of cases with instability of <10%). Genomic instability also varied widely across chromosomal arms, with the highest frequency of LOH on 9p (33% of informative single nucleotide polymorphisms), CN loss on 3p (33%), and CN gain on 3q (48%). Twenty-two LOH regions were identified: four on 9p, seven on 9q, four on 13q, two on 17p, and five on 17q. Three CN loss regions-3p12.3, 4p15.1, and 9p21.3-were detected. Twelve CN gain regions were found, including six on 3q, one on 7q, four on 8q, and one on 11q. One of the most gene-rich of these CN gain regions was 11q13.1-13.4, where 26 genes also had RNA expression data available. CN gain was significantly correlated with increased RNA expression in over 80% of these genes. Our findings show the potential utility of combining CN analysis and gene expression data to identify genes involved in esophageal carcinogenesis.

Replication of a genome-wide case-control study of esophageal squamous cell carcinoma.

In a previous pilot case-control study of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) and matched controls from a high-risk area in China, we identified 38 single nucleotide polymorphisms (SNPs) associated with ESCC located in or near one of 33 genes. In our study, we attempted to replicate the results of these 38 gene-related SNPs in a new sample of 300 ESCC cases and 300 matched controls from the same study conducted in Shanxi Province, China. Among 36 evaluable SNPs, 4 were significant in one or more analyses, including SNPs located in EPHB1, PGLYRP2, PIK3C3 and SLC9A9, although the odds ratios (ORs) for these genotypes were modest. Associations were found with EPHB1/rs1515366 (OR 0.92, 95% CI 0.86-0.99; p = 0.019), PIK3C3/rs52911 (OR 0.93, 95% CI 0.88-0.99; p = 0.02) and PGLYRP2/rs959117 (OR 0.93, 95% CI, 0.86-1.01; p = 0.061) in general linear models (additive mode); and the genotype distribution differed between cases and controls for SLC9A9/rs956062 (p = 0.024). To examine these 4 genes in more detail, 40 HapMap-based tag SNPs from these 4 genes were evaluated in the same subjects and 7 additional SNPs associated with ESCC were identified. Further confirmation of these findings in other populations and other studies are needed to determine if the signals from these SNPs are indirectly associated due to linkage disequilibrium, or are directly related to biologic function and the development of ESCC.

Evaluation of BRCA2 in the genetic susceptibility of familial esophageal cancer.

Previous studies of esophageal squamous cell carcinoma (ESCC) have shown a high frequency of allelic loss on chromosome 13q, infrequent somatic mutations in BRCA2, and a suggested association between a positive family history (FH+) of upper gastrointestinal cancer and germline BRCA2 mutations. In all, 70 ESCC patients (44 FH+ and 26 FH-) were examined by direct full sequencing of germline DNA for BRCA2 mutations. In addition, 28 family members of three of these patients and 232 unrelated healthy blood bank donor controls were examined for the mutations identified in the 70 ESCC patients. Five BRCA2 germline mutations, including three not previously reported (N1600del, A2054P, and V2109I), were identified in six of 44 FH+ patients, but none of 26 FH- patients (14 vs 0%, P=0.078), consistent with our previous findings (3/34 or 9% FH+ vs 0/22 or 0% FH-, P=0.27). The cumulative frequency of BRCA2 germline mutations in ESCC patients in this and our previous study combined is 12%, with all mutations found in FH+ as opposed to FH- cases (9/78 or 12% FH+ vs 0/48 or 0% FH-, P=0.013). We conclude that germline mutations in BRCA2 in ESCC patients from this high-risk area of China are more frequent in FH+ than FH- cases, suggesting that BRCA2 may play a role in genetic susceptibility to familial ESCC.