Mutations In Gastric Cancer Research Articles

MUC16 mutation predicts a favorable clinical outcome and correlates decreased Warburg effect in gastric cancer

Mutations in oncogenes or tumor suppressors can reprogram tumor metabolism by controlling multiple metabolic changes including glycolysis, glutaminolysis, increased autophagy, and macropinocytosis. Somatic mutations are essential for the development and growth of gastric cancer (GC), but the precise roles of these mutations in GC glucose metabolism remain largely unknown. In this study, we examined cancer genomes in 375 GC samples and demonstrated several glycolysis-related mutations in GC. Of note, loss-of-function mutation in MUC16 gene was identified. Mutated MUC16 predicted a better prognosis in GC patients. Gene set enrichment analysis suggested that mutated MUC16 status was associated with down-regulation of PI3K/Akt/mTOR signaling and Myc expression. GC cells with MUC16 mutations had reduced glycolytic capacity. Subsequently, genetic silencing of MUC16 in SNU16 and SNU5 cells led to significant reduction in glucose uptake, lactate production, extracellular acidification rate, and colony formation ability, indicating the critical regulatory roles of MUC16 in GC glycolysis and tumorigenesis. Specifically, western blotting showed that MUC16 knockdown inhibited PI3K/Akt/mTOR signaling, and reduced the protein level of Myc, which acts as a key transcription factor in regulating glycolysis. Taken together, our findings identify the MUC16-PI3K/Akt/mTOR-Myc axis as a critical signaling cascade that couples genomic mutations to metabolic reprogramming in GC.

Landscape of somatic mutations in gastric cancer assessed using next-generation sequencing analysis.

Gastric cancer is a highly heterogeneous disease and the second leading cause of cancer-associated mortality. However, the genomic basis of gastric cancer is not completely understood and the underlying genetic heterogeneity has not been well studied. In the present study, 1,021 genes were sequenced and the somatic mutations of 45 formalin-fixed, paraffin-embedded gastric adenocarcinoma samples were assessed using next-generation sequencing technologies. In the present study, a median sequencing coverage depth of 708-fold was achieved. Somatic genomic alterations were detected in 37/45 patients (82.4%) and the most frequent genetic alterations identified were tumor protein P53 (TP53) gene mutations. Mutations in MLL4, ERBB3, FBXW7, MLL3, MTOR, NOTCH1, PIK3CA, KRAS, ERBB4 and EGFR were also detected. Patients with TP53 mutations had a higher number of somatic mutations, and the total number of somatic mutations was weakly correlated with patient age. These results provided data on the intratumoral heterogeneity of gastric cancer and may be used in order to develop personalized cancer therapy.

PIK3CA mutation in gastric cancer and the role of microsatellite instability status in mutations of exons 9 and 20 of the PIK3CA gene

A better understanding of molecular gastric cancer (GC) entities may help in tailored treatments of that neoplasm. The PIK3CA mutation is one of the most important in many cancers. We performed a comparison of clinical and pathological data of the PIK3CA mutation in GC patients. The analysis was done on 472 patients operated on in 1 center. Polymerase chain reaction (PCR) was used for the screening of PIK3CA (exon 9 and 20). For microsatellite instability (MSI) we used 5 quasi-monomorphic mononucleotide repeats - BAT-26, BAT-25, NR-24, NR-21, and NR-27. The clinical and pathological data was analyzed. PIK3CA mutation was observed in 10 out of 472 GC patients (2.1%). Nine out of 10 were MSI (9 of 111 MSI patients - 8.1%). Half of the 10 patients had mutations in exon 9 and the other half in exon 20. A majority of patients with the PIK3CA mutation had MSI (p < 0.001). The 5-year survival of MSI patients with the PIK3CA mutation was 40% and without the mutation, 70.4% (p = 0.309). For patients with the mutation in exon 9, the 5-year survival was 0%, and for those with the mutation in exon 20, 80% (p = 0.031). The Cox proportional hazards regression analysis did not show that PIK3CA is statistically correlated with a worse overall survival. PIK3CA mutation in GC is a rare finding. It is strongly associated with the MSI molecular subgroup, presenting a worse outcome than other MSI patients. A completely different outcome is associated with the mutation in exon 9 compared to the mutation in exon 20, with the latter being more favorable.

KRAS Codon 12 and 13 Mutations in Gastric Cancer in the Northeast Iran

KRAS mutations are reported in many types of cancers including pancreas, lung, colon, breast,and gastric (GC). High frequency of KRAS mutation is observed in the pancreas,colon, and lung cancers; they commonly arise in codon 12 and 13 of exon 2. Due to the lack of information about the frequency of KRAS mutations in the Northeast of Iran, the currentstudy aimed at evaluating KRAS frequency in cases with GC in this region. A total of120 formalin-fixed, paraffin-embedded blocks of patients with GC were assessed. The assays to detect KRAS in codon 12 and13 were obtained through the peptide nucleic acid (PNA)-clamp. Totally 87 male and 33 female patients were analyzed in the current study. The mean age of the subjects was 55years.The most common tumoral fragment was located on the body with 48 cases (40%) and the less frequent was related to fondues with six cases (5%).Of the 120 GC samples, 16(13.3%) caseshad codon 12 KRAS mutation, and 16.7% had codon 13 mutations. There were no significant relationships between gender,age, and KRAS mutations in the studied specimens. In conclusion, the overall frequency of KRAS codon 12 and 13 mutations in GC was 30% in the current study population.Frequency of KRAS codon 12 and 13 mutations hadsignificant correlation with tumors location. Different pathogenic mechanismsare suggested for GC according to tumor location. The current study resultsmay be an important diagnostic tool for physicians managing atrophic gastritis.

Systematic Inspection of the Clinical Relevance of TP53 Missense Mutations in Gastric Cancer.

The "guardian of the genome," TP53, is one of the most frequently mutated genes of all cancers. Despite the important biological roles of TP53, the clinical relevance of TP53 mutations, in gastric cancer (GC), remains largely unknown. Here, we systematically assessed clinical relevance, in terms of TP53 mutation positions, finding substantial variability. Thus, we hypothesized that the position of the TP53 mutation might affect clinical outcomes in GC. We systematically inspected missense mutations in TP53, from a TCGA (The Cancer Genome Atlas) GC dataset in UCSC Xena repository. Specifically, we examined five aspects of each mutational position: (1) the whole gene body; (2) known hot-spots; (3) the DNA-binding domain; (4) the secondary structure of the domain; and (5) individual mutation positions. We then analyzed the clinical outcomes for each aspect. These results showed that, in terms of secondary structure, patients with mutations in turn regions showed poor prognosis, compared to those with mutations in beta strand regions (log rank ${\text{p}}= {{0.043}}$p=0.043). Also, in terms of individual mutation positions, patients having mutations at R248 showed poorer survival than other patients having mutations at different TP53 positions (log rank ${\text{p}}= {{0.035}}$p=0.035).

K-RAS mutation in gastric cancer and its link with microsatellite instability status

K-RAS mutation in gastric cancer and its link with microsatellite instability status

Novel Systemic Therapies for Advanced Gastric Cancer.

Gastric cancer (GC) is the second leading cause of cancer mortality and the fourth most commonly diagnosed malignant diseases. While continued efforts have been focused on GC treatment, the introduction of trastuzumab marked the beginning of a new era of target-specific treatments. Considering the diversity of mutations in GC, satisfactory results obtained from various target-specific therapies were expected, yet most of them were unsuccessful in controlled clinical trials. There are several possible reasons underlying the failures, including the absence of patient selection depending on validated predictive biomarkers, the inappropriate combination of drugs, and tumor heterogeneity. In contrast to targeted agents, immuno-oncologic agents are designed to regulate and boost immunity, are not target-specific, and may overcome tumor heterogeneity. With the successful establishment of predictive biomarkers, including Epstein-Barr virus pattern, microsatellite instability status, and programmed death-ligand 1 (PD-L1) expression, as well as ideal combination regimens, a new frontier in the immuno-oncology of GC treatment is on the horizon. Since the field of immuno-oncology has witnessed innovative, practice-changing successes in other cancer types, several trials on GC are ongoing. Among immuno-oncologic therapies, immune checkpoint inhibitors are the mainstay of clinical trials performed on GC. In this article, we review target-specific agents currently used in clinics or are undergoing clinical trials, and highlight the future clinical application of immuno-oncologic agents in inoperable GC.

Function of tumor necrosis factor alpha before and after mutation in gastric cancer

PurposeTo explore the cause of functional changes of tumor necrosis factor alpha (TNF-α) in development of gastric cancer through the structural changes of each site in TNF-α before and after mutation.MethodsThree typical mutant sites (TNF-α-308G/A, 857C/T and 863C/A of TNF-α) were chosen and methods like ab initio modeling was adopted for 3D modeling of TNF-α before and after mutation, besides, the structural changes were also analyzed.ResultsMutation of TNF-α-308G/A led to the production of multiple helical structures and that of 863C/A caused the production of one helical structure in its adjacent region. Mutation of 857C/T, however, did not cause the change in the basic structure of TNF-α.ConclusionsStructural changes of TNF-α may have a significant effect on development of gastric cancer.

KRAS Mutation in Gastric Cancer and Prognostication Associated with Microsatellite Instability Status.

Microsatellite instability (MSI) is one of the subgroups based on the new molecular classification of gastric cancer (GC). In this study, we analyzed the role of KRAS status in MSI GC and the impact of MSI status on KRAS mutation. We performed analysis on 595 GC patients. Polymerase chain reaction (PCR) was used for the screening of KRAS mutation (exon 2) and 5 quasi-monomorphic mononucleotide repeats, namely, BAT-26, BAT-25, NR -24, NR-21, and NR-27 were used to determine the MSI status. The KRAS and MSI status were then compared with clinicopathologic data of the GC patients. MSI GC was found in 20.3% of all cases. KRAS mutation was seen in 24 patients; 18 were MSI (75%) and 6 were microsatellite stable (MSS) (25%). MSI GC patients with KRAS mutation were older and mostly female, but MSS presented more advanced T and N stage of the disease, more cardia tumors, and adjuvant treatment. Five-year survival was 72.2% for KRAS mutation patients with MSI and 0% for MSS (p<0.001). Although KRAS mutations in GC are linked with MSI in the majority of cases, KRAS mutations with MSS status presented with a poor prognosis and a worse outcome. In multivariate analysis, MSI was associated with better survival (p<0.001) but KRAS was with worse survival (p=0.304). Our study suggests that KRAS mutations are based on MSI status rather than different codon subtypes of mutation, and such a division could be used to determine the GC patient outcome.

Abstract 636: Comprehensive analysis of T cells responsive to neoantigens derived from tumor-specific genetic mutations

Abstract Neoantigens derived from tumor-specific genetic mutations can be recognized as foreign by the host immune system, and might be suitable as target for cancer immunotherapy possibly due to their higher immunogenicity. In this study, to really know the immunogenicity of tumor-specific neoantigens, we comprehensively investigated T cell responses against neoantigens derived from genetic mutations in gastric cancer. Using next-generation sequencing, 156 missense mutations were identified in tumor cells from two gastric cancer patients. From them, we selected 30 potentially immunogenic amino acid sequences, which were derived from the mutations and predicted to potentially bind to HLA-class I (A*0201, A*0206, or A*2402) by an epitope prediction server, IEBD. We synthesized 30 kinds of 27mer long peptides, in which the mutated sequences were located in the center, and then cultured peripheral blood mononuclear cells (PBMC) from healthy donors in the presence of the synthetic peptides to evaluate whether they could really induce antigen-specific T cell responses. In the analysis with PBMC from 18 healthy donors, 27/30 (90%) synthetic peptides showed an ability to induce antigen-specific T cell responses in at least one donor, assessed by cytokine production assay. Among them, 15 peptides were immunogenic in more than one donor. The antigen-specific T cell responses were detected more frequently in CD4+ T cells (70%) than in CD8+ T cells (43%). The specificity of T cell responses to mutated sequences, but not to the corresponding wild type sequences, were confirmed in 5 of 8 (63%) peptides examined. In addition, antigen-specific T cell responses induced by mutated peptides were shown to be much higher than those induced by the corresponding wild type peptides. These findings clearly demonstrated high immunogenicity and specificity of neoantigens derived from tumor-specific genetic mutations. Further studies would be recommended to develop a novel immunotherapeutic approach, “personalized cancer vaccination”, targeting mutation-derived neoantigens. Citation Format: Tetsuro Sasada, Junya Ohtake, Satoshi Wada, Erika Yada, Shintaro Yoshida. Comprehensive analysis of T cells responsive to neoantigens derived from tumor-specific genetic mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 636. doi:10.1158/1538-7445.AM2017-636

Epstein–Barr virus-associated gastric cancer reveals intratumoral heterogeneity of PIK3CA mutations

BackgroundRecent whole-genome sequencing identified four molecular subtypes of gastric cancer (GC), of which the subgroup of Epstein–Barr virus-associated GC (EBVaGC) showed a significant enrichment of PIK3CA mutations. We here aimed to validate independently the enrichment of PIK3CA mutations in EBVaGC of a Central European GC cohort, to correlate EBV status with clinico-pathological patient characteristics and to test for a major issue of GC, intratumoral heterogeneity.Patients and methodsIn a first step, 484 GCs were screened for EBV and PIK3CA hot spot mutations of exon 9/20 using EBER in situ hybridization and pyrosequencing, respectively. Secondly, an extended sequencing of PIK3CA also utilizing next generation sequencing was carried out in all EBVaGCs and 96 corresponding lymph node metastases.ResultsTwenty-two GCs were EBER-positive, all being of latency type I. Intratumoral heterogeneity of EBER-positivity was found in 18% of EBVaGCs. Twenty-three GCs held PIK3CA mutations in hot spot regions of exon 9 or 20, being significantly more common in EBVaGCs (P < 0.001). Subsequent extended sequencing of PIK3CA of EBVaGCs showed that 14% harvested three to five different PIK3CA genotypes (including wildtype) in the same primary tumor, albeit in histologically and spatially distinct tumor areas, and that intratumoral heterogeneity of PIK3CA was also present in the corresponding lymph node metastases.ConclusionsOur findings unravel issues of tumor heterogeneity and illustrate that the assessment of the EBV status in tissue biopsies might carry the risk of sampling errors, which may significantly hamper adequate molecular tumor classification in a more clinical setting. Moreover, this is the first report of intratumoral heterogeneity of PIK3CA mutations in GC, and our findings lead to the conclusion that PIK3CA mutant and -wildtype tumor subclones are skilled to metastasize independently to different regional lymph nodes.

Unique characteristics of ARID1A mutation and protein level in gastric and colorectal cancer: A meta-analysis.

Background/Aim:Recently, AT-rich interactive domain-containing 1A protein (ARID1A) has been identified as a novel tumor suppressor gene in gastric cancer (GC) and colorectal cancer (CRC). However, the clinicopathologic value of ARID1A mutation or protein level in GC and CRC patients is controversial. Hence, we conducted a meta-analysis on the relationship between ARID1A aberrations and clinicopathologic parameters in GC and CRC.Materials and Methods:Relevant published studies were selected from PubMed and EMBASE. The effect sizes of ARID1A mutation or level on the patient's clinicopathologic parameters were calculated by prevalence rate or odds ratio (OR) or hazard ratio (HR), respectively. The effect sizes were combined using a random-effects model.Results:The frequency of ARID1A mutation and loss of ARID1A protein expression in GC patients was 17% and 27%, respectively. The loss of ARID1A protein expression of GC patients was significantly associated with advanced tumor depth (OR = 1.8, P = 0.004), lymph node metastasis (OR = 1.4, P = 0.001), and unfavorable adjusted overall survival (HR = 1.5, P < 0.001). ARID1A mutation of GC was significantly associated with microsatellite instability (MSI) (OR = 24.5, P < 0.001) and EBV infection (OR = 2.6, P = 0.001). The frequency of ARID1A mutation and ARID1A protein expression loss in CRC patients was approximately 12–13%. Interestingly, the loss of ARID1A protein expression in CRC patients was significantly associated with poorly differentiated grade (OR = 4.0, P < 0.001) and advanced tumor depth (OR = 1.8, P = 0.012).Conclusion:Our meta-analysis revealed that ARID1A alterations may be involved in the carcinogenesis of GC by EBV infection and MSI. The loss of ARID1A protein expression may be a marker of poor prognosis in GC and CRC patients.

Construction of a combinatorial pipeline using two somatic variant calling methods for whole exome sequence data of gastric cancer.

High-throughput next-generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer, forming the basis for personalized medicine in the clinical setting. Although the advent of many computational algorithms leads to higher accuracy in somatic variant calling, no standard method exists due to the limitations of each method. Here, we constructed a new pipeline. We combined two different somatic variant callers with different algorithms, Strelka and VarScan 2, and evaluated performance using whole exome sequencing data obtained from 19 Japanese cases with gastric cancer (GC); then, we characterized these tumors based on identified driver molecular alterations. More single nucleotide variants (SNVs) and small insertions/deletions were detected by Strelka and VarScan 2, respectively. SNVs detected by both tools showed higher accuracy for estimating somatic variants compared with those detected by only one of the two tools and accurately showed the mutation signature and mutations of driver genes reported for GC. Our combinatorial pipeline may have an advantage in detection of somatic mutations in GC and may be useful for further genomic characterization of Japanese patients with GC to improve the efficacy of GC treatments. J. Med. Invest. 64: 233-240, August, 2017.

Clinical Relevance and Molecular Phenotypes in Gastric Cancer, of TP53 Mutations and Gene Expressions, in Combination With Other Gene Mutations.

While altered TP53 is the most frequent mutation in gastric cancer (GC), its association with molecular or clinical phenotypes (e.g., overall survival, disease-free survival) remains little known. To that end, we can use genome-wide approaches to identify altered genes significantly related to mutated TP53. Here, we identified significant differences in clinical outcomes, as well as in molecular phenotypes, across specific GC tumor subpopulations, when combining TP53 with other signaling networks, including WNT and its related genes NRXN1, CTNNB1, SLITRK5, NCOR2, RYR1, GPR112, MLL3, MTUS2, and MYH6. Moreover, specific GC subpopulations indicated by dual mutation of NRXN1 and TP53 suggest different drug responses, according to the Connectivity Map, a pharmacological drug-gene association tool. Overall, TP53 mutation status in GC is significantly relevant to clinical or molecular categories. Thus, our approach can potentially provide a patient stratification strategy by dissecting previously unknown multiple TP53-mutated patient groups.

354. KRAS mutation in gastric cancer- molecular, and clinico-pathological characteristic

354. KRAS mutation in gastric cancer- molecular, and clinico-pathological characteristic

353. PIK3CA mutation in gastric cancer and the role of different codon mutations in the new molecular division of that neoplasm

353. PIK3CA mutation in gastric cancer and the role of different codon mutations in the new molecular division of that neoplasm

Prognostic and clinical impact of PIK3CA mutation in gastric cancer: pyrosequencing technology and literature review.

BackgroundPhosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutations that activate the PI3K/AKT signaling pathway have been observed in several types of carcinoma and have been associated with patient prognosis. However, the significance of PIK3CA mutations in gastric cancer remains unclear. This retrospective study investigated the relationship between PIK3CA mutations and clinical outcomes in patients with gastric cancer. Additionally, we reviewed the rate of PIK3CA mutations in gastric cancer and the association between PIK3CA mutations and prognosis in human cancers.MethodsThe study included 208 patients with gastric cancer who underwent surgical resection at Kumamoto University Hospital, Japan, between January 2001 and August 2010. Mutations in PIK3CA exons 9 and 20 were quantified by pyrosequencing assays.ResultsPIK3CA mutations were detected in 25 (12 %) of the 208 patients. Ten patients had c.1634A > G (p.E545G), 10 had c.1624G > A (p.E542K), 13 had c.1633G > A (p.E545K), nine had c.3139C > T (p.H1047R), and 1 had c.3140A > G (p.H1047Y) mutations. PIK3CA mutations were not significantly associated with any clinical, epidemiologic, or pathologic characteristic. Kaplan–Meier analysis showed no significant differences in disease-free survival (log rank P = 0.84) and overall survival (log rank P = 0.74) between patients with and without PIK3CA mutations.ConclusionsMutations in PIK3CA did not correlate with prognosis in patients with gastric cancer, providing additional evidence for the lack of relationship between the two.

Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer.

Gastric cancer and esophageal cancer are the second and sixth leading causes of cancer-related death worldwide. Multiple genomic alterations underlying gastric cancer and esophageal squamous cell carcinoma (ESCC) have been identified, but the full spectrum of genomic structural variations and mutations have yet to be uncovered. Here, we report the results of whole-genome sequencing of 30 samples comprising tumor and blood from 15 patients, four of whom presented with ESCC, seven with gastric cardia adenocarcinoma (GCA), and four with gastric noncardia adenocarcinoma. Analyses revealed that an A>C mutation was common in GCA, and in addition to the preferential nucleotide sequence of A located 5 prime to the mutation as noted in previous studies, we found enrichment of T in the 5 prime base. The A>C mutations in GCA suggested that oxidation of guanine may be a potential mechanism underlying cancer mutagenesis. Furthermore, we identified genes with mutations in gastric cancer and ESCC, including well-known cancer genes, TP53, JAK3, BRCA2, FGF2, FBXW7, MSH3, PTCH, NF1, ERBB2, and CHEK2, and potentially novel cancer-associated genes, KISS1R, AMH, MNX1, WNK2, and PRKRIR Finally, we identified recurrent chromosome alterations in at least 30% of tumors in genes, including MACROD2, FHIT, and PARK2 that were often intragenic deletions. These structural alterations were validated using the The Cancer Genome Atlas dataset. Our studies provide new insights into understanding the genomic landscape, genome instability, and mutation profile underlying gastric cancer and ESCC development. Cancer Res; 76(7); 1714-23. ©2016 AACR.

An epidermal growth factor receptor exon 19 mutation in a mucin-producing gastric cancer sample from a Chinese patient.

To determine whether a subgroup of gastric cancer patients might benefit from epidermal growth factor receptor-tyrosine kinase inhibitors. A total of 103 gastric cancer samples were collected for this study. High-resolution melting and deoxyribonucleic acid sequencing were used to detect epidermal growth factor receptor mutations in exons 19 and 21. Polymerase chain reaction-high-resolution melting was successfully performed on all 103 samples. Aberrant melting curves were found in only one sample. Sanger sequencing revealed a 15 bp deletion (c.2235_2249del; p.Glu746_Ala750del) in epidermal growth factor receptor exon 19. The sample was from a male patient, and the pathological diagnosis was a mucin-producing gastric cancer with lymph node metastasis. To date, this is the first report on epidermal growth factor receptor exon 19 mutation in gastric cancer. An epidermal growth factor receptor mutation in exon 19 was identified in mucin-producing gastric cancer sample from a male patient. This mutation indicates that the small subgroup of patients with mucin-producing gastric cancer might benefit from epidermal growth factor receptor-tyrosine kinase inhibitors.

Research advances of K-ras mutation in the prognosis and targeted therapy of gastric cancer

K-ras mutations have been described in 30% of human cancers with significantly different mutation frequencies. High K-ras mutation frequency is found in many cancers such as pancreas and lung cancers, whereas, gastric cancer has a relatively low K-ras mutation frequency. In recent years, numerous researches have focused on the K-ras mutation in gastric cancer. This review summarizes the K-ras mutation frequency in gastric cancer, the relationship of K-ras mutation with clinicopathologic features and prognosis of gastric cancer patients, targeted therapy for K-ras mutated gastric cancer, some small-molecular inhibitors of K-ras, and development of targeted therapy drugs for K-ras signaling pathway in gastric cancer.