Mutations In Gastric Cancer Research Articles

ARID1A Mutations in Gastric Cancer: A Review with Focus on Clinicopathological Features, Molecular Background and Diagnostic Interpretation.

AT-rich interaction domain 1 (ARID1A) is a pivotal gene with a significant role in gastrointestinal tumors which encodes a protein referred to as BAF250a or SMARCF1, an integral component of the SWI/SNF (SWItch/sucrose non-fermentable) chromatin remodeling complex. This complex is instrumental in regulating gene expression by modifying the structure of chromatin to affect the accessibility of DNA. Mutations in ARID1A have been identified in various gastrointestinal cancers, including colorectal, gastric, and pancreatic cancers. These mutations have the potential to disrupt normal SWI/SNF complex function, resulting in aberrant gene expression and potentially contributing to the initiation and progression of these malignancies. ARID1A mutations are relatively common in gastric cancer, particularly in specific adenocarcinoma subtypes. Moreover, such mutations are more frequently observed in specific molecular subtypes, such as microsatellite stable (MSS) cancers and those with a diffuse histological subtype. Understanding the presence and implications of ARID1A mutations in GC is of paramount importance for tailoring personalized treatment strategies and assessing prognosis, particularly given their potential in predicting patient response to novel treatment strategies including immunotherapy, poly(ADP) ribose polymerase (PARP) inhibitors, mammalian target of rapamycin (mTOR) inhibitors, and enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2) inhibitors.

Abstract 3639: ARID1 mutations may serve as a predictor of MSI and TMB levels in gastric cancer

Abstract Background: ARID1A is a gene that produces a protein called BAF250a, which is a component of the chromatin remodeling complex. This complex plays a critical role in regulating gene expression by altering the structure of chromatin. ARID1A mutations and MSI-H are mutually exclusive in endometrial cancer, but not in ovarian cancer. ARID1A mutations are associated with high TMB in certain types of cancer, such as endometrial and gastric cancer. The relationship between ARID1B mutations and MSI-H/TMB is complex, and this study aims to clarify it in gastric cancer. Methods: The formalin-fixed paraffin-embedded (FFPE) tissues 337 patients with gastric cancer who have underwent next-generation sequencing (NGS) include 733 genes from Nov, 2019 to Mar, 2023 in 3DMed Clinical Laboratory Inc. were investigated in this study. These patients are still being followed up. Result: In this study, 337 patients with gastric cancer were analyzed for ARID1A and ARID1B mutations, MSI-H status, and TMB levels. The results showed that 17.8% of the patients had ARID1A mutations, 8.9% had ARID1B mutations, and 3.6% had both mutations. Additionally, 7.7% of the all patients had MSI-H. The study found that patients with ARID1 mutations had significantly higher rates of MSI-H compared to unselected patients. Specifically, 35% of patients with ARID1A mutations, 30% with ARID1B mutations, and 75% with both mutations had MSI-H, compared to 7.7% in unselected patients. Furthermore, TMB levels were higher in patients with ARID1A or ARID1B mutations compared to wild-type and unselected patients (p<0.0001). There was no significant difference observed between patients with ARID1A and ARID1B mutation subgroups in terms of TMB levels (p = 0.3515). However, TMB levels were lower in patients with ARID1A or ARID1B mutations compared to patients with both mutations (p = 0.0036, p = 0.0104). These findings suggest that ARID1 mutations may cause genomic and chromosomal instability in gastric cancer, leading to higher rates of MSI-H and TMB. Conclusion: The study highlights the potential clinical significance of ARID1 mutations as a biomarker for predicting MSI-H and TMB levels in gastric cancer, which could help guide personalized treatment strategies for patients with this disease. However, further research is needed to confirm these findings and to determine the clinical implications of ARID1 mutations in gastric cancer. Citation Format: Chunsheng Xu, Bo Lian, Yujie Dai, Weiming Duan, Feilong Zhao, Mengbin Li. ARID1 mutations may serve as a predictor of MSI and TMB levels in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3639.

Exploration of BRCA1 and BRCA2 mutations in gastric cancer patients through next generation sequencing: implications for diagnosis and therapy.

The study aims to characterize BRCA1/2 mutations in Pakistani gastric cancer (GC) patients, identifying unique pathogenic variants and evaluating their potential as diagnostic biomarkers, while also exploring therapeutic avenues for personalized treatment strategies. In this study, we investigated the role of Breast Cancer gene 1 (BRCA1) and Breast Cancer gene 2 (BRCA2) mutations in Pakistani GC patients and their functional implications using Next-Generation Sequencing (NGS). Through NGS, we identified a total of 19 mutations in BRCA1 and 11 mutations in BRCA2, all with high mutation quality scores. In silico analysis revealed one pathogenic mutation in BRCA1 and one in BRCA2, indicating a potential link to disease development. Notably, two pathogenic mutations (BRCA1 p.Ala1823Ser and BRCA2 p.Gln92fs) were exclusively observed in the Pakistani GC population, suggesting unique genetic markers. Further examination utilizing The Cancer Genome Atlas (TCGA) data confirmed the absence of these mutations in non-Pakistani GC samples, emphasizing their specificity. Sanger sequencing validated these findings. Real Time Quantitative PCR (RT-qPCR) analysis indicated significantly decreased BRCA1/2 gene expression in samples harboring pathogenic mutations, suggesting their potential as biomarkers for GC diagnosis. Immunohistochemistry corroborated this by showing reduced protein expression levels in mutated samples. Enrichment analysis highlighted associations of BRCA1/2 genes with DNA damage response pathways and cancer-related processes. DrugBank exploration revealed potential therapeutic agents targeting mutated BRCA1/2, such as Cisplatin and Estradiol, offering new avenues for treatment. Our study identifies novel BRCA1/2 mutations specific to Pakistani GC patients, suggesting a distinct genetic susceptibility profile. These findings not only contribute to understanding GC pathogenesis but also hold implications for personalized treatment strategies in this population.

Mutational separation and clinical outcomes of TP53 and CDH1 in gastric cancer.

Gastric cancer (GC) is a deadly tumor with the fifth highest occurrence and highest global mortality rates. Owing to its heterogeneity, the underlying mechanism of GC remains unclear, and chemotherapy offers little benefit to individuals. To investigate the clinical outcomes of TP53 and CDH1 mutations in GC. In this study, 202 gastric adenocarcinoma tumor tissues and their corresponding normal tissues were collected. A total of 490 genes were identified using target capture. Through t-test and Wilcoxon rank-sum test, somatic mutations, microsatellite instability, and clinical statistics, including overall survival, were detected, compared, and calculated. The mutation rates of 32 genes, including TP53, SPEN, FAT1, and CDH1 exceeded 10%. TP53 mutations had a slightly lower overall occurrence rate (33%). The TP53 mutation rate was significantly higher in advanced stages (stage III/IV) than that in early stages (stage I/II) (P < 0.05). In contrast, CDH1 mutations were significantly associated with diffuse GC. TP53 is related to poor prognosis of advanced-stage tumors; nevertheless, CDH1 corresponds to a diffuse type of cancer. TP53 is exclusively mutated in CDH1 and is primarily affected by two distinct GC mechanisms. Different somatic mutation patterns in TP53 and CDH1 indicate two major mechanisms of GC.

RHOA drivers take alternate routes in gastric cancer.

Oncogenic small guanosine triphosphatases (GTPases) are often characterized by a limited set of activating mutations that affect their intrinsic biochemical function, but RHOA-which is frequently mutated in gastric cancer-appears not to have read the instruction manual. Having previously characterized the Y42C RHOA mutation in gastric cancer, in this issue of Science Signaling, Schaefer et al. take on the slightly less common L57V mutation and find that individual RHOA mutations can have different and unpredictable signaling outcomes.

ALDOC regulated the biological function and immune infiltration of gastric cancer cells.

The role of ALDOC which is an important regulator involved in tumor metabolic reprogramming and immune microenvironment in GC remains unclear. Therefore, we investigated the feasibility of ALDOC as a prognostic marker and therapeutic target. We verified the expression of ALDOC in GC and its effect on the prognosis of GC patients by analyzing clinical data. The regulation of ALDOC on the biological behavior of GC cells was confirmed by experiments. The potential mechanism of miRNA regulating GC immune cell infiltration by inhibiting ALDOC was explored by experiments and bioinformatic analysis. We further analyzed the effect of ALDOC on somatic mutations in gastric cancer, and constructed a prognostic model based on ALDOC and related immune molecules. ALDOC is overexpressed in GC cells and tissues, which promotes malignant biological behavior of GC cells and is an independent risk factor for poor prognosis of GC patients. MiR-19a-5p promotes the expression of ALDOC by down-regulating ETS1, leading to poor prognosis in GC patients. ALDOC is significantly associated with immune infiltration in GC, regulates macrophage differentiation and promotes the progression of GC. ALDOC is significantly correlated with TMB and MSI of gastric cancer, and affects somatic mutation of gastric cancer. The prognostic model has good predictive efficiency. ALDOC is a potential prognostic marker and therapeutic target with abnormal immune-mediated effects. The prognostic model based on ALDOC provides a reference for prognosis prediction and individualized treatment of GC patients.

Identification of a subpopulation of patients with gastric cancer responsive to PARP inhibitors.

432 Background: Treatment with PARP inhibitors (PARPi) has been approved in some tumors bearing a deficient Homologous Recombination (HR) system. Despite negative results of clinical trials conducted on the overall population of gastric cancer (GC) patients, we wondered whether a PARPi therapeutic strategy might represent a window of opportunity for a subpopulation of these patients. 7-12% of gastric cancers exhibit a mutational signature associated with HR failure, suggesting that these patients might benefit from PARPi. Methods: To analyze responsiveness to PARPi we exploited a proprietary human Gastro-Esophageal Adenocarcinoma (GEA) annotated platform of Patient-Derived Xenografts (PDXs) and PDX-derived primary cells on which we performed in vivo and in vitro experiments. Results: We selected 10 PDXs with loss-of-function mutations in HR pathway genes. Cell viability assays and preclinical trials showed that treatment with PARPi was effective in PDXs harbouring BRCA2 germline mutations and somatic inactivation of the second allele in a microsatellite stable background. PARPi responsive tumors were sensitive to oxaliplatin as well. Evaluation of HR deficiency and mutational signatures efficiently stratified responder vs non-responder PDXs. A retrospective analysis on 57 GEA patients showed that those carrying BRCA2 inactivating variants had longer PFS upon platinum-based regimens (used as proxy). In 5 out of 7 BRCA2 germline mutated patients we identified the p.K3326* variant, currently classified as “benign”. However, familial history of cancer, the absence of RAD51 foci in the tumor cells and a high HR deficiency score suggest a deleterious effect for this mutation in gastric cancer. Conclusions: PARP inhibition could represent a new therapeutic perspective for BRCA2 mutated and/or high HRD score GEA patients, including familial intestinal gastric cancer patients.

Landscape of exitrons in gastric cancer.

SummaryBackgroundExitron is a new type of non-canonical alternative splicing. Accumulating evidence implies exitron may have pathological function and contribute to another source of anti-tumor immunogenicity in various cancers. Its role in gastric cancer remains poorly understood. Large-scale, multi-omics analysis could comprehensively characterize the landscape of exitrons in gastric cancer, reveal undiscovered mechanism and hopefully identify molecular biomarkers for predicting immunotherapy response.MethodsWe collected datasets from five studies for analysis. RNA sequencing was used for exitron identification. Somatic mutations were detected by whole exome sequencing. Neopeptides were confirmed by proteome mass spectrometry.Findings42174 gastric cancer-specific exitrons (GCSEs) were identified in 632 patients. GCSEs were clinically relevant to gender, age, Lauren type, tumor stage and prognosis. Tissue specificity test and pathogenic exitron prediction revealed their unique functional impact. GCSEs were mutually exclusive with mutations and demonstrated both unique and complementary function against TP53 mutation in gastric cancer. We further established splicing regulatory network to reveal upstream regulation of exitron splicing. We also evaluated the immunogenicity and diagnostic potential of GCSEs. Evidence of GCSEs-derived neopeptide expression was validated by whole proteome mass spectrometry. PD-1 and Siglecs were significantly increased in high neoantigen load patients. But exitron-related biomarkers failed to predict immunotherapy response, possibly due to small sample size and insufficient sequencing depth.InterpretationThe present study provided a comprehensive multidimensional landscape of gastric cancer exitrons and underscores insights into underexplored mechanism in gastric cancer pathology.FundingThe Guangdong Provincial Key Laboratory of Precision Medicine for Gastroinstestinal Cancer (2020B121201004), the Guangdong Provincial Major Talents Project (No. 2019JC05Y361) and National Natural Science Foundation of China (grant number:82172960 and 81872013).

Bioinformatics Analysis Based on TCGA: MUC16 Mutation Correlates with Clinical Outcome in Gastric Cancer.

The prognosis of gastric cancer (GC) is difficult to predict due to the disease's complex genetic and phenotypic characteristics. MUC16 has been reported to be involved in the progression of several tumors. In this study, we aimed to explore whether MUC16 mutation had any impact on the prognosis or treatments of GC patients. Additionally, this analysis uncovered possible critical pathways related with these systems. On the cBioPortal, we were able to locate the pertinent data of patients with MUC16 mutations. And then, GSEA analysis identified differences in mRNA levels between mutant and wild-type MUC16 patients in terms of biological function annotation and pathways. The KEGG and GO analyses were also performed using the differentially expressed genes (DEGs). There were 139 individuals with GC who had the MUC16 mutation, which accounts for 32 percent, and the remaining patients had the MUC16 wild type. Survival assays revealed that patients with the MUC16 mutation had longer overall survival and disease-free survival. GSEA analysis revealed that cell cycle, cysteine and methionine metabolism, Huntington's disease, one carbon pool by folate, pyrimidine metabolism, pyruvate metabolism, RNA degradation, spliceosome, and valine leucine and isoleucine degradation were distinctly enriched in patients with MUC16 mutation type. Moreover, we identified 323 DEGs. Among them, 162 genes were upregulated, and 161 genes were downregulated. GO and KEGG assays indicated DEGs as enriched in pancreatic secretion, neuroactive ligand-receptor interaction, protein digestion and absorption, fat digestion and absorption, and glycerolipid metabolism. Overall, our data revealed that the MUC16 mutation in GC may affect the development of patients by altering several genes and pathways, indicating the importance of MUC16 mutation in the treatments of GC on an individual basis.

Association of FLG mutation with tumor mutation load and clinical outcomes in patients with gastric cancer.

Background: Stomach adenocarcinoma (STAD) is one of the most frequently diagnosed cancers in the world with a poor prognosis due to genetic heterogeneity. The present study aimed to explore potential prognostic predictors and therapeutic targets that can be used for STAD treatment. Methods: We collected relevant data of STAD patients from the Cancer Genome Atlas (TCGA), including somatic mutation, transcriptome, and survival data. We performed a series of analyses such as tumor mutational burden (TMB), immune infiltration, and copy number variation (CNV) analysis to evaluate the potential mechanism of filaggrin (FLG) mutation in gastric cancer. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and gene set enrichment analysis (GSEA) were performed for annotation of differentially expressed genes (DEGs). The STRING online database was used to construct the protein–protein interaction (PPI) and ceRNA network and hub genes were identified. Univariate and multivariate Cox regression analyses were used to determine the effect of selected DEGs on tumor prognosis. Results: The FLG-mutant group (FLG-MT) showed a higher mutation load and immunogenicity in gastric cancer. GO and KEGG analyses identified and ranked unique biologic processes and immune-related pathway maps that correlated with the FLG-mutant target. GSEA analysis showed that several tumorigenesis and metastasis-related pathways were indeed enriched in FLG-mutant tumor tissue. Both cell cycle–related pathways and the DNA damage and repair associated pathways were also enriched in the FLG-MT group. The FLG mutations resulted in increased gastric cancer sensitivity to 24 chemotherapeutic drugs. The ceRNA network was established using Cytoscape and the PPI network was established in the STRING database. The results of the prognostic information further demonstrated that the OS and DFS were significantly higher in FLG mutation carriers, and the FLG gene mutation might be a protective factor. Conclusion: The multiple molecular mechanisms of the FLG gene in STAD are worthy of further investigation and may reveal novel therapeutic targets and biomarkers for STAD treatment.

Abstract 5752: Loss-of-function mutations in ACVR2A are correlated with microsatellite instability in gastric and colorectal cancer

Abstract Background: The activin type II receptor (ACVR2), which is a member of the transforming growth factor beta (TGF-β) receptor family, is frequently mutated in colorectal cancer (CRC) and gastric cancer (GC). However, the incidence of ACVR2 mutations in MSI-H patients remains unclear. The aim of this study is to evaluate ACVR2A mutation characteristics and to examine its associations between the high microsatellite instability (MSI-H) and ACVR2A mutations in CRC and GC. Materials and Methods: We analyzed data from two cohorts: a Chinese cohort and the TCGA cohort. The Chinese cohort consisted of 1960 patients with CRC and GC, including 140 MSI-H samples and 1820 MSS samples. MSI status of these patients was derived from tumor-normal paired sequence data by targeted next generation sequencing (NGS). The TCGA cohort consists of 570 patients whose MSI status was determined. NGS data and clinical information were downloaded from the cBioPortal database (https://www.cbioportal.org). The abundance of tumor immune infiltrates was estimated by the Tumor Immune Estimation Resource (TIMER) 2.0 algorithm using gene expression data. Results: In the Chinese cohort, ACVR2A mutations were identified in 204 (18.6%) of 1960 patients, including 125 (61%) MSI-H patients and 79 (39%) MSS patients. Meanwhile, in all 140 MSI-H samples, 125 (90%) samples harbored AVCR2A mutation. The main variant of ACVR2A is loss of function mutation (ACVR2ALOF), including p.K437del(65%, 132/204), p.D96del(5%, 11/204), p.Asp96ins(4%, 9/204), and etc. ACVR2ALOF were detected in 161 patients (78.9%, 161/204), of which 125 (77%) were MSI-H and 36 (22%) were MSS. In the TCGA cohort, there were 102 (102/570) MSI-H samples, and 43% (44/102) of MSI-H samples carried ACVR2A mutation. Compared to the Chinese cohort, the ACVR2A mutation frequency in MSI-H samples was significantly lower in the TCGA cohort (43% vs 90%, p&amp;lt;0.01). The ACVR2ALOF mutations were observed in 30 MSI-H samples and 6 MSS samples. In both cohorts, patients with ACVR2ALOF mutations exhibited higher TMB (p&amp;lt;0.05) and PD-L1 expression (p&amp;lt;0.0001) than those without ACVR2ALOF mutations. Furthermore, in the TCGA cohort, we found that the Tumor Infiltrating Lymphocytes (TILs) of CD4+ T cells and macrophage cells were significantly lower in ACVR2ALOF samples than those without ACVR2ALOF mutations (p&amp;lt;0.05). Conclusions: The ACVR2ALOF was strongly correlated with MSI-H in patients of CRC and GC in both cohorts, especially in the Chinese population. Patients with ACVR2ALOF mutations have similar genomic characteristics to MSI-H, with high TMB, high PD-L1 expression, and therefore can serve as a potential biomarker for selecting candidates for immunotherapy. Citation Format: Yongning Jia, Hongling Yuan, Yaqun Xin, Fei Pang, Fei Shan, Shuangxi Li, Honglin Zhu, Ziyu Li. Loss-of-function mutations in ACVR2A are correlated with microsatellite instability in gastric and colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5752.

Detection of a novel panel of 24 genes with high frequencies of mutation in gastric cancer based on next-generation sequencing.

BACKGROUNDGastric cancer is a leading cause of cancer-related mortality worldwide. Many somatic mutations have been identified based on next-generation sequencing; they likely play a vital role in cancer treatment selection. However, next-generation sequencing has not been widely used to diagnose and treat gastric cancer in the clinic.AIMTo test the mutant gene frequency as a guide for molecular diagnosis and personalized therapy in gastric cancer by use of next-generation sequencing.METHODSWe constructed a panel of 24 mutant genes to detect somatic nucleotide variations and copy number variations based on a next-generation sequencing technique. Our custom panel included high-mutation frequency cancer driver and tumour suppressor genes. Mutated genes were also analyzed using the cBioPortal database. The clinical annotation of important variant mutation sites was evaluated in the ClinVar database. We searched for candidate drugs for targeted therapy and immunotherapy from the OncoKB database.RESULTSIn our study, the top 16 frequently mutated genes were TP53(58%), ERBB2(28%), BRCA2 (23%), NF1 (19%), PIK3CA (14%), ATR (14%), MSH2 (12%), FBXW7 (12%), BMPR1A (12%), ERBB3 (11%), ATM (9%), FGFR2 (8%), MET (8%), PTEN (6%), CHD4 (6%), and KRAS (5%). TP53 is a commonly mutated gene in gastric cancer and has a similar frequency to that in the cBioPortal database. 33 gastric cancer patients (51.6%) with microsatellite stability and eight patients (12.5%) with microsatellite instability-high were investigated. Enrichment analyses demonstrated that high-frequency mutated genes had transmembrane receptor protein kinase activity. We discovered that BRCA2, PIK3CA, and FGFR2 gene mutations represent promising biomarkers in gastric cancer.CONCLUSIONWe developed a powerful panel of 24 genes with high frequencies of mutation that could detect common somatic mutations. The observed mutations provide potential targets for the clinical treatment of gastric cancer.

SOCS3 gene silencing does not occur through methylation and mutations in gastric cancer.

Gastric cancer (GC) is ranked the third leading cause of cancer-related deaths worldwide. Mutations and epigenetic alterations in several essential genes, including p53, KRAS, PIK3CA, FAT4 and ARID1A, are often reported. Furthermore, loss of SOCS3 expression was reported in GC, suggesting its tumor suppressor role. To assess the mutational and methylation status of SOCS3, we performed gene panel exome sequencing on 47 human GC samples. The SOCS3 gene was rarely mutated, suggesting alternative regulation mechanisms, such as promoter hypermethylation and/or long non-coding RNAs (lncRNAs). We first explored SOCS3 promoter methylation status in 44 human GC samples by methylation-specific PCR (MS-PCR). Thirteen out of forty-four patients (29.5%) displayed a methylation pattern. Then, to see whether SOCS3 expression is silenced by CpG methylation, we examined publicly available databases (cbioportal and The Cancer Genome Atlas (TCGA)). The analysis revealed β values lower than 0.1, indicating hypo-methylation in healthy and GC samples. Moreover, moderate methylation (β < 0.4) and high methylation (β > 0.4) did not affect the free survival, suggesting that methylation is unlikely to be the mechanism rulingSOCS3silencing in GC. Next, to assess the regulatory effects of lncRNAs on SOCS3, we silenced the AC125807.2-lncRNA and quantified the SOCS3 gene expression in AGS and NCI-N87 gastric cancer cell line. SOCS3 was found to be downregulated following AC125807.2-lncRNA silencing in AGS cells, suggesting the potential implication of lncRNA AC125807.2 in SOCS3 regulation. However, in NCI-N87 cells, there was no significant change in SOCS3 expression. In conclusion, neither mutations nor hypermethylation was associated with the SOCS3downregulation in GC, and alternative mechanisms, including non-coding RNAs-mediated gene silencing, may be proposed.

Integrated DNA and RNA sequencing reveals early drivers involved in metastasis of gastric cancer

Gastric cancer (GC) is the second cause of cancer-related death and metastasis is an important cause of death. Considering difficulties in searching for metastatic driver mutations, we tried a novel strategy here. We conducted an integrative genomic analysis on GC and identified early drivers lead to metastasis. Whole-exome sequencing (WES), transcriptomes sequencing and targeted-exome sequencing (TES) were performed on tumors and matched normal tissues from 432 Chinese GC patients, especially the comparative analysis between higher metastatic-potential (HMP) group with T1 stage and lymph-node metastasis, and lower metastatic-potential (LMP) group without lymph-nodes or distant metastasis. HMP group presented higher mutation load and heterogeneity, enrichment in immunosuppressive signaling, more immune cell infiltration than LMP group. An integrated mRNA-lncRNA signature based on differentially expressed genes was constructed and its prognostic value was better than traditional TNM stage. We identified 176 candidate prometastatic mutations by WES and selected 8 genes for following TES. Mutated TP53 and MADCAM1 were significantly associated with poor metastasis-free survival. We further demonstrated that mutated MADCAM1 could not only directly promote cancer cells migration, but also could trigger tumor metastasis by establishing immunosuppressive microenvironment, including promoting PD-L1-mediated immune escape and reprogramming tumor-associated macrophages by regulating CCL2 through Akt/mTOR axis. In conclusion, GCs with different metastatic-potential are distinguishable at the genetic level and we revealed a number of potential metastatic driver mutations. Driver mutations in early-onset metastatic GC could promote metastasis by establishing an immunosuppressive microenvironment. This study provided possibility for future target therapy of GC.

TP53 Co-Mutational Features and NGS-Calibrated Immunohistochemistry Threshold in Gastric Cancer.

PurposeTP53 is the most frequently mutated gene in gastric cancer and it can be potentially used for gastric cancer diagnosis and screening. However, standardized clinical approaches that could accurately and cost-effectively detect TP53 mutations in gastric cancer are largely lagged behind.Patients and MethodsWe conducted next-generation sequencing (NGS) analysis of 425 cancer-related genes in 42 gastric cancer patients in our cohort. A 1313-patient cohort derived from the cBioPortal database was used for validation. We performed immunohistochemistry (IHC) staining with four commonly used p53 antibodies, and the NGS results were used as the gold standard to optimize the IHC threshold for each antibody.ResultsBy NGS analysis, we found that around 80% of gastric cancer patients in our cohort harbored TP53 alterations. Genetic alterations of BRCA1/2 or KMT2B were mostly exclusive with TP53 mutations, so were the MSI status or low grade of tumors. These results were further validated using the data from cBioPortal. We then used the NGS-derived TP53 status to optimize four commonly used IHC antibodies for detecting TP53 mutations. We showed that all antibodies could achieve more than 93% accuracy when proper IHC positivity thresholds were used, especially for the SP5 antibody that could reach 100% sensitivity and specificity with the 20% threshold.ConclusionOur results indicated that exclusivity between TP53 and BRCA mutations could be potentially used as a cost-effective way to predict BRCA status. Also, setting proper IHC thresholds for each specific antibody is critical to accurately detect TP53 mutations and facilitate disease diagnosis.

Correlation between LRP1B Mutations and Tumor Mutation Burden in Gastric Cancer.

Background It has been shown that low-density lipoprotein receptor-related protein 1B (LRP1B) mutations correlate with tumor mutation burden (TMB) and prognosis in patients with melanoma and non-small-cell lung cancer, while the relationship between LRP1B mutations and TMB in gastric cancer needs further study. This study is aimed at exploring the relationship between LRP1B mutations and TMB in gastric cancer. Methods Mutation frequency profiles of the genes in patients with gastric cancer in TCGA-STAD dataset were analyzed by bioinformatics analysis. The relationship among LRP1B mutations, TMB, and patient clinical features in gastric cancer was investigated by the chi-square test. The TMB prediction capacity based on LRP1B mutation status was evaluated by ROC curves. ResultsLRP1B is one of the top 10 genes with high gene mutation frequency in gastric cancer. The mutation status of LRP1B in gastric cancer patients was significantly correlated with age and TP53 and MUC16 mutation status. The result of ROC curve analysis revealed that the mutation status of LRP1B could be considered as an indicator of the degree of TMB in patients with gastric cancer. Conclusion This study presented the relationship between TMB and LRP1B mutations in gastric cancer, providing a novel perspective for gastric cancer prognosis and therapy.

A detailed understanding of the COL10A1 and SOX9 genes interaction based on potentially damaging mutations in gastric cancer using computational techniques

Gastric cancer (GC) has limited effective treatment options and is followed up with biomarkers that have insufficient sensitivity and specificity. Recent studies on Collagen Type X Alpha 1 Chain (COL10A1) show that the COL10A1 gene may be a diagnostic and/or prognostic biomarker for different cancer types. Moreover, its relationship with the Sex determining Region Y (SRY)-related High-Mobility Group (HMG) box (SOX9) gene which is also a transcription factor, was discovered recently, and co-expression of these two genes are associated with the development of GC. However, to the best of our knowledge, there is no study in the literature on how potential damaging mutations in the SOX9 and COL10A1 genes can affect their interactions. The aim of this study is to investigate the interactions of wild-type and potentially damaging mutated structures of COL10A1 and SOX9 genes. Thus, outputs for drug development and therapeutic strategies for GC can be obtained. For this purpose, structure validation and energy minimization analyses as well as docking and binding affinity calculations were performed. As a result, it was found that all investigated mutations (P563S, I588L, T624A, H165R and N110T) increased the binding affinity between the COL10A1-SOX9 complex, especially the N110T and H165R mutants in SOX9. As a conclusion, the N110T and H165R mutants in SOX9 may contribute to tumor progression. Therefore, it is important to consider these mutations for future therapeutic strategies. Communicated by Ramaswamy H. Sarma

P-147 Epigenetic gene somatic mutations in gastric cancer

P-147 Epigenetic gene somatic mutations in gastric cancer

Sensitive Detection of Single-Nucleotide Polymorphisms by Solid Nanopores Integrated With DNA Probed Nanoparticles.

Single-nucleotide polymorphisms (SNPs) are the abundant forms of genetic variations, which are closely associated with serious genetic and inherited diseases, even cancers. Here, a novel SNP detection assay has been developed for single-nucleotide discrimination by nanopore sensing platform with DNA probed Au nanoparticles as transport carriers. The SNP of p53 gene mutation in gastric cancer has been successfully detected in the femtomolar concentration by nanopore sensing. The robust biosensing strategy offers a way for solid nanopore sensors integrated with varied nanoparticles to achieve single-nucleotide distinction with high sensitivity and spatial resolution, which promises tremendous potential applications of nanopore sensing for early diagnosis and disease prevention in the near future.

Frequency of homologous recombination-related (HRR) genes mutations in gastric cancer.

4031 Background: Homologous recombination deficiency (HRD) might contribute to predict response of immunotherapy and Chemotherapy response and PARP inhibitor (PARPi) therapy. The HRD phenotype has been defined as the presence of a non-silent somatic mutation in homologous recombination-related (HRR) genes. We aimed to analyze the mutational pattern of HRR genes and the relationship between HRR-related genes and clinical outcomes in gastric cancer. Methods: We prospectively sequenced 386 Chinese patients with gastric cancer using next-generation sequencing techniques with 808 cancer-related genes. 440 patients with WES data from the TCGA project were included. The 15 HRR genes were selected on clinical evidence of sensitivity to PARP inhibitors and immunotherapy. Correlations between HRR genes and clinical outcomes were identified via bioinformatic analysis using TCGA datasets. Results: In the Chinese cohort, 10.4% (40/386) patients exhibited genomic alterations in HRR genes. The frequently mutated genes were BRCA2 (2.3%), ATM (1.8%), CDK12 (1.8%), BRCA1 (1.0%), CHEK2(1.0%), PALB2(0.8%), BARD1 (0.5%), RAD51B (0.5%), and RAD54L (0.3%). 8.3% patients had at least one somatic HRR genes mutation. Pathogenic germline variants were identified in 2.1% (8/386) patients. No participants carried both germline and somatic HRR gene mutations. In TCGA cohort, 19.1% (841/440) patients had at least one somatic mutation in an HRR gene. The frequently mutated genes were BRCA2 (6.4%), ATM (6.4%), CDK12 (3.2%), BRCA1 (3.2%), BARD1 (2.3%), PALB2 (2.3%), HEK2 (1.6%), CHEK1 (1.4%), BROP1 (1.1%), RAD54L (1.1%), FANCL (0.9%), RAD51D (0.9%), RAD51C (0.7%), PPP2R2A (0.5%), and RAD51B (0.5%). Chinese cohort had lower frequently somatic mutation of HRR genes compared to that in TCGA cohort (8.3% vs 19.1%, p &lt; 0.001). Interestingly, in the TCGA cohort, patients with HRR-mut had significantly elevated tumor mutational burden, microsatellite instability status and enhanced immune activity than patients with HRR-wt. In the MSK-IMPACT cohort comprising 49 patients treated with ICIs, patients with HRR-mut had significantly better overall survival compared to those in patients with HRR-wt (p = 0.027). Conclusions: Our data suggest that patients with altered HRR genes may be rational candidates for precision oncology treatment and provide new opportunities to predict the tumor response to multiple treatments, such as immunotherapeutic combine PARP inhibitor (PARPi) therapy. Exploring other biomarkers of HRD to predict the response to PARPi and immunotherapeutic in GC is necessary.