scholarly journals Whole genome and transcriptome sequencing of matched primary and peritoneal metastatic gastric carcinoma

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
J. Zhang ◽  
J. Y. Huang ◽  
Y. N. Chen ◽  
F. Yuan ◽  
H. Zhang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Peritoneal Metastasis ◽  
Transcriptome Sequencing ◽  
Fusion Gene ◽  
Metastatic Cancer ◽  
Cancer Case ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Average Survival ◽  
Prevalent Form

Abstract Gastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease. Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6-month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control. We identified 27 mutated genes, of which 19 genes are reported in COSMIC database (ZNF208, CRNN, ATXN3, DCTN1, RP1L1, PRB4, PRB1, MUC4, HS6ST3, MUC17, JAM2, ITGAD, IREB2, IQUB, CORO1B, CCDC121, AKAP2, ACAN and ACADL) and eight genes have not previously been described in gastric cancer (CCDC178, ARMC4, TUBB6, PLIN4, PKLR, PDZD2, DMBT1and DAB1).Additionally,GPX4 and MPND in 19q13.3-13.4 region, is characterized as a novel fusion-gene. This study disclosed novel biological markers and tumorigenic pathways that would predict gastric cancer occurring peritoneal metastasis.

scholarly journals Integrated analysis of whole genome and transcriptome sequencing in a young patient with gastric cancer provides insights for precision therapy

2020 ◽  
Vol 20 (4) ◽  
pp. 1-1
Author(s):  
Kongwang Hu ◽  
Weiqiang Yu ◽  
Olugbenga Ajayi ◽  
Longlong Li ◽  
Zhiguo Huang ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Young Patient ◽  
Transcriptome Sequencing ◽  
Integrated Analysis ◽  
Whole Genome ◽  
Precision Therapy

scholarly journals Transcriptomic and Genomic Testing to Guide Individualized Treatment in Chemoresistant Gastric Cancer Case

Biomedicines ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 67 ◽  
Author(s):  
Alexey Moisseev ◽  
Eugene Albert ◽  
Dan Lubarsky ◽  
David Schroeder ◽  
Jeffrey Clark
Keyword(s):  
Gastric Cancer ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Regional Lymph Node ◽  
Residual Tumor ◽  
Cancer Case ◽  
Sequencing Analysis ◽  
Tumor Biopsy ◽  
Whole Exome ◽  
Initial Biopsy

Gastric cancer is globally the fifth leading cause of cancer death. We present a case report describing the unique genomic characteristics of an Epstein–Barr virus-negative gastric cancer with esophageal invasion and regional lymph node metastasis. Genomic tests were performed first with the stomach biopsy using platforms FoundationOne, OncoDNA, and Oncopanel at Dana Farber Institute. Following neoadjuvant chemotherapy, residual tumor was resected and the stomach and esophageal residual tumor samples were compared with the initial biopsy by whole exome sequencing and molecular pathway analysis platform Oncobox. Copy number variation profiling perfectly matched the whole exome sequencing results. A moderate agreement was seen between the diagnostic platforms in finding mutations in the initial biopsy. Final data indicate somatic activating mutation Q546K in PIK3CA gene, somatic frameshifts in PIH1D1 and FBXW7 genes, stop-gain in TP53BP1, and a few somatic mutations of unknown significance. RNA sequencing analysis revealed upregulated expressions of MMP7, MMP9, BIRC5, and PD-L1 genes and strongly differential regulation of several molecular pathways linked with the mutations identified. According to test results, the patient received immunotherapy with anti-PD1 therapy and is now free of disease for 2 years. Our data suggest that matched tumor and normal tissue analyses have a considerable advantage over tumor biopsy-only genomic tests in stomach cancer.

scholarly journals The Value of Serum Immunoglobulin G Glycome in the Preoperative Discrimination of Peritoneal Metastasis from Advanced Gastric Cancer

2019 ◽  
Vol 10 (12) ◽  
pp. 2811-2821 ◽  
Author(s):  
Ruihuan Qin ◽  
Yupeng Yang ◽  
Wenjun Qin ◽  
Jing Han ◽  
Hao Chen ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Advanced Gastric Cancer ◽  
Immunoglobulin G ◽  
Peritoneal Metastasis ◽  
Serum Immunoglobulin

Identification of novel autoantibodies in ascites of relapsed paclitaxel-resistant gastric cancer with peritoneal metastasis using immunome protein microarrays and proteomics

2021 ◽  
pp. 1-10
Author(s):  
Zhongyin Yang ◽  
Chao Yan ◽  
Wentao Liu ◽  
Wei Xu ◽  
Chen Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Effective Treatment ◽  
Peritoneal Metastasis ◽  
Quantitative Proteomics ◽  
Poor Prognosis ◽  
Protein Microarrays ◽  
Tandem Mass ◽  
Tandem Mass Tag ◽  
Resistant Group ◽  
Potential Biomarkers

BACKGROUND: Gastric cancer (GC) patients with peritoneal metastasis usually have extremely poor prognosis. Intraperitoneal infusion of paclitaxel (PTX) provides an effective treatment, but relapse and PTX-resistance are unavoidable disadvantages, and it is difficult to monitor the occurrence of PTX-resistance. OBJECTIVE: The aim of this study was to explore novel autoantibodies in the ascites of individuals with relapsed PTX-resistant GC with peritoneal metastasis. METHODS: Ascites samples were collected before PTX infusion and after the relapse in 3 GC patients. To determine the expression of significantly changed proteins, we performed autoantibody profiling with immunome protein microarrays and tandem mass tag (TMT) quantitative proteomics, and then, the overlapping proteins were selected. RESULTS: Thirty-eight autoantibodies that were differentially expressed between the ascites in the untreated group and relapsed PTX-resistant group were identified. For confirmation of the results, TMT quantitative proteomics was performed, and 842 dysregulated proteins were identified. Four proteins, TPM3, EFHD2, KRT19 and vimentin, overlapped between these two assays. CONCLUSIONS: Our results first revealed that TPM3, EFHD2, KRT19 and vimentin were novel autoantibodies in the ascites of relapsed PTX-resistant GC patients. These autoantibodies may be used as potential biomarkers to monitor the occurrence of PTX-resistance.

scholarly journals Matrix metalloprotease–14 is a Target Enzyme for Detecting Peritoneal Metastasis in Gastric Cancer

2021 ◽  
pp. 102420
Author(s):  
Soichiro Ogawa ◽  
Hidemasa Kubo ◽  
Yasutoshi Murayama ◽  
Takeshi Kubota ◽  
Masayuki Yubakami ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Peritoneal Metastasis ◽  
Matrix Metalloprotease ◽  
Target Enzyme

scholarly journals Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.)

2021 ◽  
Vol 22 (13) ◽  
pp. 6641
Author(s):  
Chen Li ◽  
Meng Kou ◽  
Mohamed Hamed Arisha ◽  
Wei Tang ◽  
Meng Ma ◽  
...  
Keyword(s):  
High Temperature ◽  
Metabolic Pathways ◽  
Transcriptome Sequencing ◽  
Ipomoea Batatas ◽  
Sequencing Analysis ◽  
Storage Roots ◽  
Metabolic Analysis ◽  
Cooking Process

The saccharification of sweetpotato storage roots is a common phenomenon in the cooking process, which determines the edible quality of table use sweetpotato. In the present study, two high saccharified sweetpotato cultivars (Y25, Z13) and one low saccharified cultivar (X27) in two growth periods (S1, S2) were selected as materials to reveal the molecular mechanism of sweetpotato saccharification treated at high temperature by transcriptome sequencing and non-targeted metabolome determination. The results showed that the comprehensive taste score, sweetness, maltose content and starch change of X27 after steaming were significantly lower than those of Y25 and Z13. Through transcriptome sequencing analysis, 1918 and 1520 differentially expressed genes were obtained in the two periods of S1 and S2, respectively. Some saccharification-related transcription factors including MYB families, WRKY families, bHLH families and inhibitors were screened. Metabolic analysis showed that 162 differentially abundant metabolites related to carbohydrate metabolism were significantly enriched in starch and sucrose capitalization pathways. The correlation analysis between transcriptome and metabolome confirmed that the starch and sucrose metabolic pathways were significantly co-annotated, indicating that it is a vitally important metabolic pathway in the process of sweetpotato saccharification. The data obtained in this study can provide valuable resources for follow-up research on sweetpotato saccharification and will provide new insights and theoretical basis for table use sweetpotato breeding in the future.

scholarly journals Whole-Genome DNA Methylation Analysis in Hydrogen Peroxide Overproducing Transgenic Tobacco Resistant to Biotic and Abiotic Stresses

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 178
Author(s):  
Ana L. Villagómez-Aranda ◽  
Luis F. García-Ortega ◽  
Irineo Torres-Pacheco ◽  
Ramón G. Guevara-González
Keyword(s):  
Hydrogen Peroxide ◽  
Dna Methylation ◽  
Transgenic Tobacco ◽  
Stress Responses ◽  
Abiotic Stresses ◽  
Methylation Status ◽  
Physiological Adaptation ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
Biotic And Abiotic Stresses

Epigenetic regulation is a key component of stress responses, acclimatization and adaptation processes in plants. DNA methylation is a stable mark plausible for the inheritance of epigenetic traits, such that it is a potential scheme for plant breeding. However, the effect of modulators of stress responses, as hydrogen peroxide (H2O2), in the methylome status has not been elucidated. A transgenic tobacco model to the CchGLP gene displayed high H2O2 endogen levels correlated with biotic and abiotic stresses resistance. The present study aimed to determine the DNA methylation status changes in the transgenic model to obtain more information about the molecular mechanism involved in resistance phenotypes. The Whole-genome bisulfite sequencing analysis revealed a minimal impact of overall levels and distribution of methylation. A total of 9432 differential methylated sites were identified in distinct genome regions, most of them in CHG context, with a trend to hypomethylation. Of these, 1117 sites corresponded to genes, from which 83 were also differentially expressed in the plants. Several genes were associated with respiration, energy, and calcium signaling. The data obtained highlighted the relevance of the H2O2 in the homeostasis of the system in stress conditions, affecting at methylation level and suggesting an association of the H2O2 in the physiological adaptation to stress functional linkages may be regulated in part by DNA methylation.

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