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

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.

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Integrated analysis of whole genome and transcriptome sequencing reveals a frameshift mutation associated with recessive embryonic lethality in Holstein cattle

Animal Genetics ◽

10.1111/age.13160 ◽

2021 ◽

Author(s):

Y. Yang ◽

J. Si ◽

X. Lv ◽

D. Dai ◽

L. Liu ◽

...

Keyword(s):

Transcriptome Sequencing ◽

Frameshift Mutation ◽

Embryonic Lethality ◽

Integrated Analysis ◽

Holstein Cattle ◽

Whole Genome

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Comprehensive Analysis of SFRP Family Members Prognostic Value and Immune Infiltration in Gastric Cancer

Life ◽

10.3390/life11060522 ◽

2021 ◽

Vol 11 (6) ◽

pp. 522

Author(s):

Dehua Liu ◽

Chenyu Sun ◽

Nahyun Kim ◽

Chandur Bhan ◽

John Pocholo Whitaker Tuason ◽

...

Keyword(s):

Gastric Cancer ◽

Wnt Signaling ◽

Signaling Pathway ◽

Prognostic Value ◽

Immune Cell ◽

System Development ◽

Wnt Signaling Pathway ◽

Immune System Development ◽

Precision Therapy ◽

Gastric Cancer Patients

Gastric cancer (GC) is the fifth most common cancer globally. Secreted frizzled-related proteins (SFRP) are important elements associated with the Wnt signaling pathway, and its dysregulated expression is found in multiple cancers. However, the function of distinct SFRPs in GC remains poorly understood. We investigated the differential expression, prognostic value, and immune cell infiltration of SFRPs in gastric cancer patients from the Oncomine, Gene Expression Profiling Interactive Analysis (GEPIA), UALCAN, Kaplan–Meier plotter, cBioPortal, STRING, Gene-MANIA, DAVID, MethSurv, and TIMER databases. We found that the expression levels of SFRP2 and SFRP4 were significantly increased in GC tissues, whereas the SFRP1 and SFRP5 expressions were reduced. SFRP1, SFRP2, and SFRP5 were significantly correlated with the clinical cancer stage in GC patients. Higher expression of SFRPs was associated with short overall survival (OS) in GC patients. Besides, high SFRPs methylation showed favorable OS in GC patients. The functions of SFRPs were primarily related to the Wnt signaling pathway, immune system development, and basal cell carcinoma. The expression of SFRPs was strongly correlated with immune infiltrating cells, including CD4+ T cells and macrophages in GC. Our study indicated that SFRPs could be potential targets of precision therapy and prognostic biomarkers for the survival of GC patients.

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Comprehensive analysis of the genetic landscape of 21 cases with blastic plasmacytoid dendritic cell neoplasm by whole genome and whole transcriptome sequencing

Leukemia & Lymphoma ◽

10.1080/10428194.2021.1924372 ◽

2021 ◽

pp. 1-4

Author(s):

Isolde Summerer ◽

Wencke Walter ◽

Manja Meggendorfer ◽

Wolfgang Kern ◽

Torsten Haferlach ◽

...

Keyword(s):

Dendritic Cell ◽

Transcriptome Sequencing ◽

Plasmacytoid Dendritic Cell ◽

Comprehensive Analysis ◽

Whole Genome ◽

Cell Neoplasm ◽

Genetic Landscape ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

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MA23.09 Fusion Genes Identified from Whole Genome and Whole Transcriptome Sequencing of Malignant Pleural Mesothelioma Tumours

Journal of Thoracic Oncology ◽

10.1016/j.jtho.2019.08.697 ◽

2019 ◽

Vol 14 (10) ◽

pp. S344-S345

Author(s):

T.M. Chee ◽

H. Oey ◽

K. Fong ◽

I. Yang ◽

L. Krause ◽

...

Keyword(s):

Malignant Pleural Mesothelioma ◽

Transcriptome Sequencing ◽

Pleural Mesothelioma ◽

Whole Genome ◽

Fusion Genes ◽

Whole Transcriptome Sequencing ◽

Whole Transcriptome

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Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Cancer Research ◽

10.1158/0008-5472.can-17-0833 ◽

2017 ◽

Vol 77 (23) ◽

pp. 6538-6550 ◽

Cited By ~ 17

Author(s):

Dylan Z. Kelley ◽

Emily L. Flam ◽

Evgeny Izumchenko ◽

Ludmila V. Danilova ◽

Hildegard A. Wulf ◽

...

Keyword(s):

Head And Neck ◽

Integrated Analysis ◽

Open Chromatin ◽

Whole Genome ◽

Head And Neck Tumor ◽

Rna Seq ◽

Neck Tumor ◽

Integration Sites

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Screening Driving Transcription Factors in the Processing of Gastric Cancer

Gastroenterology Research and Practice ◽

10.1155/2016/8431480 ◽

2016 ◽

Vol 2016 ◽

pp. 1-9 ◽

Cited By ~ 5

Author(s):

Guangzhong Xu ◽

Kai Li ◽

Nengwei Zhang ◽

Bin Zhu ◽

Guosheng Feng

Keyword(s):

Gastric Cancer ◽

Transcription Factors ◽

Regulatory Network ◽

Target Genes ◽

Transcriptional Regulatory Network ◽

Expression Profiles ◽

Functional Enrichment ◽

Regulatory Mechanisms ◽

Integrated Analysis ◽

Transcriptional Regulatory

Background. Construction of the transcriptional regulatory network can provide additional clues on the regulatory mechanisms and therapeutic applications in gastric cancer.Methods. Gene expression profiles of gastric cancer were downloaded from GEO database for integrated analysis. All of DEGs were analyzed by GO enrichment and KEGG pathway enrichment. Transcription factors were further identified and then a global transcriptional regulatory network was constructed.Results. By integrated analysis of the six eligible datasets (340 cases and 43 controls), a bunch of 2327 DEGs were identified, including 2100 upregulated and 227 downregulated DEGs. Functional enrichment analysis of DEGs showed that digestion was a significantly enriched GO term for biological process. Moreover, there were two important enriched KEGG pathways: cell cycle and homologous recombination. Furthermore, a total of 70 differentially expressed TFs were identified and the transcriptional regulatory network was constructed, which consisted of 566 TF-target interactions. The top ten TFs regulating most downstream target genes were BRCA1, ARID3A, EHF, SOX10, ZNF263, FOXL1, FEV, GATA3, FOXC1, and FOXD1. Most of them were involved in the carcinogenesis of gastric cancer.Conclusion. The transcriptional regulatory network can help researchers to further clarify the underlying regulatory mechanisms of gastric cancer tumorigenesis.

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