scholarly journals Gastrointestinal Goblet Cell Adenocarcinomas Harbor Distinctive Clinicopathological, Immune, and Genomic Landscape

2021 ◽  
Vol 11 ◽  
Author(s):  
Dong-Liang Lin ◽  
Li-Li Wang ◽  
Peng Zhao ◽  
Wen-Wen Ran ◽  
Wei Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Differential Gene Expression ◽  
Differentially Expressed Genes ◽  
Colorectal Adenocarcinoma ◽  
Signet Ring Cell ◽  
Cell Component ◽  
Signet Ring ◽  
Differential Gene ◽  
Ring Cell

Goblet cell adenocarcinoma (GCA) is a rare amphicrine tumor and difficult to diagnose. GCA is traditionally found in the appendix, but extra-appendiceal GCA may be underestimated. Intestinal adenocarcinoma with signet ring cell component is also very rare, and some signet ring cell carcinomas are well cohesive, having some similar morphological features to GCAs. It is necessary to differentiate GCA from intestinal adenocarcinomas with cohesive signet ring cell component (IACSRCC). The goal of this study is to find occurrence of extra-appendiceal GCA and characterize the histological, immunohistochemical, transcriptional, and immune landscape of GCA. We collected 12 cases of GCAs and 10 IACSRCCs and reviewed the clinicopathologic characters of these cases. Immunohistochemical stains were performed with synaptophysin, chromogranin A, CD56, somatostatin receptor (SSTR) 2, and Ki-67. Whole transcriptome RNA-sequencing was performed, and data were used to analyze differential gene expression and predict immune cell infiltration levels in GCA and IACSRCC. RNA-sequencing data for colorectal adenocarcinoma were gathered from TCGA data portal. Of the 12 patients with GCA, there were 4 women and 8 men. There were three appendiceal cases and nine extra-appendiceal cases. GCAs were immunohistochemically different from IACSRCC. GCA also had different levels of B-cell and CD8+ T-cell infiltration compared to both colorectal adenocarcinoma and cohesive IACSRCCs. Differential gene expression analysis showed distinct gene expression patterns in GCA compared to colorectal adenocarcinoma, with a number of cancer-related differentially expressed genes, including upregulation of TMEM14A, GOLT1A, DSCC1, and HSD17B8, and downregulation of KCNQ1OT1 and MXRA5. GCA also had several differentially expressed genes compared to IACSRCCs, including upregulation of PRSS21, EPPIN, RPRM, TNFRSF12A, and BZRAP1, and downregulation of HIST1H2BE, TCN1, AC069363.1, RP11-538I12.2, and REG4. In summary, the number of extra-appendiceal GCA was underestimated in Chinese patients. GCA can be seen as a distinct morphological, immunohistochemical, transcriptomic, and immunological entity. The classic low-grade component of GCA and the immunoreactivity for neuroendocrine markers are the key points to diagnosing GCA.

scholarly journals ViDGER: An R package for integrative interpretation of differential gene expression results of RNA-seq data

2018 ◽  
Author(s):  
Adam McDermaid ◽  
Brandon Monier ◽  
Jing Zhao ◽  
Qin Ma
Keyword(s):  
Gene Expression ◽  
Rna Sequencing ◽  
Differential Gene Expression ◽  
Differentially Expressed Genes ◽  
R Package ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Differential Gene

AbstractDifferential gene expression (DGE) is one of the most common applications of RNA-sequencing (RNA-seq) data. This process allows for the elucidation of differentially expressed genes (DEGs) across two or more conditions. Interpretation of the DGE results can be non-intuitive and time consuming due to the variety of formats based on the tool of choice and the numerous pieces of information provided in these results files. Here we present an R package, ViDGER (Visualization of Differential Gene Expression Results using R), which contains nine functions that generate information-rich visualizations for the interpretation of DGE results from three widely-used tools, Cuffdiff, DESeq2, and edgeR.

scholarly journals Differentially expressed genes for atrial fibrillation identified by RNA sequencing from paired human left and right atrial appendages

2019 ◽  
Vol 51 (8) ◽  
pp. 323-332 ◽  
Author(s):  
Alison M. Thomas ◽  
Claudia P. Cabrera ◽  
Malcolm Finlay ◽  
Kulvinder Lall ◽  
Muriel Nobles ◽  
...  
Keyword(s):  
Gene Expression ◽  
Atrial Fibrillation ◽  
Sinus Rhythm ◽  
Rna Sequencing ◽  
Differential Gene Expression ◽  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Right Atrial ◽  
Differential Gene ◽  
Left And Right

Atrial fibrillation is a significant worldwide contributor to cardiovascular morbidity and mortality. Few studies have investigated the differences in gene expression between the left and right atrial appendages, leaving their characterization largely unexplored. In this study, differential gene expression was investigated in atrial fibrillation and sinus rhythm using left and right atrial appendages from the same patients. RNA sequencing was performed on the left and right atrial appendages from five sinus rhythm (SR) control patients and five permanent AF case patients. Differential gene expression in both the left and right atrial appendages was analyzed using the Bioconductor package edgeR. A selection of differentially expressed genes, with relevance to atrial fibrillation, were further validated using quantitative RT-PCR. The distribution of the samples assessed through principal component analysis showed distinct grouping between left and right atrial appendages and between SR controls and AF cases. Overall 157 differentially expressed genes were identified to be downregulated and 90 genes upregulated in AF. Pathway enrichment analysis indicated a greater involvement of left atrial genes in the Wnt signaling pathway whereas right atrial genes were involved in clathrin-coated vesicle and collagen formation. The differing expression of genes in both left and right atrial appendages indicate that there are different mechanisms for development, support and remodeling of AF within the left and right atria.

scholarly journals Clinicopathologic and Molecular Features of Colorectal Adenocarcinoma with Signet-Ring Cell Component

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0156659 ◽  
Author(s):  
Qing Wei ◽  
Xicheng Wang ◽  
Jing Gao ◽  
Jian Li ◽  
Jie Li ◽  
...  
Keyword(s):  
Colorectal Adenocarcinoma ◽  
Signet Ring Cell ◽  
Cell Component ◽  
Molecular Features ◽  
Signet Ring ◽  
Ring Cell

Higher incidence of EGFR exon 19 deletion in younger (age 40 or younger) patients with adenocarcinoma of the lung.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. 7044-7044
Author(s):  
Eri Sugiyama ◽  
Koichi Goto ◽  
Genichiro Ishii ◽  
Shigeki Umemura ◽  
Kiyotaka Yoh ◽  
...  
Keyword(s):  
Elderly Patients ◽  
Lung Adenocarcinoma ◽  
Signet Ring Cell ◽  
Egfr Mutations ◽  
Cell Component ◽  
Younger Patients ◽  
Signet Ring ◽  
Exon 19 Deletion ◽  
Ring Cell ◽  
Exon 19

7044 Background: The proportion of younger patients (≤ 40 years) with lung cancer is reported to be 2-5%. The most frequent histologic type of them is adenocarcinoma, however little is known about the pathological and molecular characteristics of younger patients with lung adenocarcinoma. Methods: Between July 1992 and April 2011, a total of 7443 patients were diagnosed as lung cancer in National Cancer Center Hospital East and 165 patients of whom (2.2%) who were 40 years or younger were identified. Among them, 44 patients with adenocarcinoma who underwent surgical resection were selected for this study. In addition, 185 elderly patients with > 40 years who underwent surgical resection matching gender and smoking status were selected as a control group. Histological predominant growth pattern and any coexisting variant pattern, the status of EGFR mutations were compared between these two groups. Results: The median age in ≤ 40 years patients was 37 years (range, 21 to 40 years) and that in elderly patients was 68 years (range, 42 to 83 years). Between these two groups, there were no significant differences in the distribution of histological predominant growth patterns (lepidic; 31.8% vs. 26.5%, papillary; 34.1% vs. 37.3%, acinar; 9.1% vs. 16.2%, and solid; 25.0% vs. 20.0%, p=0.78) and the incidence of EGFR mutations (40.9% vs. 45.9%; p=0.55). However, signet-ring cell component were significantly found in the younger patients than elderly (11.4% vs. 0%; p<0.01). The incidence of EGFR exon 19 deletion was significantly higher in younger patients than elderly, in contrast, that of EGFR exon 21 L858R was significantly higher in elderly patients (exon 19 del; 31.7% vs. 18.9%, L858R; 4.6% vs. 25.4%, p=0.0091). Three of 17 adenocarcinomas (17.7%) with EGFR-wild type in younger patients showed positive for ALK translocation. Conclusions: Younger patients with lung adenocarcinoma showed significantly higher proportion of EGFR exon 19 deletion genotype and containing histologically signet-ring cell component comparing with elderly patients. EGFR exon 19 deletion genotype may be related to pathogenesis of lung adenocarcinoma in younger patients.

Signet ring cell colorectal cancer: Genomic insights into a rare subpopulation of colorectal adenocarcinoma.

2017 ◽  
Vol 35 (4_suppl) ◽  
pp. 606-606
Author(s):  
Krittiya Korphaisarn ◽  
Van Karlyle Morris ◽  
Michael J. Overman ◽  
David R. Fogelman ◽  
Imad Shureiqui ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Colorectal Adenocarcinoma ◽  
Cpg Island ◽  
Signet Ring Cell ◽  
Molecular Characteristics ◽  
Advanced Tumor Stage ◽  
Molecular Features ◽  
Advanced Tumor ◽  
Signet Ring ◽  
Ring Cell

606 Background: Colorectal signet ring cell carcinoma (SRCC) has been shown to be associated with advanced tumor stage at presentation and worse outcomes. Due to the rarity of this subtype, 1% of all colorectal adenocarcinoma (CRC), little is known about its molecular characteristics. We aimed to characterize the molecular alterations of this subgroup. Methods: Metastatic CRC (mCRC) patients (pts) with signet ring cell (SC) histology who had tumors evaluated with next generation sequencing between February 2009 and November 2015 were reviewed. SC mCRC were classified into 2 groups; SRCC (>50% of signet cells) and adenocarcinoma (AC) with SC component. Genomic alterations, microsatellite instability (MSI) and CpG island methylator phenotype (CIMP) status noted in SC mCRC were compared to non-SC mCRC pts from the Assessment of Targeted Therapies Against Colorectal Cancer program at MD Anderson Cancer Center using Pearson’s χ 2 test. Results: A total of 665 mCRC pts were included in this study. 93 pts (14%) had SC histology of which 30 (32.3%) pts were SRCC. The Table below shows key cancer genes mutation frequencies. Conclusions: Colorectal SRCC has distinct molecular features compared with non-SC and AC with SC component CRC. The frequencies of KRAS, PIK3CA and APC mutations were lower than the frequencies reported in non-SC CRC. SRCC was not associated with MSI-H or CIMP-H tumor in this study. Further studies on identification of activated pathways underlying this worse prognosis and potential therapeutic targets are required. [Table: see text]

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