1
|
Alvi MA, McArt DG, Kelly P, Fuchs MA, Alderdice M, McCabe CM, Bingham V, McGready C, Tripathi S, Emmert-Streib F, Loughrey MB, McQuaid S, Maxwell P, Hamilton PW, Turkington R, James JA, Wilson RH, Salto-Tellez M. Comprehensive molecular pathology analysis of small bowel adenocarcinoma reveals novel targets with potential for clinical utility. Oncotarget 2016; 6:20863-74. [PMID: 26315110 PMCID: PMC4673235 DOI: 10.18632/oncotarget.4576] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 07/20/2015] [Indexed: 01/22/2023] Open
Abstract
Small bowel accounts for only 0.5% of cancer cases in the US but incidence rates have been rising at 2.4% per year over the past decade. One-third of these are adenocarcinomas but little is known about their molecular pathology and no molecular markers are available for clinical use. Using a retrospective 28 patient matched normal-tumor cohort, next-generation sequencing, gene expression arrays and CpG methylation arrays were used for molecular profiling. Next-generation sequencing identified novel mutations in IDH1, CDH1, KIT, FGFR2, FLT3, NPM1, PTEN, MET, AKT1, RET, NOTCH1 and ERBB4. Array data revealed 17% of CpGs and 5% of RNA transcripts assayed to be differentially methylated and expressed respectively (p < 0.01). Merging gene expression and DNA methylation data revealed CHN2 as consistently hypermethylated and downregulated in this disease (Spearman −0.71, p < 0.001). Mutations in TP53 which were found in more than half of the cohort (15/28) and Kazald1 hypomethylation were both were indicative of poor survival (p = 0.03, HR = 3.2 and p = 0.01, HR = 4.9 respectively). By integrating high-throughput mutational, gene expression and DNA methylation data, this study reveals for the first time the distinct molecular profile of small bowel adenocarcinoma and highlights potential clinically exploitable markers.
Collapse
Affiliation(s)
- Muhammad A Alvi
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Darragh G McArt
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Paul Kelly
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Marc-Aurel Fuchs
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Matthew Alderdice
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Clare M McCabe
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Victoria Bingham
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Claire McGready
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Shailesh Tripathi
- Computational Biology and Machine Learning Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Frank Emmert-Streib
- Computational Biology and Machine Learning Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Maurice B Loughrey
- Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Stephen McQuaid
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Perry Maxwell
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Peter W Hamilton
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Richard Turkington
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jacqueline A James
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| | - Richard H Wilson
- Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen's University Belfast, Belfast, Northern Ireland, UK.,Tissue Pathology, Belfast Health and Social Care Trust, Belfast, Northern Ireland, UK
| |
Collapse
|
2
|
Chen M, Lin WR, Lu CH, Chen CC, Huang YC, Liao WL, Tsai FJ. Chimerin 2 genetic polymorphisms are associated with non-proliferative diabetic retinopathy in Taiwanese type 2 diabetic patients. J Diabetes Complications 2014; 28:460-3. [PMID: 24854763 DOI: 10.1016/j.jdiacomp.2014.04.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/01/2014] [Accepted: 04/11/2014] [Indexed: 12/12/2022]
Abstract
AIM To investigate whether chimerin 2 (CHN2) genetic polymorphisms were associated with the susceptibility to diabetic retinopathy (DR) in Taiwanese individuals with type 2 diabetes. METHODS This case-control study comprised of 171 individuals with DR and 548 without DR. Four rs39059, rs2023908, rs1002630 and rs1362363 polymorphism of CHN2 were genotyped for each subjects. All subjects underwent a complete ophthalmologic examination, and basic information (age, gender, age at diagnosis of diabetes, and ocular history of the patient) was record. Several clinical parameters (systolic and diastolic blood pressure, waist and hip circumferences, body mass index levels, fasting glucose and HbA1c) were measured. RESULTS Logistic regressions were used to analyze odds ratios between SNPs and DR after controlling for gender, systolic blood pressure, waist and hip ratio, duration of diabetes, serum HbA1c levels and nephropathy classification. A protective effect of rs1002630 (GA+AA) and rs1362363 (AG+GG) [odds ratio (OR) (95% confidence interval)=0.45 (0.22-0.88), 0.66 (0.44-0.99), respectively) was observed. Furthermore, the protective effect of rs1002630 was observed when compared subjects with non-proliferative DR with subjects without DR [OR=0.25 (95%C.I. = 0.09-0.73)]. CONCLUSIONS This study showed that the rs1002630 of CHN2 were associated with DR risk and non-proliferative DR risk in Taiwanese individuals with type 2 diabetes. Variations at this locus may contribute to the pathogenesis of DR.
Collapse
Affiliation(s)
- Marcelo Chen
- Department of Urology, Mackay Memorial Hospital, Taipei, Taiwan; Mackay Medicine, Nursing and Management College, Taipei, Taiwan; School of Medicine, Mackay Medical College, New Taipei City, Taiwan
| | - Wun-Rong Lin
- Department of Urology, Mackay Memorial Hospital, Taipei, Taiwan
| | - Chieh-Hsiang Lu
- Division of Endocrinology and Metabolism of Internal Medicine, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ching-Chu Chen
- Division of Endocrinology and Metabolism, Department of Medicine, China Medical University Hospital, Taichung, Taiwan; School of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - Yu-Chuen Huang
- School of Chinese Medicine, China Medical University, Taichung, Taiwan; Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Wen-Ling Liao
- Center for Personalized Medicine, China Medical University Hospital, Taichung, Taiwan; Graduate Institute of Integrate Medicine, School of Chinese Medicine, China Medical University, Taichung, Taiwan.
| | - Fuu-Jen Tsai
- School of Chinese Medicine, China Medical University, Taichung, Taiwan; Genetics Center, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan.
| |
Collapse
|