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Xia J, Zhang H, Guan Q, Wang S, Li Y, Xie J, Li M, Huang H, Yan H, Chen T. Qualitative diagnostic signature for pancreatic ductal adenocarcinoma based on the within-sample relative expression orderings. J Gastroenterol Hepatol 2021; 36:1714-1720. [PMID: 33150986 DOI: 10.1111/jgh.15326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 10/18/2020] [Accepted: 10/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of pancreatic cancer, which is one of the most aggressive malignant neoplasms with a 9.3% five-year survival rate. The pathological biopsy is the current golden standard for confirming suspicious lesions of PDAC, but it is not entirely reliable because of the insufficient sampling amount and inaccurate sampling location. Therefore, developing a robust signature to aid the accurate diagnosis of PDAC is critical. METHODS Based on the within-sample relative expression orderings of gene pairs, we identified a qualitative signature to discriminate both PDAC and adjacent samples from both chronic pancreatitis and normal samples in the training datasets and validated it in other independent datasets produced by different laboratories with different measuring platforms. RESULTS A six-gene-pair signature was identified in the training data and validated in eight independent datasets. For surgical samples, 96.63% of 356 PDAC tissues, 100% of 11 pancreatitis tissues of non-cancer patients, and 23 of 24 normal pancreatic tissues were correctly classified. Especially, 59 of 60 cancer-adjacent normal tissues of PDAC patients were correctly identified as PDAC. For biopsy samples, all of 11 PDAC biopsy tissues were correctly classified as PDAC. CONCLUSION The signature can distinguish both PDAC and PDAC-adjacent normal tissues from both chronic pancreatitis and normal tissues of non-cancer patients even when the sampling locations are inaccurate, which can aid the diagnosis of PDAC.
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Affiliation(s)
- Jie Xia
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Huarong Zhang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qingzhou Guan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Shanshan Wang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yawei Li
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiajing Xie
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Meifeng Li
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Haiyan Huang
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Haidan Yan
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Ting Chen
- Department of Bioinformatics, Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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Li M, Chen H, He J, Xie J, Xia J, Liu H, Shi Y, Guo Z, Yan H. A qualitative classification signature for post-surgery 5-fluorouracil-based adjuvant chemoradiotherapy in gastric cancer. Radiother Oncol 2020; 155:65-72. [PMID: 33065189 DOI: 10.1016/j.radonc.2020.10.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 09/23/2020] [Accepted: 10/07/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND PURPOSE Currently, 5-fluorouracil (5-FU)-based adjuvant chemoradiotherapy (ACRT) is a preferred regimen for post-surgery gastric cancer (GC). However, the survival outcome of 5-FU-based ACRT varies greatly among different GC patients. Thus, it is necessary to classify which patients may benefit from 5-FU-based ACRT. MATERIALS AND METHODS We collected 577 GC and 84 adjacent normal samples for training and 675 GC samples for validation. Based on the within-sample relative expression orderings (REOs) of gene expression levels, reversal gene pairs were selected, and the pairs correlating with overall survival (OS) of GC patients receiving 5-FU-based ACRT were identified as candidates. Finally, an optimized set of candidate gene pairs was selected as a classification signature in training data and validated in validation data. RESULTS A signature consisting of 34 gene pairs was identified in training data and validated in three independent datasets. The classified low-risk group had better OS than the classified high-risk group. We also analyzed the recurrent free survival or disease free survival (RFS/DFS) of the validation datasets, and the similar results were shown. Furthermore, although the signature was identified based on the OS of GC patients receiving ACRT, it was not a prognostic signature for patients treated with surgery alone, but may be a potential signature for 5-FU-based chemotherapy alone. CONCLUSIONS The signature can accurately classify GC patients who may benefit from 5-FU-based ACRT, which could aid clinicians in tailoring more effective GC treatments.
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Affiliation(s)
- Meifeng Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Haifeng Chen
- Department of General Surgery, Fuzhou Second Hospital Affiliated to Xiamen University, China.
| | - Jun He
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Jiajing Xie
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Jie Xia
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Hui Liu
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Yidan Shi
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Zheng Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
| | - Haidan Yan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.
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Chen R, He J, Wang Y, Guo Y, Zhang J, Peng L, Wang D, Lin Q, Zhang J, Guo Z, Li L. Qualitative transcriptional signatures for evaluating the maturity degree of pluripotent stem cell-derived cardiomyocytes. Stem Cell Res Ther 2019; 10:113. [PMID: 30925936 PMCID: PMC6440140 DOI: 10.1186/s13287-019-1205-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [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: 11/12/2018] [Revised: 02/22/2019] [Accepted: 03/03/2019] [Indexed: 12/29/2022] Open
Abstract
Background Pluripotent stem cell-derived cardiomyocytes (PSC-CMs) are widely used models for regenerative medicine and disease research. However, PSC-CMs are usually immature in morphology and functionality and the maturity of PSC-CMs could not be determined accurately. In order to reasonably interpret the experimental results obtained by PSC-CMs, it is necessary to evaluate the maturity of PSC-CMs and find the key genes related to maturation. Methods Using the gene expression profiles of normal adult cardiac tissue and embryonic stem cell (ESC) samples, we identified gene pairs with identically relative expression orderings (REOs) within adult cardiac tissue but reversely identical in ESCs. Then, for a PSC-CM model, we calculated the maturity score as the percentage of these gene pairs that exhibit the same REOs in adult cardiac tissue. Lastly, the CellComp method was used to identify the maturation-related genes. Results The maturity score increased gradually from 0.8401 for 18-week fetal cardiac tissue to 0.9997 for adult cardiac tissue. For four human PSC-CM models, the mature scores increased with prolonged culture time but were all below 0.8. The genes involved in energy metabolism, angiogenesis, immunity, and proliferation were dysregulated in the 1-year PSC-CMs compared with adult cardiac tissue. Conclusion We proposed a qualitative transcriptional signature to score the maturity degree of PSC-CMs. This score can reasonably track the maturity of PSC-CMs and be used to compare different PSC-CM culture methods. Electronic supplementary material The online version of this article (10.1186/s13287-019-1205-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rou Chen
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jun He
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Yumei Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - You Guo
- Medical Big Data and Bioinformatics Research Center, First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Juan Zhang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Luying Peng
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Duo Wang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qin Lin
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Zhang
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zheng Guo
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China.
| | - Li Li
- Key Laboratory of Arrhythmias, Ministry of Education, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.
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Cai H, Li X, Li J, Liang Q, Zheng W, Guan Q, Guo Z, Wang X. Identifying differentially expressed genes from cross-site integrated data based on relative expression orderings. Int J Biol Sci 2018; 14:892-900. [PMID: 29989020 PMCID: PMC6036750 DOI: 10.7150/ijbs.24548] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [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: 12/25/2017] [Accepted: 02/02/2018] [Indexed: 12/13/2022] Open
Abstract
It is a basic task in high-throughput gene expression profiling studies to identify differentially expressed genes (DEGs) between two phenotypes. But the weakly differential expression signals between two phenotypes are hardly detectable with limited sample sizes. To solve this problem, many researchers tried to combine multiple independent datasets using meta-analysis or batch effect adjustment algorithms. However, these algorithms may distort true biological differences between two phenotypes and introduce unacceptable high false rates, as demonstrated in this study. These problems pose critical obstacles for analyzing the transcriptional data in The Cancer Genome Atlas where there are many small-scale batches of data. Previously, we developed RankComp to detect DEGs for individual disease samples through exploiting the incongruous relative expression orderings between two phenotypes and further improved it here to identify DEGs using multiple independent datasets. We demonstrated the improved RankComp can directly analyze integrated cross-site data to detect DEGs between two phenotypes without the need of batch effect adjustments. Its usage was illustrated in detecting weak differential expression signals of breast cancer drug-response data using combined datasets from multiple experiments.
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Affiliation(s)
- Hao Cai
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Xiangyu Li
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Jing Li
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Qirui Liang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Weicheng Zheng
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.,Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Qingzhou Guan
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Zheng Guo
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou 350122, China.,Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
| | - Xianlong Wang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
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Guan Q, Yan H, Chen Y, Zheng B, Cai H, He J, Song K, Guo Y, Ao L, Liu H, Zhao W, Wang X, Guo Z. Quantitative or qualitative transcriptional diagnostic signatures? A case study for colorectal cancer. BMC Genomics 2018; 19:99. [PMID: 29378509 PMCID: PMC5789529 DOI: 10.1186/s12864-018-4446-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 09/26/2017] [Accepted: 01/11/2018] [Indexed: 12/20/2022] Open
Abstract
Background Due to experimental batch effects, the application of a quantitative transcriptional signature for disease diagnoses commonly requires inter-sample data normalization, which would be hardly applicable under common clinical settings. Many cancers might have qualitative differences with the non-cancer states in the gene expression pattern. Therefore, it is reasonable to explore the power of qualitative diagnostic signatures which are robust against experimental batch effects and other random factors. Results Firstly, using data of technical replicate samples from the MicroArray Quality Control (MAQC) project, we demonstrated that the low-throughput PCR-based technologies also exist large measurement variations for gene expression even when the samples were measured in the same test site. Then, we demonstrated the critical limitation of low stability for classifiers based on quantitative transcriptional signatures in applications to individual samples through a case study using a support vector machine and a naïve Bayesian classifier to discriminate colorectal cancer tissues from normal tissues. To address this problem, we identified a signature consisting of three gene pairs for discriminating colorectal cancer tissues from non-cancer (normal and inflammatory bowel disease) tissues based on within-sample relative expression orderings (REOs) of these gene pairs. The signature was well verified using 22 independent datasets measured by different microarray and RNA_seq platforms, obviating the need of inter-sample data normalization. Conclusions Subtle quantitative information of gene expression measurements tends to be unstable under current technical conditions, which will introduce uncertainty to clinical applications of the quantitative transcriptional diagnostic signatures. For diagnosis of disease states with qualitative transcriptional characteristics, the qualitative REO-based signatures could be robustly applied to individual samples measured by different platforms. Electronic supplementary material The online version of this article (10.1186/s12864-018-4446-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qingzhou Guan
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Haidan Yan
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Yanhua Chen
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Baotong Zheng
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Hao Cai
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Jun He
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Kai Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - You Guo
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.,Department of Preventive Medicine, School of Basic Medicine Sciences, Gannan Medical University, Ganzhou, 341000, China
| | - Lu Ao
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Huaping Liu
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China
| | - Wenyuan Zhao
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China
| | - Xianlong Wang
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China.
| | - Zheng Guo
- Fujian Key Laboratory of Medical Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, 350122, China. .,Fujian Key Laboratory of Tumor Microbiology, Fujian Medical University, Fuzhou, 350122, China. .,College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150086, China.
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