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Olatunji I, Cui F. Multimodal AI for prediction of distant metastasis in carcinoma patients. FRONTIERS IN BIOINFORMATICS 2023; 3:1131021. [PMID: 37228671 PMCID: PMC10203594 DOI: 10.3389/fbinf.2023.1131021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 04/24/2023] [Indexed: 05/27/2023] Open
Abstract
Metastasis of cancer is directly related to death in almost all cases, however a lot is yet to be understood about this process. Despite advancements in the available radiological investigation techniques, not all cases of Distant Metastasis (DM) are diagnosed at initial clinical presentation. Also, there are currently no standard biomarkers of metastasis. Early, accurate diagnosis of DM is however crucial for clinical decision making, and planning of appropriate management strategies. Previous works have achieved little success in attempts to predict DM from either clinical, genomic, radiology, or histopathology data. In this work we attempt a multimodal approach to predict the presence of DM in cancer patients by combining gene expression data, clinical data and histopathology images. We tested a novel combination of Random Forest (RF) algorithm with an optimization technique for gene selection, and investigated if gene expression pattern in the primary tissues of three cancer types (Bladder Carcinoma, Pancreatic Adenocarcinoma, and Head and Neck Squamous Carcinoma) with DM are similar or different. Gene expression biomarkers of DM identified by our proposed method outperformed Differentially Expressed Genes (DEGs) identified by the DESeq2 software package in the task of predicting presence or absence of DM. Genes involved in DM tend to be more cancer type specific rather than general across all cancers. Our results also indicate that multimodal data is more predictive of metastasis than either of the three unimodal data tested, and genomic data provides the highest contribution by a wide margin. The results re-emphasize the importance for availability of sufficient image data when a weakly supervised training technique is used. Code is made available at: https://github.com/rit-cui-lab/Multimodal-AI-for-Prediction-of-Distant-Metastasis-in-Carcinoma-Patients.
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Tsyganov MM, Tsydenova IA, Markovich VA, Ibragimova MK, Rodionov EO, Tuzikov SA, Litvyakov NV. Expression heterogeneity of ABC-transporter family genes and chemosensitivity genes in gastric tumor, carcinomatosis and lymph node metastases. ADVANCES IN MOLECULAR ONCOLOGY 2022. [DOI: 10.17650/2313-805x-2022-9-4-78-88] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Introduction. Metastatic tumors (particularly gastric cancer) have been found to be characterized by heterogeneity between the primary tumor and metastases. This type of heterogeneity comes to the fore when treating primary-metastatic forms of tumor and is an important reason for the low effectiveness of their treatment. In this regard, comparative analysis of ABC-transporter gene expression and chemosensitivity genes will allow to characterize to a certain extent the resistance and sensitivity of primary tumor, carcinomatosis and metastases to therapy and provide the basis for personalized treatment approach.Aim. To evaluate expression heterogeneity of ABC-transporter genes and chemosensitivity genes in gastric tumor, carcinomatosis and lymph node metastases.Materials and methods. Overall 41 patients with disseminated gastric cancer stage IV with carcinomatosis of peritoneum were included in the investigation. All patients underwent surgery according to Roux palliative gastrectomy. After surgery patients underwent chemotherapy depending on indications. RNA was isolated using RNeasy Plus mini kit (Qiagen, Germany). The expression level of ABC transporter genes (ABCB1, ABCC1, ABCC2, ABCC5, ABCG1, ABCG2) and chemosensitivity genes (BRCA1, RRM1, ERCC1, TOP1, TOP2α, TUBβ3, TYMS, GSTP1) was assessed by reverse transcription polymerase chain reaction (RT-PCR) in primary tumor, carcinomatosis and lymph node metastases.Results. The expression levels of the genes under study were shown to vary widely. For ABC transporter genes, ABCG1 (3.1 ± 1.1; max 32.0), ABCG2 (7.9 ± 2.3; max 54.1), ABCG2 (9.6 ± 3.8; max 101.0) were the most expressed genes in gastric tumor tissue, carcinomatosis and lymph node metastasis, respectively. Hyperexpression among chemosensitivity genes at all three sites was characteristic only of TOP2α (17.2 ± 6.0; max. 161.9; 10.8 ± 4.1; max. 105.1; 35.3 ± 0.8; max. 439.6, respectively). We found that TOP2α and BRCA1 gene expression levels were higher in lymph node metastasis compared with gastric tumor tissue and carcinomatosis (at p = 0.005 and p = 0.001). Whereas ABCC1 gene expression was statistically significantly higher in carcinomatosis (p = 0.03).Conclusion. Thus, a high level of expression heterogeneity is observed in gastric cancer, which affects the expression patterns of various genes in different localizations. The expression profile can be used to determine the level of heterogeneity and approach to personalized therapy tactics.
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Affiliation(s)
- M. M. Tsyganov
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences; Siberian State Medical University, Ministry of Health of Russia
| | - I. A. Tsydenova
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - V. A. Markovich
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - M. K. Ibragimova
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences; Siberian State Medical University, Ministry of Health of Russia; National Research Tomsk State University
| | - E. O. Rodionov
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - S. A. Tuzikov
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - N. V. Litvyakov
- Cancer Research Institute of the Tomsk National Research Medical Center of the Russian Academy of Sciences
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Malpeli G, Barbi S, Innamorati G, Alloggio M, Filippini F, Decimo I, Castelli C, Perris R, Bencivenga M. Landscape of Druggable Molecular Pathways Downstream of Genomic CDH1/Cadherin-1 Alterations in Gastric Cancer. J Pers Med 2022; 12:jpm12122006. [PMID: 36556227 PMCID: PMC9784514 DOI: 10.3390/jpm12122006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/03/2022] [Accepted: 11/24/2022] [Indexed: 12/09/2022] Open
Abstract
Loss of CDH1/Cadherin-1 is a common step towards the acquisition of an abnormal epithelial phenotype. In gastric cancer (GC), mutation and/or downregulation of CDH1/Cadherin-1 is recurrent in sporadic and hereditary diffuse GC type. To approach the molecular events downstream of CDH1/Cadherin-1 alterations and their relevance in gastric carcinogenesis, we queried public databases for genetic and DNA methylation data in search of molecular signatures with a still-uncertain role in the pathological mechanism of GC. In all GC subtypes, modulated genes correlating with CDH1/Cadherin-1 aberrations are associated with stem cell and epithelial-to-mesenchymal transition pathways. A higher level of genes upregulated in CDH1-mutated GC cases is associated with reduced overall survival. In the diffuse GC (DGC) subtype, genes downregulated in CDH1-mutated compared to cases with wild type CDH1/Cadherin-1 resulted in being strongly intertwined with the DREAM complex. The inverse correlation between hypermethylated CpGs and CDH1/Cadherin-1 transcription in diverse subtypes implies a common epigenetic program. We identified nonredundant protein-encoding isoforms of 22 genes among those differentially expressed in GC compared to normal stomach. These unique proteins represent potential agents involved in cell transformation and candidate therapeutic targets. Meanwhile, drug-induced and CDH1/Cadherin-1 mutation-related gene expression comparison predicts FIT, GR-127935 hydrochloride, amiodarone hydrochloride in GC and BRD-K55722623, BRD-K13169950, and AY 9944 in DGC as the most effective treatments, providing cues for the design of combined pharmacological treatments. By integrating genetic and epigenetic aspects with their expected functional outcome, we unveiled promising targets for combinatorial pharmacological treatments of GC.
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Affiliation(s)
- Giorgio Malpeli
- Department of Surgical, Odontostomatologic, Maternal and Child Sciences, University of Verona, 37134 Verona, Italy
- Correspondence:
| | - Stefano Barbi
- Department of Diagnostics and Public Health, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Giulio Innamorati
- Department of Surgical, Odontostomatologic, Maternal and Child Sciences, University of Verona, 37134 Verona, Italy
| | - Mariella Alloggio
- General and Upper GI Surgery Division, Department and of Surgical, Odontostomatologic, Maternal and Child Sciences, University of Verona, 37134 Verona, Italy
| | - Federica Filippini
- General and Upper GI Surgery Division, Department and of Surgical, Odontostomatologic, Maternal and Child Sciences, University of Verona, 37134 Verona, Italy
| | - Ilaria Decimo
- Section of Pharmacology, Department of Diagnostic and Public Health, University of Verona, 37134 Verona, Italy
| | - Claudia Castelli
- Pathology Unit, Department of Diagnostics and Public Health, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Roberto Perris
- Department of Biosciences, COMT-Centre for Molecular and Translational Oncology, University of Parma, 43124 Parma, Italy
| | - Maria Bencivenga
- General and Upper GI Surgery Division, Department and of Surgical, Odontostomatologic, Maternal and Child Sciences, University of Verona, 37134 Verona, Italy
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Recurrence patterns after curative gastrectomy for pStage II/III gastric cancer: Exploratory analysis of the randomized controlled JCOG1001 trial. EUROPEAN JOURNAL OF SURGICAL ONCOLOGY 2022; 49:838-844. [PMID: 36424261 DOI: 10.1016/j.ejso.2022.11.093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/30/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Peritoneal, lymph node, and hematogenous recurrence patterns are common after potentially curative surgery for gastric cancer. However, clinicopathological characteristics associated with each recurrence type have rarely been comprehensively reported among patients who received a unified treatment strategy and follow-up protocol. Understanding these recurrence patterns would help with early detection of recurrence and a personalized follow-up plan. We investigated the initial recurrence patterns after curative gastrectomy using data from the randomized clinical JCOG1001 trial. METHODS Of 1204 patients enrolled in JCOG1001, 932 pStage II/III patients were included. Initial recurrence dates and patterns were recorded by attending physicians according to the protocol. Risk factors for hematogenous, lymph node, and peritoneal recurrence were determined by univariable and multivariable analyses using the Fine-Gray model. RESULTS Overall, 253 patients developed recurrence. Hematogenous recurrence was the most frequent pattern (n = 115), followed by peritoneal (n = 104) and lymph node recurrence (n = 70). Differentiated type (p = 0.0028), pT4 (p = 0.0466), and pN3 (p < 0.0001) were associated with hematogenous recurrence; however, D2+ lymphadenectomy reduced it (p = 0.0161). Patients with large (≥5 cm) tumors (p = 0.0312), pT4 (p < 0.0001), pN3 (p = 0.0013), and undifferentiated histologic type (p = 0.0001) had significantly higher rates of peritoneal recurrence. Extended lymph node metastasis (pN3) was the only risk factor (p < 0.0001) for lymph node recurrence. CONCLUSIONS Clinicopathological features differed according to the recurrence patterns. Vigilant follow-up with an understanding of recurrence patterns might be beneficial for some high-risk patients.
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Lu M, Xiao L, Xu B, Gao Q. Identification of Novel Genes and Associated Drugs in Advanced Clear Cell Renal Cell Carcinoma by Bioinformatic Methods. TOHOKU J EXP MED 2022; 258:79-90. [PMID: 35896362 DOI: 10.1620/tjem.2022.j059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Meiqi Lu
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Liangxiang Xiao
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Bo Xu
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University
| | - Qing Gao
- Department of Nephrology, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University.,The Third Clinical Medical College, Fujian Medical University
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Gastric cancer biomarker analysis in patients treated with different adjuvant chemotherapy regimens within SAMIT, a phase III randomized controlled trial. Sci Rep 2022; 12:8509. [PMID: 35595817 PMCID: PMC9123164 DOI: 10.1038/s41598-022-12439-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Accepted: 03/23/2022] [Indexed: 12/23/2022] Open
Abstract
Biomarkers for selecting gastric cancer (GC) patients likely to benefit from sequential paclitaxel treatment followed by fluorinated-pyrimidine-based adjuvant chemotherapy (sequential paclitaxel) were investigated using tissue samples of patients recruited into SAMIT, a phase III randomized controlled trial. Total RNA was extracted from 556 GC resection samples. The expression of 105 genes was quantified using real-time PCR. Genes predicting the benefit of sequential paclitaxel on overall survival, disease-free survival, and cumulative incidence of relapse were identified based on the ranking of p-values associated with the interaction between the biomarker and sequential paclitaxel or monotherapy groups. Low VSNL1 and CD44 expression predicted the benefit of sequential paclitaxel treatment for all three endpoints. Patients with combined low expression of both genes benefitted most from sequential paclitaxel therapy (hazard ratio = 0.48 [95% confidence interval, 0.30-0.78]; p < 0.01; interaction p-value < 0.01). This is the first study to identify VSNL1 and CD44 RNA expression levels as biomarkers for selecting GC patients that are likely to benefit from sequential paclitaxel treatment followed by fluorinated-pyrimidine-based adjuvant chemotherapy. Our findings may facilitate clinical trials on biomarker-oriented postoperative adjuvant chemotherapy for patients with locally advanced GC.
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Predicting peritoneal recurrence by artificial intelligence. Lancet Digit Health 2022; 4:e293-e294. [DOI: 10.1016/s2589-7500(22)00065-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022]
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Qiao J, Tian Y, Cheng X, Liu Z, Zhou J, Gu L, Zhang B, Zhang L, Ji J, Xing R, Deng D. CDKN2A Deletion Leading to Hematogenous Metastasis of Human Gastric Carcinoma. Front Oncol 2022; 11:801219. [PMID: 35004325 PMCID: PMC8733704 DOI: 10.3389/fonc.2021.801219] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/06/2021] [Indexed: 12/24/2022] Open
Abstract
Introduction Somatic copy number deletion (SCND) of CDKN2A gene is the most frequent event in cancer genomes. Whether CDKN2A SCND drives human cancer metastasis is far from clear. Hematogenous metastasis is the main reason of human gastric carcinoma (GC) death. Thus, prediction GC metastasis is eagerly awaited. Method GC patients (n=408) enrolled in both a cross-sectional and a prospective cohorts were analysed. CDKN2A SCND was detected with a quantitative PCR assay (P16-Light). Association of CDKN2A SCND and GC metastasis was evaluated. Effect of CDKN2A SCND by CRISPR/Cas9 on biological behaviors of cancer cells was also studied. Results CDKN2A SCND was detected in 38.9% of GCs from patients (n=234) enrolled in the cross-sectional cohort. Association analysis showed that more CDKN2A SCND was recognized in GCs with hematogenous metastasis than those without (66.7% vs. 35.7%, p=0.014). CDKN2A SCND was detected in 36.8% of baseline pN0M0 GCs from patients (n=174) enrolled in the prospective study, the relationship between CDKN2A SCND and hematogenous metastasis throughout the follow-up period (62.7 months in median) was also significant (66.7% vs. 34.6%, p=0.016). Using CDKN2A SCND as a biomarker for predicting hematogenous metastasis of GCs, the prediction sensitivity and specificity were 66.7% and 65.4%. The results of functional experiments indicated that CDKN2A SCND could obviously downregulate P53 expression that consequently inhibited the apoptosis of MGC803 GC and HEK293T cells. This may account for hematogenous metastasis of GCs by CDKN2A SCND. Conclusion CDKN2A SCND may drive GC metastasis and could be used as a predictor for hematogenous metastasis of GCs.
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Affiliation(s)
- Juanli Qiao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Yuan Tian
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Xiaojing Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Liankun Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Baozhen Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Lianhai Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Jiafu Ji
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Beijing, China
| | - Rui Xing
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Tumor Biology, Peking University Cancer Hospital and Institute, Beijing, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Beijing, China
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Tazawa H, Suzuki T, Saito A, Ishikawa A, Komo T, Sada H, Shimada N, Hadano N, Onoe T, Sudo T, Shimizu Y, Kuraoka K, Tashiro H. Utility of TMPRSS4 as a Prognostic Biomarker and Potential Therapeutic Target in Patients with Gastric Cancer. J Gastrointest Surg 2022; 26:305-313. [PMID: 34379296 PMCID: PMC8821072 DOI: 10.1007/s11605-021-05101-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/14/2021] [Indexed: 01/31/2023]
Abstract
BACKGROUND Transmembrane serine protease 4 (TMPRSS4) belongs to the family of type II transmembrane serine proteases that are known to be upregulated in many malignant tumors. However, there is a paucity of studies documenting the clinical impact and biological effects of TMPRSS4 on gastric cancer (GC) patients who underwent surgery. METHODS Tissues samples were obtained from 105 patients with GC who underwent gastrectomy followed by adjuvant chemotherapy, excluding those at stage I. The expression of TMPRSS4 was examined through immunohistochemical analysis. The association between TMPRSS4 expression and clinico-pathological features as well as prognosis was assessed. Moreover, the effects of TMPRSS4 expression on cell migration and sensitivity to 5-FU were investigated. RESULTS The expression rate of TMPRSS4 was 56.3% (59/105) in GC cases. The expression of TMPRSS4 was positively correlated with the depth of tumor (T) and venous (V) invasion. The 5-year overall survival (OS) and recurrence-free survival (RFS) rates of the TMPRSS4-positive group was significantly lower than that of the TMPRSS4-negative group (p=0.0001 and p=0.005, respectively). Especially, there was significant differences in OS and RFS of patients with stage III cancer between the two groups (p=0.0064 and 0.012, respectively). Multivariate analysis demonstrated that TMPRSS4 expression and the stage of cancer were crucial prognostic factors for RFS. TMPRSS4-silenced GC cells exhibited increased sensitivity to 5-FU when compared with the non-specific control siRNA-transfected cells. CONCLUSION TMPRSS4 can be considered as a potential prognostic biomarker, especially for stage III, and a promising therapeutic target for GC.
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Affiliation(s)
- Hirofumi Tazawa
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan.
| | - Takahisa Suzuki
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biochemical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akihisa Saito
- Department of Diagnostic Pathology, Kure Medical Center・Chugoku Cancer Center, Kure, Hiroshima, Japan
| | - Akira Ishikawa
- Department of Diagnostic Pathology, Kure Medical Center・Chugoku Cancer Center, Kure, Hiroshima, Japan
| | - Toshiaki Komo
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Haruki Sada
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Norimitsu Shimada
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Naoto Hadano
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Takashi Onoe
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Takeshi Sudo
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Yosuke Shimizu
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan
| | - Kazuya Kuraoka
- Department of Diagnostic Pathology, Kure Medical Center・Chugoku Cancer Center, Kure, Hiroshima, Japan
| | - Hirotaka Tashiro
- Department of Surgery, Kure Medical Center・Chugoku Cancer Center, 737-0023, 3-1, Kure, Hiroshima, Japan.
- Department of Gastroenterological and Transplant Surgery, Graduate School of Biochemical and Health Sciences, Hiroshima University, Hiroshima, Japan.
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Ji Y, Gao L, Zhang C, Sun X, Dai L, Ji Z, Zhang J, Zhang Z, Cao W, Zhao Y, Zhang L. Identification of the hub genes and prognostic indicators of gastric cancer and correlation of indicators with tumor-infiltrating immune cell levels. J Cancer 2021; 12:4025-4038. [PMID: 34093807 PMCID: PMC8176244 DOI: 10.7150/jca.52105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/25/2021] [Indexed: 12/29/2022] Open
Abstract
Aims: To identify the hub genes and prognostic indicators of gastric cancer (GC) and determine the correlation between prognostic indicators and the tumor-infiltrating immune cell levels so as to provide useful information for future GC diagnosis and treatment. Methods: The Cancer Genome Atlas (TCGA) stomach adenocarcinoma dataset and two microarray datasets were used to screen the overlapping differentially expressed genes (DEGs) between normal gastric and GC tissue samples. Hub genes were screened via protein-protein interaction networks and module analysis of the overlapping DEGs. Their expression was validated at the cell level and tissue level using the ONCOMINE database. The prognostic indicators of overall survival (OS) and disease-free survival was identified by Cox proportional hazards regression analysis based on tumor grade and cancer stage. The expression of hub genes was validated at the cell level. The correlation of prognostic indicators with the tumor-infiltrating immune cell levels was analyzed using Tumor IMmune Estimation Resource. Results: Ten hub genes, namely CDC6, CDC20, BUB1B, TOP2A, CDK1, AURKA, CCNA2, CCNB1, MAD2L1, and KIF11, were screened and their upregulation in the GC tissue was verified. Three prognostic factors, namely LUM, VCAN, and EFNA4, were identified; their expression was higher in GC cells than in normal cells. LUM, VCAN, and EFNA4 were correlated with tumor-infiltrating immune cell levels in GC. Significance: The identified hub genes and prognostic indicators of GC could be useful indicators for future GC diagnosis and treatment.
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Affiliation(s)
- Yun Ji
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450007, China.,Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Lu Gao
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450007, China.,Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Can Zhang
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450007, China.,Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Xu Sun
- Integrated TCM and Western Medicine Department, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou 450008, China
| | - Liping Dai
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Zhenyu Ji
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Jianying Zhang
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Zhida Zhang
- BGI College, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450007, China.,Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Wei Cao
- Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450000, China
| | - Yang Zhao
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China
| | - Liguo Zhang
- Henan Institute of Medical and Pharmaceutical Science, Zhengzhou University, No. 40 Daxue Road, Zhengzhou 450052, China.,Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou University, Zhengzhou 450000, China
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Fujiya K, Terashima M, Ohshima K, Aizawa D, Sugino T, Serizawa M, Nakamura K, Nagashima T, Hatakeyama K, Urakami K, Akiyama Y, Tsubosa Y, Kitagawa Y, Yamaguchi K. MAGEA10 expression is a predictive marker of early hepatic recurrence after curative gastrectomy for gastric and gastroesophageal junction cancer. Gastric Cancer 2021; 24:341-351. [PMID: 32965606 DOI: 10.1007/s10120-020-01123-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Resection for hepatic recurrence after gastrectomy in patients with gastric cancer may be curative; however, the prediction of hepatic recurrence remains intractable. Therefore, we aimed to explore predictive markers for hepatic recurrence in gastric and gastroesophageal junction cancer based on genetic information. METHODS This study recruited 154 patients who underwent curative gastrectomy for pathological stage II or III primary gastric and gastroesophageal junction adenocarcinoma. Genes associated with hepatic recurrence were comprehensively analyzed using whole-exome sequencing and gene expression profiling (GEP), followed by immunohistochemistry analysis for MAGEA10. The cumulative incidences of hepatic recurrence, relapse-free survival, and overall survival were evaluated. RESULTS A total of 12 patients with early hepatic recurrences were found within 2 years of surgery. Although there were no distinct gene mutations in recurrent patients, upregulation of MAGEA10 was identified in patients with early hepatic recurrence using GEP analysis. Immunostaining for MAGEA10 stained the cell nuclei in 29 (18.8%) of 154 samples. Furthermore, protein expression of MAGEA10 on immunohistochemistry was significantly related to a high MAGEA10 mRNA expression, high cumulative incidences of hepatic recurrence, and poor relapse-free survival. Overall survival did not differ significantly between positive and negative immunohistochemical staining for MAGEA10. The sensitivity and specificity of MAGEA10 staining for early hepatic recurrence were 58.3% and 84.5%, respectively. CONCLUSIONS MAGEA10 represents a promising predictive marker for early hepatic recurrence after curative gastrectomy for gastric and gastroesophageal junction cancer.
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Affiliation(s)
- Keiichi Fujiya
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
| | - Masanori Terashima
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Daisuke Aizawa
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Takashi Sugino
- Division of Pathology, Shizuoka Cancer Center, Shizuoka, Japan
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Nakamura
- Division of Gastric Surgery, Shizuoka Cancer Center, 1007 Shimonagakubo, Nagaizumi-cho, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
- SRL, Inc., Tokyo, Japan
| | - Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuto Akiyama
- Immunotherapy Division, Shizuoka Cancer Center Research Institute, Shizuoka, Japan
| | - Yasuhiro Tsubosa
- Division of Esophageal Surgery, Shizuoka Cancer Center, Shizuoka, Japan
| | - Yuko Kitagawa
- Department of Surgery, Keio University School of Medicine, Tokyo, Japan
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12
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Song D, Tian J, Hu Y, Wei Y, Lu H, Wang Y, Guan Q, Zhou Y. Identification of biomarkers associated with diagnosis and prognosis of gastroesophageal junction adenocarcinoma-a study based on integrated bioinformatics analysis in GEO and TCGA database. Medicine (Baltimore) 2020; 99:e23605. [PMID: 33371094 PMCID: PMC7748358 DOI: 10.1097/md.0000000000023605] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022] Open
Abstract
Gastroesophageal junction adenocarcinoma (GEJAC) is a malignant tumor with high mortality. Its incidence has increased sharply all over the world in recent years. The study aims to search for potential biomarkers for the diagnosis and prognosis of GEJAC based on the Gene Expression Omnibus database (GEO) database and The Cancer Genome Atlas (TCGA) database.Microarray dataset (GSE96668 and GSE74553) of GEJAC was downloaded from the GEO. After screening overlapping differentially expressed genes (DEGs) by GEO2R and Wayne map, functional enrichment analysis of the DEGs was performed by the DAVID database. Then, a protein-protein interaction (PPI) network was constructed, and the hub gene was identified by using STRING and Cytoscape, as well as the diagnostic value of hub genes was evaluated by the receiver operating characteristic (ROC) curves. Finally, the gene transcriptome profiles of gastric cancer named TCGA-STAD were downloaded from TCGA database to screen the potential prognostic genes and construct the prognostic risk model using Cox proportional hazards regression. Meanwhile, the Kaplan-Meier curve and time-dependent ROC curve were adopted to test the prognostic value of the prognostic gene signature.In this study, we identified 10 hub genes that might have high diagnostic value for GEJAC, and inferred that they might be involved in the occurrence and development of GEJAC. Moreover, we conducted a survival prediction model consisting of 6 genes and proved that they have value to some extent in predicting prognosis for GEJAC patients.
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Affiliation(s)
- Danlei Song
- The First Clinical Medical School of Lanzhou University
- Department of Gastroenterology
- Key Laboratory for Gastrointestinal Diseases of Gansu Province
| | - Jiming Tian
- The First Clinical Medical School of Lanzhou University
- Department of Obstetrics and Gynecology
| | - Yuping Hu
- The First Clinical Medical School of Lanzhou University
- Hospital of Reproductive Medicinal
| | - Yongjian Wei
- The First Clinical Medical School of Lanzhou University
- The Fifth Department of General Surgery
| | - Hong Lu
- Department of Gastroenterology
- Key Laboratory for Gastrointestinal Diseases of Gansu Province
| | - Yuping Wang
- Department of Gastroenterology
- Key Laboratory for Gastrointestinal Diseases of Gansu Province
| | - Quanlin Guan
- Department of Oncology Surgery, The First Hospital of Lanzhou University, Lanzhou, China
| | - Yongning Zhou
- Department of Gastroenterology
- Key Laboratory for Gastrointestinal Diseases of Gansu Province
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13
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Hou G, Deng J, You X, Chen J, Jiang Y, Qian T, Bi Y, Song B, Xu Y, Yang X. Mining topoisomerase isoforms in gastric cancer. Gene 2020; 754:144859. [PMID: 32535049 DOI: 10.1016/j.gene.2020.144859] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/20/2020] [Accepted: 06/05/2020] [Indexed: 01/04/2023]
Abstract
DNA topoisomerases essentially remove topological strains generated during DNA replication, transcription, DNA repair, and other cytogenetic processes. However, distinct expression level and prognostic significance of individual topoisomerase isoforms in gastric cancer (GC) remain largely unexplored. In this study, we utilized Oncomine and Kaplan-Meier plotter database to detect the mRNA expression level of individual topoisomerase isoforms as well as assess their prognostic significance in GC patients. With the exception of TOP3B and TOP2B, levels of all topoisomerase isoforms were found to be elevated in GC patients when compared to the normal tissues. Elevated expression of TOP1 and TOP1MT was relevant to longer overall survival (OS) in GC and gastric intestinal type adenocarcinoma (GITA) patients, but not in diffuse gastric adenocarcinoma (DFA) patients. Increased expression of TOP2A and TOP2B was related to better OS in GC, as well as in GITA and DFA patients. In contrast, increased expression TOP3A and TOP3B was associated with shorter OS in GC, as well as in GITA and DFA patients. We also applied the Tumor IMmune Estimation Resource (TIMER) tool to assess the correlations between distinct topoisomerase isoforms and the infiltrating immune cell landscape. Furthermore, we found that down-regulating the expression of TOP3A by shRNA significantly inhibited the proliferation and colony formation in GC cells compared to control shRNA treated cells. Thus our study lays the framework for utilizing topoisomerases in better understanding the complexity and heterogeneity of GC and for developing strategies for novel customized therapy in GC patients.
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Affiliation(s)
- Guoxin Hou
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Jingjing Deng
- Department of Respiratory, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xin You
- The First Department of Chemotherapy, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Jing Chen
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Yiming Jiang
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Tingting Qian
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Yanyu Bi
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Binbin Song
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Yufen Xu
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China
| | - Xinmei Yang
- Department of Oncology, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, Zhejiang, China.
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14
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Serum CXCL13 and PECAM-1 can be used as diagnostic and prognostic markers in elderly patients with gastric cancer. Clin Transl Oncol 2020; 23:130-138. [PMID: 32500259 DOI: 10.1007/s12094-020-02403-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/13/2020] [Indexed: 02/07/2023]
Abstract
PURPOSE To investigate the application value of serum CXC Chemokine-13 (CXCL-13) and platelet endothelial cell adhesion molecule-1 (PECAM-1) in elderly patients with gastric cancer (GC). METHODS Ninety-eight elderly GC patients admitted to the Affiliated Hexian Memorial Hospital of Southern Medical University were selected as a research group, and 60 healthy subjects of the same age and in relatively good health who underwent physical examination at the same period were selected as a control group. Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of CXCL13 and PECAM-1 in serum. The clinical diagnosis and prognostic value of serum CXCL13 and PECAM-1 in elderly GC patients were analyzed. RESULTS The levels of CXCL13 and PECAM-1 in serum of the research group were significantly higher than those of the control group (P < 0.001). The AUC value of combined diagnosis of elderly GC patients by serum CXCL13 and PECAM-1 was 0.950, and that of combined evaluation of prognosis of patients was 0.849. Serum CXCL13 and PECAM-1 were significantly related to TNM staging, differentiation degree and tumor diameter in elderly GC patients (P < 0.05). High levels of CXCL13 and PECAM-1 were significantly associated with lower 5-year OS (P < 0.05). CONCLUSION Elderly GC patients with higher TNM staging, longer tumor diameters, high levels of CXCL13 and PECAM-1 had an increased risk of poor prognosis. Serum CXCL13 and PECAM-1 can be used as effective indicators for diagnosis and prognosis of elderly patients with GC, and can predict the 5-year OS in patients.
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15
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Wang B, Shen Y, Zou Y, Qi Z, Huang G, Xia S, Gao R, Li F, Huang Z. TOP2A Promotes Cell Migration, Invasion and Epithelial-Mesenchymal Transition in Cervical Cancer via Activating the PI3K/AKT Signaling. Cancer Manag Res 2020; 12:3807-3814. [PMID: 32547216 PMCID: PMC7251484 DOI: 10.2147/cmar.s240577] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 04/22/2020] [Indexed: 12/19/2022] Open
Abstract
Background/Objective Topoisomerases type IIA (TOP2A) was identified to present with a high-expression pattern in cervical cancer. However, TOP2A role in the progression of cervical cancer remains unknown. Here, we aimed to explore the effect and reveal the underlying mechanism of TOP2A in the migration, invasion and epithelial–mesenchymal transition (EMT) of cervical cancer. Materials and Methods The expression profiles of TOP2A in 20 paired cervical cancer tissues and the paracancerous normal tissues were detected by using Western blotting assay. Transwell chambers were used to test cell migration and invasion abilities. Cell morphology and the expressions of E-cadherin and N-cadherin were detected to assess cell EMT. LY294002 was used to inhibit the activation of PI3K/AKT signaling. Results Compared with the paracancerous normal tissues, TOP2A was overexpressed in 85% (17/20) cervical cancer tissues. Repression of TOP2A expression in SiHa cells significantly weakened cell migration and invasion abilities, reduced cell numbers in shuttle shape and increased E-cadherin expression while decreased E-cadherin expression. To the opposite, overexpression of TOP2A in Hela cells induced opposite results. In addition, the expression of p-AKT was increased when TOP2A was overexpressed in Hela cells, and p-AKT expression was decreased when TOP2A was silenced in SiHa cells. Moreover, suppression of the PI3K/AKT signaling with LY294002 treatment apparently rescued TOP2A-mediated promotions in cell migration, invasion and EMT in Hela cells. Conclusion This study reveals that TOP2A is abnormally overexpressed in cervical cancer tissues, and TOP2A overexpression leads to cell migration, invasion and EMT via activating PI3K/AKT signaling.
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Affiliation(s)
- Bi Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education, Guizhou Medical University, Guiyang, Guizhou, People's Republic of China.,Department of Paediatrics, Maternal and Child Health Hospital of Guiyang City, Guiyang, Guizhou, People's Republic of China
| | - Yaping Shen
- Department of Interventional Radiology, The Affiliated Baiyun Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Yin Zou
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Zhengjun Qi
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Guijia Huang
- Department of Oncology, The Second Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Shan Xia
- Department of Gynecologic Oncology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Rui Gao
- Guiyang Customs Guizhou International Travel Healthcare Center, Guiyang, Guizhou, People's Republic of China
| | - Fenghu Li
- Department of Gynecologic Oncology, The Affiliated Cancer Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
| | - Zhi Huang
- Department of Interventional Radiology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, People's Republic of China
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16
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Zhang H, Zou J, Yin Y, Zhang B, Hu Y, Wang J, Mu H. Bioinformatic analysis identifies potentially key differentially expressed genes in oncogenesis and progression of clear cell renal cell carcinoma. PeerJ 2019; 7:e8096. [PMID: 31788359 PMCID: PMC6883955 DOI: 10.7717/peerj.8096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/12/2022] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is one of the most common and lethal types of cancer within the urinary system. Great efforts have been made to elucidate the pathogeny. However, the molecular mechanism of ccRCC is still not well understood. The aim of this study is to identify key genes in the carcinogenesis and progression of ccRCC. The mRNA microarray dataset GSE53757 was downloaded from the Gene Expression Omnibus database. The GSE53757 dataset contains tumor and matched paracancerous specimens from 72 ccRCC patients with clinical stage I to IV. The linear model of microarray data (limma) package in R language was used to identify differentially expressed genes (DEGs). The protein–protein interaction (PPI) network of the DEGs was constructed using the search tool for the retrieval of interacting genes (STRING). Subsequently, we visualized molecular interaction networks by Cytoscape software and analyzed modules with MCODE. A total of 1,284, 1,416, 1,610 and 1,185 up-regulated genes, and 932, 1,236, 1,006 and 929 down-regulated genes were identified from clinical stage I to IV ccRCC patients, respectively. The overlapping DEGs among the four clinical stages contain 870 up-regulated and 645 down-regulated genes. The enrichment analysis of DEGs in the top module was carried out with DAVID. The results showed the DEGs of the top module were mainly enriched in microtubule-based movement, mitotic cytokinesis and mitotic chromosome condensation. Eleven up-regulated genes and one down-regulated gene were identified as hub genes. Survival analysis showed the high expression of CENPE, KIF20A, KIF4A, MELK, NCAPG, NDC80, NUF2, TOP2A, TPX2 and UBE2C, and low expression of ACADM gene could be involved in the carcinogenesis, invasion or recurrence of ccRCC. Literature retrieval results showed the hub gene NDC80, CENPE and ACADM might be novel targets for the diagnosis, clinical treatment and prognosis of ccRCC. In conclusion, the findings of present study may help us understand the molecular mechanisms underlying the carcinogenesis and progression of ccRCC, and provide potential diagnostic, therapeutic and prognostic biomarkers.
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Affiliation(s)
- Haiping Zhang
- Department of Derma Science Laboratory, Wuxi NO.2 People's Hospital affiliated to Nanjing Medical University, Wuxi, Jiangsu, China
| | - Jian Zou
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
| | - Ying Yin
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
| | - Bo Zhang
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
| | - Yaling Hu
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
| | - Jingjing Wang
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
| | - Huijun Mu
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China.,Wuxi Institute of Translational Medicine, Wuxi, Jiangsu, China
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17
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Maezawa Y, Sakamaki K, Oue N, Kimura Y, Hashimoto I, Hara K, Kano K, Aoyama T, Hiroshima Y, Yamada T, Yamamoto N, Ogata T, Ito H, Cho H, Shiozawa M, Yoshikawa T, Morinaga S, Rino Y, Yasui W, Masuda M, Miyagi Y, Oshima T. High gamma-glutamyl hydrolase and low folylpolyglutamate synthetase expression as prognostic biomarkers in patients with locally advanced gastric cancer who were administrated postoperative adjuvant chemotherapy with S-1. J Cancer Res Clin Oncol 2019; 146:75-86. [PMID: 31754833 PMCID: PMC6942012 DOI: 10.1007/s00432-019-03087-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 11/15/2019] [Indexed: 12/24/2022]
Abstract
Purpose The enzymes gamma-glutamyl hydrolase (GGH) and folylpolyglutamate synthetase (FPGS) regulate intracellular folate concentrations needed for cell proliferation, DNA synthesis, and repair. High GGH expression affects 5-FU thymidylate synthase (TS) inhibition and is a risk factor for various malignancies. Here, the clinical significance of GGH and FPGS expression was investigated in Stage II/III gastric cancer patients undergoing postoperative adjuvant chemotherapy with S-1. Methods Surgical specimens of cancer tissue and adjacent normal mucosa, obtained from 253 patients with previously untreated gastric cancer, were examined. GGH and FPGS mRNA expression was measured by qPCR to evaluate their clinicopathological significance in gastric cancer patients after curative resection. Results While FPGS expression showed no significant differences between the cancerous and normal samples, GGH expression was higher in cancer tissue than in adjacent normal mucosa. High GGH expression was correlated with age, histological type, and vascular invasion. Overall survival (OS) of patients with high GGH mRNA expression was significantly poorer than of patients with low GGH expression. Multivariate analysis showed that high GGH expression was an independent prognostic factor of OS (HR: 2.58, 95% CI 1.29–5.16). Patients who received S-1 adjuvant treatment showed a significantly poor OS between high GGH/low FPGS and low GGH/high FPGS. Patients without adjuvant treatment showed no significant difference. Conclusion GGH expression was significantly higher in gastric cancer tissue than in adjacent normal mucosa. High GGH and low FPGS expression is a useful independent predictor of poor outcomes in stage II/III gastric cancer patients undergoing postoperative adjuvant chemotherapy with S-1.
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Affiliation(s)
- Yukio Maezawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Kentaro Sakamaki
- Department of Biostatistics Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8658, Japan
| | - Naohide Oue
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Science, Hiroshima, 734-8551, Japan
| | - Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Itaru Hashimoto
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Kentaro Hara
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Kazuki Kano
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Toru Aoyama
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Yukihiko Hiroshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Takanobu Yamada
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Naoto Yamamoto
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Takashi Ogata
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Hiroyuki Ito
- Department of Thoracic Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Haruhiko Cho
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
- Department of Surgery, Tokyo Metropolitan Cancer and Infectious Disease Center Komagome Hospital, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Manabu Shiozawa
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Takaki Yoshikawa
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
- Department of Gastric Surgery, National Cancer Center Hospital, Chuo-ku, Tokyo, 104-0045, Japan
| | - Soichiro Morinaga
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan
| | - Yasushi Rino
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Wataru Yasui
- Department of Molecular Pathology, Hiroshima University Institute of Biomedical and Health Science, Hiroshima, 734-8551, Japan
| | - Munetaka Masuda
- Department of Surgery, Yokohama City University, Yokohama, Kanagawa, 236-0004, Japan
| | - Yohei Miyagi
- Kanagawa Cancer Center Research Institute, Yokohama, Kanagawa, 241-8515, Japan
| | - Takashi Oshima
- Department of Gastrointestinal Surgery, Kanagawa Cancer Center, Yokohama, Kanagawa, 241-8515, Japan.
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18
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Zhang J, Li D, Zhang Y, Ding Z, Zheng Y, Chen S, Wan Y. Integrative analysis of mRNA and miRNA expression profiles reveals seven potential diagnostic biomarkers for non‑small cell lung cancer. Oncol Rep 2019; 43:99-112. [PMID: 31746439 PMCID: PMC6908938 DOI: 10.3892/or.2019.7407] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to explore specific molecular targets for the diagnosis and treatment of non-small cell lung cancer (NSCLC). The expression profiles of microRNAs (miRNAs) and mRNAs were downloaded from the GEO (GSE102286 and GSE101929) and TCGA databases. After data preprocessing, differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in cancer and normal tissues were selected and used to construct a DEM-DEG regulatory network and a protein-protein interaction (PPI) network. The genes and miRNAs in these networks were subjected to functional enrichment and survival analyses. Several key DEMs and DEGs were verified using RT-qPCR, and the results were statistically interpreted using a multivariate logistic regression analysis. In this study, 25 DEMs and 789 DEGs common to all datasets were identified, which were then used for the construction of a DEM-DEG regulatory network and a PPI network module. Survival analyses of 19 DEMs in the DEM-DEG regulatory network and 36 DEGs in the PPI network module revealed that 34 DEGs (including TOP2A, CCNB1, BIRC5, and TTK) and two miRNAs (miR-21-5p and miR-31-5p) were significantly associated with NSCLC prognosis. Moreover, RT-qPCR analysis identified three DEGs and five DEMs that had changes in expression consistent with those observed in the bioinformatic analysis. Finally, a multivariate logistic regression analysis of the data showed that TOP2A, CCNB1, BIRC5, miR-21-5p, miR-193b-3p, miR-210-3p and miR-31-5p could be combined for the diagnosis of NSCLC. In conclusion, TOP2A, CCNB1, BIRC5, miR-21-5p, miR-193b-3p, miR-210-3p and miR-31-5p may therefore serve as important biomarkers and diagnostic targets for NSCLC.
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Affiliation(s)
- Jie Zhang
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Dong Li
- Department of Ear‑Nose‑Throat, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Yueming Zhang
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Zongli Ding
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Yulong Zheng
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
| | - Song Chen
- Institute of Medicinal Biotechnology, Jiangsu College of Nursing, Huai'an, Jiangsu 223300, P.R. China
| | - Yufeng Wan
- Department of Respiratory Diseases, The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, Jiangsu 223002, P.R. China
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19
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Liu Z, Cheng X, Zhang L, Zhou J, Deng D, Ji J. A panel of DNA methylated markers predicts metastasis of pN 0M 0 gastric carcinoma: a prospective cohort study. Br J Cancer 2019; 121:529-536. [PMID: 31431673 PMCID: PMC6889426 DOI: 10.1038/s41416-019-0552-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The aim of this prospective study was to evaluate the feasibility of predicting GC metastasis using CDH1, GFRA1, P16 and ZNF382 DNA methylation as biomarkers. METHODS 198 GC patients without metastasis at the time of surgery resection were recruited into the double-blind cohort (NCT02159339). Gene methylation was analysed using MethyLight assays. GC metastasis and survival data were obtained from 178 patients with 94.7% compliance during follow-up. RESULTS Twenty six cases of metastasis and 5 cases of recurrence were observed in 178 cases (17.4%) during the follow-up (median, 62.7 months). The GC metastasis rate for GFRA1 methylation-positive patients was significantly reduced compared with GFRA1 methylation-negative patients (odds ratio [OR]: 0.23, 95% confidence interval [CI] 0.08-0.66). Similar results were also observed using ZNF382 methylation as a predictor (OR: 0.17, 95% CI 0.06-0.47). A risk score including methylation of GFRA1 and ZNF382 was generated. The metastasis rate was significantly increased in high-risk GC patients (OR: 4.71, 95% CI: 1.85-12.00). GC patients with high risk had a shorter overall survival, especially for patients with stage I GC (P = 0.024). CONCLUSIONS The combination of GFRA1 and ZNF382 methylation is a biomarker panel for the prediction of GC metastasis.
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Affiliation(s)
- Zhaojun Liu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Xiaojing Cheng
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Lianhai Zhang
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Jing Zhou
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China
| | - Dajun Deng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Division of Etiology, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China.
| | - Jiafu Ji
- Department of Gastrointestinal Surgery, Peking University Cancer Hospital and Institute, Fu-Cheng-Lu, No. 52, Haidian District, Beijing, 100142, China.
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20
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Li DF, Wang NN, Chang X, Wang SL, Wang LS, Yao J, Li ZS, Bai Y. Bioinformatics analysis suggests that COL4A1 may play an important role in gastric carcinoma recurrence. J Dig Dis 2019; 20:391-400. [PMID: 31069993 DOI: 10.1111/1751-2980.12758] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 04/25/2019] [Accepted: 05/06/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Cancer recurrence is a complicated problem for clinicians that contributes to poor prognosis. This study aimed to use advanced gastric carcinoma genes profiles to predict increased risk of cancer recurrence in order to identify patients in need of adjuvant therapy for prognosis improvement. METHODS Differentially expressed genes were identified for advanced gastric carcinoma by analyzing the GSE2685 from the Gene Expression Omnibus database (GEO) using R package. The candidate genes were then obtained by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, protein-protein interaction analysis and survival analysis. Logistic regression analysis was performed to determine the relationship between candidate genes and the recurrence of gastric carcinoma. RESULTS Collagen type IV alpha 1 (COL4A1) was overexpressed in gastric carcinoma tissue by analyzing the GSE2685 gene expression profiles from the Gene Expression Omnibus database. COL4A1 was also overexpressed in gastric carcinoma tissue from the Cancer Genome Atlas dataset and further determined that higher COL4A1 expression led to poorer overall survival. A univariate analysis suggested that COL4A1 was strongly correlated with T stage and gastric carcinoma recurrence (P = 0.014 and 0.041, respectively). Moreover, a multiple logistic regression analysis indicated that COL4A1 was significantly associated with gastric carcinoma recurrence (hazard ratio 1.605, 95% confidence interval 1.063-2.677, P = 0.008). CONCLUSIONS COL4A1 may promote gastric carcinoma recurrence and could be used as a therapeutic target for gastric carcinoma recurrence.
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Affiliation(s)
- De Feng Li
- Department of Gastroenterology, Second Clinical Medicine School (Shenzhen People's Hospital), Jinan University, Shenzhen, Guangdong Province, China.,Integrated Chinese and Western Medicine Postdoctoral Research Station, Jinan University, Guangzhou, Guangdong Province, China.,Department of Gastroenterology, First Affiliated Hospital of the University of South China, Hengyang, Hunan Province, China
| | - Nan Nan Wang
- Department of Gastroenterology, First Affiliated Hospital of the University of South China, Hengyang, Hunan Province, China
| | - Xin Chang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shu Ling Wang
- Department of Gastroenterology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Li Sheng Wang
- Department of Gastroenterology, Second Clinical Medicine School (Shenzhen People's Hospital), Jinan University, Shenzhen, Guangdong Province, China
| | - Jun Yao
- Department of Gastroenterology, Second Clinical Medicine School (Shenzhen People's Hospital), Jinan University, Shenzhen, Guangdong Province, China
| | - Zhao Shen Li
- Department of Gastroenterology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yu Bai
- Department of Gastroenterology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
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21
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Sarathi A, Palaniappan A. Novel significant stage-specific differentially expressed genes in hepatocellular carcinoma. BMC Cancer 2019; 19:663. [PMID: 31277598 PMCID: PMC6612102 DOI: 10.1186/s12885-019-5838-3] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 06/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Liver cancer is among top deadly cancers worldwide with a very poor prognosis, and the liver is a vulnerable site for metastases of other cancers. Early diagnosis is crucial for treatment of the predominant liver cancers, namely hepatocellular carcinoma (HCC). Here we developed a novel computational framework for the stage-specific analysis of HCC. METHODS Using publicly available clinical and RNA-Seq data of cancer samples and controls and the AJCC staging system, we performed a linear modelling analysis of gene expression across all stages and found significant genome-wide changes in the log fold-change of gene expression in cancer samples relative to control. To identify genes that were stage-specific controlling for confounding differential expression in other stages, we developed a set of six pairwise contrasts between the stages and enforced a p-value threshold (< 0.05) for each such contrast. Genes were specific for a stage if they passed all the significance filters for that stage. The monotonicity of gene expression with cancer progression was analyzed with a linear model using the cancer stage as a numeric variable. RESULTS Our analysis yielded two stage-I specific genes (CA9, WNT7B), two stage-II specific genes (APOBEC3B, FAM186A), ten stage-III specific genes including DLG5, PARI, NCAPG2, GNMT and XRCC2, and 35 stage-IV specific genes including GABRD, PGAM2, PECAM1 and CXCR2P1. Overexpression of DLG5 was found to be tumor-promoting contrary to the cancer literature on this gene. Further, GABRD was found to be signifincantly monotonically upregulated across stages. Our work has revealed 1977 genes with significant monotonic patterns of expression across cancer stages. NDUFA4L2, CRHBP and PIGU were top genes with monotonic changes of expression across cancer stages that could represent promising targets for therapy. Comparison with gene signatures from the BCLC staging system identified two genes, HSP90AB1 and ARHGAP42. Gene set enrichment analysis indicated overrepresented pathways specific to each stage, notably viral infection pathways in HCC initiation. CONCLUSIONS Our study identified novel significant stage-specific differentially expressed genes which could enhance our understanding of the molecular determinants of hepatocellular carcinoma progression. Our findings could serve as biomarkers that potentially underpin diagnosis as well as pinpoint therapeutic targets.
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Affiliation(s)
- Arjun Sarathi
- Department of Bioengineering, School of Chemical and BioTechnology, SASTRA deemed University, Thanjavur, Tamil Nadu 613401 India
| | - Ashok Palaniappan
- Department of Bioinformatics, School of Chemical and BioTechnology, SASTRA deemed University, Thanjavur, Tamil Nadu 613401 India
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22
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Shuto K, Mori M, Kosugi C, Narushima K, Nakabayashi S, Fujisiro T, Sato A, Hayano K, Shimizu H, Koda K. Hepatic blood flow by perfusion computed tomography as an imaging biomarker for patients with gastric cancer. Oncol Lett 2019; 17:3267-3276. [PMID: 30867759 PMCID: PMC6396202 DOI: 10.3892/ol.2019.9969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/17/2019] [Indexed: 11/19/2022] Open
Abstract
Perfusion computed tomography (PCT) is a less invasive imaging modality that provides information about tissue hemodynamics at the capillary level. The present study aimed to investigate the correlation between hepatic perfusion and gastric cancer progression. A total of 136 patients with gastric adenocarcinoma were evaluated in the present study. Prior to initial treatment, liver PCT was performed across the hepatic hilar plane and the hepatic blood flow (HBF) was measured using the dual-input deconvolution method. HBF was compared with clinicopathological factors, patient prognosis and circulating serum proangiogenic cytokines. The median HBF was 217 ml/min/100 g tissue. Patients with high HBF had larger tumors (43 mm vs. 71, P<0.001) and more advanced tumor-node stages (P<0.001 for both). When both patient groups of operable and inoperable were compared by their respective median HBF values, each high-HBF group had a significantly worse prognosis (P=0.002 and P=0.024), notably in the inoperable group, with <1-year survival. In 17 postoperative recurrent patients, the high-HBF at recurrence group also had a significantly worse postrecurrent prognosis (P=0.019). HBF was an independent prognostic factor (hazard ratio, 2.019; P=0.048) and was strongly associated with serum vascular endothelial growth factor level (R=0.607, P<0.001). HBF was significantly correlated with gastric cancer progression, and is an easily measured imaging biomarker reflecting patient survival.
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Affiliation(s)
- Kiyohiko Shuto
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
| | - Mikito Mori
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
| | - Chihiro Kosugi
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
| | - Kazuo Narushima
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
| | - Satoko Nakabayashi
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
| | - Takeshi Fujisiro
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Asami Sato
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Koichi Hayano
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Hiroaki Shimizu
- Department of Frontier Surgery, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Keiji Koda
- Department of Surgery, Teikyo University Chiba Medical Center, Ichihara, Chiba 299-0111, Japan
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23
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Li QW, Ma L, Qiu B, Yang H, Zhu YJ, Qiang MY, Liu SR, Chen NB, Guo JY, Cai LZ, Wang JY, Zhang X, Liu H. Differential expression profiles of long noncoding RNAs in synchronous multiple and solitary primary esophageal squamous cell carcinomas: A microarray analysis. J Cell Biochem 2019; 120:2439-2453. [PMID: 30324748 DOI: 10.1002/jcb.27536] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/07/2018] [Indexed: 01/24/2023]
Abstract
As a unique subtype of esophageal cancer, synchronous multiple primary esophageal squamous cell carcinomas (ESCCs) mostly occur in Asian patients with alcohol and/or tobacco abuse, or with a family history of cancer. Multiple ESCCs are associated with poor clinical outcomes. Growing evidence has addressed that long noncoding RNAs (lncRNAs) are involved in the carcinogenesis of various malignancies. We compared the lncRNA and messenger RNA (mRNA) profiles between solitary and multiple ESCC tissues through microarray analysis, aiming at studying their different mechanisms in tumor development. As a result, in multiple ESCCs, a total of 5257 lncRNAs and 3371 mRNAs were consistently differentially expressed compared with solitary ESCC, including 2986 upregulated and 2271 downregulated lncRNAs, and 2313 upregulated, and 1058 downregulated mRNAs. We validated the results in four differentially expressed lncRNAs using quantitative real-time polymerase chain reaction. There were 38 and 20 pathways significantly related to up- and downregulated transcripts. The pathways associated with mostly enriched up- and downregulated mRNAs were hsa01200 (carbon metabolism) and hsa05221 (acute myeloid leukemia- homo sapiens [human]). Gene ontology analysis suggested that upregulated and downregulated mRNAs were mainly enriched in bounding membrane of organelle involved in the cellular component and positive regulation of transport involved in the biological process. Further analysis identified 189 differentially expressed paired antisense lncRNAs and relative sense mRNA, as well as 2134 differentially expressed long intergenic noncoding RNAs and their adjacent mRNA pairs. In conclusion, the aberrantly expressed lncRNAs might play a role in the carcinogenesis of multiple ESCCs and could be candidates as diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Qi-Wen Li
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Li Ma
- Department of Radiation Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong, China
| | - Bo Qiu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hong Yang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yu-Jia Zhu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Meng-Yun Qiang
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Song-Ran Liu
- Department of Pathology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Nai-Bin Chen
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jin-Yu Guo
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ling-Zhi Cai
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Jun-Ye Wang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xu Zhang
- Department of Thoracic Surgery, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China
| | - Hui Liu
- Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China.,Lung Cancer Research Center, Sun Yat-sen University, Guangzhou, Guangdong, China
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24
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Peng L, Guo JC, Long L, Pan F, Zhao JM, Xu LY, Li EM. A Novel Clinical Six-Flavoprotein-Gene Signature Predicts Prognosis in Esophageal Squamous Cell Carcinoma. BIOMED RESEARCH INTERNATIONAL 2019; 2019:3869825. [PMID: 31815134 PMCID: PMC6878914 DOI: 10.1155/2019/3869825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 02/05/2023]
Abstract
Flavoproteins and their interacting proteins play important roles in mitochondrial electron transport, fatty acid degradation, and redox regulation. However, their clinical significance and function in esophageal squamous cell carcinoma (ESCC) are little known. Here, using survival analysis and machine learning, we mined 179 patient expression profiles with ESCC in GSE53625 from the Gene Expression Omnibus (GEO) database and constructed a signature consisting of two flavoprotein genes (GPD2 and PYROXD2) and four flavoprotein interacting protein genes (CTTN, GGH, SRC, and SYNJ2BP). Kaplan-Meier analysis revealed the signature was significantly associated with the survival of ESCC patients (mean survival time: 26.77 months in the high-risk group vs. 54.97 months in the low-risk group, P < 0.001, n = 179), and time-dependent ROC analysis demonstrated that the six-gene signature had good predictive ability for six-year survival for ESCC (AUC = 0.86, 95% CI: 0.81-0.90). We then validated its prediction performance in an independent set by RT-PCR (mean survival: 15.73 months in the high-risk group vs. 21.1 months in the low-risk group, P=0.032, n = 121). Furthermore, RNAi-mediated knockdown of genes in the flavoprotein signature led to decreased proliferation and migration of ESCC cells. Taken together, CTTN, GGH, GPD2, PYROXD2, SRC, and SYNJ2BP have an important clinical significance for prognosis of ESCC patients, suggesting they are efficient prognostic markers and potential targets for ESCC therapy.
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Affiliation(s)
- Liu Peng
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jin-Cheng Guo
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Lin Long
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Feng Pan
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Jian-Mei Zhao
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Institute of Oncologic Pathology, Shantou University Medical College, Shantou 515041, Guangdong, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, Guangdong, China
- Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou 515041, Guangdong, China
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25
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Liu X, Wu J, Zhang D, Bing Z, Tian J, Ni M, Zhang X, Meng Z, Liu S. Identification of Potential Key Genes Associated With the Pathogenesis and Prognosis of Gastric Cancer Based on Integrated Bioinformatics Analysis. Front Genet 2018; 9:265. [PMID: 30065754 PMCID: PMC6056647 DOI: 10.3389/fgene.2018.00265] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/02/2018] [Indexed: 12/23/2022] Open
Abstract
Background and Objective: Despite striking advances in multimodality management, gastric cancer (GC) remains the third cause of cancer mortality globally and identifying novel diagnostic and prognostic biomarkers is urgently demanded. The study aimed to identify potential key genes associated with the pathogenesis and prognosis of GC. Methods: Differentially expressed genes between GC and normal gastric tissue samples were screened by an integrated analysis of multiple gene expression profile datasets. Key genes related to the pathogenesis and prognosis of GC were identified by employing protein–protein interaction network and Cox proportional hazards model analyses. Results: We identified nine hub genes (TOP2A, COL1A1, COL1A2, NDC80, COL3A1, CDKN3, CEP55, TPX2, and TIMP1) which might be tightly correlated with the pathogenesis of GC. A prognostic gene signature consisted of CST2, AADAC, SERPINE1, COL8A1, SMPD3, ASPN, ITGBL1, MAP7D2, and PLEKHS1 was constructed with a good performance in predicting overall survivals. Conclusion: The findings of this study would provide some directive significance for further investigating the diagnostic and prognostic biomarkers to facilitate the molecular targeting therapy of GC.
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Affiliation(s)
- Xinkui Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Jiarui Wu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Dan Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Zhitong Bing
- Evidence Based Medicine Center, School of Basic Medical Science, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China.,Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Jinhui Tian
- Evidence Based Medicine Center, School of Basic Medical Science, Lanzhou University, Lanzhou, China.,Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, Lanzhou, China
| | - Mengwei Ni
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Xiaomeng Zhang
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Ziqi Meng
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
| | - Shuyu Liu
- Department of Clinical Chinese Pharmacy, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing, China
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26
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Zhang R, Xu J, Zhao J, Bai JH. Proliferation and invasion of colon cancer cells are suppressed by knockdown of TOP2A. J Cell Biochem 2018; 119:7256-7263. [PMID: 29761838 DOI: 10.1002/jcb.26916] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 04/04/2018] [Indexed: 12/23/2022]
Abstract
Recent research has shown that TOP2A plays an important role in the tumorigenesis of many malignancies, such as breast cancer, ovarian cancer, and prostate cancer. However, few studies have been conducted on TOP2A expression and functions in colon cancer. In the present study, we found that TOP2A expression was obviously elevated in colon cancer tissues compared to adjacent non-cancerous tissues. Depletion of TOP2A in HCT116 and SW480 colon cancer cells by transfection of specific small interfering RNA significantly suppressed proliferation and inhibited invasion of cells, even induced apoptosis as indicated by both MTT assay, Annexin V/propidium iodide staining, and Transwell assay. Furthermore, we explored the underlying mechanisms. Knockdown of TOP2A not only affects the expression of cell apoptosis-related (Bcl-2 and Bax) and invasion-related proteins (MMP-2 and MMP-9), but also reduced the phosphorylation levels of ERK and AKT. In conclusion, we showed that TOP2A was upregulated in colon cancer tissue samples and that TOP2A may serve as an oncogene in colon cancer.
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Affiliation(s)
- Rui Zhang
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning Province, P.R. China
| | - Jian Xu
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning Province, P.R. China
| | - Jian Zhao
- Department of Colorectal Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning Province, P.R. China
| | - Jing H Bai
- Department of Internal Medicine, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Insititute, Shenyang, Liaoning Province, P.R. China
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