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Zhang S, Jiang Y, Shi L, Wei T, Lai Z, Feng X, Li S, Tang D. Identification and analysis of key genes related to efferocytosis in colorectal cancer. BMC Med Genomics 2024; 17:198. [PMID: 39107816 PMCID: PMC11304617 DOI: 10.1186/s12920-024-01967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
The impact of efferocytosis-related genes (ERGs) on the diagnosis of colorectal cancer (CRC) remains unclear. In this study, efferocytosis-associated biomarkers for the diagnosis of CRC were identified by integrating data from transcriptome sequencing and public databases. Finally, the expression of biomarkers was validated by real-time quantitative polymerase chain reaction (RT-qPCR). Our study may provide a reference for CRC diagnosis. BACKGROUND It has been shown that some efferocytosis related genes (ERGs) are associated with the development of cancer. However, it is still uncertain how ERGs may influence the diagnosis of colorectal cancer (CRC). METHODS In our study, the CRC cohorts were gained from transcriptome sequencing and the gene expression omnibus (GEO) database (GSE71187). Efferocytosis related biomarkers with diagnostic utility for CRC were identified through combining differentially expressed analysis, machine learning algorithms, and receiver operating characteristic (ROC) analysis. Then, infiltration abundance of immune cells between CRC and control was evaluated. The regulatory networks (including mRNA-miRNA-lncRNA and miRNA/transcription factors (TF)-mRNA networks) were created. Finally, the expression of biomarkers was validated via real-time quantitative polymerase chain reaction (RT-qPCR). RESULTS There were 3 biomarkers (ELMO3, P2RY12, and PDK4) related diagnosis for CRC patients gained. ELMO3 was highly expressed in CRC group, while P2RY12 and PDK4 was lowly expressed. Besides, the infiltrating abundance of 3 immune cells between CRC and control groups was significantly differential, namely activated CD4 memory T cells, macrophages M0, and resting mast cells. We then constructed a mRNA-miRNA-lncRNA network containing 3 mRNAs, 33 miRNAs, and 22 lncRNAs, and a miRNA/TF-mRNA network including 3 mRNAs, 33 miRNAs, and 7 TFs. Additionally, RT-qPCR results revealed that the expression trends of all biomarkers were consistent with the transcriptome sequencing data and GSE71187. CONCLUSION Taken together, this study provides three efferocytosis related biomarkers (ELMO3, P2RY12, and PDK4) for diagnosis of CRC, providing a scientific reference for further studies of CRC.
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Affiliation(s)
- Shengliang Zhang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Ying Jiang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Lei Shi
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Tianning Wei
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Zhiwen Lai
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Xuan Feng
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Shiyuan Li
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China
| | - Detao Tang
- Department of Gastrointestinal and Breast Surgery, Guizhou University of Traditional Chinese Medicine, The First Affiliated Hospital of Guizhou University of Traditional Chinese Medicine of China, Guizhou, China.
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Sun Z, Wang H, Xu Y, Liu Y, Wang L, Zhou R, Zhou R, Ma W, Zhang T. High expression of NXPH4 correlates with poor prognosis, metabolic reprogramming, and immune infiltration in colon adenocarcinoma. J Gastrointest Oncol 2024; 15:641-667. [PMID: 38756632 PMCID: PMC11094489 DOI: 10.21037/jgo-23-956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/15/2024] [Indexed: 05/18/2024] Open
Abstract
Background Colon adenocarcinoma (COAD) is a prevalent gastrointestinal malignant disease with high mortality rate, and identification of novel prognostic biomarkers and therapeutic targets is urgently needed. Although neurexophilin 4 (NXPH4) has been investigated in several tumors, its role in COAD remains unclear. The aim of this study was to explore the prognostic value and potential functions of NXPH4 in COAD. Methods The expression of NXPH4 in COAD were analyzed using The Cancer Genome Atlas (TCGA) and datasets from the Gene Expression Omnibus (GEO) database. The prognostic value of NXPH4 was determined using Kaplan-Meier analysis and Cox regression analysis. To investigate the possible mechanism underlying the role of NXPH4 in COAD, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and gene set enrichment analysis (GSEA) were employed. The correlation between NXPH4 expression and immune cell infiltration levels was examined thorough single-sample gene set enrichment analysis (ssGSEA). Furthermore, the competing endogenous RNA (ceRNA) regulatory network that may be involved in NXPH4 in COAD was predicted and constructed through a variety of databases. Results NXPH4 expression was significantly higher in COAD tissue compared with normal colon tissues. Meanwhile, high expression of NXPH4 was associated with poor prognosis in COAD patients. GO-KEGG and GSEA analyses indicated that NXPH4 was associated with glycolysis and hypoxia pathway, and may promote COAD progression and metastasis by modulating metabolic reprogramming. ssGSEA analysis demonstrated that NXPH4 expression also associated with immune infiltration. Furthermore, we identified various microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) as upstream regulators of NXPH4 in COAD. Conclusions The present study revealed that high expression of NXPH4 is associated with tumor progression, metabolic reprogramming, and immune infiltration. These findings suggest that NXPH4 could serve as a reliable prognostic biomarker and a promising therapeutic target in COAD.
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Affiliation(s)
- Zhe Sun
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Haodi Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Yao Xu
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Yichi Liu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Lu Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
| | - Ruijie Zhou
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Runlong Zhou
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Wenjian Ma
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Qilu Institute of Technology, Jinan, China
| | - Tongcun Zhang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin, China
- Institute of Biology and Medicine, College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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Li G, Huang J, Chen S, He Y, Wang Z, Peng J. High Expression of ATP6V1C2 Predicts Unfavorable Overall Survival in Patients With Colon Adenocarcinoma. Front Genet 2022; 13:930876. [PMID: 36212133 PMCID: PMC9532742 DOI: 10.3389/fgene.2022.930876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 06/21/2022] [Indexed: 12/05/2022] Open
Abstract
Aims: Colon adenocarcinoma (COAD) is responsible for 90% of all colorectal cancer cases and is one of the most common causes of cancer-related deaths worldwide. ATP6V1s (cytosolic V1 domain of vacuolar adenosine triphosphatase) participate in the biological process of transporting hydrogen ions and are implicated in tumor growth and metastasis. ATP6V1C2 as a family member has been documented to associate with esophageal carcinoma and renal clear cell carcinoma, while its roles in COAD remain elusive. Methods: The expression status, potential molecular mechanism, and prognostic value of ATP6V1C2 in COAD were investigated using The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. In addition, its biological roles in COAD were explored through in vitro studies. Results: ATP6V1C2 showed a significantly higher expression level in COAD compared with matched non-cancerous tissues. High expression of ATP6V1C2 predicted a shorter overall survival both in TCGA and GEO COAD datasets, and ATP6V1C2 was identified as an independent factor associated with overall survival in COAD. Bioinformatic analyses showed that high expression of ATP6V1C2 was associated with high epithelial–mesenchymal transition (EMT) score and Wnt signaling pathway was significantly enriched from differentially expressed genes between ATP6V1C2-high and -low group. We also found that high expression of ATP6V1C2 could decrease pathway activity of CD8 T effector implicated in tumor microenvironment (TME). In vitro study revealed that ATP6V1C2 knockdown resulted in aberrant expression of Wnt- and EMT-related genes and inhibited COAD cell proliferation and growth. Conclusion: This is the first study to reveal the molecular functions of ATP6V1C2 in COAD. Our study suggests that overexpressed ATP6V1C2 might promote EMT by activating Wnt signaling pathway, resulting in cancer metastasis and poor prognosis. This study paves the way for understanding potential molecular mechanisms and therapeutic perspectives in COAD.
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Affiliation(s)
- Guanghua Li
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Jiahua Huang
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Sile Chen
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
| | - Yulong He
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
- Digestive Medical Center, Sun Yat-sen University Seventh Affiliated Hospital, Shenzhen, China
- *Correspondence: Yulong He, ; Zhixiong Wang, ; Jianjun Peng,
| | - Zhixiong Wang
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
- *Correspondence: Yulong He, ; Zhixiong Wang, ; Jianjun Peng,
| | - Jianjun Peng
- Gastrointestinal Surgery Center, Sun Yat-sen University First Affiliated Hospital, Guangzhou, China
- *Correspondence: Yulong He, ; Zhixiong Wang, ; Jianjun Peng,
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Construction of a Novel MYC-Associated ceRNA Regulatory Network to Identify Prognostic Biomarkers in Colon Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3216285. [PMID: 35847359 PMCID: PMC9277212 DOI: 10.1155/2022/3216285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Colorectal cancer (CRC) includes colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ). Competitive endogenous RNA (ceRNA) is crucial for cancer pathogenesis. Abnormal expression of MYC is generally associated with a poor colon adenocarcinoma prognosis. The present study aimed to identify a novel MYC-associated ceRNA regulatory network and identify potential prognostic markers associated with COAD. We obtained the transcriptome sequencing profiles of 462 COAD cases from the TCGA database and analyzed differentially expressed genes (DEGs) in MYC high expression (MYChigh) and MYC low expression (Myclow) tumors. We identified an important lncRNA, LINC00114, which effectively predicts overall survival and plays a protective role in COAD. Moreover, the LINC00114/miR-216a-5p axis was identified as a clinical prognostic model. The predicted target genes of the LINC00114/miR-216a-5p axis include uromodulin Like 1 (UMODL1) and oncoprotein induced transcript 3 (OIT3), which are closely related to the survival and prognosis of COAD patients. In summary, we constructed a novel ceRNA regulatory network and identified potential biomarkers for the targeted therapy and prognosis of COAD.
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Combined Efficacy of CXCL5, STC2, and CHI3L1 in the Diagnosis of Colorectal Cancer. JOURNAL OF ONCOLOGY 2022; 2022:7271514. [PMID: 35646113 PMCID: PMC9142324 DOI: 10.1155/2022/7271514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 12/23/2022]
Abstract
Objective To improve the diagnostic capacity of serum biomarkers for colorectal cancer (CRC), we introduced three novel indicators, namely, the C-X-C motif chemokine ligand 5 (CXCL5), stanniocalcin 2 (STC2), and chitinase 3 like 1 (CHI3L1) and assessed their performances in the detection of CRC. Methods A total of 887 serum samples (153 health, 342 polyps, and 392 CRCs) were collected. Concentrations of CXCL5, STC2, and CHI3L1 were measured by the ELISA. CEA and CA199 were determined by electrochemiluminescence. Binary logistic regression was used to build the combination model. ROC analysis was used to evaluate the performance of biomarkers alone or in combination. Results Model_2 that based on CXCL5, STC2, and CHI3L1 was the best approach in discriminating CRC from non-CRC controls (AUC, 0.943 (0.922–0.960); sensitivity, 0.848; specificity, 0.917; and accuracy, 0.887 in the training cohort and 0.959 (95% CI 0.927–0.980), 0.878, 0.917, and 0.900 in the testing cohort, respectively). In the detection of early CRC, Model_2 revealed AUC, sensitivity, specificity, and accuracy of 0.925 (0.897–0.947), 0.793, 0.917, and 0.886 in the training cohort and those of 0.926 (0.979–0.959), 0.786, 0.931, and 0.898 in the testing cohort. Furthermore, Model_2 exhibited an excellent diagnostic performance in CEA-negative cases (0.938 (0.913–0.957), 0.826, 0.917, and 0.888 in the training cohort and 0.961 (0.925–0.983), 0.887, 0.931, and 0.918 in the testing cohort). As used alone, STC2 achieved the capacities that is second only to that of Model_2 (0.866 (0.837–0.892), 0.859, 0.842, and 0.853 in the training cohort and 0.887 (0.842–0.923), 0.922, 0.799, and 0.853 in the testing cohort). STC2 alone also yielded acceptable results for early CRC detection (0.815 (0.776–0.849), 0.767, 0.849, and 0.829 in the training cohort and 0.870 (0.812–0.914), 0.952, 0.799, and 0.833 in the testing cohort). Moreover, STC2 maintained diagnostic accuracy for CRC patients with negative CEA (0.874 (0.842–0.901), 0.862, 0.849, and 0.853 in the training cohort and 0.898 (0.848–0.936), 0.930, 0.801, and 0.842 in the testing cohort). In comparison, the performances of the CEA and CA199 based Model_1 were far from satisfactory, especially in early cases (0.767 (0.726–0.805), 0.491, 0.863, and 0.771 in the training cohort and 0.817 (0.754–0.870), 0.476, 0.889, and 0.796 in the testing cohort). Conclusions STC2 was a promising serum biomarker for CRC diagnosis either used alone or in combination with CXCL5 and CHI3L1.
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Lacalamita A, Piccinno E, Scalavino V, Bellotti R, Giannelli G, Serino G. A Gene-Based Machine Learning Classifier Associated to the Colorectal Adenoma-Carcinoma Sequence. Biomedicines 2021; 9:biomedicines9121937. [PMID: 34944753 PMCID: PMC8698794 DOI: 10.3390/biomedicines9121937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Colorectal cancer (CRC) carcinogenesis is generally the result of the sequential mutation and deletion of various genes; this is known as the normal mucosa–adenoma–carcinoma sequence. The aim of this study was to develop a predictor-classifier during the “adenoma-carcinoma” sequence using microarray gene expression profiles of primary CRC, adenoma, and normal colon epithelial tissues. Four gene expression profiles from the Gene Expression Omnibus database, containing 465 samples (105 normal, 155 adenoma, and 205 CRC), were preprocessed to identify differentially expressed genes (DEGs) between adenoma tissue and primary CRC. The feature selection procedure, using the sequential Boruta algorithm and Stepwise Regression, determined 56 highly important genes. K-Means methods showed that, using the selected 56 DEGs, the three groups were clearly separate. The classification was performed with machine learning algorithms such as Linear Model (LM), Random Forest (RF), k-Nearest Neighbors (k-NN), and Artificial Neural Network (ANN). The best classification method in terms of accuracy (88.06 ± 0.70) and AUC (92.04 ± 0.47) was k-NN. To confirm the relevance of the predictive models, we applied the four models on a validation cohort: the k-NN model remained the best model in terms of performance, with 91.11% accuracy. Among the 56 DEGs, we identified 17 genes with an ascending or descending trend through the normal mucosa–adenoma–carcinoma sequence. Moreover, using the survival information of the TCGA database, we selected six DEGs related to patient prognosis (SCARA5, PKIB, CWH43, TEX11, METTL7A, and VEGFA). The six-gene-based classifier described in the current study could be used as a potential biomarker for the early diagnosis of CRC.
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Affiliation(s)
- Antonio Lacalamita
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Emanuele Piccinno
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Viviana Scalavino
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Roberto Bellotti
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy;
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Gianluigi Giannelli
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Grazia Serino
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
- Correspondence:
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Bourdakou MM, Spyrou GM, Kolios G. Colon Cancer Progression Is Reflected to Monotonic Differentiation in Gene Expression and Pathway Deregulation Facilitating Stage-specific Drug Repurposing. Cancer Genomics Proteomics 2021; 18:757-769. [PMID: 34697067 DOI: 10.21873/cgp.20295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Colon cancer is one of the most common cancer types and the second leading cause of death due to cancer. Many efforts have been performed towards the investigation of molecular alterations during colon cancer progression. However, the identification of stage-specific molecular markers remains a challenge. The aim of this study was to develop a novel computational methodology for the analysis of alterations in differential gene expression and pathway deregulation across colon cancer stages in order to reveal stage-specific biomarkers and reinforce drug repurposing investigation. MATERIALS AND METHODS Transcriptomic datasets of colon cancer were used to identify (a) differentially expressed genes with monotonicity in their fold changes (MEGs) and (b) perturbed pathways with ascending monotonic enrichment (MEPs) related to the number of the participating differentially expressed genes (DEGs), across the four colon cancer stages. Through an in silico drug repurposing pipeline we identified drugs that regulate the expression of MEGs and also target the resulting MEPs. RESULTS Our methodology highlighted 15 MEGs and 32 candidate repurposed drugs that affect their expression. We also found 51 MEPs divided into two groups according to their rate of DEG content alteration across colon cancer stages. Focusing on the target MEPs of the highlighted repurposed drugs, we found that one of them, the neuroactive ligand-receptor interaction, was targeted by the majority of the candidate drugs. Moreover, we observed that two of the drugs (PIK-75 and troglitazone) target the majority of the resulting MEPs. CONCLUSION These findings highlight significant genes and pathways that can be used as stage-specific biomarkers and facilitate the discovery of new potential repurposed drugs for colon cancer. We expect that the computational methodology presented can be applied in a similar way to the analysis of any progressive disease.
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Affiliation(s)
- Marilena M Bourdakou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George M Spyrou
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece;
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Acharjee A, Agarwal P, Nash K, Bano S, Rahman T, Gkoutos GV. Immune infiltration and prognostic and diagnostic use of LGALS4 in colon adenocarcinoma and bladder urothelial carcinoma. Am J Transl Res 2021; 13:11353-11363. [PMID: 34786063 PMCID: PMC8581917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 06/03/2021] [Indexed: 06/13/2023]
Abstract
Colon adenocarcinoma (COAD) is a common tumor of the gastrointestinal tract with a high mortality rate. Current research has identified many genes associated with immune infiltration that play a vital role in the development of COAD. In this study, we analysed the prognostic and diagnostic features of such immune-related genes in the context of colonic adenocarcinoma (COAD). We analysed 17 overlapping gene expression profiles of COAD and healthy samples obtained from TCGA-COAD and public single-cell sequencing resources, to identify potential therapeutic COAD targets. We evaluated the abundance of immune infiltration with those genes using the TIMER (Tumor Immune Estimation Resource) deconvolution method. Subsequently, we developed predictive and survival models to assess the prognostic value of these genes. The LGALS4 (Galectin-4) gene was found to be significantly (P<0.05) downregulated in COAD and bladder urothelial carcinoma (BLCA) compared to healthy samples. We identified LGALS4 as a prognostic and diagnostic marker for multiple cancer types, including COAD and BLCA. Our analysis reveals a series of novel candidate drug targets, as well as candidate molecular markers, that may explain the pathogenesis of COAD and BLCA. LGALS4 gene is associated with multiple cancer types and is a possible prognostic, as well as diagnostic, marker of COAD and BLCA.
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Affiliation(s)
- Animesh Acharjee
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of BirminghamB15 2TT, UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation TrustB15 2TT, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital BirminghamBirmingham, B15 2WB, UK
| | - Prasoon Agarwal
- KTH Royal Institute of Technology, School of Electrical Engineering and Computer ScienceStockholm, Sweden
- Science for Life LaboratorySolna, Sweden
| | - Katrina Nash
- College of Medical and Dental Sciences, University of BirminghamBirmingham, B15 2TT, UK
| | - Subia Bano
- Elvesys Microfluidic Innovation CentreParis 75011, France
| | - Taufiq Rahman
- Department of Pharmacology, Tennis Court Road, University of CambridgeCambridge, CB2 1PD
| | - Georgios V Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, University of BirminghamB15 2TT, UK
- Institute of Translational Medicine, University Hospitals Birmingham NHS, Foundation TrustB15 2TT, UK
- NIHR Surgical Reconstruction and Microbiology Research Centre, University Hospital BirminghamBirmingham, B15 2WB, UK
- MRC Health Data Research UK (HDR UK)
- NIHR Experimental Cancer Medicine CentreBirmingham, B15 2TT, UK
- NIHR Biomedical Research Centre, University Hospital BirminghamBirmingham, B15 2TT, UK
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Ahluwalia P, Kolhe R, Gahlay GK. The clinical relevance of gene expression based prognostic signatures in colorectal cancer. Biochim Biophys Acta Rev Cancer 2021; 1875:188513. [PMID: 33493614 DOI: 10.1016/j.bbcan.2021.188513] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer (CRC) is one of the most prevalent cancers, with more than one million new cases every year. In the last few decades, several advancements in therapeutic and preventative levels have reduced the mortality rate, but new biomarkers are required for improved prognosis. The alterations at the genetic and epigenetic level have been recognized as major players in tumorigenesis. The products of gene expression in the form of mRNA, microRNA, and long-noncoding RNA, have started to emerge as important regulatory molecules, playing an important role in cancer. Gene-expression based prognostic risk scores, which quantify and compare their expression, have emerged as promising biomarkers with enormous clinical value. These composite multi-gene models in which more than one gene is used to predict prognosis have been shown to be significantly effective in identifying patients with multiple clinico-pathological risks like overall mortality, response to chemotherapy, risk of metastasis, etc. The advent of microarray and advanced sequencing technologies have led to the generation of large datasets like TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus), which have fueled the search for new biomarkers. Continuous evaluation of these candidate biomarkers in clinical settings is promising to improve the management of CRC. These composite gene signatures provide potential in identifying high-risk patients, which might help clinicians to better manage these patients and design appropriate personalized therapeutic interventions. In this review, we emphasize on composite prognostic scores from diverse resources with clinical utility in CRC.
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Affiliation(s)
- Pankaj Ahluwalia
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India; Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Gagandeep K Gahlay
- Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, India.
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Zhang B, Wang Y, Li H, Feng L, Li W, Cheng S. Identification of Prognostic Biomarkers for Multiple Solid Tumors Using a Human Villi Development Model. Front Cell Dev Biol 2020; 8:492. [PMID: 32656211 PMCID: PMC7325693 DOI: 10.3389/fcell.2020.00492] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/25/2020] [Indexed: 01/03/2023] Open
Abstract
The processes of embryonic development that rely on epithelial-mesenchymal transition (EMT) for the implantation of trophoblast cells are co-opted by tumors, reflecting their inherent uncontrolled characteristics and leading to invasion and metastasis. Although tumorigenesis and embryogenesis have similar EMT characteristics, trophoblasts have been shown to exhibit "physiological metastasis" or be "pseudo-malignant," resulting in different outcomes. The gene co-expression network is the basis of embryonic development and tumorigenesis. We hypothesize that if the gene co-expression network in tumors is "off-track" from that in villi, it is more likely to develop into malignant tumors and have a worse prognosis, and we proposed the "off-track theory" for the first time. In this study, we examined gene co-expression networks in villi and multiple solid tumors. Through network functional enrichment analyses, we found that most tumors and villi exhibited a significantly enriched EMT, but the genes that performed this function were not identical. Then, we identified the "off-track genes" in the EMT-related gene interaction network using the "off-track theory," and through survival analysis, we discovered that the risk score of "off-track genes" was associated with poor survival of cancer patients. Our study indicated that villi development is a reliable and strictly regulated model that can illuminate the trajectory of human cancer development and that the gene co-expression networks in tumor development are "off-track" from those in villi. These "off-track genes" may have a substantial impact on tumor development and could reveal novel prognostic biomarkers.
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Affiliation(s)
- Botao Zhang
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China.,State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanjing Wang
- Department of Gynecological Oncology, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | - Hongxia Li
- Department of Obstetrics and Gynecology, Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wenbin Li
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Wu Y, Zhang S, Yan J. IRF1 association with tumor immune microenvironment and use as a diagnostic biomarker for colorectal cancer recurrence. Oncol Lett 2020; 19:1759-1770. [PMID: 32194669 PMCID: PMC7039159 DOI: 10.3892/ol.2020.11289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 11/27/2019] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer (CRC) is considered to be one of the most lethal cancer types globally, and its recurrence is a major treatment challenge. Identifying the factors involved when determining the risk of CRC recurrence is required to improve personalized therapy for patients with CRC. Based on the GSE39582 dataset, the present study demonstrated that a higher ratio of M1 macrophages and activated memory CD4+ T cells indicated a better recurrence-free survival (RFS) time for CRC, using CIBERSORT and Pearson's correlation analysis. Through weighted correlation network analysis (WGCNA), an immune-associated module was identified that was significantly positively correlated with the ratio of M1 macrophages and activated memory CD4+ T cells. In this module, using WGCNA and a protein-protein interaction network, interferon regulatory factor 1 (IRF1), chemokine ligand 5, ubiquitin/ISG15-conjugating enzyme E2 L6, guanylate binding protein 1 and interleukin 2 receptor subunit beta were identified as hub genes. Among these genes, univariate Cox and multivariate Cox analysis revealed that IRF1 may be a potential diagnostic biomarker for RFS in patients with CRC. This was further validated using The Cancer Genome Atlas data. Gene set enrichment analysis demonstrated that IRF1 influenced the genes and pathways that are associated with immune cell recruitment and activation. Additionally, the DNA methylation of cg27587780 and cg15375424 CpG sites in the IRF1 gene region was indicated to be negatively correlated with IRF1 mRNA expression and positively correlated with the recurrence of CRC. Collectively, the results of the present study demonstrated that IRF1 may be a potential diagnostic biomarker for RFS in patients with CRC.
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Affiliation(s)
- Yanfang Wu
- Department of Gastroenterology, The Fourth People's Hospital of Shaanxi, Xi'an, Shanxi 710032, P.R. China
| | - Shuju Zhang
- Hunan Children's Research Institute, Hunan Children's Hospital, University of South China, Changsha, Hunan 410007, P.R. China
| | - Jun Yan
- Center of Hepatobiliary Pancreatic Disease, Beijing Tsinghua Changgung Hospital, Beijing 102218, P.R. China
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12
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Chen J, Chen QL, Wang WH, Chen XL, Hu XQ, Liang ZQ, Cao YB, Cao YM, Su SB. Prognostic and predictive values of CXCL10 in colorectal cancer. Clin Transl Oncol 2020; 22:1548-1564. [PMID: 32016676 DOI: 10.1007/s12094-020-02299-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 01/09/2020] [Indexed: 01/05/2023]
Abstract
BACKGROUND The role of CXCL10 in progression and prognosis of colorectal cancer (CRC) has been studied for years, yet results remain controversial. AIM This study aims to explore the relationship between CXCL10 and CRC progression and prognosis. METHODS We evaluated plasma CXCL10 in CRC patients using ELISA. We also performed a meta-analysis of the associations between CXCL10 and overall survival (OS), disease-free survival (DFS), disease-specific survival (DSS), relapse-free survival (RFS), and clinicopathological features. Finally, correlations between CXCL10 and methylation or immune infiltration were performed using TCGA data. RESULTS ELISA analysis showed that CXCL10 was associated with age, red blood cells, blood platelets, and blood urea nitrogen. A separate analysis of 3,763 patients from 24 studies revealed that there were significant associations between low CXCL10 expression and OS (HR 1.25, 95% CI 1.01-1.53), DFS (HR 1.65, 95% CI 1.17-2.34), and RFS (HR 1.43, 95% CI 1.20-1.71) in CRC. Additionally, downregulated CXCL10 expression was significantly correlated with age [odds ratio (OR) 1.31, 95% CI 1.13-1.52], metastasis (OR 1.34, 95% CI 1.11-1.63), recurrence (OR 1.46, 95% CI 1.16-1.83), tumor location (OR 1.88, 95% CI 1.58-2.24), differentiation (OR 0.57, 95% CI 0.35-0.93), microsatellite instability (OR 0.23, 95% CI 0.15-0.35), BRAF mutation (OR 1.62, 95% CI 1.25-2.08), p53 mutation (OR 0.28, 95% CI 0.16-0.47), and CIMP (OR 0.27, 95% CI 0.17-0.43). Furthermore, significant associations were observed between CXCL10 and methylation and immune infiltration. CONCLUSIONS The study suggests that CXCL10 might be a potential target for the treatment of CRC. TRIAL REGISTRATION NCT03189992. Registered 4 June 2017, https://www.clinicaltrials.gov/ct2/show/study/NCT03189992?term=NCT03189992&rank=1 .
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Affiliation(s)
- J Chen
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China.,Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.,Shanghai TCM-Integrated Institute of Vascular Anomalies, Shanghai, 200082, China.,Institute of Vascular Anomalies, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Q-L Chen
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - W-H Wang
- Department of Medical Oncology, Shuguang Hospital Affiliated Baoshan Branch, Shanghai University of Traditional Chinese Medicine, Shanghai, 201901, China
| | - X-L Chen
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - X-Q Hu
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.,Department of Medical Oncology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Z-Q Liang
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Y-B Cao
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China.,Shanghai TCM-Integrated Institute of Vascular Anomalies, Shanghai, 200082, China.,Institute of Vascular Anomalies, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 200082, China
| | - Y-M Cao
- Shanghai TCM-Integrated Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200082, China.,Shanghai TCM-Integrated Institute of Vascular Anomalies, Shanghai, 200082, China.,Institute of Vascular Anomalies, Shanghai Academy of Traditional Chinese Medicine, Shanghai, 200082, China
| | - S-B Su
- Research Center for Traditional Chinese Medicine Complexity System, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
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13
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Liu Q, Deng J, Wei X, Yuan W, Ma J. Integrated analysis of competing endogenous RNA networks revealing five prognostic biomarkers associated with colorectal cancer. J Cell Biochem 2019; 120:11256-11264. [PMID: 30756409 DOI: 10.1002/jcb.28403] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 11/29/2018] [Accepted: 12/06/2018] [Indexed: 01/24/2023]
Abstract
Colorectal cancer (CRC) is a common malignant tumor with high morbidity and mortality around the world. The aim of this study was to determine the genes significantly associated with the overall survival (OS) of CRC patients and predict their function in the competing endogenous RNA (ceRNA) regulation networks. We constructed the lncRNA-miRNA-mRNA networks according to the differentially expressed RNAs from the The Cancer Genome Atlas data sets of 561 CRC patients. Twelve differentially expressed messenger RNAs from the ceRNA networks were selected through a univariate Cox proportional hazards regression. Then, these genes were analyzed by using multivariate Cox proportional hazards stepwise regression to construct a prognostic model in which five genes (tensin 1, clusterin, proteolipid protein 1, epiregulin, and transcription factor Spi-B) were included. The Kaplan-Meier risk survival analysis showed that this five-gene signature independently predicted a 5-year overall survival in CRC patients (P < 0.001). Furthermore, significance was verified according to two irrelevant Gene Expression Omnibus (GEO) data sets (GSE38832 and GSE39582). The verified five-gene model of CRC can be used to predict patient prognosis and will inform postoperational evaluation and follow-up strategies.
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Affiliation(s)
- Qian Liu
- Department of Colorectal Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Junjie Deng
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xundong Wei
- Department of Biotherapy, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Wei Yuan
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jie Ma
- Department of Biotherapy, Beijing Hospital, National Center of Gerontology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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14
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An N, Zhao C, Yu Z, Yang X. Identification of prognostic genes in colorectal cancer through transcription profiling of multi-stage carcinogenesis. Oncol Lett 2018; 17:432-441. [PMID: 30655784 DOI: 10.3892/ol.2018.9632] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 07/09/2018] [Indexed: 01/02/2023] Open
Abstract
Colorectal cancer is a complex multistage process following the adenoma-carcinoma sequence. Additional research on the basis of molecular dysregulations, particularly in the precancerous stage, may provide insight into the realization of potential biomarkers and therapeutic targets for the disease. In the present study, the expression profile of human multistage colorectal mucosa tissues, including healthy, adenoma and adenocarcinoma samples, was downloaded. Genes that were consistently differentially expressed in precancerous tissues and cancer samples were collected. Based on a merged biological network, the biggest connected component composed of these identified genes and their one-step neighbors were retrieved to conduct random walk with restart algorithm, in order to identify genes significantly affected during carcinogenesis. Therefore, 35 genes significantly affected by carcinogenic dysregulation were successfully identified. Survival and Cox analysis indicated that the expression of these genes was an independent prognostic factor confirmed by six cohorts. In summary, based on the transcription profile of multi-stage carcinogenesis and bioinformatics analysis, 35 genes significantly associated with patient survival were successfully identified, which may serve as promising therapeutic targets for the disease.
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Affiliation(s)
- Ning An
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Chen Zhao
- Department of Anatomy, School of Basic Medicine, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Zhuang Yu
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
| | - Xue Yang
- Department of Oncology, Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, P.R. China
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15
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Huang Z, Yang Q, Huang Z. Identification of Critical Genes and Five Prognostic Biomarkers Associated with Colorectal Cancer. Med Sci Monit 2018; 24:4625-4633. [PMID: 29973580 PMCID: PMC6065283 DOI: 10.12659/msm.907224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a common malignant tumor with high incidence and mortality worldwide. The aim of this study was to evaluate the association between differentially expressed genes (DEGs), which may function as biomarkers for CRC prognosis and therapies, and the clinical outcome in patients with CRC. MATERIAL AND METHODS A total of 116 normal mucous tissue and 930 CRC tissue datasets were downloaded from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA). After screening DEGs based on limma package in R. Gene Ontology (GO) and KEGG enrichment analysis as well as the protein-protein interaction (PPI) networks were performed to predict the function of these DEGs. Meanwhile, Cox proportional hazards regression was used to build a prognostic model of these DEGs. Then, Kaplan-Meier risk analysis was used to test the model in TCGA datasets and validation datasets. RESULTS In the present study, 300 DEGs with 100 upregulated genes and 200 downregulated genes were identified. The PPI networks including 162 DEGs and 256 nodes were constructed and 2 modules with high degree were selected. Moreover, 5 genes (MMP1, ACSL6, SMPD1, PPARGC1A, and HEPACAM2) were identified using the Cox proportional hazards stepwise regression. Kaplan-Meier risk curve in the TCGA and validation cohorts showed that high-risk group had significantly poor overall survival than the low-risk group. CONCLUSIONS Our study provided insights into the mechanisms of CRC formation and found 5 prognostic genes, which could potentially inform further studies and clinical therapies.
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Affiliation(s)
- Zuoliang Huang
- School of Medical Laboratory, Shao Yang University, Shaoyang, Hunan, China (mainland)
| | - Qin Yang
- School of Medical Laboratory, Shao Yang University, Shaoyang, Hunan, China (mainland)
| | - Zezhi Huang
- School of Medical Laboratory, Shao Yang University, Shaoyang, Hunan, China (mainland)
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16
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Catacchio I, Scattone A, Silvestris N, Mangia A. Immune Prophets of Lung Cancer: The Prognostic and Predictive Landscape of Cellular and Molecular Immune Markers. Transl Oncol 2018; 11:825-835. [PMID: 29729581 PMCID: PMC6050352 DOI: 10.1016/j.tranon.2018.04.006] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 02/07/2023] Open
Abstract
Lung cancer is the leading cause of cancer deaths throughout the world. The majority of patients are diagnosed with locally advanced or metastatic disease when surgery, the best curative option, is no longer feasible. Thus, the prognosis of lung cancer remains poor and heterogeneous and new biomarkers are needed. As the immune system plays a pivotal role in cancer, the study of tumor microenvironment, with regard to the immune component, may provide valuable information for a better comprehension of the pathogenesis and progression of the disease. Through a detailed and critical evaluation of the most recent publications on this topic, we provide evidences of the prognostic and predictive significance of immune markers in tumor and in peripheral blood of lung cancer patients: from the landscape of immune cells (macrophages, neutrophils, lymphocytes and natural killer) and their cytokines, to the analysis of immune-checkpoints (PD-L1 and CTLA4), up to the genetic and epigenetic regulation of the immune response (immune gene signatures and miRNA). We also argue about the lights and shadows related to immune marker use in clinical practice, emphasizing on one hand the importance of their assessment in the choice of therapeutic treatment, on the other, the difficulty in their determination and reproducibility of literature data. The following review gives a foundation and a suggestion for future studies investigating tumor immunology in lung cancer.
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Affiliation(s)
- Ivana Catacchio
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori, Bari 70124, Italy
| | - Anna Scattone
- Pathology Department, IRCCS-Istituto Tumori, Bari 70124, Italy
| | | | - Anita Mangia
- Functional Biomorphology Laboratory, IRCCS-Istituto Tumori, Bari 70124, Italy.
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17
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Riley JM, Cross AW, Paulos CM, Rubinstein MP, Wrangle J, Camp ER. The clinical implications of immunogenomics in colorectal cancer: A path for precision medicine. Cancer 2018; 124:1650-1659. [PMID: 29315503 DOI: 10.1002/cncr.31214] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/10/2017] [Indexed: 12/15/2022]
Abstract
Colorectal cancer (CRC) remains the third most common malignancy and the second-leading cause of cancer-related deaths in the United States. Large multi-omic databases, such as The Cancer Genome Atlas and the International Colorectal Cancer Subtyping Consortium, have identified distinct molecular subtypes related to anatomy. The identification of genomic alterations in CRC is now critical because of the recent success and US Food and Drug Administration approval of pembrolizumab and nivolumab for microsatellite-instable tumors. In parallel, landmark studies have established the prognostic significance of the CRC tumor-infiltrating lymphocyte and the clinical impact of the tumor immune microenvironment. As a result, there is a growing appreciation for immunogenomics, the interconnected relation between tumor genomics and the immune microenvironment. The clinical implications of CRC immunogenomics continue to expand, and it will likely serve as a guide for next-generation immunotherapy strategies for improving outcomes for this disease. Cancer 2018;124:1650-9. © 2018 American Cancer Society.
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Affiliation(s)
- Jenny M Riley
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina.,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - Ashley W Cross
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina
| | - Chrystal M Paulos
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
| | - Mark P Rubinstein
- Department of Pathology, Medical University of South Carolina, Charleston, South Carolina.,Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, South Carolina
| | - John Wrangle
- Department of Medicine, Medical University of South Carolina, Charleston, South Carolina.,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
| | - E Ramsay Camp
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina.,Department of Surgery, Medical University of South Carolina, Charleston, South Carolina
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18
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Gutiérrez ML, Corchete LA, Sarasquete ME, Del Mar Abad M, Bengoechea O, Fermiñán E, Anduaga MF, Del Carmen S, Iglesias M, Esteban C, Angoso M, Alcazar JA, García J, Orfao A, Muñoz-Bellvís L, Sayagués JM. Prognostic impact of a novel gene expression profile classifier for the discrimination between metastatic and non-metastatic primary colorectal cancer tumors. Oncotarget 2017; 8:107685-107700. [PMID: 29296198 PMCID: PMC5746100 DOI: 10.18632/oncotarget.22591] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/28/2017] [Indexed: 02/06/2023] Open
Abstract
Despite significant advances have been achieved in the genetic characterization of sporadic colorectal cancer (sCRC), the precise genetic events leading to the development of distant metastasis remain poorly understood. Thus, accurate prediction of metastatic disease in newly-diagnosed sCRC patients remains a challenge. Here, we evaluated the specific genes and molecular pathways associated with the invasive potential of colorectal tumor cells, through the assessment of the gene expression profile (GEP) of coding and non-coding genes in metastatic (MTX) vs. non-metastatic (non-MTX) primary sCRC tumors followed for >5 years. Overall, MTX tumors showed up-regulation of genes associated with tumor progression and metastatic potential while non-MTX cases displayed GEP associated with higher cell proliferation, activation of DNA repair and anti-tumoral immune/inflammatory responses. Based on only 19 genes a specific GEP that classifies sCRC tumors into two MTX-like and non-MTX-like molecular subgroups was defined which shows an independent prognostic impact on patient overall survival, particularly when it is combined with the lymph node status at diagnosis. In summary, we show an association between the global GEP of primary sCRC cells and their metastatic potential and defined a GEP-based classifier that provides the basis for further prognostic stratification of sCRC patients who are at risk of distant metastases.
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Affiliation(s)
- María Laura Gutiérrez
- Cytometry Service-NUCLEUS, Cancer Research Center, IBMCC-CSIC/USAL, Department of Medicine, University of Salamanca, Institute of Biomedical Research of Salamanca, Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Salamanca, Spain
| | - Luis Antonio Corchete
- Cancer Research Center and Service of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - María Eugenia Sarasquete
- Cancer Research Center and Service of Hematology, University Hospital of Salamanca, Salamanca, Spain
| | - María Del Mar Abad
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Oscar Bengoechea
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Encarna Fermiñán
- Genomics Unit, Cancer Research Center, IBMCC-CSIC/USAL, Salamanca, Spain
| | - María Fernanda Anduaga
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Sofía Del Carmen
- Department of Pathology, University Hospital of Salamanca, Salamanca, Spain
| | - Manuel Iglesias
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Carmen Esteban
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - María Angoso
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Jose Antonio Alcazar
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Jacinto García
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - Alberto Orfao
- Cytometry Service-NUCLEUS, Cancer Research Center, IBMCC-CSIC/USAL, Department of Medicine, University of Salamanca, Institute of Biomedical Research of Salamanca, Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Salamanca, Spain
| | - Luis Muñoz-Bellvís
- Service of General and Gastrointestinal Surgery, Institute of Biomedical Research of Salamanca, Salamanca, Spain
| | - José María Sayagués
- Cytometry Service-NUCLEUS, Cancer Research Center, IBMCC-CSIC/USAL, Department of Medicine, University of Salamanca, Institute of Biomedical Research of Salamanca, Biomedical Research Networking Centre Consortium-CIBER-CIBERONC, Salamanca, Spain
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19
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Qiu Z, Sun W, Gao S, Zhou H, Tan W, Cao M, Huang W. A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma. PeerJ 2017; 5:e4062. [PMID: 29158988 PMCID: PMC5695251 DOI: 10.7717/peerj.4062] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/29/2017] [Indexed: 12/25/2022] Open
Abstract
Background Oral tongue squamous cell carcinoma (OTSCC) is the most common subtype of oral cancer. A predictive gene signature is necessary for prognosis of OTSCC. Methods Five microarray data sets of OTSCC from the Gene Expression Omnibus (GEO) and one data set from The Cancer Genome Atlas (TCGA) were obtained. Differentially expressed genes (DEGs) of GEO data sets were identified by integrated analysis. The DEGs associated with prognosis were screened in the TCGA data set by univariate survival analysis to obtain a gene signature. A risk score was calculated as the summation of weighted expression levels with coefficients by Cox analysis. The signature was used to distinguish carcinoma, estimated by receiver operator characteristic curves and the area under the curve (AUC). All were validated in the GEO and TCGA data sets. Results Integrated analysis of GEO data sets revealed 300 DEGs. A 16-gene signature and a risk score were developed after survival analysis. The risk score was effective to stratify patients into high-risk and low-risk groups in the TCGA data set (P < 0.001). The 16-gene signature was valid to distinguish the carcinoma from normal samples (AUC 0.872, P < 0.001). Discussion We identified a useful 16-gene signature for prognosis of OTSCC patients, which could be applied to clinical practice. Further studies were needed to prove the findings.
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Affiliation(s)
- Zeting Qiu
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.,Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wei Sun
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Shaowei Gao
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Huaqiang Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wulin Tan
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Minghui Cao
- Department of Anesthesiology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Wenqi Huang
- Department of Anesthesiology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
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20
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Østrup O, Dagenborg VJ, Rødland EA, Skarpeteig V, Silwal-Pandit L, Grzyb K, Berstad AE, Fretland ÅA, Mælandsmo GM, Børresen-Dale AL, Ree AH, Edwin B, Nygaard V, Flatmark K. Molecular signatures reflecting microenvironmental metabolism and chemotherapy-induced immunogenic cell death in colorectal liver metastases. Oncotarget 2017; 8:76290-76304. [PMID: 29100312 PMCID: PMC5652706 DOI: 10.18632/oncotarget.19350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/26/2017] [Indexed: 01/05/2023] Open
Abstract
Background Metastatic colorectal cancer (CRC) is associated with highly variable clinical outcome and response to therapy. The recently identified consensus molecular subtypes (CMS1-4) have prognostic and therapeutic implications in primary CRC, but whether these subtypes are valid for metastatic disease is unclear. We performed multi-level analyses of resectable CRC liver metastases (CLM) to identify molecular characteristics of metastatic disease and evaluate the clinical relevance. Methods In this ancillary study to the Oslo-CoMet trial, CLM and tumor-adjacent liver tissue from 46 patients were analyzed by profiling mutations (targeted sequencing), genome-wide copy number alteration (CNAs), and gene expression. Results Somatic mutations and CNAs detected in CLM were similar to reported primary CRC profiles, while CNA profiles of eight metastatic pairs suggested intra-patient divergence. A CMS classifier tool applied to gene expression data, revealed the cohort to be highly enriched for CMS2. Hierarchical clustering of genes with highly variable expression identified two subgroups separated by high or low expression of 55 genes with immune-related and metabolic functions. Importantly, induction of genes and pathways associated with immunogenic cell death (ICD) was identified in metastases exposed to neoadjuvant chemotherapy (NACT). Conclusions The uniform classification of CLM by CMS subtyping may indicate that novel class discovery approaches need to be explored to uncover clinically useful stratification of CLM. Detected gene expression signatures support the role of metabolism and chemotherapy in shaping the immune microenvironment of CLM. Furthermore, the results point to rational exploration of immune modulating strategies in CLM, particularly by exploiting NACT-induced ICD.
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Affiliation(s)
- Olga Østrup
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vegar Johansen Dagenborg
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Einar Andreas Rødland
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Veronica Skarpeteig
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Krzysztof Grzyb
- Department of Pathology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Audun Elnæs Berstad
- Department of Radiology, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Åsmund Avdem Fretland
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Gunhild Mari Mælandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Pharmacy, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Anne Hansen Ree
- Department of Oncology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Bjørn Edwin
- Department of Hepato-Pancreato-Biliary Surgery, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- The Intervention Centre, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Vigdis Nygaard
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Kjersti Flatmark
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Department of Gastroenterological Surgery, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
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21
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Zhu H, Dai M, Chen X, Chen X, Qin S, Dai S. Integrated analysis of the potential roles of miRNA‑mRNA networks in triple negative breast cancer. Mol Med Rep 2017. [PMID: 28627677 PMCID: PMC5561991 DOI: 10.3892/mmr.2017.6750] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Triple negative breast cancer (TNBC) is a type of breast cancer where the tumor cells are negative for the estrogen, progesterone and human epidermal growth factor 2 receptors. To date, expression profiling of microRNA (miRNA/miR) and mRNA sequences have been widely applied for the diagnosis of TNBC. In the present study, an integrated analysis of miRNA‑mRNA profiling arrays was performed. A total of five dysregulated miRNAs in patients with TNBC were identified, including upregulated miR‑558 expression and downregulated miR‑320d‑1, miR‑548v, miR‑99a and miR‑21 expression. In addition, 49 potential target mRNA sequences were identified. Bioinformatics analyses were performed on the identified miRNAs and mRNAs, including gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes pathway and miRNA‑mRNA network analyses. A total of 31 GO terms and three signaling pathways were identified. The results indicated that the differentially expressed miRNAs and their potential target mRNAs may affect the pathogenesis of TNBC, and may therefore be considered as promising biomarkers for the early diagnosis and targeted therapy of patients with TNBC.
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Affiliation(s)
- Huiru Zhu
- Department of Galactophore, The Third Affiliated Hospital of Guangxi University of Chinese Medicine, Liuzhou, Guangxi 545001, P.R. China
| | - Meiyu Dai
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Xiaoli Chen
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Xiang Chen
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Shini Qin
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
| | - Shengming Dai
- Department of Clinical Laboratory, The Fourth Affiliated Hospital of Guangxi Medical University, Liuzhou, Guangxi 545005, P.R. China
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22
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An N, Yang X, Zhang Y, Shi X, Yu X, Cheng S, Zhang K, Wang G. Cell cycle related genes up-regulated in human colorectal development predict the overall survival of late-stage colorectal cancer patients. MOLECULAR BIOSYSTEMS 2016; 12:541-52. [PMID: 26672738 DOI: 10.1039/c5mb00761e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
A tumor can be perceived as a special "organ" that undergoes aberrant and poorly regulated organogenesis. Embryonic development and carcinogenesis share striking similarities in their cellular behavior and underlying molecular mechanisms. This intimate association makes embryonic development a viable reference model for studying cancer thereby circumventing the potentially misleading complexity of tumor heterogeneity. Therefore, on the basis of global expression profile, the genes simultaneously activated (up-regulated in terms of expression profile) or suppressed (down-regulated) in both the embryonic development and cancer stage, probably contain profound information on the molecular mechanism of cancer. In this study, the Affymetrix expression profile of 1593 colorectal cancer samples was downloaded from Gene Expression Omnibus. The 1396 differentially expressed probes were robustly obtained using 660 colorectal normal and cancer samples, the expression pattern of which was analyzed using our human colorectal developmental data. All of these 1396 probes were classified into 27 distinct patterns based on their expression patterns during the developmental process. By means of gene set enrichment analysis, we collected 393 V probes simultaneously up-regulated in both development and carcinogenesis and 207 A probes down-regulated in both. Functional enrichment analysis indicated that the V probes were significantly related to cell cycle regulation. Notably, 28 cell-cycle related probes within the V probe group were found to be significantly associated with an overall survival of Stage III/IV patients (GSE17536 cross validation, n = 96, p = 5.70 × 10(-3); GSE29621, n = 36, p = 1.70 × 10(-3); GSE39084, n = 38, p = 0.05; GSE39582, n = 264, p = 0.047; GSE17537, n = 36, p = 5.90 × 10(-3)).
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Affiliation(s)
- Ning An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China.
| | - Xue Yang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China.
| | - Yueming Zhang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China.
| | - Xiaoyu Shi
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China.
| | - Xuexin Yu
- College of Bioinformatics Science and Technology, Harbin Medical University, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China.
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College & Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China.
| | - Guiqi Wang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China.
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23
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Nearchou A, Pentheroudakis G. The significance of tumor-associated immune response in molecular taxonomy, prognosis and therapy of colorectal cancer patients. ANNALS OF TRANSLATIONAL MEDICINE 2016; 4:271. [PMID: 27563658 DOI: 10.21037/atm.2016.05.54] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The importance of host immune response in colorectal cancer (CRC) has been constantly revealed through the last 10 years. A number of relevant immune markers have been introduced as prognostic and are now been used alone or in combination with each other in clinical practice. Efforts establishing a worldwide consensus on the implications of immune-profiles in conjunction to other factors are designed in the right direction in order to more effectively categorize patients with CRC in groups that might benefit from currently used or future applied therapies. On the other hand, a number of clinical trials have evolved the application of immunotherapies in patients with CRC both in the adjuvant and palliative setting.
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Affiliation(s)
- Andreas Nearchou
- Department of Oncology-Pathology, Karolinska Institute, Stockholm, Sweden
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24
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Feng L, Tong R, Liu X, Zhang K, Wang G, Zhang L, An N, Cheng S. A network-based method for identifying prognostic gene modules in lung squamous carcinoma. Oncotarget 2016; 7:18006-20. [PMID: 26919109 PMCID: PMC4951267 DOI: 10.18632/oncotarget.7632] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 02/13/2016] [Indexed: 12/23/2022] Open
Abstract
Similarities in gene expression between both developing embryonic and precancerous tissues and cancer tissues may help identify much-needed biomarkers and therapeutic targets in lung squamous carcinoma. In this study, human lung samples representing ten successive time points, from embryonic development to carcinogenesis, were used to construct global gene expression profiles. Differentially expressed genes with similar expression in precancerous and cancer samples were identified. Using a network-based greedy searching algorithm to analyze the training cohort (n = 69) and three independent testing cohorts, we successfully identified a significant 22-gene module in which expression levels were correlated with overall survival in lung squamous carcinoma patients.
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Affiliation(s)
- Lin Feng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Run Tong
- Department of Respiratory and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohong Liu
- Department of Gynecology and Obstetrics, Maternal and Child Health Care Hospital of Haidian, Beijing, China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Guiqi Wang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Zhang
- Department of Endoscopy, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ning An
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
| | - Shujun Cheng
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Peking Union Medical College and Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Beijing, China
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