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Han X, Song D, Cui Y, Shi Y, Gu X. Pan-cancer analyses of immunogenic cell death-derived gene signatures: Potential biomarkers for prognosis and immunotherapy. Cancer Rep (Hoboken) 2024; 7:e2073. [PMID: 38627900 PMCID: PMC11021686 DOI: 10.1002/cnr2.2073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 03/15/2024] [Accepted: 03/30/2024] [Indexed: 04/19/2024] Open
Abstract
BACKGROUND Immunogenic cell death (ICD) is a type of regulated cell death that is capable of initiating an adaptive immune response. Induction of ICD may be a potential treatment strategy, as it has been demonstrated to activate the tumor-specific immune response. AIMS The biomarkers of ICD and their relationships with the tumor microenvironment, clinical features, and immunotherapy response are not fully understood in a clinical context. Therefore, we conducted pan-cancer analyses of ICD gene signatures across 33 cancer types from The Cancer Genome Atlas database. METHODS AND RESULTS We identified key genes that had strong relationships with survival and the tumor microenvironment, contributing to a better understanding of the role of ICD genes in cancer therapy. In addition, we predicted therapeutic agents that target ICD genes and explored the potential mechanisms by which gemcitabine induce ICD. Moreover, we developed an ICD score based on the ICD genes and found it to be associated with patient prognosis, clinical features, tumor microenvironment, radiotherapy access, and immunotherapy response. A high ICD score was linked to the immune-hot phenotype, while a low ICD score was linked to the immune-cold phenotype. CONCLUSION We uncovered the potential of ICD gene signatures as comprehensive biomarkers for ICD in pan-cancer. Our research provides novel insights into immuno-phenotypic assessment and cancer therapeutic strategies, which could help to broaden the application of immunotherapy to benefit more patients.
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Affiliation(s)
- Xiaodan Han
- Department of Radiation OncologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Di Song
- Zhengzhou UniversityZhengzhouChina
| | - Yongliang Cui
- Department of Respiratory MedicineZhengzhou Central HospitalZhengzhouChina
| | - Yonggang Shi
- Department of Radiation OncologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
| | - Xiaobin Gu
- Department of Radiation OncologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhouChina
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Cartry J, Bedja S, Boilève A, Mathieu JRR, Gontran E, Annereau M, Job B, Mouawia A, Mathias P, De Baère T, Italiano A, Besse B, Sourrouille I, Gelli M, Bani MA, Dartigues P, Hollebecque A, Smolenschi C, Ducreux M, Malka D, Jaulin F. Implementing patient derived organoids in functional precision medicine for patients with advanced colorectal cancer. J Exp Clin Cancer Res 2023; 42:281. [PMID: 37880806 PMCID: PMC10598932 DOI: 10.1186/s13046-023-02853-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/06/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Patient Derived Organoids (PDOs) emerged as the best technology to develop ex vivo tumor avatars. Whether drug testing on PDOs to identify efficient therapies will bring clinical utility by improving patient survival remains unclear. To test this hypothesis in the frame of clinical trials, PDO technology faces three main challenges to be implemented in routine clinical practices: i) generating PDOs with a limited amount of tumor material; ii) testing a wide panel of anti-cancer drugs; and iii) obtaining results within a time frame compatible with patient disease management. We aimed to address these challenges in a prospective study in patients with colorectal cancer (CRC). METHODS Fresh surgical or core needle biopsies were obtained from patients with CRC. PDOs were established and challenged with a panel of 25 FDA-approved anti-cancer drugs (chemotherapies and targeted therapies) to establish a scoring method ('chemogram') identifying in vitro responders. The results were analyzed at the scale of the cohort and individual patients when the follow-up data were available. RESULTS A total of 25 PDOs were successfully established, harboring 94% concordance with the genomic profile of the tumor they were derived from. The take-on rate for PDOs derived from core needle biopsies was 61.5%. A chemogram was obtained with a 6-week median turnaround time (range, 4-10 weeks). At least one hit (mean 6.16) was identified for 92% of the PDOs. The number of hits was inversely correlated to disease metastatic dissemination and the number of lines of treatment the patient received. The chemograms were compared to clinical data obtained from 8 patients and proved to be predictive of their response with 75% sensitivity and specificity. CONCLUSIONS We show that PDO-based drug tests can be achieved in the frame of routine clinical practice. The chemogram could provide clinicians with a decision-making tool to tailor patient treatment. Thus, PDO-based functional precision oncology should now be tested in interventional trials assessing its clinical utility for patients who do not harbor activable genomic alterations or have developed resistance to standard of care treatments.
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Affiliation(s)
- Jérôme Cartry
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France.
| | - Sabrina Bedja
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Alice Boilève
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Jacques R R Mathieu
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Emilie Gontran
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Maxime Annereau
- Département de Pharmacie Clinique, Gustave Roussy, 94805, Villejuif, France
| | - Bastien Job
- Inserm US23, Plateforme de Bioinformatique, Gustave Roussy, 94805, Villejuif, France
| | - Ali Mouawia
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Pierre Mathias
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
| | - Thierry De Baère
- Département de Radiologie Interventionnelle, Gustave Roussy, 94805, Villejuif, France
- UFR Médecine, Université Paris-Saclay, 94270, Le Kremlin-Bicêtre, France
| | - Antoine Italiano
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, 94805, France
- Gustave Roussy, Unité de Médecine de Précision, 94805, Villejuif, France
| | - Benjamin Besse
- Gustave Roussy, Unité de Médecine de Précision, 94805, Villejuif, France
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, 94805, Villejuif, France
| | | | - Maximiliano Gelli
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
- Département de Chirurgie Viscérale, Gustave Roussy, 94805, Villejuif, France
| | | | - Peggy Dartigues
- Département de Pathologie, Gustave Roussy, 94805, Villejuif, France
| | - Antoine Hollebecque
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, 94805, France
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, 94805, Villejuif, France
| | - Cristina Smolenschi
- Département d'Innovation Thérapeutique et d'Essais Précoces, Gustave Roussy, Villejuif, 94805, France
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, 94805, Villejuif, France
| | - Michel Ducreux
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, 94805, Villejuif, France
| | - David Malka
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France
- Département de Médecine Oncologique, Gustave Roussy, Université Paris-Saclay, 94805, Villejuif, France
- Département d'Oncologie Médicale, Institut Mutualiste Montsouris, Paris, France
| | - Fanny Jaulin
- Inserm U-1279, Gustave Roussy, Université Paris-Saclay, Villejuif, F-94805, France.
- Département de Recherche, Gustave Roussy, 94800, Villejuif, France.
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Sai Krishna AVS, Ramu A, Hariharan S, Sinha S, Donakonda S. Characterization of tumor microenvironment in glioblastoma multiforme identifies ITGB2 as a key immune and stromal related regulator in glial cell types. Comput Biol Med 2023; 165:107433. [PMID: 37660569 DOI: 10.1016/j.compbiomed.2023.107433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 07/06/2023] [Accepted: 08/28/2023] [Indexed: 09/05/2023]
Abstract
Glioblastoma multiforme (GBM) is the most aggressive form of brain tumor characterized by inter and intra-tumor heterogeneity and complex tumor microenvironment. To uncover the molecular targets in this milieu, we systematically identified immune and stromal interactions at the glial cell type level that leverages on RNA-sequencing data of GBM patients from The Cancer Genome Atlas. The perturbed genes between the high vs low immune and stromal scored patients were subjected to weighted gene co-expression network analysis to identify the glial cell type specific networks in immune and stromal infiltrated patients. The intramodular connectivity analysis identified the highly connected genes in each module. Combining it with univariable and multivariable prognostic analysis revealed common vital gene ITGB2, between the immune and stromal infiltrated patients enriched in microglia and newly formed oligodendrocytes. We found following unique hub genes in immune infiltrated patients; COL6A3 (microglia), ITGAM (oligodendrocyte precursor cells), TNFSF9 (microglia), and in stromal infiltrated patients, SERPINE1 (microglia) and THBS1 (newly formed oligodendrocytes, oligodendrocyte precursor cells). To validate these hub genes, we used external GBM patient single cell RNA-sequencing dataset and this identified ITGB2 to be significantly enriched in microglia, newly formed oligodendrocytes, T-cells, macrophages and adipocyte cell types in both immune and stromal datasets. The tumor infiltration analysis of ITGB2 showed that it is correlated with myeloid dendritic cells, macrophages, monocytes, neutrophils, B-cells, fibroblasts and adipocytes. Overall, the systematic screening of tumor microenvironment components at glial cell types uncovered ITGB2 as a potential target in primary GBM.
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Affiliation(s)
- A V S Sai Krishna
- Chromatin Biology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bengaluru, India
| | - Alagammai Ramu
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Srimathangi Hariharan
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Swati Sinha
- Department of Biotechnology, Faculty of Life and Allied Health Sciences, MS Ramaiah University of Applied Sciences, Bengaluru, India
| | - Sainitin Donakonda
- Institute of Molecular Immunology and Experimental Oncology, Klinikum Rechts Der Isar, Technical University of Munich, Munich, Germany.
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Yin Y, Luo Y, He K. Landscape of immunocytes infiltration and prognostic immune-related genes in hepatocellular carcinoma. Asian J Surg 2023; 46:4251-4260. [PMID: 36746728 DOI: 10.1016/j.asjsur.2023.01.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/04/2022] [Accepted: 01/10/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND /Objective: The therapeutic efficacy and prognosis of patients with hepatocellular carcinoma (HCC) remain unsatisfactory, and further studies are supposed to provide more effective treatment strategies. Immune cells in extracellular matrix play an important role in the therapeutic effect and prognosis of hepatocellular carcinoma. METHOD To explore the mechanism of immune cells, we analysed the relationship between immune infiltration and gene expression profile through public databases. Patients were divided into high and low groups according to immune score by the ESTIMATE algorithm. It was found that the prognosis and clinical data of patients with liver cancer were correlated with immune scores. RESULTS Using the CIBERSORT method, we identified 21 types of immunocytes infiltration in HCC and demonstrated that these immune cells have clinical and prognostic implications. According to immune score, 590 differentially expressed genes were identified, and 6 key immune-related genes were screened by univariate COX analysis and lasso regression. In addition, the expression of EGLN3, KLRB1, MSC and HMOX1 was found to be correlated with immune cells (B cells, CD4+ T cells, CD8+ T cells, neutrophils, macrophages and dendritic cells) in HCC by the TIMER algorithm. CONCLUSIONS These findings provide new clues to understanding the mechanisms of immune cells in HCC and lay the foundation for the development of new prognostic strategies in HCC.
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Affiliation(s)
- Yanze Yin
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China; Shanghai Institute of Transplantation, Shanghai, China
| | - Yi Luo
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China; Shanghai Institute of Transplantation, Shanghai, China
| | - Kang He
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Engineering Research Center of Transplantation and Immunology, Shanghai, China; Shanghai Institute of Transplantation, Shanghai, China.
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Lee H, Ha S, Choi S, Do S, Yoon S, Kim YK, Kim WY. Oncogenic Impact of TONSL, a Homologous Recombination Repair Protein at the Replication Fork, in Cancer Stem Cells. Int J Mol Sci 2023; 24:ijms24119530. [PMID: 37298484 DOI: 10.3390/ijms24119530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
We investigated the role of TONSL, a mediator of homologous recombination repair (HRR), in stalled replication fork double-strand breaks (DSBs) in cancer. Publicly available clinical data (tumors from the ovary, breast, stomach and lung) were analyzed through KM Plotter, cBioPortal and Qomics. Cancer stem cell (CSC)-enriched cultures and bulk/general mixed cell cultures (BCCs) with RNAi were employed to determine the effect of TONSL loss in cancer cell lines from the ovary, breast, stomach, lung, colon and brain. Limited dilution assays and ALDH assays were used to quantify the loss of CSCs. Western blotting and cell-based homologous recombination assays were used to identify DNA damage derived from TONSL loss. TONSL was expressed at higher levels in cancer tissues than in normal tissues, and higher expression was an unfavorable prognostic marker for lung, stomach, breast and ovarian cancers. Higher expression of TONSL is partly associated with the coamplification of TONSL and MYC, suggesting its oncogenic role. The suppression of TONSL using RNAi revealed that it is required in the survival of CSCs in cancer cells, while BCCs could frequently survive without TONSL. TONSL dependency occurs through accumulated DNA damage-induced senescence and apoptosis in TONSL-suppressed CSCs. The expression of several other major mediators of HRR was also associated with worse prognosis, whereas the expression of error-prone nonhomologous end joining molecules was associated with better survival in lung adenocarcinoma. Collectively, these results suggest that TONSL-mediated HRR at the replication fork is critical for CSC survival; targeting TONSL may lead to the effective eradication of CSCs.
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Affiliation(s)
- Hani Lee
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sojung Ha
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - SeokGyeong Choi
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Soomin Do
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Sukjoon Yoon
- Department of Biological Sciences, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Yong Kee Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Muscle Physiome Research Center, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Research Institute of Pharmacal Research, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women's University, Seoul 04310, Republic of Korea
- Research Institute of Pharmacal Research, Sookmyung Women's University, Seoul 04310, Republic of Korea
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Yoshikawa A, Nakamura Y. Molecular Basis of HER2-Targeted Therapy for HER2-Positive Colorectal Cancer. Cancers (Basel) 2022; 15:183. [PMID: 36612185 PMCID: PMC9818808 DOI: 10.3390/cancers15010183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) amplification has emerged as a biomarker in colorectal cancer (CRC), occurring in 1-4% of metastatic CRC (mCRC). In addition to conventional methods, such as immunohistochemistry and fluorescence in situ hybridization, next-generation sequencing-based tissue or circulating tumor DNA analysis has recently been used to identify HER2 amplification and assess HER2 overexpression. Prospective clinical trials have demonstrated the efficacy of HER2-targeted therapies in HER2-positive mCRC. The TRIUMPH study, a phase II study of dual HER2 antibodies, i.e., pertuzumab plus trastuzumab, demonstrated promising efficacy for patients with HER2-positive mCRC confirmed by tissue-and/or blood-based techniques, which led to the regulatory approval of this combination therapy in Japan. The mechanisms associated with efficacy and resistance have also been explored in translational studies that incorporate liquid biopsy in prospective trials. In particular, HER2 copy number and co-alterations have repeatedly been reported as biomarkers related to efficacy. To improve the therapeutic efficacy of the current strategy, many clinical trials with various HER2-targeted agents are ongoing. This review discusses the molecular basis of HER2-targeted therapeutic strategies for patients with HER2-positive mCRC.
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Affiliation(s)
- Ayumu Yoshikawa
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-0882, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa 277-0882, Japan
- International Research Promotion Office, National Cancer Center Hospital East, Kashiwa 277-0882, Japan
- Translational Research Support Section, National Cancer Center Hospital East, Kashiwa 277-0882, Japan
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Zhao H, Song N, Feng H, Lei Q, Zheng Y, Liu J, Liu C, Chai Z. Construction and validation of a prognostic model for gastrointestinal stromal tumors based on copy number alterations and clinicopathological characteristics. Front Oncol 2022; 12:1055174. [PMID: 36620561 PMCID: PMC9811389 DOI: 10.3389/fonc.2022.1055174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Background The increasing incidence of gastrointestinal stromal tumors (GISTs) has led to the discovery of more novel prognostic markers. We aim to establish an unsupervised prognostic model for the early prediction of the prognosis of future patients with GISTs and to guide clinical treatment. Methods We downloaded the GISTs dataset through the cBioPortal website. We extracted clinical information and pathological information, including the microsatellite instability (MSI) score, fraction genome altered (FGA) score, tumor mutational burden (TMB), and copy number alteration burden (CNAB), of patients with GISTs. For survival analysis, we used univariate Cox regression to analyze the contribution of each factor to prognosis and calculated a hazard ratio (HR) and 95% confidence interval (95% CI). For clustering groupings, we used the t-distributed stochastic neighbor embedding (t-SNE) method for data dimensionality reduction. Subsequently, the k-means method was used for clustering analysis. Results A total of 395 individuals were included in the study. After dimensionality reduction with t-SNE, all patients were divided into two subgroups. Cluster 1 had worse OS than cluster 2 (HR=3.45, 95% CI, 2.22-5.56, P<0.001). The median MSI score of cluster 1 was 1.09, and the median MSI score of cluster 2 was 0.24, which were significantly different (P<0.001). The FGA score of cluster 1 was 0.28, which was higher than that of cluster 2 (P<0.001). In addition, both the TMB and CNAB of cluster 1 were higher than those of cluster 2, and the P values were less than 0.001. Conclusion Based on the CNA of GISTs, patients can be divided into high-risk and low-risk groups. The high-risk group had a higher MSI score, FGA score, TMB and CNAB than the low-risk group. In addition, we established a prognostic nomogram based on the CNA and clinicopathological characteristics of patients with GISTs.
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Affiliation(s)
- Heng Zhao
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China
| | - Nuohan Song
- Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China,China University of Political Science and Law, Beijing, China
| | - Hao Feng
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Qiang Lei
- Department of Research and Development, Shandong Benran Biotechnology Co., Ltd., Jinan, China
| | - Yingying Zheng
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Jing Liu
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Chunyan Liu
- Department of Oncology, Shandong Key Laboratory of Rheumatic Disease and Translational Medicine, Shandong Provincial Qianfoshan Hospital, The First Affiliated Hospital of Shandong First Medical University, Jinan, China,*Correspondence: Chunyan Liu, ; Zhengbin Chai,
| | - Zhengbin Chai
- Department of Clinical Laboratory Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China,*Correspondence: Chunyan Liu, ; Zhengbin Chai,
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Huang B, Su W, Yu D. Data-driven analysis to identify prognostic immune-related biomarkers in BRAF mutated cutaneous melanoma microenvironment. Front Genet 2022; 13:1081418. [DOI: 10.3389/fgene.2022.1081418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022] Open
Abstract
Skin cutaneous melanoma is one of the deadly diseases, and more than 50% of the patients have BRAF gene mutations. Evidence suggests that oncogenic BRAF modulates the immune system’s ability to recognize SKCM cells. Due to the complexity of the tumor microenvironment (TME) and a lack of a rational mechanistic basis, it is urgent to investigate the immune infiltration and identify prognostic biomarkers in BRAF mutated SKCM patients. Multiple methods including ESTIMATE algorithm, differential gene analysis, prognostic analysis and immune infiltration analysis were performed to investigate the tumor microenvironment. Based on the patient’s immune score and stromal score, immune-related genes DEGs were identified. Functional analysis revealed that these genes were mainly enriched in biological processes such as immune response, defense response and positive regulation of immune system. Furthermore, we analyzed the immune infiltrating cell components of BRAF mutated patients and revealed 4 hub genes associated with overall survival time. Several cells (Monocyte, Macrophage and Gamma delta cells) have been found to be significantly decreased in immune-high BRAF mutated SKCM group. While CD4+T, CD8+T, CD4 naïve, Tr1, Th2 and many T cell subsets were significantly increased in immune-high group. These immune cells and genes were closely related to each other. This study revealed that the dysregulation of immune function and immune cells may contribute to the poor outcomes of BRAF mutated patients. It is of great significance to our further understanding of the TME and immune dysfunction in BRAF mutated SKCM.
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Díez-Villanueva A, Sanz-Pamplona R, Solé X, Cordero D, Crous-Bou M, Guinó E, Lopez-Doriga A, Berenguer A, Aussó S, Paré-Brunet L, Obón-Santacana M, Moratalla-Navarro F, Salazar R, Sanjuan X, Santos C, Biondo S, Diez-Obrero V, Garcia-Serrano A, Alonso MH, Carreras-Torres R, Closa A, Moreno V. COLONOMICS - integrative omics data of one hundred paired normal-tumoral samples from colon cancer patients. Sci Data 2022; 9:595. [PMID: 36182938 PMCID: PMC9526730 DOI: 10.1038/s41597-022-01697-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
Colonomics is a multi-omics dataset that includes 250 samples: 50 samples from healthy colon mucosa donors and 100 paired samples from colon cancer patients (tumor/adjacent). From these samples, Colonomics project includes data from genotyping, DNA methylation, gene expression, whole exome sequencing and micro-RNAs (miRNAs) expression. It also includes data from copy number variation (CNV) from tumoral samples. In addition, clinical data from all these samples is available. The aims of the project were to explore and integrate these datasets to describe colon cancer at molecular level and to compare normal and tumoral tissues. Also, to improve screening by finding biomarkers for the diagnosis and prognosis of colon cancer. This project has its own website including four browsers allowing users to explore Colonomics datasets. Since generated data could be reuse for the scientific community for exploratory or validation purposes, here we describe omics datasets included in the Colonomics project as well as results from multi-omics layers integration.
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Affiliation(s)
- Anna Díez-Villanueva
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Rebeca Sanz-Pamplona
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Xavier Solé
- Molecular Biology CORE, Center for Biomedical Diagnostics, Hospital Clínic de Barcelona, 08036, Barcelona, Spain
- Translational Genomic and Targeted Therapeutics in Solid Tumors, August Pi i Sunyer Biomedical Research Institute (IDIBAPS), 08036, Barcelona, Spain
| | - David Cordero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Marta Crous-Bou
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO) - Bellvitge Biomedical Research Institute (IDIBELL). L'Hospitalet de Llobregat, Barcelona, 08908, Spain
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Elisabet Guinó
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adriana Lopez-Doriga
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Antoni Berenguer
- Rheumatology Department - Parc Taulí Research and Innovation Institute (I3PT), Barcelona, Spain
| | - Susanna Aussó
- TIC Salut Social Foundation. Ministry of Health of Generalitat de Catalunya, Barcelona, Spain
| | | | - Mireia Obón-Santacana
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Ferran Moratalla-Navarro
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Ramon Salazar
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Xavier Sanjuan
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Pathology Service, Bellvitge University Hospital (HUB), Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Medical Oncology Department. Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Oncology (CIBERONC), Madrid, Spain
| | - Sebastiano Biondo
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
- Digestive Surgery Service, Bellvitge University Hospital (HUB). Hospitalet de Llobregat, Barcelona, Spain
| | - Virginia Diez-Obrero
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
| | - Ainhoa Garcia-Serrano
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Maria Henar Alonso
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain
| | - Robert Carreras-Torres
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Adria Closa
- The John Curtin School of Medical Research, Australian National University, Canberra, Australia
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, Australia
| | - Víctor Moreno
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO). Hospitalet de Llobregat, Barcelona, Spain.
- Colorectal Cancer Group, ONCOBELL, Bellvitge Biomedical Research Institute (IDIBELL). Hospitalet de Llobregat, Barcelona, Spain.
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and health Sciences and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, Barcelona, Spain.
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10
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Bhardwaj V, Sharma A, Parambath SV, Gul I, Zhang X, Lobie PE, Qin P, Pandey V. Machine Learning for Endometrial Cancer Prediction and Prognostication. Front Oncol 2022; 12:852746. [PMID: 35965548 PMCID: PMC9365068 DOI: 10.3389/fonc.2022.852746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
Endometrial cancer (EC) is a prevalent uterine cancer that remains a major contributor to cancer-associated morbidity and mortality. EC diagnosed at advanced stages shows a poor therapeutic response. The clinically utilized EC diagnostic approaches are costly, time-consuming, and are not readily available to all patients. The rapid growth in computational biology has enticed substantial research attention from both data scientists and oncologists, leading to the development of rapid and cost-effective computer-aided cancer surveillance systems. Machine learning (ML), a subcategory of artificial intelligence, provides opportunities for drug discovery, early cancer diagnosis, effective treatment, and choice of treatment modalities. The application of ML approaches in EC diagnosis, therapies, and prognosis may be particularly relevant. Considering the significance of customized treatment and the growing trend of using ML approaches in cancer prediction and monitoring, a critical survey of ML utility in EC may provide impetus research in EC and assist oncologists, molecular biologists, biomedical engineers, and bioinformaticians to further collaborative research in EC. In this review, an overview of EC along with risk factors and diagnostic methods is discussed, followed by a comprehensive analysis of the potential ML modalities for prevention, screening, detection, and prognosis of EC patients.
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Affiliation(s)
- Vipul Bhardwaj
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Arundhiti Sharma
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | | | - Ijaz Gul
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Xi Zhang
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Peter E. Lobie
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Shenzhen Bay Laboratory, Shenzhen, China
| | - Peiwu Qin
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Vijay Pandey
- Tsinghua Berkeley Shenzhen Institute, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
- *Correspondence: Vijay Pandey,
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11
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Miao X, Zou H, Pan L, Cheng J, Wu Y, Chen R, Su Y, Du H, Ding X. Circ_0110940 Exerts an Antiapoptotic and Pro-Proliferative Effect in Gastric Cancer Cells via the miR-1178-3p/SLC38A6 Axis. Journal of Oncology 2022; 2022:1-12. [PMID: 35813866 PMCID: PMC9262524 DOI: 10.1155/2022/3494057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Revised: 06/02/2022] [Accepted: 06/08/2022] [Indexed: 12/14/2022]
Abstract
Circular RNAs (circRNAs) are essential regulators in human cancers, including gastric cancer, by the miRNA/mRNA axis. A previous study identified the upregulation of circ_0110940 in human gastric cancer tissues. The present study performed in vitro assays to reveal the functions of circ_0110940 and its downstream miRNA/mRNA axis in gastric cancer cells. Traditional proliferation and apoptosis assays including colony formation, EdU staining, and Annexin V-PI staining assays were conducted. A luciferase reporter assay was performed to assess the binding between miR-1178-3p and circ_0110940 or SLC38A. We found the significant upregulation of circ_0110940 in human gastric cancer cells AGS and MKN45. Circ_0110940 was a stable circRNA and exerted an antiproliferative and proapoptotic effect in AGS and MKN45. Circ_0110940 binded with miR-1178-3p, which further targeted SLC38A6 3′UTR. Circ_0110940 degraded miR-1178-3p, and miR-1178-3p degraded SLC38A6. Thus, circ_0110940 has a positive effect on SLC38A6 expression. Furthermore, SLC38A6 rescued the effects of circ_0110940 knockdown on gastric cancer cell proliferation and apoptosis. In conclusion, circ_0110940 exerted an antiapoptotic and pro-proliferative effect in gastric cancer cells via the miR-1178-3p/SLC38A6 axis, which may provide basis for the targeted therapy of gastric cancer.
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12
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Lahoz S, Archilla I, Asensio E, Hernández‐Illán E, Ferrer Q, López‐Prades S, Nadeu F, Del Rey J, Sanz‐Pamplona R, Lozano JJ, Castells A, Cuatrecasas M, Camps J. Copy-number intratumor heterogeneity increases the risk of relapse in chemotherapy-naive stage II colon cancer. J Pathol 2022; 257:68-81. [PMID: 35066875 PMCID: PMC9790656 DOI: 10.1002/path.5870] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/17/2021] [Accepted: 01/13/2022] [Indexed: 12/30/2022]
Abstract
Optimal selection of high-risk patients with stage II colon cancer is crucial to ensure clinical benefit of adjuvant chemotherapy. Here, we investigated the prognostic value of genomic intratumor heterogeneity and aneuploidy for disease recurrence. We combined targeted sequencing, SNP arrays, fluorescence in situ hybridization, and immunohistochemistry on a retrospective cohort of 84 untreated stage II colon cancer patients. We assessed the clonality of copy-number alterations (CNAs) and mutations, CD8+ lymphocyte infiltration, and their association with time to recurrence. Prognostic factors were included in machine learning analysis to evaluate their ability to predict individual relapse risk. Tumors from recurrent patients displayed a greater proportion of CNAs compared with non-recurrent (mean 31.3% versus 23%, respectively; p = 0.014). Furthermore, patients with elevated tumor CNA load exhibited a higher risk of recurrence compared with those with low levels [p = 0.038; hazard ratio (HR) 2.46], which was confirmed in an independent cohort (p = 0.004; HR 3.82). Candidate chromosome-specific aberrations frequently observed in recurrent cases included gain of the chromosome arm 13q (p = 0.02; HR 2.67) and loss of heterozygosity at 17q22-q24.3 (p = 0.05; HR 2.69). CNA load positively correlated with intratumor heterogeneity (R = 0.52; p < 0.0001). Consistently, incremental subclonal CNAs were associated with an elevated risk of relapse (p = 0.028; HR 2.20), which we did not observe for subclonal single-nucleotide variants and small insertions and deletions. The clinico-genomic model rated an area under the curve of 0.83, achieving a 10% incremental gain compared with clinicopathological markers (p = 0.047). In conclusion, tumor aneuploidy and copy-number intratumor heterogeneity were predictive of poor outcome and improved discriminative performance in early-stage colon cancer. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sara Lahoz
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ivan Archilla
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Elena Asensio
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Eva Hernández‐Illán
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Queralt Ferrer
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Sandra López‐Prades
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Ferran Nadeu
- Molecular Pathology of Lymphoid NeoplasmsInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Cáncer (CIBERONC)BarcelonaSpain
| | - Javier Del Rey
- Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
| | - Rebeca Sanz‐Pamplona
- Unit of Biomarkers and SusceptibilityOncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL) and CIBERESPl'Hospitalet de LlobregatSpain
| | - Juan José Lozano
- Bioinformatics PlatformCentro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD)MadridSpain
| | - Antoni Castells
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Miriam Cuatrecasas
- Pathology Department, Biomedical Diagnostic Center, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain
| | - Jordi Camps
- Translational Colorectal Cancer Genomics, Gastrointestinal and Pancreatic Oncology TeamInstitut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of BarcelonaBarcelonaSpain,Department of Cell Biology, Physiology and Immunology, Faculty of MedicineUniversity Autonomous of BarcelonaBellaterraSpain
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Lu C, Hu D, Zheng J, Cao S, Zhu J, Chen X, Huang S, Yao J, Xu Y. A Six-Gene Risk Model Based on the Immune Score Reveals Prognosis in Intermediate-Risk Acute Myeloid Leukemia. BioMed Research International 2022; 2022:1-9. [PMID: 35528167 PMCID: PMC9076319 DOI: 10.1155/2022/4010786] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/30/2022] [Indexed: 12/17/2022]
Abstract
Tumor microenvironment (TME) has been revealed as an important determinant of diagnosis and treatment response in AML patients. The scores of immune and stromal cell scores of AML in the intermediate-risk group from The Cancer Genome Atlas (TCGA) database were calculated using the Estimation of STromal and Immune cells in MAlignant Tumor tissues using Expression data algorithm. Differentially expressed genes were identified between high and low scores. Gene set enrichment and pathway analyses were performed. A risk score model based on TME for six immune-related genes was established and validated. Patients with a lower immune score had a longer overall survival than those with a higher score (P = 0.044). A total of 805 intersected genes as differentially expressed genes were identified and selected according to the comparison of both immune and stromal scores. The functional enrichment analysis shows that these genes are mainly associated with the immune/inflammatory response. The risk score model based on TME for six immune-related genes (including MEF2C, ENPP2, FAM107A, CD37, TNFAIP8L2, and CASS4) was established and validated in the TCGA database and well validated in the TARGET database (P = 0.005). A key microenvironment-related gene signature was identified that affects the outcomes of AML patients in the intermediate-risk group and might serve as therapeutic targets.
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Tan ES, Knepper TC, Wang X, Permuth JB, Wang L, Fleming JB, Xie H. Copy Number Alterations as Novel Biomarkers and Therapeutic Targets in Colorectal Cancer. Cancers (Basel) 2022; 14:2223. [PMID: 35565354 PMCID: PMC9101426 DOI: 10.3390/cancers14092223] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 04/21/2022] [Accepted: 04/24/2022] [Indexed: 12/10/2022] Open
Abstract
In colorectal cancer, somatic mutations have played an important role as prognostic and predictive biomarkers, with some also functioning as therapeutic targets. Another genetic aberration that has shown significance in colorectal cancer is copy number alterations (CNAs). CNAs occur when a change to the DNA structure propagates gain/amplification or loss/deletion in sections of DNA, which can often lead to changes in protein expression. Multiple techniques have been developed to detect CNAs, including comparative genomic hybridization with microarray, low pass whole genome sequencing, and digital droplet PCR. In this review, we summarize key findings in the literature regarding the role of CNAs in the pathogenesis of colorectal cancer, from adenoma to carcinoma to distant metastasis, and discuss the roles of CNAs as prognostic and predictive biomarkers in colorectal cancer.
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Affiliation(s)
- Elaine S. Tan
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Todd C. Knepper
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jennifer B. Permuth
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12901 USF Magnolia Drive Tampa, Tampa, FL 33612, USA;
| | - Jason B. Fleming
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
| | - Hao Xie
- Department of Gastrointestinal Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive Tampa, Tampa, FL 33612, USA; (E.S.T.); (J.B.P.); (J.B.F.)
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Wang Q, Li X, Wang Y, Qiu J, Wu J, He Y, Li J, Kong Q, Han J, Jiang Y. Development and Validation of a Three-Gene Prognostic Signature Based on Tumor Microenvironment for Gastric Cancer. Front Genet 2022; 12:801240. [PMID: 35178071 PMCID: PMC8843853 DOI: 10.3389/fgene.2021.801240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/27/2021] [Indexed: 12/24/2022] Open
Abstract
Gastric cancer (GC), which has high morbidity and low survival rate, is one of the most common malignant tumors in the world. The increasing evidences show that the tumor microenvironment (TME) is related to the occurrence and progression of tumors and the prognosis of patients. In this study, we aimed to develop a TME-based prognostic signature for GC. We first identified the differentially expressed genes (DEGs) related to the TME using the Wilcoxon rank-sum test in a training set of GC. Univariate Cox regression analysis was used to identify prognostic-related DEGs. To decrease the overfitting, we performed the least absolute shrinkage and selection operator (LASSO) regression to reduce the number of signature genes and obtained three genes (LPPR4, ADAM12, NOX4). Next, the multivariate Cox regression was performed to construct the risk score model, and a three-gene prognostic signature was developed. According to the signature, patients were classified into high-risk and low-risk groups with significantly different survival. The signature was then applied to three independent validated sets and obtained the same results. We conducted the time-dependent Receiver Operating Characteristic (ROC) curve analysis to evaluate our signature. We further evaluated the differential immune characters between high-risk and low-risk patients to reveal the potential immune mechanism of the impact on the prognosis of the model. Overall, we identified a three-gene prognostic signature based on TME to predict the prognosis of patients with GC and facilitate the development of a precise treatment strategy.
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Affiliation(s)
- Qian Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiangmei Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yahui Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiayue Qiu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiashuo Wu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yalan He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ji Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qingfei Kong
- College of Basic Medical Science, Harbin Medical University, Harbin, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ying Jiang
- College of Basic Medical Science, Heilongjiang University of Chinese Medicine, Harbin, China
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16
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Huai Q, Guo W, Han L, Kong D, Zhao L, Song P, Peng Y, Gao S. Identification of prognostic genes and tumor-infiltrating immune cells in the tumor microenvironment of esophageal squamous cell carcinoma and esophageal adenocarcinoma. Transl Cancer Res 2022; 10:1787-1803. [PMID: 35116502 PMCID: PMC8797718 DOI: 10.21037/tcr-20-3078] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/07/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Esophageal cancer (EC) is a highly aggressive malignancy that is classified as esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC). Infiltrating stromal/immune cells, a major component of the tumor immune microenvironment (TIME), have prognostic significance in various cancers. METHODS In this study we investigated genes and immune factors in the tumor microenvironment (TME) of ESCC and EAC that can serve as prognostic biomarkers. Stromal and immune scores were calculated using the Estimation of Stromal and Immune Cells in Malignant Tumor Tissues Using Expression Data (ESTIMATE) algorithm based on gene expression profiles of patient-derived tumor tissues in The Cancer Genome Atlas database. The correlation between ESTIMATE scores and survival rates in EC were analyzed. A comparison of high and low stromal/immune score groups revealed multiple differentially expressed genes (DEGs) as candidate prognostic genes; their role in immune-related biological processes was evaluated by functional and protein-protein interaction (PPI) network analyses, and the genes were validated using Gene Expression Omnibus datasets. Additionally, 22 tumor-infiltrating immune cell (TIIC) subsets were analyzed using the CIBERSORT algorithm. RESULTS Median stromal score was higher whereas immune score was lower in ESCC than in EAC (both P<0.01). Stromal score was lower in female as compared to male ESCC patients (P<0.05), and was significantly correlated with T stage (P<0.05). In EAC, median immune score was higher in female as compared to male patients (P<0.05) and was correlated with tumor-node-metastasis stage (P<0.05). The identified DEGs were mainly involved in lymphocyte (especially T-lymphocyte) activation and carbohydrate binding. Moreover, the levels of infiltrating resting-stage dendritic cells, CD8+ T cells, naïve B cells, activated mast cells, and resting memory CD4+ T cells were significantly correlated with EC prognosis (P<0.05). CONCLUSIONS The immune microenvironment of ESCC and EAC are quite different. We have found genes with prognostic value in multiple tumor databases.
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Affiliation(s)
- Qilin Huai
- Department of Graduate School, Zunyi Medical University, Zunyi, China.,Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Wei Guo
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liankui Han
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Demiao Kong
- Department of Thoracic Surgery, Guizhou Provincial People's Hospital, Guiyang, China
| | - Liang Zhao
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Peng Song
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Peng
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shugeng Gao
- Department of Thoracic Surgery, 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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Colangelo T, Carbone A, Mazzarelli F, Cuttano R, Dama E, Nittoli T, Albanesi J, Barisciano G, Forte N, Palumbo O, Graziano P, di Masi A, Colantuoni V, Sabatino L, Bianchi F, Mazzoccoli G. Loss of circadian gene Timeless induces EMT and tumor progression in colorectal cancer via Zeb1-dependent mechanism. Cell Death Differ 2022; 29:1552-1568. [PMID: 35034102 PMCID: PMC9345857 DOI: 10.1038/s41418-022-00935-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
The circadian gene Timeless (TIM) provides a molecular bridge between circadian and cell cycle/DNA replication regulatory systems and has been recently involved in human cancer development and progression. However, its functional role in colorectal cancer (CRC), the third leading cause of cancer-related deaths worldwide, has not been fully clarified yet. Here, the analysis of two independent CRC patient cohorts (total 1159 samples) reveals that loss of TIM expression is an unfavorable prognostic factor significantly correlated with advanced tumor stage, metastatic spreading, and microsatellite stability status. Genome-wide expression profiling, in vitro and in vivo experiments, revealed that TIM knockdown induces the activation of the epithelial-to-mesenchymal transition (EMT) program. Accordingly, the analysis of a large set of human samples showed that TIM expression inversely correlated with a previously established gene signature of canonical EMT markers (EMT score), and its ectopic silencing promotes migration, invasion, and acquisition of stem-like phenotype in CRC cells. Mechanistically, we found that loss of TIM expression unleashes ZEB1 expression that in turn drives the EMT program and enhances the aggressive behavior of CRC cells. Besides, the deranged TIM-ZEB1 axis sets off the accumulation of DNA damage and delays DNA damage recovery. Furthermore, we show that the aggressive and genetically unstable 'CMS4 colorectal cancer molecular subtype' is characterized by a lower expression of TIM and that patients with the combination of low-TIM/high-ZEB1 expression have a poorer outcome. In conclusion, our results as a whole suggest the engagement of an unedited TIM-ZEB1 axis in key pathological processes driving malignant phenotype acquisition in colorectal carcinogenesis. Thus, TIM-ZEB1 expression profiling could provide a robust prognostic biomarker in CRC patients, supporting targeted therapeutic strategies with better treatment selection and patients' outcomes.
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Affiliation(s)
- Tommaso Colangelo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Annalucia Carbone
- Fondazione IRCCS Casa Sollievo della Sofferenza, Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy
| | - Francesco Mazzarelli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Roberto Cuttano
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Elisa Dama
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Teresa Nittoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy
| | - Jacopo Albanesi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, 00154, Rome, (RM), Italy
| | - Giovannina Barisciano
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Nicola Forte
- UOC- Patologia Clinica-Settore Anatomia Patologica, Ospedale Fatebenefratelli, Viale Principe di Napoli, 14/A, 82100, Benevento, (BN), Italy
| | - Orazio Palumbo
- Fondazione IRCCS Casa Sollievo della Sofferenza, Division of Medical Genetics, Viale Padre Pio, 7d, 71013, San Giovanni Rotondo, (FG), Italy
| | - Paolo Graziano
- Pathology Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy
| | - Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale G. Marconi, 446, 00154, Rome, (RM), Italy
| | - Vittorio Colantuoni
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Lina Sabatino
- Department of Sciences and Technologies, University of Sannio, Via Traiano, 3, 82100, Benevento, (BN), Italy
| | - Fabrizio Bianchi
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cancer Biomarkers Unit, Viale Padre Pio 7, 71013, San Giovanni Rotondo, (FG), Italy.
| | - Gianluigi Mazzoccoli
- Fondazione IRCCS Casa Sollievo della Sofferenza, Department of Medical Sciences, Division of Internal Medicine and Chronobiology Laboratory, Viale Cappuccini snc, 71013, San Giovanni Rotondo, (FG), Italy.
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Tang B, Yan R, Zhu J, Cheng S, Kong C, Chen W, Fang S, Wang Y, Yang Y, Qiu R, Lu C, Ji J. Integrative analysis of the molecular mechanisms, immunological features and immunotherapy response of ferroptosis regulators across 33 cancer types. Int J Biol Sci 2022; 18:180-198. [PMID: 34975326 PMCID: PMC8692154 DOI: 10.7150/ijbs.64654] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/20/2021] [Indexed: 02/06/2023] Open
Abstract
Ferroptosis is a recently described mode of cell death caused by the accumulation of intracellular iron and lipid reactive oxygen species (ROS), which play critical roles in tumorigenesis and cancer progression. However, the underlying molecular mechanisms and promising biomarkers of ferroptosis among cancers remain to be elucidated. In this study, 30 ferroptosis regulators in ferroptosis-related signaling pathways were identified and analyzed in 33 cancer types. We found transcriptomic aberrations and evaluated the prognostic value of ferroptosis regulators across 33 cancer types. Then, we predicted and validated potential transcription factors (including E2F7, KLF5 and FOXM1) and therapeutic drugs (such as cyclophosphamide, vinblastine, and gefitinib) that target ferroptosis regulators in cancer. Moreover, we explored the molecular mechanisms of ferroptosis and found that signaling pathways such as the IL-1 and IL-2 pathways are closely associated with ferroptosis. Additionally, we found that ferroptosis regulators have a close relationship with immunity-related parameters, including the immune score, immune cell infiltration level, and immune checkpoint protein level. Finally, we determined a ferroptosis score using GSVA method. We found that the ferroptosis score effectively predicted ferroptotic cell death in tumor samples. And ferroptosis score is served as an independent prognostic indicator for the incidence and recurrence of cancers. More importantly, patients with high ferroptosis scores received greater benefit from immunotherapy. We aslo created an online webserver based on the nomogram prognostic model to predict the survival in immunotherapy cohort. The reason for this outcome is partially the result of patients with a high ferroptosis rate also having high immune scores, HLA-related gene expression and immune checkpoint protein expression, such as PDL2 and TIM3. Moreover, patients with high ferroptosis scores exhibited CD8 T cell and TIL infiltration and immune-related signaling pathway enrichment. In summary, we systematically summarize the molecular characteristics, clinical relevance and immune features of ferroptosis across cancers and show that the ferroptosis score can be used as a prognostic factor and for the evaluation of immunotherapy effects.
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Affiliation(s)
- Bufu Tang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310016, China
| | - Ruochen Yan
- School of Medicine, Zhejiang University, Hangzhou 310012, China
| | - Jinyu Zhu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Shimiao Cheng
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Chunli Kong
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Weiqian Chen
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Shiji Fang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Yajie Wang
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Yang Yang
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Rongfang Qiu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
| | - Chenying Lu
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
| | - Jiansong Ji
- Key Laboratory of Imaging Diagnosis and Minimally Invasive Intervention Research, Lishui Hospital, School of Medicine, Zhejiang University, Lishui 323000, China
- Department of Radiology, the Fifth Affiliated Hospital of Wenzhou Medical University, Lishui 323000, China
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Yu S, Wang Y, Peng K, Lyu M, Liu F, Liu T. Establishment of a Prognostic Signature of Stromal/Immune-Related Genes for Gastric Adenocarcinoma Based on ESTIMATE Algorithm. Front Cell Dev Biol 2021; 9:752023. [PMID: 34900998 PMCID: PMC8652145 DOI: 10.3389/fcell.2021.752023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/01/2021] [Indexed: 11/13/2022] Open
Abstract
Different subtypes of gastric cancer differentially respond to immune checkpoint inhibitors (ICI). This study aimed to investigate whether the Estimation of STromal and Immune cells in Malignant Tumor tissues using Expression data (ESTIMATE) algorithm is related to the classification and prognosis of gastric cancer and to establish an ESTIMATE-based gene signature to predict the prognosis for patients. The immune/stromal scores of 388 gastric cancer patients from TCGA were used in this analysis. The upregulated differentially expressed genes (DEGs) in patients with high stromal/immune scores were identified. The immune-related hub DEGs were selected based on protein-protein interaction (PPI) analysis. The prognostic values of the hub DEGs were evaluated in the TCGA dataset and validated in the GSE15460 dataset using the Kaplan-Meier curves. A prognostic signature was built using the hub DEGs by Cox proportional hazards model, and the accuracy was assessed using receiver operating characteristic (ROC) analysis. Different subtypes of gastric cancer had significantly different immune/stromal scores. High stromal scores but not immune scores were significantly associated with short overall survivals of TCGA patients. Nine hub DEGs were identified in PPI analysisThe expression of these hub DEG negatively correlated with the overall survival in the TCGA cohort, which was validated in the GSE15460 cohort. A 9-gene prognostic signature was constructed. The risk factor of patients was calculated by this signature. High-risk patients had significantly shorter overall survival than low-risk patients. ROC analysis showed that the prognostic model accurately identified high-risk individuals within different time frames. We established an effective 9-gene-based risk signature to predict the prognosis of gastric cancer patients, providing guidance for prognostic stratification.
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Affiliation(s)
- Shan Yu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Wang
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ke Peng
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Minzhi Lyu
- Department of Biostatistics, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-Based Medicine, Fudan University, Shanghai, China
| | - Fenglin Liu
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tianshu Liu
- Department of Medical Oncology, Zhongshan Hospital, Fudan University, Shanghai, China.,Center of Evidence-Based Medicine, Fudan University, Shanghai, China
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20
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Zhang S, Lv M, Cheng Y, Wang S, Li C, Qu X. Immune landscape of advanced gastric cancer tumor microenvironment identifies immunotherapeutic relevant gene signature. BMC Cancer 2021; 21:1324. [PMID: 34893046 PMCID: PMC8665569 DOI: 10.1186/s12885-021-09065-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Background Advanced gastric cancer (AGC) is a disease with poor prognosis due to the current lack of effective therapeutic strategies. Immune checkpoint blockade treatments have shown effective responses in patient subgroups but biomarkers remain challenging. Traditional classification of gastric cancer (GC) is based on genomic profiling and molecular features. Therefore, it is critical to identify the immune-related subtypes and predictive markers by immuno-genomic profiling. Methods Single-sample gene-set enrichment analysis (ssGSEA) and ESTIMATE algorithm were used to identify the immue-related subtypes of AGC in two independent GEO datasets. Weighted gene co-expression network analysis (WGCNA) and Molecular Complex Detection (MCODE) algorithm were applied to identify hub-network of immune-related subtypes. Hub genes were confirmed by prognostic data of KMplotter and GEO datasets. The value of hub-gene in predicting immunotherapeutic response was analyzed by IMvigor210 datasets. MTT assay, Transwell migration assay and Western blotting were performed to confirm the cellular function of hub gene in vitro. Results Three immune-related subtypes (Immunity_H, Immunity_M and Immunity_L) of AGC were identified in two independent GEO datasets. Compared to Immunity_L, the Immuntiy_H subtype showed higher immune cell infiltration and immune activities with favorable prognosis. A weighted gene co-expression network was constructed based on GSE62254 dataset and identified one gene module which was significantly correlated with the Immunity_H subtype. A Hub-network which represented high immune activities was extracted based on topological features and Molecular Complex Detection (MCODE) algorithm. Furthermore, ADAM like decysin 1 (ADAMDEC1) was identified as a seed gene among hub-network genes which is highly associated with favorable prognosis in both GSE62254 and external validation datasets. In addition, high expression of ADAMDEC1 correlated with immunotherapeutic response in IMvigor210 datasets. In vitro, ADAMDEC1 was confirmed as a potential protein in regulating proliferation and migration of gastric cancer cell. Deficiency of ADAMDEC1 of gastric cancer cell also associated with high expression of PD-L1 and Jurkat T cell apoptosis. Conclusions We identified immune-related subtypes and key tumor microenvironment marker in AGC which might facilitate the development of novel immune therapeutic targets. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-09065-z.
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Affiliation(s)
- Simeng Zhang
- Department of Medical Oncology, the First Hospital of China Medical University, 110001, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, China
| | - Mengzhu Lv
- Department of Plastic Surgery, the First Hospital of China Medical University, Shenyang, 110001, China
| | - Yu Cheng
- Department of Medical Oncology, the First Hospital of China Medical University, 110001, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, China
| | - Shuo Wang
- Department of Medical Oncology, the First Hospital of China Medical University, 110001, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, China
| | - Ce Li
- Department of Medical Oncology, the First Hospital of China Medical University, 110001, Shenyang, China.,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China.,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001, China.,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, China
| | - Xiujuan Qu
- Department of Medical Oncology, the First Hospital of China Medical University, 110001, Shenyang, China. .,Key Laboratory of Anticancer Drugs and Biotherapy of Liaoning Province, the First Hospital of China Medical University, Shenyang, 110001, China. .,Liaoning Province Clinical Research Center for Cancer, Shenyang, 110001, China. .,Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, Shenyang, 110001, China.
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21
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Xia T, Meng L, Zhao Z, Li Y, Wen H, Sun H, Zhang T, Wei J, Li F, Liu C. Bioinformatics prediction and experimental verification identify MAD2L1 and CCNB2 as diagnostic biomarkers of rhabdomyosarcoma. Cancer Cell Int 2021; 21:634. [PMID: 34838000 PMCID: PMC8626952 DOI: 10.1186/s12935-021-02347-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/16/2021] [Indexed: 12/19/2022] Open
Abstract
Background Rhabdomyosarcoma (RMS) is a malignant soft-tissue tumour. In recent years, the tumour microenvironment (TME) has been reported to be associated with the development of tumours. However, the relationship between the occurrence and development of RMS and TME is unclear. The purpose of this study is to identify potential tumor microenvironment-related biomarkers in rhabdomyosarcoma and analyze their molecular mechanisms, diagnostic and prognostic significance. Methods We first applied bioinformatics method to analyse the tumour samples of 125 patients with rhabdomyosarcoma (RMS) from the Gene Expression Omnibus database (GEO). Differential genes (DEGs) that significantly correlate with TME and the clinical staging of tumors were extracted. Immunohistochemistry (IHC) was applied to validate the expression of mitotic arrest deficient 2 like 1 (MAD2L1) and cyclin B2 (CCNB2) in RMS tissue. Then, we used cell function and molecular biology techniques to study the influence of MAD2L1 and CCNB2 expression levels on the progression of RMS. Results Bioinformatics results show that the RMS TME key genes were screened, and a TME-related tumour clinical staging model was constructed. The top 10 hub genes were screened through the establishment of a protein–protein interaction (PPI) network, and then Gene Expression Profiling Interactive Analysis (GEPIA) was conducted to measure the overall survival (OS) of the 10 hub genes in the sarcoma cases in The Cancer Genome Atlas (TCGA). Six DEGs of statistical significance were acquired. The relationship between these six differential genes and the clinical stage of RMS was analysed. Further analysis revealed that the OS of RMS patients with high expression of MAD2L1 and CCNB2 was worse and the expression of MAD2L1 and CCNB2 was related to the clinical stage of RMS patients. Gene set enrichment analysis (GSEA) revealed that the genes in MAD2L1 and CCNB2 groups with high expression were mainly related to the mechanism of tumour metastasis and recurrence. In the low-expression MAD2L1 and CCNB2 groups, the genes were enriched in the metabolic and immune pathways. Immunohistochemical results also confirmed that the expression levels of MAD2L1 (30/33, 87.5%) and CCNB2 (33/33, 100%) were remarkably higher in RMS group than in normal control group (0/11, 0%). Moreover, the expression of CCNB2 was related to tumour size. Downregulation of MAD2L1 and CCNB2 suppressed the growth, invasion, migration, and cell cycling of RMS cells and promoted their apoptosis. The CIBERSORT immune cell fraction analysis indicated that the expression levels of MAD2L1 and CCNB2 affected the immune status in the TME. Conclusions The expression levels of MAD2L1 and CCNB2 are potential indicators of TME status changes in RMS, which may help guide the prognosis of patients with RMS and the clinical staging of tumours.
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Affiliation(s)
- Tian Xia
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Lian Meng
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Zhijuan Zhao
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Yujun Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Hao Wen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Hao Sun
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Tiantian Zhang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Jingxian Wei
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China. .,Department of Pathology and Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China.
| | - Chunxia Liu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi, 832002, China. .,Department of Pathology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510260, China.
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Zhang X, Ping S, Wang A, Li C, Zhang R, Song Z, Gao C, Wang F. Development and Validation of an Immune-Related Gene Pairs Signature in Grade II/III Glioma. Int J Gen Med 2021; 14:8611-8620. [PMID: 34849006 PMCID: PMC8627264 DOI: 10.2147/ijgm.s335052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/08/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Gliomas are prevalent primary intracerebral malignant tumors. Increasing evidence indicates an association between the immune signature and Grade II/III glioma prognosis. Thus, we aimed to develop an immune-related gene pair (IRGP) signature that can be used as a prognostic tool in Grade II/III glioma. METHODS The gene expression levels and clinical information of Grade II/III glioma patients were collected from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) databases. The TCGA data were randomly divided into a training cohort (n = 249) and a validation cohort (n = 162), and a CGGA dataset served as an external validation group (n = 605). IRGPs significantly associated with prognosis were selected by Cox regression. Gene set enrichment analysis and filtration were performed with the IRGPs. RESULTS Within a set of 1991 immune genes, 8 IRGPs including 15 unique genes that significantly affect survival constituted a gene signature. In the validation datasets, the IRGP signature significantly stratified patients with Grade II/III glioma into low- and high-risk groups (P < 0.001), and the IRGP index was found to be an independent prognostic factor through univariate and multivariate analyses (P < 0.05). Additionally, 26 functional pathways were identified through the intersection of Gene Set Enrichment Analysis (GSEA) and Gene Ontology (GO) enrichment analysis. CONCLUSION The IRGP signature demonstrated good prognostic value for Grade II/III gliomas, which may provide new insights into individual treatment for glioma patients. The IRGPs might function through the identified 26 functional pathways.
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Affiliation(s)
- Xu Zhang
- Department of Neurosurgery, Baoding No.1 Central Hospital, Baoding, People’s Republic of China
| | - Shuai Ping
- Department of Orthopaedics, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People’s Republic of China
| | - Anni Wang
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Can Li
- Department of Neurosurgery, Chengdu Sixth People’s Hospital, Chengdu, People’s Republic of China
| | - Rui Zhang
- Ningxia Key Laboratory of Cerebrocranial Disease, Incubation Base of National Key Laboratory, Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Zimu Song
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Caibin Gao
- Department of Neurosurgery, General Hospital of Ningxia Medical University, Yinchuan, People’s Republic of China
| | - Feng Wang
- Department of Neurosurgery, People's Hospital of Ningxia Hui Autonomous Region Yinchuan, Yinchuan, People’s Republic of China
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Guo T, Wang Z, Liu Y. Establishment and verification of a prognostic tumor microenvironment-based and immune-related gene signature in colon cancer. J Gastrointest Oncol 2021; 12:2172-2191. [PMID: 34790383 DOI: 10.21037/jgo-21-522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background Gastrointestinal malignant cancers affect many sites in the intestinal tract, including the colon. In this study, we purposed to improve prognostic predictions for colon cancer (CC) patients by establishing a novel biosignature of immune-related genes (IRGs) based on the tumor microenvironment (TME). Methods Using the estimation of stromal and immune cells in malignant tumor tissues using expression data (ESTIMATE) algorithm, we calculated the stromal and immune scores of every CC patient extracted from The Cancer Genome Atlas (TCGA). We then identified 4 immune-related messenger RNA (mRNA) biosignatures through a Cox and least absolute shrinkage and selection operator (LASSO) univariate analysis, and a Cox multivariate analysis. Relationships between tumor immune infiltration and the risk score were evaluated through the CIBERSORT algorithm and Tumor Immune Estimation Resource (TIMER) database. Results Our studies showed that individuals who had a high immune score (P=0.017) and low stromal score (P=0.041) had a favorable overall survival (OS) rate. By comparing high/low scores cohort, 220 differentially expressed genes (DEGs) were determined. Then an immune-related four-mRNA biosignature, including PDIA2, NAFTC1, VEGFC, and CD1B was identified. Kaplan-Meier, calibration, and receiver operating characteristic (ROC) curves verified the model's performance. By using univariate and multivariate Cox analyses, we found each biosignature was an independent risk factor for assessing a CC patient's survival. Three external GEO cohorts validated its good efficiency in estimating OS among individuals with CC. Moreover, the signature was also related to infiltration of several cells of the immune system in the tumor microenvironment. Conclusions The resultant model in our study included 4 IRGs associated with the TME. These IRGs can be utilized as an auxiliary variable to estimate and help improve the prognosis of individuals with CC.
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Affiliation(s)
- Tianyu Guo
- Department of Hepatobiliary Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Zhe Wang
- Department of Gastrointestinal Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
| | - Yefu Liu
- Department of Hepatobiliary Surgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, China
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Li M, Li H, Zhou C, Li X, Gong J, Chen C, Zhang Y. Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of hepatocellular carcinoma (HCC). Medicine (Baltimore) 2021; 100:e27332. [PMID: 34596136 PMCID: PMC8483847 DOI: 10.1097/md.0000000000027332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 08/30/2021] [Accepted: 09/02/2021] [Indexed: 01/05/2023] Open
Abstract
ABSTRACT Growing evidence supports that the tumor microenvironment plays a key role in the development and progression of tumors. But immune microenvironment of hepatocellular carcinoma (HCC) has not yet been fully explored. In the present investigation, the clinical value and prognostic significance of immune-related genes in HCC were investigated.The immune and stromal scores of HCC were calculated through the application of Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data Algorithm based on the Cancer Genome Atlas database. Differentially expressed genes were identified using the "edgeR" package of the R software. Functional annotation and pathway enrichment were performed using "ggplots2" and "clusterProfiler" packages in R software. Protein-protein interaction network was constructed using STRING, and the hub genes were identified through the Cytoscape. Survival analysis was performed using Kaplan-Meier methods. Tumor Immune Estimation Resource algorithm was used to view the immune landscape of the microenvironment in HCC.Firstly, the immune and stromal scores of HCC were calculated and we found that the immune and stromal scores of HCC were closely related to the patients' prognosis. Then the differentially expressed genes were identified respectively stratified by the median value of the immune and stromal scores, and the immune-related genes that related to the prognosis in HCC patients were further identified. Functional enrichment analysis and protein-protein interaction networks further showed that these genes mainly participated in immune-related biological process. In addition, dendritic cells were found to be the most abundant in the microenvironment of HCC through Tumor Immune Estimation Resource algorithm and were significantly associated with the patients' prognosis. To robust the results, the immune-related genes were validated in an independent dataset from the Gene Expression Omnibus database.We arrived at a more comprehensive understanding of the microenvironment of HCC and extracted 7 immune-related genes that were significantly associated with the recurrence survival of HCC.
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Islam F, Gopalan V, Lu CT, Pillai S, Lam AK. Identification of novel mutations and functional impacts of EPAS1 in colorectal cancer. Cancer Med 2021; 10:5557-5573. [PMID: 34250767 PMCID: PMC8366083 DOI: 10.1002/cam4.4116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Endothelial PAS domain‐containing protein 1 (EPAS1) has implications in many cancers. However, the molecular behaviours, functional roles and mutational status of EPAS1 have never been studied in colorectal carcinoma (CRC). The study aims to examine the genetic alterations and functional roles of EPAS1 in CRC. In addition, the clinical impacts of EPAS1 in CRC were studied. Significant EPAS1 DNA amplification (63.4%; n = 52/82) and consequent mRNA overexpression (72%; n = 59/82) were noted in patients with CRC. In CRC, 16% (n = 13/82) of the patients had mutations in the EPAS1 coding sequence and most of the mutated samples exhibited aberrant DNA changes and mRNA overexpression. We have identified two novel variants, c.1084C>T; p.L362L and c.1121T>G; p.F374C in CRC. These EPAS1 aberrations in CRC were correlated with clinicopathological parameters, including tumour size, histological grade, T‐stages, cancer perforation as well as the presence of synchronous cancer. Also, reduced cell proliferation, wound healing, migration and invasion were noted in colon cancer cells followed by EPAS1 silencing. To conclude, the results obtained from the current study indicated that EPAS1 plays important role in colorectal carcinogenesis, thus, could be useful as a prognostic marker and as a target for therapy development.
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Affiliation(s)
- Farhadul Islam
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia.,Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi, Bangladesh
| | - Vinod Gopalan
- School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia
| | - Cu Tai Lu
- Department of Surgery, Gold Coast University Hospital, Southport, Queensland, Australia
| | - Suja Pillai
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Alfred K Lam
- School of Biomedical Sciences, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,School of Medicine and Dentistry, Griffith University, Gold Coast, Queensland, Australia
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Yingjuan W, Li Z, Wei C, Xiaoyuan W. Identification of prognostic genes and construction of a novel gene signature in the skin melanoma based on the tumor microenvironment. Medicine (Baltimore) 2021; 100:e26017. [PMID: 34032721 PMCID: PMC8154473 DOI: 10.1097/md.0000000000026017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 04/29/2021] [Indexed: 01/04/2023] Open
Abstract
Skin melanoma remains a highly prevalent and yet deadly form of cancer, with the exact degree of melanoma-associated mortality being strongly dependent upon the local tumor microenvironment. The exact composition of stromal and immune cells within this microenvironmental region has the potential to profoundly impact melanoma progression and prognosis. As such, the present study was designed with the goal of clarifying the predictive relevance of stromal and immune cell-related genes in melanoma patients through comprehensive bioinformatics analyses. We therefore analyzed melanoma sample gene expression within The Cancer Genome Atlas database and employed the ESTIMATE algorithm as a means of calculating both stromal and immune scores that were in turn used for identifying differentially expressed genes (DEGs). Subsequently, univariate analyses were used to detect DEGs associated with melanoma patient survival, and through additional functional enrichment analyses, we determined that these survival-related DEGs are largely related to inflammatory and immune responses. A prognostic signature comprised of 10 genes (IL15, CCL8, CLIC2, SAMD9L, TLR2, HLA.DQB1, IGHV1-18, RARRES3, GBP4, APOBEC3G) was generated. This 10-gene signature effectively separated melanoma patients into low- and high-risk groups based upon their survival. These low- and high-risk groups also exhibited distinct immune statuses and differing degrees of immune cell infiltration. In conclusion, our results offer novel insights into a number of microenvironment-associated genes that impact survival outcomes in melanoma patients, potentially highlighting these genes as viable therapeutic targets.
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Abstract
The infiltration degree of immune and stromal cells has been shown clinically significant in tumor microenvironment (TME). However, the utility of stromal and immune components in Gastric cancer (GC) has not been investigated in detail. In the present study, ESTIMATE and CIBERSORT algorithms were applied to calculate the immune/stromal scores and the proportion of tumor-infiltrating immune cell (TIC) in GC cohort, including 415 cases from The Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) were screened by Cox proportional hazard regression analysis and protein-protein interaction (PPI) network construction. Then ADAMTS12 was regarded as one of the most predictive factors. Further analysis showed that ADAMTS12 expression was significantly higher in tumor samples and correlated with poor prognosis. Gene Set Enrichment Analysis (GSEA) indicated that in high ADAMTS12 expression group gene sets were mainly enriched in cancer and immune-related activities. In the low ADAMTS12 expression group, the genes were enriched in the oxidative phosphorylation pathway. CIBERSORT analysis for the proportion of TICs revealed that ADAMTS12 expression was positively correlated with Macrophages M0/M1/M2 and negatively correlated with T cells follicular helper. Therefore, ADAMTS12 might be a tumor promoter and responsible for TME status and tumor energy metabolic conversion.
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Affiliation(s)
- Yangming Hou
- grid.412463.60000 0004 1762 6325Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Avenue, Harbin, 150086 Heilongjiang China
| | - Yingjuan Xu
- grid.64924.3d0000 0004 1760 5735Department of Obstetrics and Gynecology, China-Japan Union Hospital, Jilin University, No. 126 Xiantai Avenue, Changchun, 130033 China
| | - Dequan Wu
- grid.412463.60000 0004 1762 6325Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, No. 246 Xuefu Avenue, Harbin, 150086 Heilongjiang China
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Jiang Z, Shi Y, Zhao W, Zhang Y, Xie Y, Zhang B, Tan G, Wang Z. Development of an Immune-Related Prognostic Index Associated With Glioblastoma. Front Neurol 2021; 12:610797. [PMID: 34093386 PMCID: PMC8172186 DOI: 10.3389/fneur.2021.610797] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Although the tumor microenvironment (TME) is known to influence the prognosis of glioblastoma (GBM), the underlying mechanisms are not clear. This study aims to identify hub genes in the TME that affect the prognosis of GBM. Methods: The transcriptome profiles of the central nervous systems of GBM patients were downloaded from The Cancer Genome Atlas (TCGA). The ESTIMATE scoring algorithm was used to calculate immune and stromal scores. The application of these scores in histology classification was tested. Univariate Cox regression analysis was conducted to identify genes with prognostic value. Subsequently, functional enrichment analysis and protein–protein interaction (PPI) network analysis were performed to reveal the pathways and biological functions associated with the genes. Next, these prognosis genes were validated in an independent GBM cohort from the Chinese Glioma Genome Atlas (CGGA). Finally, the efficacy of current antitumor drugs targeting these genes against glioma was evaluated. Results: Gene expression profiles and clinical data of 309 GBM samples were obtained from TCGA database. Higher immune and stromal scores were found to be significantly correlated with tissue type and poor overall survival (OS) (p = 0.15 and 0.77, respectively). Functional enrichment analysis identified 860 upregulated and 162 downregulated cross genes, which were mainly linked to immune response, inflammatory response, cell membrane, and receptor activity. Survival analysis identified 228 differentially expressed genes associated with the prognosis of GBM (p ≤ 0.05). A total of 48 hub genes were identified by the Cytoscape tool, and pathway enrichment analysis of the genes was performed using Database for Annotation, Visualization and Integrated Discovery (DAVID). The 228 genes were validated in an independent GBM cohort from the CGGA. In total, 10 genes were found to be significantly associated with prognosis of GBM. Finally, 14 antitumor drugs were identified by drug–gene interaction analysis. Conclusions: Here, 10 TME-related genes and 14 corresponding antitumor agents were found to be associated with the prognosis and OS of GBM.
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Affiliation(s)
- Zhengye Jiang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Yanxi Shi
- Department of Cardiology, Jiaxing Second Hospital, Jiaxing, China
| | - Wenpeng Zhao
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Yaya Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Yuanyuan Xie
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Bingchang Zhang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Guowei Tan
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
| | - Zhanxiang Wang
- Department of Neurosurgery, Xiamen Key Laboratory of Brain Center, The First Affiliated Hospital of Xiamen University, Xiamen, China.,School of Medicine, Institute of Neurosurgery, Xiamen University, Xiamen, China
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Gui CP, Wei JH, Chen YH, Fu LM, Tang YM, Cao JZ, Chen W, Luo JH. A new thinking: extended application of genomic selection to screen multiomics data for development of novel hypoxia-immune biomarkers and target therapy of clear cell renal cell carcinoma. Brief Bioinform 2021; 22:6273240. [PMID: 34237133 DOI: 10.1093/bib/bbab173] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/30/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022] Open
Abstract
Increasing evidences show the clinical significance of the interaction between hypoxia and immune in clear cell renal cell carcinoma (ccRCC) microenvironment. However, reliable prognostic signatures based on a combination of hypoxia and immune have not been well established. Moreover, many studies have only used RNA-seq profiles to screen the prognosis feature of ccRCC. Presently, there is no comprehensive analysis of multiomics data to mine a better one. Thus, we try and get it. First, t-SNE and ssGSEA analysis were used to establish tumor subtypes related to hypoxia-immune, and we investigated the hypoxia-immune-related differences in three types of genetic or epigenetic characteristics (gene expression profiles, somatic mutation, and DNA methylation) by analyzing the multiomics data from The Cancer Genome Atlas (TCGA) portal. Additionally, a four-step strategy based on lasso regression and Cox regression was used to construct a satisfying prognostic model, with average 1-year, 3-year and 5-year areas under the curve (AUCs) equal to 0.806, 0.776 and 0.837. Comparing it with other nine known prognostic biomarkers and clinical prognostic scoring algorithms, the multiomics-based signature performs better. Then, we verified the gene expression differences in two external databases (ICGC and SYSU cohorts). Next, eight hub genes were singled out and seven hub genes were validated as prognostic genes in SYSU cohort. Furthermore, it was indicated high-risk patients have a better response for immunotherapy in immunophenoscore (IPS) analysis and TIDE algorithm. Meanwhile, estimated by GDSC and cMAP database, the high-risk patients showed sensitive responses to six chemotherapy drugs and six candidate small-molecule drugs. In summary, the signature can accurately predict the prognosis of ccRCC and may shed light on the development of novel hypoxia-immune biomarkers and target therapy of ccRCC.
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Affiliation(s)
- Cheng-Peng Gui
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jin-Huan Wei
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yu-Hang Chen
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Liang-Min Fu
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yi-Ming Tang
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jia-Zheng Cao
- Affiliated Jiangmen Hospital, Sun Yat-sen University, Jiangmen, Guangdong, China
| | - Wei Chen
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jun-Hang Luo
- First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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Abstract
Tumor microenvironment (TME) is involved in the occurrence and development of hepatocellular carcinoma (HCC), and immune cells in the TME have been implicated in its progression and treatment. However, the association of genes involved in the TME with HCC prognosis remains unclear. Thus, in this study, we obtained transcriptomic and clinicopathological data of patients with HCC from The Cancer Genome Atlas to identify key genes in TME associated with HCC prognosis. Stromal and immune cell scores were calculated using the ESTIMATE method, and differentially expressed genes (DEGs) were determined. We identified 830 DEGs, which were further subjected to survival analyses and functional enrichment analysis. Next, we identified prognostic TME-associated DEGs, established a protein-protein interaction (PPI) network, and performed Cox analysis.Consequently, four key prognostic genes (CXCL5, CXCL8, IL18RAP, and TREM2) associated with TME, were identified, in which CXCL5 and IL18RAP may be potential independent prognostic factors. Age, clinical stage, N stage, and risk score were also determined as significant prognostic variables. CIBERSORT was used to predict the constitution and relative content of the immune cells, wherein M0 macrophages were the most closely related to the key genes. In conclusion, CXCL5, CXCL8, IL18RAP, and TREM2 were associated with HCC prognosis and were important for immune cell invasion into the TME. Additionally, IL18RAP expression may contribute toward favorable prognosis in patients with HCC. Consequently, these genes may serve as potential biomarkers and immunotherapeutic targets for HCC.
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Affiliation(s)
- Tianbing Wang
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bang Chen
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tao Meng
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhiqiang Liu
- Department of General Surgery, Anhui NO.2 Provinicial People's Hospital, Hefei, China
| | - Wenyong Wu
- Department of General Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, China.,Department of General Surgery, Anhui NO.2 Provinicial People's Hospital, Hefei, China
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Li C, Liu T, Liu Y, Zhang J, Zuo D. Prognostic value of tumour microenvironment-related genes by TCGA database in rectal cancer. J Cell Mol Med 2021; 25:5811-5822. [PMID: 33949771 PMCID: PMC8184694 DOI: 10.1111/jcmm.16547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 03/15/2021] [Accepted: 03/30/2021] [Indexed: 12/20/2022] Open
Abstract
Rectal cancer is a common malignant tumour and the progression is highly affected by the tumour microenvironment (TME). This study intended to assess the relationship between TME and prognosis, and explore prognostic genes of rectal cancer. The gene expression profile of rectal cancer was obtained from TCGA and immune/stromal scores were calculated by Estimation of Stromal and Immune cells in Malignant Tumors using Expression data (ESTIMATE) algorithm. The correlation between immune/stromal scores and survival time as well as clinical characteristics were evaluated. Differentially expressed genes (DEGs) were identified according to the stromal/immune scores, and the functional enrichment analyses were conducted to explore functions and pathways of DEGs. The survival analyses were conducted to clarify the DEGs with prognostic value, and the protein‐protein interaction (PPI) network was performed to explore the interrelation of prognostic DEGs. Finally, we validated prognostic DEGs using data from the Gene Expression Omnibus (GEO) database by PrognoScan, and we verified these genes at the protein levels using the Human Protein Atlas (HPA) databases. We downloaded gene expression profiles of 83 rectal cancer patients from The Cancer Genome Atlas (TCGA) database. The Kaplan‐Meier plot demonstrated that low‐immune score was associated with worse clinical outcome (P = .034), metastasis (M1 vs. M0, P = .031) and lymphatic invasion (+ vs. ‐, P < .001). A total of 540 genes were screened as DEGs with 539 up‐regulated genes and 1 down‐regulated gene. In addition, 60 DEGs were identified associated with overall survival. Functional enrichment analyses and PPI networks showed that the DEGs are mainly participated in immune process, and cytokine‐cytokine receptor interaction. Finally, 19 prognostic genes were verified by GSE17536 and GSE17537 from GEO, and five genes (ADAM23, ARHGAP20, ICOS, IRF4,MMRN1) were significantly different in tumour tissues compared with normal tissues at the protein level. In summary, our study demonstrated the associations between TME and prognosis as well as clinical characteristics of rectal cancer. Moreover, we explored and verified microenvironment‐related genes, which may be the potential key prognostic genes of rectal cancer. Further clinical samples and functional studies are needed to validate this finding.
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Affiliation(s)
- Chao Li
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Tao Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yi Liu
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Jiantao Zhang
- Department of Colorectal and Anal Surgery, The First Hospital of Jilin University, Changchun, China
| | - Didi Zuo
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
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Lin J, Wu C, Ma D, Hu Q. Identification of P2RY13 as an immune-related prognostic biomarker in lung adenocarcinoma: A public database-based retrospective study. PeerJ 2021; 9:e11319. [PMID: 33996281 PMCID: PMC8106393 DOI: 10.7717/peerj.11319] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/31/2021] [Indexed: 12/17/2022] Open
Abstract
Background Lung adenocarcinoma (LUAD) is the leading histological subtype of non-small cell lung cancer (NSCLC). Methods In the present study, the gene matrixes of LUAD were downloaded from The Cancer Genome Atlas to infer immune and stromal scores with the ‘Estimation of Stromal and Immune cells in Malignant Tumor tissues using Expression data’ (ESTIMATE) algorithm and identified immune-related differentially expressed genes (DEGs) between the high- and low-stromal/immune score groups. Next, all DEGs were subjected to univariate Cox regression and survival analyses to screen out prognostic biomarkers in the tumor microenvironment (TME), and were validated in the Gene Expression Omnibus database. Single-sample gene set enrichment analysis (ssGSEA) was performed to assess the level of tumor-infiltrating immune cells (TIICs) and immune functions, and GSEA was used to identified pathways altered by prognostic biomarkers. Results Survival analysis showed that LUAD in the high-immune and stromal score group had a better clinical prognosis. A total of 303 immune-related DEGs were detected. Univariate Cox regression and survival analyses revealed that P2Y purinoceptor 13 (P2RY13) was a favorable factor for the prognosis of LUAD. ssGSEA and Spearman correlation analysis demonstrated that P2RY13 was highly correlated with various TIICs and immune functions. Several immune-associated pathways were enriched between the high- and low-expression P2RY13 groups. Conclusion P2RY13 may be a potential prognostic indicator and is highly associated with the TME in LUAD. However, further experimental studies are required to validate the present findings.
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Affiliation(s)
- Jiang Lin
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Chunlei Wu
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Dehua Ma
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
| | - Quanteng Hu
- Department of Thoracic Surgery, Taizhou Hospital of Zhejiang Province, Affiliated to Wenzhou Medical University, Taizhou, Zhejiang, China
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Xu Y, Xu Y, Wang C, Xia B, Mu Q, Luan S, Fan J. Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment. PeerJ 2021; 9:e11375. [PMID: 33987033 PMCID: PMC8103916 DOI: 10.7717/peerj.11375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/08/2021] [Indexed: 11/20/2022] Open
Abstract
Background Ovarian cancer is one of the leading causes of female deaths worldwide. Ovarian serous cystadenocarcinoma occupies about 90% of it. Effective and accurate biomarkers for diagnosis, outcome prediction and personalized treatment are needed urgently Methods Gene expression profile for OSC patients was obtained from the TCGA database. The ESTIMATE algorithm was used to calculate immune scores and stromal scores of expression data of ovarian serous cystadenocarcinoma samples. Survival results between high and low groups of immune and stromal score were compared and differentially expressed genes (DEGs) were screened out by limma package. The Gene Ontology (GO), the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and the protein-protein interaction (PPI) network analysis were performed with the g:Profiler database, the Cytoscape and Search Tool for the Retrieval of Interacting Genes (STRING-DB). Survival results between high and low immune and stromal score groups were compared. Kaplan-Meier plots based on TCGA follow up information were generated to evaluate patients’ overall survival. Results Eighty-six upregulated DEGs and one downregulated DEG were identified. Three modules, which included 49 nodes were chosen as important networks. Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were considered to be correlated with poor overall survival. Conclusion Seven DEGs (VSIG4, TGFBI, DCN, F13A1, ALOX5AP, GPX3, SFRP4) were correlated with poor overall survival in our study. This new set of genes can become strong predictor of survival, individually or combined. Further investigation of these genes is needed to validate the conclusion to provide novel understanding of tumor microenvironment with ovarian serous cystadenocarcinoma prognosis and treatment.
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Affiliation(s)
- Youzheng Xu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
| | - Yixin Xu
- Department of Neurology, Qingdao Municipal Hospital, Qingdao, China
| | - Chun Wang
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
| | - Baoguo Xia
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
| | - Qingling Mu
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
| | - Shaohong Luan
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
| | - Jun Fan
- Department of Gynecology, Qingdao Municipal Hospital, Qingdao, China
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Hou Y, Wang X, Wang J, Sun X, Liu X, Hu H, Fan W, Zhang X, Wu D. Cyclin B1 acts as a tumor microenvironment-related cancer promoter and prognostic biomarker in hepatocellular carcinoma. J Int Med Res 2021; 49:3000605211016265. [PMID: 34044639 PMCID: PMC8168034 DOI: 10.1177/03000605211016265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 04/19/2021] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVES The present study aimed to develop a gene signature based on the ESTIMATE algorithm in hepatocellular carcinoma (HCC) and explore possible cancer promoters. METHODS The ESTIMATE and CIBERSORT algorithms were applied to calculate the immune/stromal scores and the proportion of tumor-infiltrating immune cells (TICs) in a cohort of HCC patients. The differentially expressed genes (DEGs) were screened by Cox proportional hazards regression analysis and protein-protein interaction (PPI) network construction. Cyclin B1 (CCNB1) function was verified using experiments. RESULTS The stromal and immune scores were associated with clinicopathological factors and recurrence-free survival (RFS) in HCC patients. In total, 546 DEGs were up-regulated in low score groups, 127 of which were associated with RFS. CCNB1 was regarded as the most predictive factor closely related to prognosis of HCC and could be a cancer promoter. Gene Set Enrichment Analysis (GSEA) and CIBERSORT analyses indicated that CCNB1 levels influenced HCC tumor microenvironment (TME) immune activity. CONCLUSIONS The ESTIMATE signature can be used as a prognosis tool in HCC. CCNB1 is a tumor promoter and contributes to TME status conversion.
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Affiliation(s)
- Yangming Hou
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xin Wang
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Junwei Wang
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xuemei Sun
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinbo Liu
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Han Hu
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Wenzhe Fan
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Xinchen Zhang
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Dequan Wu
- Department of Hepatic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Chen D, Xiong L, Zhang L, Yu H, Xu Y, Wang M, Jiang X, Xiong Z. CSF1R is a Prognostic Biomarker and Correlated with Immune Cell Infiltration in the Gastric Cancer Microenvironment. Pharmgenomics Pers Med 2021; 14:445-457. [PMID: 33880056 PMCID: PMC8053503 DOI: 10.2147/pgpm.s301303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/15/2021] [Indexed: 01/22/2023]
Abstract
Purpose The tumor microenvironment (TME) plays a crucial role in the progression and prognosis of gastric cancer (GC). This study investigated TME-associated genes and explored their roles in the GC microenvironment. Methods A total of 330 GC samples were extracted from TCGA. ESTIMATE and CIBERSORT algorithms were utilized to evaluate the stromal and immune scores of GC samples and the fraction of 22 immune cells infiltrated in the TME. Then, the TME-related differentially expressed genes (DEGs) were determined through integrative analysis. Protein-protein interaction (PPI) network and Cox regression analysis were conducted to analyze DEGs, and CSF1R was determined as the most crucial gene. We further probed the role of CSF1R in the GC microenvironment and evaluated the prognostic value of CSF1R. Results We identified 560 TME-related DEGs and found CSF1R associated with the development and prognosis of GC. Further analysis showed that CSF1R was involved in immune-related signaling pathways. Furthermore, CIBERSORT analysis revealed that CSF1R expression correlated with several kinds of infiltrating immune cells, including tumor-associated macrophages (TAMs), B cells, NK cells, neutrophils, eosinophils, T cells, dendritic cells, and so on. Conclusion In summary, CSF1R might take part in the modulation of immune-active status in the GC microenvironment and could be a promising biomarker for GC therapy and prognosis.
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Affiliation(s)
- Di Chen
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Lina Xiong
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Li Zhang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Honglu Yu
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yushuang Xu
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Mengmeng Wang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Xin Jiang
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Zhifan Xiong
- Department of Gastroenterology, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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Han W, Huang B, Zhao XY, Shen GL. Data mining of immune-related prognostic genes in metastatic melanoma microenvironment. Biosci Rep 2020; 40:BSR20201704. [PMID: 33169786 DOI: 10.1042/BSR20201704] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 11/03/2020] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
Skin cutaneous melanoma (SKCM) is one of the most deadly malignancies. Although immunotherapies showed the potential to improve the prognosis for metastatic melanoma patients, only a small group of patients can benefit from it. Therefore, it is urgent to investigate the tumor microenvironment in melanoma as well as to identify efficient biomarkers in the diagnosis and treatments of SKCM patients. A comprehensive analysis was performed based on metastatic melanoma samples from the Cancer Genome Atlas (TCGA) database and ESTIMATE algorithm, including gene expression, immune and stromal scores, prognostic immune‐related genes, infiltrating immune cells analysis and immune subtype identification. Then, the differentially expressed genes (DEGs) were obtained based on the immune and stromal scores, and a list of prognostic immune‐related genes was identified. Functional analysis and the protein–protein interaction network revealed that these genes enriched in multiple immune-related biological processes. Furthermore, prognostic genes were verified in the Gene Expression Omnibus (GEO) databases and used to predict immune infiltrating cells component. Our study revealed seven immune subtypes with different risk values and identified T cells as the most abundant cells in the immune microenvironment and closely associated with prognostic outcomes. In conclusion, the present study thoroughly analyzed the tumor microenvironment and identified prognostic immune‐related biomarkers for metastatic melanoma.
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Xiang S, Li J, Shen J, Zhao Y, Wu X, Li M, Yang X, Kaboli PJ, Du F, Zheng Y, Wen Q, Cho CH, Yi T, Xiao Z. Identification of Prognostic Genes in the Tumor Microenvironment of Hepatocellular Carcinoma. Front Immunol 2021; 12:653836. [PMID: 33897701 PMCID: PMC8059369 DOI: 10.3389/fimmu.2021.653836] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world. The efficacy of immunotherapy usually depends on the interaction of immunomodulation in the tumor microenvironment (TME). This study aimed to explore the potential stromal-immune score-based prognostic genes related to immunotherapy in HCC through bioinformatics analysis. Methods: ESTIMATE algorithm was applied to calculate the immune/stromal/Estimate scores and tumor purity of HCC using the Cancer Genome Atlas (TCGA) transcriptome data. Functional enrichment analysis of differentially expressed genes (DEGs) was analyzed by the Database for Annotation, Visualization, and Integrated Discovery database (DAVID). Univariate and multivariate Cox regression analysis and least absolute shrinkage and selection operator (LASSO) regression analysis were performed for prognostic gene screening. The expression and prognostic value of these genes were further verified by KM-plotter database and the Human Protein Atlas (HPA) database. The correlation of the selected genes and the immune cell infiltration were analyzed by single sample gene set enrichment analysis (ssGSEA) algorithm and Tumor Immune Estimation Resource (TIMER). Results: Data analysis revealed that higher immune/stromal/Estimate scores were significantly associated with better survival benefits in HCC within 7 years, while the tumor purity showed a reverse trend. DEGs based on both immune and stromal scores primarily affected the cytokine–cytokine receptor interaction signaling pathway. Among the DEGs, three genes (CASKIN1, EMR3, and GBP5) were found most significantly associated with survival. Moreover, the expression levels of CASKIN1, EMR3, and GBP5 genes were significantly correlated with immune/stromal/Estimate scores or tumor purity and multiple immune cell infiltration. Among them, GBP5 genes were highly related to immune infiltration. Conclusion: This study identified three key genes which were related to the TME and had prognostic significance in HCC, which may be promising markers for predicting immunotherapy outcomes.
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Affiliation(s)
- Shixin Xiang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Jing Li
- Department of Oncology and Hematology, Hospital (T.C.M) Affiliated to Southwest Medical University, Luzhou, China
| | - Jing Shen
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yueshui Zhao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xu Wu
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Mingxing Li
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Xiao Yang
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Parham Jabbarzadeh Kaboli
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Fukuan Du
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China
| | - Yuan Zheng
- Neijiang Health and Health Vocational College, Neijiang, China
| | - Qinglian Wen
- Department of Oncology, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Chi Hin Cho
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,South Sichuan Institute of Translational Medicine, Luzhou, China.,Faculty of Medicine, School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Tao Yi
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, China
| | - Zhangang Xiao
- Laboratory of Molecular Pharmacology, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, China.,Department of Pharmacy, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Wang W, Wu Q, Wang Z, Ren S, Shen H, Shi W, Xu Y. Development of a Prognostic Model for Ovarian Cancer Patients Based on Novel Immune Microenvironment Related Genes. Front Oncol 2021; 11:647273. [PMID: 33869044 PMCID: PMC8045757 DOI: 10.3389/fonc.2021.647273] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
Ovarian cancer (OV) has become the most lethal gynecological cancer. However, its treatment methods and staging system are far from ideal. In the present study, taking the advantage of large-scale public cohorts, we extracted a list of immune-related prognostic genes that differentially expressed in tumor and normal ovarian tissues. Importantly, an individualized immune-related gene based prognostic model (IPM) for OV patients were developed. Furthermore, we validated our IPM in Gene Expression Omnibus (GEO) repository and compared the immune landscape and pathways between high-risk and low-risk groups. The results of our study can serve as an important model to identify the immune subset of patients and has potential for use in immune therapeutic selection and patient management.
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Affiliation(s)
- Wei Wang
- Department of Clinical Biobank, Nantong University Affiliated Hospital, Nantong, China.,Department of Medicine, Nantong University Xinling College, Nantong, China
| | - Qianqian Wu
- Department of Clinical Biobank, Nantong University Affiliated Hospital, Nantong, China
| | - Ziheng Wang
- Department of Medicine, Nantong University Xinling College, Nantong, China
| | - Shiqi Ren
- Department of Clinical Biobank, Nantong University Affiliated Hospital, Nantong, China.,Department of Medicine, Nantong University Xinling College, Nantong, China
| | - Hanyu Shen
- Department of Medicine, Nantong University Xinling College, Nantong, China
| | - Wenyu Shi
- Department of Oncology, Affiliated Hospital of Nantong University, Nantong, China
| | - Yunzhao Xu
- Department of Clinical Biobank, Nantong University Affiliated Hospital, Nantong, China.,Department of Obstetrics and Gynecology, Nantong University Affiliated Hospital, Nantong, China
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Zheng Y, Wen Y, Cao H, Gu Y, Yan L, Wang Y, Wang L, Zhang L, Shao F. Global Characterization of Immune Infiltration in Clear Cell Renal Cell Carcinoma. Onco Targets Ther 2021; 14:2085-2100. [PMID: 33790572 PMCID: PMC7997590 DOI: 10.2147/ott.s282763] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/03/2021] [Indexed: 12/26/2022] Open
Abstract
Background Immunotherapy has revolutionized the treatment of clear cell renal cell carcinoma (ccRCC). However, the therapy is constrained by drug resistance. Therefore, further characterization of immune infiltration in ccRCC is needed to improve its efficacy. Methods Here, we adopted the CIBERSORT method to analyze the level of 22 immune cells, and analyzed the correlation of immune cells and clinical parameters in ccRCC in The Cancer Genome Atlas. We used consensus clustering to cluster ccRCC and identified differently expressed genes (DEGs) between hot and cold tumors using the "Limma" package, and then performed enrichment analysis of DEGs. Finally, we constructed and validated a Cox regression model using the "survival", "glmnet", and "survivalROC" packages, implemented in R. Results Regulatory T cells upregulated in tumor tissue increased during tumor progression, and correlated with poor overall survival in ccRCC. Consensus clustering identified four clusters of ccRCC. To elucidate the underlying mechanisms of immune cell infiltration, we subdivided these four clusters into two major types, immune hot and cold, and identified DEGs between them. The results revealed different transcription profiles in the two tumor types, with hot tumors being enriched in immune-related signaling, whereas cold tumors were enriched in extracellular matrix remodeling and the phosphatidylinositol 3-kinase-AKT (PI3K/AKT) pathway. We further identified hub genes and prognostic-related genes from the DEGs, and constructed a Cox regression model for predicting the overall survival of patients with ccRCC. The areas under the receiver operating characteristics curve for the risk model for the training, testing, and external Zhengzhou validation cohorts were 0.834, 0.733, and 0.812, respectively. Notably, gene sets in the prediction model could also predict the overall survival of patients receiving immunotherapy. Conclusion These findings provide a comprehensive characterization of immune infiltration in ccRCC, while the constructed model can be used effectively to predict the overall survival of ccRCC patients.
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Affiliation(s)
- Yan Zheng
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yibo Wen
- Clinical Systems Biology Laboratories, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Huixia Cao
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yue Gu
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Lei Yan
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Yanliang Wang
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Limeng Wang
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Lina Zhang
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
| | - Fengmin Shao
- Henan Provincial Key Laboratory of Kidney Disease and Immunology, Henan Provincial People's Hospital, Zhengzhou, 450052, Henan, People's Republic of China
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Xia ZN, Wang XY, Cai LC, Jian WG, Zhang C. IGLL5 is correlated with tumor-infiltrating immune cells in clear cell renal cell carcinoma. FEBS Open Bio 2021; 11:898-910. [PMID: 33449444 PMCID: PMC7931224 DOI: 10.1002/2211-5463.13085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 02/06/2023] Open
Abstract
Renal cell carcinomas (RCCs) account for about 90% of renal tumors, and their major histological subtype is ccRCC (clear cell RCC). Increasing evidence has indicated that the tumor microenvironment plays a significant role in the occurrence and development of ccRCC. In this study, we used ESTIMATE and CIBERSORT computational methods to calculate the proportion of immune and stromal components and the rate of TICs (tumor‐infiltrating immune cells) in 539 ccRCC samples from The Cancer Genome Atlas database. By examining the intersection of the differentially expressed genes obtained by the protein–protein interaction network and Cox regression analysis, we identified only one overlapping gene: IGLL5 (immunoglobulin lambda‐like polypeptide 5). We report that IGLL5 expression is correlated with TICs. Furthermore, our immunoinfiltration analyses revealed that three types of TIC are positively correlated with IGLL5 expression. IGLL5 may have potential as a prognostic biomarker of ccRCC.
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Affiliation(s)
- Zhi-Nan Xia
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Xing-Yuan Wang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Li-Cheng Cai
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Wen-Gang Jian
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
| | - Cheng Zhang
- Department of Urology, The First Affiliated Hospital of Harbin Medical University, China
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Meng D, Liu T, Ma F, Wang M. Screening the key genes of prognostic value in the microenvironment for head and neck squamous cell carcinoma. Medicine (Baltimore) 2021; 100:e24184. [PMID: 33530209 PMCID: PMC7850760 DOI: 10.1097/md.0000000000024184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 12/12/2020] [Indexed: 01/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth common malignancy worldwide. The tumor microenvironment is highly related to tumor initiation, progression, and prognosis. This study aims to screen the tumor microenvironment related key genes of prognostic value for HNSCC.The gene expression and clinical data for HNSCC were downloaded from the cancer genome atlas (TCGA). The immune/stromal/ESTIMATE scores were downloaded from the website of the MD Anderson Cancer Center. Correlation of patient gender and tumor grade with immune/stromal/ESTIMATE score was tested. Patients were divided into low and high immune/stromal/ESTIMATE score subgroups. Survival analysis was performed to evaluate the prognostic value of the immune/stromal/ESTIMATE score. Tumor microenvironment related differentially expressed genes were determined and applied for functional enrichment analysis and protein-protein interaction network was predicted. The prediction value of the common differentially expressed genes on patient survival was tested.Four hundred eighty samples with complete clinical, expression data, and immune/stromal/ESTIMATE scores were enrolled for analysis. Immune/stromal/ESTIMATE score was higher in female patients than males. A total of 44 common differentially expressed genes were screened in high and low immune/stromal/ESTIMATE score subgroups. Of the 44 genes, 7 genes (ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6) were found to be closely related to patient survival. Enrichment analysis showed that the differentially expressed genes mainly enriched in the protein-coupled receptor signaling pathway, extracellular region, G-protein coupled receptor activity, salivary secretion, and regulation of lipolysis in adipocytes. Protein-protein interaction analysis revealed that POSTN and OGN were crucial microenvironments related genes.Tumor microenvironment related genes ADGRG7, CSN3, CST8, KRT81, MUC7, MYH6, and SEZ6 are valuable predictors for HNSCC patient survival. POSTN and OGN are crucial in modulating the microenvironment and tumor biology for HNSCC.
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Yao Y, Zhang T, Qi L, Liu R, Liu G, Li J, Sun C. Identification of Four Genes as Prognosis Signatures in Lung Adenocarcinoma Microenvironment. Pharmgenomics Pers Med 2021; 14:15-26. [PMID: 33447073 PMCID: PMC7802904 DOI: 10.2147/pgpm.s283414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/01/2020] [Indexed: 01/06/2023]
Abstract
Background Tumor microenvironment (TME) cells constitute a vital element of tumor tissues. Increasing evidence has shown that immune response in the microenvironment plays an active role in tumor invasion, metastasis, and recurrence, and is an important factor affecting tumor prognosis. Our study aimed to identify the gene signatures in lung adenocarcinoma (LUAD) microenvironment for prognosis and immunotherapy. Methods In this study, we evaluated, for the first time, the stromal and immune scores of 594 patients from The Cancer Genome Atlas (TCGA) database with LUAD using the ESTIMATE algorithm. Three hundred and sixty-seven dysregulated immune-related genes were identified. Then, we performed functional enrichment analysis of these genes, and found the best gene model and construct the signature through univariate, Lasso and multivariate COX regression analysis. To assess the independently prognostic ability of the signature, the Kaplan–Meier survival analysis and Cox’s proportional hazards model were performed. Results Functional enrichment analysis and protein–protein interaction networks showed that the immune-related genes mainly played a role in immune response, activation/proliferation of immune-related cells, and chemokine activity. A prognostic model involving 6 genes was constructed and the signature was identified as an independent prognostic factor and significantly associated with the overall survival (OS) of LUAD. The area under curve (AUC) of the receiver operating characteristic curve (ROC curve) for the 6 genes signature in predicting the 3-year survival rate was 0.708. Finally, four genes (FOXN4, KLHL4, FAM83F and CCR2) can be used as candidate prognostic biomarkers for LUAD. Conclusion Our findings will help evaluate the prognosis of LUAD and provide new ideas for exploring the potential relationship between TME and LUAD treatment and prognosis.
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Affiliation(s)
- Yan Yao
- Clinical Medical Colleges, Weifang Medical University, Weifang, Shandong Province, People's Republic of China
| | - Tingting Zhang
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, People's Republic of China
| | - Lingyu Qi
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, People's Republic of China
| | - Ruijuan Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, People's Republic of China
| | - Gongxi Liu
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, People's Republic of China
| | - Jie Li
- College of First Clinical Medicine, Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, People's Republic of China
| | - Changgang Sun
- Department of Oncology, Weifang Traditional Chinese Hospital, Weifang, Shandong Province, People's Republic of China.,Innovative Institute of Chinese Medicine and Pharmacy, Shandong University of Traditional Chinese Medicine, Jinan, Shandong, People's Republic of China
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Abstract
Background Lung adenocarcinoma (LUAD) is the most common histological type of lung cancers, which is the primary cause of cancer‐related mortality worldwide. Growing evidence has suggested that tumor microenvironment (TME) plays a pivotal role in tumorigenesis and progression. Hence, we investigate the correlation of TME related genes with LUAD prognosis. Method The information of LUAD gene expression data was obtained from The Cancer Genome Atlas (TCGA). According to their immune/stromal scores calculated by the ESTIMATE algorithm, differentially expressed genes (DEGs) were identified. Then, we performed univariate Cox regression analysis on DEGs to obtain genes that are apparently bound up with LUAD survival (SurGenes). Functional annotation and protein-protein interaction (PPI) was also conducted on SurGenes. By validating the SurGenes with data sets of lung cancer from the Gene Expression Omnibus (GEO), 106 TME related SurGenes were generated. Further, intersection analysis was executed between the 106 TME related SurGenes and hub genes from PPI network, PTPRC and CD19 were obtained. Gene Set Enrichment Analysis and CIBERSORT analysis were performed on PTPRC and CD19. Based on the TCGA LUAD dataset, we conducted factor analysis and Step-wise multivariate Cox regression analysis for 106 TME related SurGenes to construct the prognostic model for LUAD survival prediction. The LUAD dataset in GEO (GSE68465) was used as the testing dataset to confirm the prognostic model. Multivariate Cox regression analysis was used between risk score from the prognostic model and clinical parameters. Result A total of 106 TME related genes were collected in our research totally, which were markedly correlated with the overall survival (OS) of LUAD patient. Bioinformatics analysis suggest them mainly concentrated on immune response, cell adhesion, and extracellular matrix. More importantly, among 106 TME related SurGenes, PTPRC and CD19 were highly interconnected nodes among PPI network and correlated with immune activity, exhibiting significant prognostic potential. The prognostic model was a weighted linear combination of the 106 genes, by which the low-OS LUAD samples could be separated from the high-OS samples with success. This model was also able to rebustly predict the situation of survival (training set: p-value < 0.0001, area under the curve (AUC) = 0.649; testing set: p-value = 0.0009, AUC = 0.617). By combining with clinical parameters, the prognostic model was optimized. The AUC achieved 0.716 for 3 year and 0.699 for 5 year. Conclusion A series of TME-related prognostic genes were acquired in this research, which could reflect immune disorders within TME, and PTPRC and CD19 show the potential to be an indicator for LUAD prognosis and tumor microenvironment modulation. The prognostic model constructed base on those prognostic genes presented a high predictive ability, and may have clinical implications in the overall survival prediction of LUAD.
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Affiliation(s)
- Juan Chen
- Respiratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Rui Zhou
- Respiratory Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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Qin XJ, Lin X, Xue G, Fan HL, Wang HY, Wu JF, Pei D. CXCL10 is a potential biomarker and associated with immune infiltration in human papillary thyroid cancer. Biosci Rep 2021; 41:BSR20203459. [PMID: 33345267 DOI: 10.1042/BSR20203459] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/23/2020] [Accepted: 12/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background: In recent years, the annual incidence of thyroid cancer (TC) has increased, with papillary thyroid cancer (PTC) identified as the most commonwinwordpathological type accounting for approximately 80% of all thyroid cancer cases. The tumor microenvironment is known to play a vital role in tumor information transmission and immune detection. Methods: In the present study, we examined gene expression data from 518 patients with PTC. The ESTIMATE algorithm was used to calculate immune and stromal scores of PTC patients. Based on a protein–protein interaction (PPI) network, functional enrichment and overall survival analyses, C-X-C motif chemokine ligand 10 (CXCL10) was identified as a core gene. We further investigated the roles of core genes of PTC in the tumor immune microenvironment using LinkedOmics, GSEA, and TIMER tools. Results: Immune, stromal and ESTIMATE scores were related to clinicopathological variables of patients with PTC, but not survival outcomes. Eight differentially expressed genes (DEGs) were associated with survival outcome. In addition, immunochemical staining experiments revealed lower expression of CXCL10 in PTC than paracancerous tissues. GSEA pathway enrichment analysis revealed downregulation of CXCL10 in multiple cancer pathways. CXCL10 and related genes were enriched in pathways related to adaptive immune response, cellular defense response and regulation of innate immune response. Conclusion: The tumor microenvironment plays a critical role in development of PTC and CXCL10 may serve as a novel target of precision therapy for this patient population.
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Aizemaiti R, Wu Z, Tang J, Yan H, Lv X. Heat shock factor 5 correlated with immune infiltration serves as a prognostic biomarker in lung adenocarcinoma. Int J Med Sci 2021; 18:448-458. [PMID: 33390814 PMCID: PMC7757139 DOI: 10.7150/ijms.51297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 11/05/2020] [Indexed: 01/09/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is the predominant subtype of lung cancer with a relatively poor prognosis. The dramatic improvements of new immunotherapy strategies have shown promising results in lung cancer patients. This study aimed to elucidate the functions of immune-associated genes in LUAD prognosis and pathogenesis by analyzing public databases. We obtained expression profiles of LUAD patients from The Cancer Genome Atlas (TCGA) database and applied the ESTIMATE algorithm to calculate immune scores and stromal scores. A series of microenvironment-related genes with prognostic value was then identified. Of note, heat shock factor 5 (HSF5) was found to be decreased in LUAD patients and positively correlated with overall survival, which was further confirmed in the Gene Expression Omnibus (GEO) database. Moreover, Gene Ontology (GO) analysis based on the correlated genes of HSF5 demonstrated that HSF5 expression was significantly associated with the immune response and inflammatory activities. Based on the Tumor IMmune Estimation Resource (TIMER) and Gene Expression Profiling Interactive Analysis (GEPIA) datasets, HSF5 expression showed strong correlations with various immune cell infiltration and diverse immune marker sets. These findings suggest that HSF5 can be used as a promising biomarker for determining prognosis and immune infiltration in LUAD patients.
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Affiliation(s)
- Rusidanmu Aizemaiti
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Zhigang Wu
- Zhejiang University School of Medicine, Yuhangtang Road 866, Hangzhou, China, 310009
| | - Jie Tang
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Haimeng Yan
- Bone Marrow Transplantation Center, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
| | - Xiayi Lv
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhejiang University, Qingchun Road 79, Hangzhou, China, 310009
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Guo JC, Yang YJ, Guo M, Zhang JQ, Zheng JF, Liu Z. Involvement of CDK11B-mediated SPDEF ubiquitination and SPDEF-mediated microRNA-448 activation in the oncogenicity and self-renewal of hepatocellular carcinoma stem cells. Cancer Gene Ther 2020; 28:1136-1149. [PMID: 33328586 DOI: 10.1038/s41417-020-00261-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 10/25/2020] [Accepted: 11/10/2020] [Indexed: 11/09/2022]
Abstract
Increasing evidence has suggested the crucial role cyclin-dependent kinases (CDKs) in the biology of hepatocellular carcinoma (HCC), a lethal malignancy with high morbidity and mortality. Hence, this study explored the modulatory effect of the putative cyclin-dependent kinase 11B (CDK11B)-mediated ubiquitination on HCC stem cells. The expression of CDK11B, SAM pointed domain-containing ETS transcription factor (SPDEF) and DOT1-like histone lysine methyltransferase (DOT1L) was determined by RT-qPCR and western blot analysis in HCC tissues and cells. The interaction among CDK11B, SPDEF, miR-448, and DOT1L was analyzed by Co-IP, ubiquitination-IP and ChIP assays, whereas their effects on the biological characteristics of HCC stem cells were assessed by sphere formation and colony formation assays. An in vivo xenograft tumor model was developed for validating the regulation of CDK11B in oncogenicity of HCC stem cells. We characterized the aberrant upregulation of CDK11B and downregulation SPDEF in HCC tissues and cells. CDK11B degraded SPDEF through ubiquitin-proteasome pathway, whereas SPDEF could bind to the miR-448 promoter and inhibit the expression of DOT1L by activating miR-448, whereby promoting self-renewal of HCC stem cells. Knockdown of CDK11B attenuated the self-renewal capability of HCC stem cells and their oncogenicity in vivo. These findings highlighted that blocking the CDK11B-induced degradation of SPDEF and enhancing miR-448-dependent inhibition of DOT1L may delay the progression of HCC by restraining self-renewal capability of HCC stem cells, representing novel targets for HCC management.
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Affiliation(s)
- Jun-Cheng Guo
- Department of Hepatobiliary Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, 570208, P. R. China
| | - Yi-Jun Yang
- Department of Hepatobiliary Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, 570208, P. R. China.
| | - Min Guo
- Psychological Research Center, Hainan General Hospital, Haikou, 570311, P. R. China
| | - Jian-Quan Zhang
- Department of Hepatobiliary Surgery, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, 570208, P. R. China.
| | - Jin-Fang Zheng
- Department of Hepatobiliary Surgery, Hainan General Hospital, Haikou, 570311, P. R. China
| | - Zhuo Liu
- School of Public Health, Hainan Medical University, Haikou, 571199, P. R. China
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Zhang Z, Wu Q, Zhu D, He G, Feng Q, Xu J. Tumor microenvironment derived signature predicting relapse-free survival in I-III cancer and preliminary experiment verification. Int Immunopharmacol 2021; 91:107243. [PMID: 33321467 DOI: 10.1016/j.intimp.2020.107243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/20/2020] [Accepted: 11/24/2020] [Indexed: 02/07/2023]
Abstract
The recurrence in colon cancer contributed to great difficulties in diagnostic and therapeutic treatment. Tumor microenvironment (TME) gains increasing attention recently. After univariate Cox analysis on relapse-free survival (RFS) and ESTIMATE analysis, WGCNA was further conducted to determine the TME and relapse-related genes in I-III colon cancer. Functional enrichment analyses were conducted. Furthermore, seven genes were screened to build a prognostic signature via LASSO and multivariate Cox analysis. Univariate followed multivariate Cox analysis all showed that the risk group calculated by the signature as a significant predictors. The ROC curves showed great prognostic in the internal training group, internal verification group, and independent external verification group. In the training group, the AUC at 1, 3, and 5 years was 0.737, 0.79, and 0.756. In addition, correlation analysis presented that the signature and genes involved in were significantly associated with the TME. Moreover, 3 of 7 genes (FAM78A, SGIP1, and MMP9) were validated to be associated with PDL1 through qRT-PCR.
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Liu S, Tian W, Li B. Prognostic Hub Genes in the Immune Microenvironment of Lung Adenocarcinoma by Estimation. Comb Chem High Throughput Screen 2020; 25:77-89. [PMID: 33308118 DOI: 10.2174/1386207323666201211090604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 10/23/2020] [Accepted: 10/24/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND The mortality of lung adenocarcinoma(LUAD) is high. Recent studies have found that the degree of immune infiltration and stromal cells in the tumour microenvironment or tumours makes a significant contribution to prognosis. METHODS During study, we screened differentially expressed genes (DEGs) of TCGA database for prognostic genes in LUAD immune microenvironment. Further, immune and stromal cells were quantified using ESTIMATE algorithm. To study the effects of immune and stromal cell-associated genes on the prognosis of LUAD, LUAD patients were divided into high and low groups according to their immune/ stromal scores. The obtained scores were found to be related to the phenotype and survival rate of LUAD patients. By selecting DEGs with high expression in immune and stromal cells, we performed functional enrichment analysis and found that most genes are associated with pathways of cancer, stimulus response and the MAPK signaling. The functions and enriched pathways of LUAD prognostic genes were shown by a protein-protein interaction (PPI) network. Nonetheless, an external database was used to validate the prognostic genes from the TCGA. RESULTS Prognostic genes were listed according to their expression position and protein function. CONCLUSION We provided a new targets for immunotherapy of LUAD, which further provides basic knowledge for future clinical research.
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Affiliation(s)
- Shanshan Liu
- Department of Clinical Laboratory, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004. China
| | - Wenjuan Tian
- Department of Clinical Laboratory, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004. China
| | - Burong Li
- Department of Clinical Laboratory, Second Affiliated Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, 710004. China
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Abstract
Background: As a common pathological type of lung cancer, lung adenocarcinoma (LUAD) is
mainly treated by surgery, chemotherapy, targeted therapy and radiotherapy.
Although a relatively mature treatment system has been established, there
are few studies on the microenvironment of LUAD. Material and Methods: The immune and stromal scores of patients from the LUAD cohort in the TCGA
database were obtained by using ESTIMATE. The relationship of immune and
stromal scores with the clinicopathological characteristics and overall
survival of LUAD patients was assessed by R. GO, KEGG and Cox regression
analyses were employed to analyze intersecting genes and to identify
reliable prognostic markers. The identified genes were also analyzed in the
GEPIA database to assess their correlations with survival, and these
relationships were verified with the Kaplan-Meier Plotter database. Results: The immune score was related to the survival time and tumor topography of
LUAD patients. There was a significant correlation between stromal score and
tumor metastasis. Through multivariate analysis, stage (HR = 1.640, 95% CI =
1.019-2.642, P = 0.042) and risk score (HR = 1.036, 95% CI
= 1.026-1.046, P < 0.001). The genes (ARHGAP15, BTLA,
CASS4, CLECL1, FAM129C, STAP1, TESPA1, and S100P) showed credible prognostic
value in LUAD patients in TCGA through GEPIA database online analysis and
verification in the Kaplan-Meier plotter database. Conclusions: In the microenvironment of lung adenocarcinoma, the differentially expressed
genes screened by immune score and stromal score have certain value in
evaluating the survival/prognosis of patients, as well as the invasion and
progression of tumors.
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Affiliation(s)
- Rongchang Zhao
- Department of Oncology, Taixing people's Hospital Affiliated to Bengbu Medical College, Taixing, China
| | - Dan Ding
- Department of Oncology, Taixing people's Hospital Affiliated to Bengbu Medical College, Taixing, China
| | - Wenyan Yu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chunrong Zhu
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yan Ding
- Department of Oncology, Taixing people's Hospital Affiliated to Bengbu Medical College, Taixing, China
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Wu F, Chen W, Kang X, Jin L, Bai J, Zhang H, Zhang X. A seven-nuclear receptor-based prognostic signature in breast cancer. Clin Transl Oncol 2021; 23:1292-303. [PMID: 33210236 DOI: 10.1007/s12094-020-02517-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/21/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Breast cancer (BRCA) is a malignant cancer that threatened the life of female with unsatisfactory prognosis. The aim of this study was to identify prognostic nuclear receptors (NRs) signature of BRCA. METHODS BRCA patient samples were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database. Consensus clustering analysis, univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) Cox regression analysis were performed to evaluate, select NRs as prognostic factors and build Risk Score model. GSEA analysis was explored to check signaling differences between High- and Low-Risk group. Nomogram model basing on age and Risk Score was established to predict the 1-, 3- and 5-year survival. Model performance was assessed by a time-dependent receiver operating characteristic (ROC) curve and calibration plot. CIBERSORT, ESTIMATE and TIMER algorithm were introduced to evaluate the immune landscape. RESULTS NR3C1, NR4A3, THRA, RXRG, NR2F6, NR1D2 and RORB were optimized as a prognostic signature for BRCA. This seven-NR-based Risk Score could effectively predict overall survival status. The area under the curve (AUC) of 1-, 3- and 5-year overall survival are 0.702, 0.734 and 0.722 in TCGA training cohort, and 0.630, 0.721 and 0.823 in GEO validation cohort, respectively. Calibration plot demonstrated satisfactory agreement between predictive and observed outcomes. Nomogram model worked well on predicting survival probabilities. Multiple cancer-related pathways were highly enriched in High-Risk group. High- and Low-Risk groups showed significant differed immune cell infiltration. There exists an obvious connection between Risk Score and immune checkpoints LAG3, PD1 and TIM3. CONCLUSION The seven-NR-based Risk Score represents a promising signature for estimating overall survival in patients with BRCA, and is correlated with the immune microenvironment.
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