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Zhang L, Xu F, Lu H, Dong X, Gao Z, Zhao Q, Weng T, Li H, Ye H. Data-independent acquisition (DIA) mass spectrometry reveals related proteins involved in the occurrence of early intestinal-type gastric cancer. Med Oncol 2023; 41:23. [PMID: 38114688 DOI: 10.1007/s12032-023-02241-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/07/2023] [Indexed: 12/21/2023]
Abstract
Identifying proteins associated with the onset of early intestinal-type gastric cancer (EIGC) can yield valuable insights into the pathogenesis of this specific subtype of gastric cancer. Data-independent acquisition mass spectroscopy (DIA-MS) was utilized to identify the differential protein between 10 cases of EIGC and atrophic gastritis with intestinal metaplasia (NGC). The expressions of IPO4, TBL1XR1, p62/SQSTM1, PKP3, and CRTAP were verified by immunohistochemistry (IHC) in 20 EIGC samples, 17 gastric low-grade intraepithelial neoplasia (LGIN) samples, and 21 healthy controls. The prognostic values of the five genes were validated in the transcriptome data by survival analysis. A total of 4,028 proteins were identified using DIA-MS and a total of 177 differential proteins were screened with log2(fold change) > 1.5. Among them, 113 proteins were significantly up-regulated, and 64 proteins were significantly down-regulated in EIGC tissues. IHC results showed that proteins IPO4, TBL1XR1, p62/SQSTM1, PKP3, and CRTAP were highly expressed in the cytoplasm of EIGC and LGIN, which was consistent with the results of DIA-MS. Among them, p62/SQSTM1 may undergo nuclear-cytoplasmic transfer. The five protein-coding genes were associated with intestinal-type gastric cancer survival and exhibited differential expression across various disease stages. The study successfully identified differentially expressed proteins between EIGC and NGC, providing potential biomarkers and valuable insights into the mechanism underlying intestinal-type gastric cancer.
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Affiliation(s)
- Liangshun Zhang
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Feng Xu
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Hongna Lu
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Xianwen Dong
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Zhiqiang Gao
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Qiaosu Zhao
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Ting Weng
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China
| | - Hong Li
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China.
| | - Hua Ye
- The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315046, Zhejiang, People's Republic of China.
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Zhong C, Yang D, Zhong L, Xie W, Sun G, Jin D, Li Y. Single-cell and bulk RNA sequencing reveals Anoikis related genes to guide prognosis and immunotherapy in osteosarcoma. Sci Rep 2023; 13:20203. [PMID: 37980450 PMCID: PMC10657454 DOI: 10.1038/s41598-023-47367-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/13/2023] [Indexed: 11/20/2023] Open
Abstract
Anoikis resistance, a notable factor in osteosarcoma, plays a significant role in tumor invasion and metastasis. This study seeks to identify a distinct gene signature that is specifically associated with the anoikis subcluster in osteosarcoma. Clinical, single-cell, and transcriptional data from TARGET and GEO datasets were used to develop a gene signature for osteosarcoma based on the anoikis subcluster. Univariate Cox and LASSO regression analyses were employed. The signature's predictive value was evaluated using time-dependent ROC and Kaplan-Meier analyses. Functional enrichment analyses and drug sensitivity analyses were conducted. Validation of three modular genes was performed using RT-qPCR and Western blotting. Signature (ZNF583, CGNL1, CXCL13) was developed to predict overall survival in osteosarcoma patients, targeting the anoikis subcluster. The signature demonstrated good performance in external validation. Stratification based on the signature revealed significantly different prognoses. The signature was an independent prognostic factor. The low-risk group showed enhanced immune cell infiltration and improved immune function. Drug sensitivity analysis indicated efficacy of chemotherapy agents. Prognostic nomograms incorporating the signature provided greater predictive accuracy and clinical utility. Signatures related to the anoikis subcluster play a significant role in osteosarcoma progression. Incorporating these findings into clinical decision-making can improve osteosarcoma treatment and patient outcomes.
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Affiliation(s)
- Cheng Zhong
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China
- Department of Orthopedics, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China
| | - Dongliang Yang
- Department of Orthopedics, Tai Shan Hospital of Traditional Chinese Medicine Affiliated to Guangzhou University of Chinese Medicine, Jiangmen, 529000, China
| | - Liping Zhong
- Department of Cardiothoracic Surgery, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China
| | - Weixing Xie
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China
| | - Guodong Sun
- Department of Orthopedics, The First Affiliated Hospital of Jinan University, Guangzhou, 510630, China
| | - Daxiang Jin
- Department of Orthopedics, The First Clinical Medical College of Guangzhou University of Chinese Medicine, Guangzhou, 515000, China.
| | - Yuming Li
- Department of Orthopedics, Jiangmen Hospital of Traditional Chinese Medicine Affiliated to Jinan University, Jiangmen, 529000, China.
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Yang X, Fu Q, Zhang W, An Q, Zhang Z, Li H, Chen X, Chen Z, Cheng Y, Chen S, Man C, Du L, Chen Q, Wang F. Overexpression of Pasteurella multocida OmpA induces transcriptional changes and its possible implications for the macrophage polarization. Microb Pathog 2023; 183:106212. [PMID: 37353176 DOI: 10.1016/j.micpath.2023.106212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Pasteurella multocida (P. multocida) is a highly infectious, zoonotic pathogen. Outer membrane protein A (OmpA) is an important virulence component of the outer membrane of P. multocida. OmpA mediates bacterial biofilm formation, eukaryotic cell infection, and immunomodulation. It is unclear how OmpA affects the host immune response. We estimated the role of OmpA in the pathogenesis of P. multocida by investigating the effect of OmpA on the immune cell transcriptome. Changes in the transcriptome of rat alveolar macrophages (NR8383) upon overexpression of P. multocida OmpA were demonstrated. A model cell line for stable transcription of OmpA was constructed by infecting NR8383 cells with OmpA-expressing lentivirus. RNA was extracted from cells and sequenced on an Illumina HiSeq platform. Key gene analysis of genes in the RNA-seq dataset were performed using various bioinformatics methods, such as gene ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Gene Set Enrichment Analysis, and Protein-Protein Interaction Analysis. Our findings revealed 1340 differentially expressed genes. Immune-related pathways that were significantly altered in rat alveolar macrophages under the effect of OmpA included focal adhesion, extracellular matrix and vascular endothelial growth factor signaling pathways, antigen processing and presentation, nucleotide oligomerization domain-like receptor and Toll-like receptor signaling pathways, and cytokine-cytokine receptor interaction. The key genes screened were Vegfa, Igf2r, Fabp5, P2rx1, C5ar1, Nedd4l, Gas6, Cxcl1, Pf4, Pdgfb, Thbs1, Col7a1, Vwf, Ccl9, and Arg1. Data of associated pathways and altered gene expression indicated that OmpA might cause the conversion of rat alveolar macrophages to M2-like. The related pathways and key genes can serve as a reference for OmpA of P. multitocida and host interaction mechanism studies.
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Affiliation(s)
- Xiaohong Yang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Qiaoyu Fu
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Wencan Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Qi An
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Zhenxing Zhang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Hong Li
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Xiangying Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Zhen Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Yiwen Cheng
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Si Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Churiga Man
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China
| | - Li Du
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China.
| | - Qiaoling Chen
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China.
| | - Fengyang Wang
- Hainan Key Lab of Tropical Animal Reproduction, Breeding and Epidemic Disease Research, Animal Genetic Engineering Key Lab of Haikou, School of Animal Science and Technology, Hainan University, Haikou, Hainan, China.
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Chen M, Zhu X, Zhang L, Zhao D. COL5A2 is a prognostic-related biomarker and correlated with immune infiltrates in gastric cancer based on transcriptomics and single-cell RNA sequencing. BMC Med Genomics 2023; 16:220. [PMID: 37723519 PMCID: PMC10506210 DOI: 10.1186/s12920-023-01659-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 09/09/2023] [Indexed: 09/20/2023] Open
Abstract
BACKGROUND There is still a therapeutic challenge in treating gastric cancer (GC) due to its high incidence and poor prognosis. Collagen type V alpha 2 (COL5A2) is increased in various cancers, yet it remains unclear how it contributes to the prognosis and immunity of GC. METHODS The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) datasets were used to download transcriptome profiling (TCGA-STAD; GSE84437), single-cell RNA sequencing (scRNA-seq) data (GSE167297) and clinical information. COL5A2 expression and its relationship with clinicopathological factors were analyzed. We conducted survival analysis and Cox regression analysis to evaluate the prognosis and independent factors of GC. Co-expressed analysis was also performed. To identify the underlying mechanism, we conducted analyses of differentially expressed genes (DEGs) and functional enrichment. The correlations between COL5A2 expression and immune cell infiltration levels and immune infiltrate gene marker sets were further explored. Additionally, we analyzed the association of COL5A2 expression with immunological checkpoint molecules. Furthermore, the relationship between COL5A2 expression and immunotherapy sensitivity was also investigated. RESULTS COL5A2 expression was elevated in GC. More than this, the scRNA-seq analysis revealed that COL5A2 expression had a spatial gradient. The upregulated COL5A2 was associated with worse overall survival. A significant correlation was found between COL5A2 overexpression and age, T classification and clinical stage in GC. COL5A2 was found to be an independent factor for the unfortunate outcome in Cox regression analysis. The co-expressed genes of COL5A2 were associated with tumor stage or poor survival. Enrichment analysis revealed that the DEGs were mainly associated with extracellular matrix (ECM)-related processes, PI3K-AKT signaling pathway, and focal adhesion. GSEA analyses revealed that COL5A2 was associated with tumor progression-related pathways. Meanwhile, COL5A2 expression was correlated with tumor-infiltrating immune cells. Moreover, immunophenoscore (IPS) analysis and PRJEB25780 cohorts showed that patients with low COL5A2 expression were highly sensitive to immunotherapy. CONCLUSIONS COL5A2 might act as a prognostic biomarker of GC prognosis and immune infiltration and may provide a therapeutic intervention strategy.
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Affiliation(s)
- Meiru Chen
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, 050000, China
- Department of Gastroenterology, Hengshui People's Hospital, Hengshui, Hebei Province, 053000, China
| | - Xinying Zhu
- Department of Gastroenterology, The Third Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, 050000, China
| | - Lixian Zhang
- Department of Gastroenterology, Hengshui People's Hospital, Hengshui, Hebei Province, 053000, China
| | - Dongqiang Zhao
- Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei Province, 050000, China.
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Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci 2023; 24:ijms24108961. [PMID: 37240307 DOI: 10.3390/ijms24108961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Transfer RNA fragments (tRFs) have gene silencing effects similarly to miRNAs, can be sorted into extracellular vesicles (EVs) and are emerging as potential circulating biomarkers for cancer diagnoses. We aimed at analyzing the expression of tRFs in gastric cancer (GC) and understanding their potential as biomarkers. We explored miRNA datasets from gastric tumors and normal adjacent tissues (NATs) from TCGA repository, as well as proprietary 3D-cultured GC cell lines and corresponding EVs, in order to identify differentially represented tRFs using MINTmap and R/Bioconductor packages. Selected tRFs were validated in patient-derived EVs. We found 613 Differentially Expressed (DE)-tRFs in the TCGA dataset, of which 19 were concomitantly upregulated in TCGA gastric tumors and present in 3D cells and EVs, but barely expressed in NATs. Moreover, 20 tRFs were expressed in 3D cells and EVs and downregulated in TCGA gastric tumors. Of these 39 DE-tRFs, 9 tRFs were also detected in patient-derived EVs. Interestingly, the targets of these 9 tRFs affect neutrophil activation and degranulation, cadherin binding, focal adhesion and the cell-substrate junction, highlighting these pathways as major targets of EV-mediated crosstalk with the tumor microenvironment. Furthermore, as they are present in four distinct GC datasets and can be detected even in low quality patient-derived EV samples, they hold promise as GC biomarkers. By repurposing already available NGS data, we could identify and cross-validate a set of tRFs holding potential as GC diagnosis biomarkers.
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Affiliation(s)
- Joaquín J Maqueda
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
| | - Mafalda Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Sérgio Marinho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sara Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Mafalda Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Nadine Saraiva
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Nuno Bonito
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Joana Carvalho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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Cheng X, Liu Z, Liang W, Zhu Q, Wang C, Wang H, Zhang J, Li P, Gao Y. ECM2, a prognostic biomarker for lower grade glioma, serves as a potential novel target for immunotherapy. Int J Biochem Cell Biol 2023; 158:106409. [PMID: 36997057 DOI: 10.1016/j.biocel.2023.106409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Extracellular matrix protein 2 (ECM2), which regulates cell proliferation and differentiation, has recently been reported as a prognostic indicator for multiple cancers, but its value in lower grade glioma (LGG) remains unknown. In this study, LGG transcriptomic data of 503 cases in The Cancer Genome Atlas (TCGA) database and 403 cases in The Chinese Glioma Genome Atlas (CGGA) database were collected to analyze ECM2 expression patterns and the relationship with clinical characteristics, prognosis, enriched signaling pathways, and immune-related markers. In addition, a total of 12 laboratory samples were used for experimental validation. Wilcoxon or Kruskal-Wallis tests demonstrated highly expressed ECM2 in LGG was positively associated with malignant histological features and molecular features such as recurrent LGG and isocitrate dehydrogenase (IDH) wild-type. Also, Kaplan-Meier (KM) curves proved high ECM2 expression could predict shorter overall survival in LGG patients, as multivariate analysis and meta-analysis claimed ECM2 was a deleterious factor for LGG prognosis. In addition, the enrichment of immune-related pathways for ECM2, for instance JAK-STAT pathway, was obtained by Gene Set Enrichment Analysis (GSEA) analysis. Furthermore, positive relationships between ECM2 expression with immune cells infiltration and cancer-associated fibroblasts (CAFs), iconic markers (CD163), and immune checkpoints (CD274, encoding PD-L1) were proved by Pearson correlation analysis. Finally, laboratory experiments of RT-qPCR and immunohistochemistry showed high expression of ECM2, as well as CD163 and PD-L1 in LGG samples. This study identifies ECM2, for the first time, as a subtype marker and prognostic indicator for LGG. ECM2 could also provide a reliable guarantee for further personalized therapy, synergizing with tumor immunity, to break through the current limitations and thus reinvigorating immunotherapy for LGG. AVAILABILITY OF DATA AND MATERIALS: Raw data from all public databases involved in this study are stored in the online repository (chengMD2022/ECM2 (github.com)).
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Feng J, Tang X, Song L, Zhou Z, Jiang Y, Huang Y. A telomerase regulation-related lncRNA signature predicts prognosis and immunotherapy response for gastric cancer. J Cancer Res Clin Oncol 2023; 149:135-146. [PMID: 36333566 DOI: 10.1007/s00432-022-04456-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Telomeres are involved in the development and progression of gastric cancer (GC). However, the association of telomerase regulation-related lncRNAs with prognosis and immunotherapy responsiveness in gastric cancer is unclear. METHODS This study systematically evaluated the relationship between lncRNAs co-expressed with 67 telomerase regulatory genes and gastric cancer prognosis. The risk scores of the samples were calculated based on telomerase regulation-related lncRNAs with prognostic value, and the samples were classified into high-/low-risk groups. The prognostic value of risk groups was then evaluated, a GC prognostic prediction model based on risk groups and clinical characteristics was established, and the prediction accuracy of the model was clarified by receiving operating characteristic (ROC) curves and calibration curves. Finally, the value of risk grouping in GC immunotherapy sensitivity was predicted by comparing MSI status and tumor mutation load between the high- and low-risk groups. RESULTS We identified 13 lncRNAs with prognostic value co-expressed with telomerase regulatory genes and observed that the prognosis of the low-risk group was significantly better than that of the high-risk group. Meanwhile, a GC overall survival (OS) prediction model based on risk grouping and clinical characteristics was developed, and ROC curves and calibration curves confirmed the good predictive ability of the model. In addition, the low-risk group exhibited a higher tumor mutation load and MSI-H, suggesting a possible benefit of immunotherapy. CONCLUSION We found that telomerase regulation-related lncRNAs have prognostic value in GC patients and contribute to the exploration of more effective immunotherapeutic strategies.
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Affiliation(s)
- Jinggao Feng
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China.
| | - Xiayu Tang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Liusong Song
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Zhipeng Zhou
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yuan Jiang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
| | - Yao Huang
- Department of Gastrointestinal and Anorectal Surgery, The Central Hospital of Yongzhou, No. 151, Xiaoshui West Road, Lingling District, Yongzhou, 425100, Hunan Province, China
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Xu F, Yan J, Peng Z, Liu J, Li Z. Comprehensive analysis of a glycolysis and cholesterol synthesis-related genes signature for predicting prognosis and immune landscape in osteosarcoma. Front Immunol 2022; 13:1096009. [PMID: 36618348 PMCID: PMC9822727 DOI: 10.3389/fimmu.2022.1096009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
Background Glycolysis and cholesterol synthesis are crucial in cancer metabolic reprogramming. The aim of this study was to identify a glycolysis and cholesterol synthesis-related genes (GCSRGs) signature for effective prognostic assessments of osteosarcoma patients. Methods Gene expression data and clinical information were obtained from GSE21257 and TARGET-OS datasets. Consistent clustering method was used to identify the GCSRGs-related subtypes. Univariate Cox regression and LASSO Cox regression analyses were used to construct the GCSRGs signature. The ssGSEA method was used to analyze the differences in immune cells infiltration. The pRRophetic R package was utilized to assess the drug sensitivity of different groups. Western blotting, cell viability assay, scratch assay and Transwell assay were used to perform cytological validation. Results Through bioinformatics analysis, patients diagnosed with osteosarcoma were classified into one of 4 subtypes (quiescent, glycolysis, cholesterol, and mixed subtypes), which differed significantly in terms of prognosis and tumor microenvironment. Weighted gene co-expression network analysis revealed that the modules strongly correlated with glycolysis and cholesterol synthesis were the midnight blue and the yellow modules, respectively. Both univariate and LASSO Cox regression analyses were conducted on screened module genes to identify 5 GCSRGs (RPS28, MCAM, EN1, TRAM2, and VEGFA) constituting a prognostic signature for osteosarcoma patients. The signature was an effective prognostic predictor, independent of clinical characteristics, as verified further via Kaplan-Meier analysis, ROC curve analysis, univariate and multivariate Cox regression analysis. Additionally, GCSRGs signature had strong correlation with drug sensitivity, immune checkpoints and immune cells infiltration. In cytological experiments, we selected TRAM2 as a representative gene to validate the validity of GCSRGs signature, which found that TRAM2 promoted the progression of osteosarcoma cells. Finally, at the pan-cancer level, TRAM2 had been correlated with overall survival, progression free survival, disease specific survival, tumor mutational burden, microsatellite instability, immune checkpoints and immune cells infiltration. Conclusion Therefore, we constructed a GCSRGs signature that efficiently predicted osteosarcoma patient prognosis and guided therapy.
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Affiliation(s)
- Fangxing Xu
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jinglong Yan
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China,*Correspondence: Jinglong Yan,
| | - Zhibin Peng
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Jingsong Liu
- Department of Orthopedics, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Zecheng Li
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Reza MS, Hossen MA, Harun-Or-Roshid M, Siddika MA, Kabir MH, Mollah MNH. Metadata analysis to explore hub of the hub-genes highlighting their functions, pathways and regulators for cervical cancer diagnosis and therapies. Discov Oncol 2022; 13:79. [PMID: 35994213 PMCID: PMC9395557 DOI: 10.1007/s12672-022-00546-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/11/2022] [Indexed: 11/25/2022] Open
Abstract
Cervical cancer (CC) is considered as the fourth most common women cancer globally.that shows malignant features of local infiltration and invasion into adjacent organs and tissues. There are several individual studies in the literature that explored CC-causing hub-genes (HubGs), however, we observed that their results are not so consistent. Therefore, the main objective of this study was to explore hub of the HubGs (hHubGs) that might be more representative CC-causing HubGs compare to the single study based HubGs. We reviewed 52 published articles and found 255 HubGs/studied-genes in total. Among them, we selected 10 HubGs (CDK1, CDK2, CHEK1, MKI67, TOP2A, BRCA1, PLK1, CCNA2, CCNB1, TYMS) as the hHubGs by the protein-protein interaction (PPI) network analysis. Then, we validated their differential expression patterns between CC and control samples through the GPEA database. The enrichment analysis of HubGs revealed some crucial CC-causing biological processes (BPs), molecular functions (MFs) and cellular components (CCs) by involving hHubGs. The gene regulatory network (GRN) analysis identified four TFs proteins and three miRNAs as the key transcriptional and post-transcriptional regulators of hHubGs. Then, we identified hHubGs-guided top-ranked FDA-approved 10 candidate drugs and validated them against the state-of-the-arts independent receptors by molecular docking analysis. Finally, we investigated the binding stability of the top-ranked three candidate drugs (Docetaxel, Temsirolimus, Paclitaxel) by using 100 ns MD-based MM-PBSA simulations and observed their stable performance. Therefore the finding of this study might be the useful resources for CC diagnosis and therapies.
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Affiliation(s)
- Md. Selim Reza
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Alim Hossen
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Harun-Or-Roshid
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Mst. Ayesha Siddika
- Microbiology Lab, Department of Veterinary and Animal Sciences, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Hadiul Kabir
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab, Department of Statistics, University of Rajshahi, Rajshahi-6205, Bangladesh
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Hossain MT, Li S, Reza MS, Feng S, Zhang X, Jin Z, Wei Y, Peng Y. Identification of circRNA Biomarker for Gastric Cancer through Integrated Analysis. Front Mol Biosci 2022; 9:857320. [PMID: 35359600 PMCID: PMC8960148 DOI: 10.3389/fmolb.2022.857320] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 01/22/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignant tumors and ranks third in cancer mortality globally. Although, a lot of advancements have been made in diagnosis and treatment of gastric cancer, there is still lack of ideal biomarker for the diagnosis and treatment of gastric cancer. Due to the poor prognosis, the survival rate is not improved much. Circular RNAs (circRNAs) are single-stranded RNAs with a covalently closed loop structure that don't have the 5'-3' polarity and a 3' polyA tail. Because of their circular structure, circRNAs are more stable than linear RNAs. Previous studies have found that circRNAs are involved in several biological processes like cell cycle, proliferation, apoptosis, autophagy, migration and invasion in different cancers, and participate in some molecular mechanisms including sponging microRNAs (miRNAs), protein translation and binding to RNA-binding proteins. Several studies have reported that circRNAs play crucial role in the occurrence and development of different types of cancers. Although, some studies have reported several circRNAs in gastric cancer, more studies are needed in searching new biomarkers for gastric cancer diagnosis and treatment. Here, we investigated potential circRNA biomarkers for GC using next-generation sequencing (NGS) data collected from 5 paired GC samples. A total of 45,783 circRNAs were identified in all samples and among them 478 were differentially expressed (DE). The gene ontology (GO) analysis of the host genes of the DE circRNAs showed that some genes were enriched in several important biological processes, molecular functions and cellular components. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that some host genes were enriched in several GC related pathways. The circRNA-miRNA-gene interaction network analysis showed that two circRNAs circCEACAM5 and circCOL1A1 were interacted with gastric cancer related miRNAs, and their host genes were also the important therapeutic and prognostic biomarkers for GC. The experimental results also validated that these two circRNAs were DE in GC compared to adjacent normal tissues. Overall, our findings suggest that these two circRNAs circCEACAM5 and circCOL1A1 might be the potential biomarkers for the diagnosis and treatment of GC.
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Affiliation(s)
- Md. Tofazzal Hossain
- University of Chinese Academy of Sciences, Beijing, China
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Song Li
- Shenzhen Science & Technology Development Exchange Center, Shenzhen Science and Technology Building, Shenzhen, China
| | - Md. Selim Reza
- University of Chinese Academy of Sciences, Beijing, China
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Shengzhong Feng
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, China
| | - Zhe Jin
- Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, China
| | - Yanjie Wei
- Center for High Performance Computing, Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yin Peng
- Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, China
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