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Wang S, Zhang M, Sun H, Li T, Hao J, Fang M, Dong J, Xu H. Multi-omics analysis of TLCD1 as a promising biomarker in pan-cancer. Front Cell Dev Biol 2024; 11:1305906. [PMID: 38559424 PMCID: PMC10978584 DOI: 10.3389/fcell.2023.1305906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/31/2023] [Indexed: 04/04/2024] Open
Abstract
Background: The TLC Domain Containing 1 (TLCD1) protein, a key regulator of phosphatidylethanolamine (PE) composition, is distributed across several cellular membranes, including mitochondrial plasma membranes. Existing research has revealed the impact of TLCD1 on the development of non-alcoholic fatty liver disease. However, there remains a gap in comprehensive pan-cancer analyses of TLCD1, and the precise role of TLCD1 in cancer patient prognosis and immunological responses remains elusive. This study aims to provide a comprehensive visualization of the prognostic landscape associated with TLCD1 across a spectrum of cancers, while shedding light on the potential links between TLCD1 expression within the tumor microenvironment and immune infiltration characteristics. Methods: TLCD1 expression data were obtained from GTEx, TCGA, and HPA data repositories. Multiple databases including TIMER, HPA, TISIDB, cBioPortal, GEPIA2, STRING, KEGG, GO, and CancerSEA were used to investigate the expression pattern, diagnostic and prognostic significance, mutation status, functional analysis, and functional status of TLCD1. In addition, we evaluated the relationship between TLCD1 expression and immune infiltration, tumor mutational burden (TMB), microsatellite instability (MSI), and immune-related genes in pan-cancer. Furthermore, the association of TLCD1 with drug sensitivity was analyzed using the CellMiner database. Results: We found that TLCD1 is generally highly expressed in pan-cancers and is significantly associated with the staging and prognosis of various cancers. Furthermore, our results also showed that TLCD1 was significantly associated with immune cell infiltration and immune regulatory factor expression. Using CellMiner database analysis, we then found a strong correlation between TLCD1 expression and sensitivity to anticancer drugs, indicating its potential as a therapeutic target. The most exciting finding is that high TLCD1 expression is associated with worse survival and prognosis in GBM and SKCM patients receiving anti-PD1 therapy. These findings highlight the potential of TLCD1 as a predictive biomarker for response to immunotherapy. Conclusion: TLCD1 plays a role in the regulation of immune infiltration and affects the prognosis of patients with various cancers. It serves as both a prognostic and immunologic biomarker in human cancer.
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Affiliation(s)
- Shengli Wang
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital Affiliated With Jinan University, Jinan University, Zhuhai, Guangdong, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Mingyue Zhang
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital Affiliated With Jinan University, Jinan University, Zhuhai, Guangdong, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Hongyan Sun
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital Affiliated With Jinan University, Jinan University, Zhuhai, Guangdong, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Tao Li
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital Affiliated With Jinan University, Jinan University, Zhuhai, Guangdong, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Jianlei Hao
- Zhuhai Institute of Translational Medicine, Zhuhai People’s Hospital Affiliated With Jinan University, Jinan University, Zhuhai, Guangdong, China
- The Biomedical Translational Research Institute, Faculty of Medical Science, Jinan University, Guangzhou, Guangdong, China
| | - Meixia Fang
- Department of Laboratory Animal, Institute of Laboratory Animal Science, Jinan University, Guangzhou, Guangdong, China
| | - Jie Dong
- Department of Clinical Laboratory, Guangzhou Twelfth People’s Hospital, Guangzhou, Guangdong, China
| | - Hongbiao Xu
- Department of Thyroid and Breast Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
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2
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Yu W, Li M, Xia J. Identification of immunogenic cell death‑related prognostic signatures in pancreatic cancer. Oncol Lett 2023; 26:473. [PMID: 37809045 PMCID: PMC10551861 DOI: 10.3892/ol.2023.14061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 08/22/2023] [Indexed: 10/10/2023] Open
Abstract
Targeting immunogenic cell death (ICD) may enable the response of pancreatic cancer to immune checkpoint inhibitors (ICIs). The aim of the present study was to elucidate the role of ICD-related genes in pancreatic cancer. Utilizing the k-means method, consensus clustering was employed to effectively group patients with pancreatic cancer. Subsequently, a set of differentially expressed genes was identified between the two subtypes related to ICD, facilitating the execution of a comprehensive enrichment analysis. Furthermore, the construction of an ICD-related prognostic signature (IRPS) was accomplished through LASSO Cox regression, thereby enabling the assessment of responses to both chemotherapy and immunotherapy. In addition, the biological functionality of 5'-nucleotidase ecto (NT5E) was elucidated through experimental investigations. Patients characterized as the ICD high subtype experienced a comparatively shorter overall survival. This subtype exhibited a noteworthy correlation with HLA families and immune checkpoint molecules, underscoring its immunological significance. Subsequently, patients with elevated IRPS risk scores displayed resistance towards immunotherapy interventions. Of note, synergistic downregulation of NT5E in combination with Gemcitabine was observed to significantly induce tumor cell apoptosis, emphasizing its potential therapeutic value. Leveraging ICD-related genes, a novel classification system was meticulously devised to comprehensively evaluate both the clinical outcomes and therapeutic responses of patients diagnosed with pancreatic cancer.
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Affiliation(s)
- Wenjing Yu
- Department of Laboratory Medicine, The 13th People's Hospital of Chongqing, Chongqing 400053, P.R. China
| | - Mei Li
- Department of Laboratory Medicine, The 13th People's Hospital of Chongqing, Chongqing 400053, P.R. China
| | - Jing Xia
- Department of Laboratory Medicine, The 13th People's Hospital of Chongqing, Chongqing 400053, P.R. China
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3
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Tang S, Roberts RD, Cheng L, Li L. Osteosarcoma Multi-Omics Landscape and Subtypes. Cancers (Basel) 2023; 15:4970. [PMID: 37894336 PMCID: PMC10605601 DOI: 10.3390/cancers15204970] [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: 06/12/2023] [Revised: 09/12/2023] [Accepted: 09/17/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma (OS) is the most common primary bone malignancy that exhibits remarkable histologic diversity and genetic heterogeneity. The complex nature of osteosarcoma has confounded precise molecular categorization, prognosis, and prediction for this disease. In this study, we performed a comprehensive multiplatform analysis on 86 osteosarcoma tumors, including somatic copy-number alteration, gene expression and methylation, and identified three molecularly distinct and clinically relevant subtypes of osteosarcoma. The subgrouping criteria was validated on another cohort of osteosarcoma tumors. Previously unappreciated osteosarcoma-type-specific changes in specific genes' copy number, expression and methylation were revealed based on the subgrouping. The subgrouping and novel gene signatures provide insights into refining osteosarcoma therapy and relationships to other types of cancer.
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Affiliation(s)
- Shan Tang
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Ryan D. Roberts
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lijun Cheng
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
| | - Lang Li
- College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH 43210, USA;
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4
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Molstad AJ, Patra RK. Dimension reduction for integrative survival analysis. Biometrics 2023; 79:1610-1623. [PMID: 35964256 DOI: 10.1111/biom.13736] [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: 08/12/2021] [Accepted: 06/20/2022] [Indexed: 11/26/2022]
Abstract
We propose a constrained maximum partial likelihood estimator for dimension reduction in integrative (e.g., pan-cancer) survival analysis with high-dimensional predictors. We assume that for each population in the study, the hazard function follows a distinct Cox proportional hazards model. To borrow information across populations, we assume that each of the hazard functions depend only on a small number of linear combinations of the predictors (i.e., "factors"). We estimate these linear combinations using an algorithm based on "distance-to-set" penalties. This allows us to impose both low-rankness and sparsity on the regression coefficient matrix estimator. We derive asymptotic results that reveal that our estimator is more efficient than fitting a separate proportional hazards model for each population. Numerical experiments suggest that our method outperforms competitors under various data generating models. We use our method to perform a pan-cancer survival analysis relating protein expression to survival across 18 distinct cancer types. Our approach identifies six linear combinations, depending on only 20 proteins, which explain survival across the cancer types. Finally, to validate our fitted model, we show that our estimated factors can lead to better prediction than competitors on four external datasets.
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Affiliation(s)
- Aaron J Molstad
- Department of Statistics and Genetics Institute, University of Florida, Gainesville, Florida, USA
| | - Rohit K Patra
- Department of Statistics, University of Florida, Gainesville, Florida, USA
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5
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Chen J, Chen S, Li B, Zhou S, Lin H. A pyroptosis-related signature predicts prognosis and indicates immune microenvironment infiltration in glioma. Cancer Med 2023; 12:5071-5087. [PMID: 36161280 PMCID: PMC9972150 DOI: 10.1002/cam4.5247] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 08/08/2022] [Accepted: 09/01/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Glioma, the most common malignant brain tumor, leads to high recurrence rates and disabilities in patients. Pyroptosis is an inflammasomes-induced programmed cell death in response to infection or chemotherapy. However, the role of pyroptosis in glioma has not yet been elucidated. METHODS RNA-seq data and clinical information of 660 gliomas and 847 samples were downloaded from the TCGA and CGGA, respectively. Then, data of 104 normal brain tissues was retrieved from the GTEx for differential expression analysis. Twelve pairs of peritumoral tissue and glioma samples were used for validation. Gene alteration status of differentially expressed pyroptosis-related regulators in gliomas was detected in cBioPortal algorithm. Consensus clustering was employed to classify gliomas based on differentially expressed pyroptosis-related regulators. Subsequently, a PS-signature was constructed using LASSO-congressional analysis for clinical application. The immune infiltration of glioma microenvironment (TME) was explored using ESTIMATE, CIBERSORT, and the other immune signatures. RESULTS cBioPortal algorithm revealed alteration of these regulators was correlated to better prognosis of gliomas. Then, our study showed that pyroptosis-related regulators can be used to sort out patients into two clusters with distinct prognostic outcome and immune status. Moreover, a PS-signature for predicting the prognosis of glioma patients was developed based on the identified subtypes. The high PS-score group showed more abundant inflammatory cell infiltration and stronger immune response, but with poorer prognosis of gliomas. CONCLUSION The findings of this study provide a therapeutic basis for future research on pyroptosis and unravel the relationship between pyroptosis and glioma prognosis. The risk signature can be utilized as a prognostic biomarker for glioma.
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Affiliation(s)
- Jia Chen
- The Fourth People's Hospital of ChengduChengduChina
- The Clinical Hospital of Chengdu Brain Science InstituteMOE Key Lab for Neuroinformation, University of Electronic Science and Technology of ChinaChengduChina
| | - Shanwei Chen
- Department of Neurosurgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical SciencesGuangzhouChina
- Shantou University Medical CollegeShantouChina
| | - Bingxian Li
- Department of Neurology, Shantou Central HospitalShantouChina
| | - Shaojiong Zhou
- Department of Neurology, Shantou Central HospitalShantouChina
| | - Han Lin
- Department of Neurosurgery, Beijing Tiantan HospitalCapital Medical UniversityBeijingChina
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6
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Chen P, Xu J, Cui Z, Wu S, Xie T, Zhang X. Multi-omics analysis of N6-methyladenosine reader IGF2BP3 as a promising biomarker in pan-cancer. Front Immunol 2023; 14:1071675. [PMID: 36761737 PMCID: PMC9905439 DOI: 10.3389/fimmu.2023.1071675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Background Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) has been reported to exhibit an oncogenic effect as an RNA-binding protein (RBP) by promoting tumor cell proliferation, migration and invasion in several tumor types. However, a pan-cancer analysis of IGF2BP3 is not currently available, and the exact roles of IGF2BP3 in prognosis and immunology in cancer patients remain enigmatic. The main aim of this study was to provide visualization of the systemic prognostic landscape of IGF2BP3 in pan-cancer and to uncover the potential relationship between IGF2BP3 expression in the tumor microenvironment and immune infiltration profile. Methods Raw data on IGF2BP3 expression were obtained from GTEx, CCLE, TCGA, and HPA data portals. We have investigated the expression patterns, diagnostic and prognostic significance, mutation landscapes, functional analysis, and functional states of IGF2BP3 utilizing multiple databases, including HPA, TISIDB, cBioPortal, GeneMANIA, GESA, and CancerSEA. Moreover, the relationship of IGF2BP3 expression with immune infiltrates, TMB, MSI and immune-related genes was evaluated in pan-cancer. IGF2BP3 with drug sensitivity analysis was performed from the CellMiner database. Furthermore, the expression of IGF2BP3 in different grades of glioma was detected by immunohistochemical staining and western blot. Results We found that IGF2BP3 was ubiquitously highly expressed in pan-cancer and significantly correlated with diagnosis, prognosis, TMB, MSI, and drug sensitivity in various types of cancer. Besides, IGF2BP3 was involved in many cancer pathways and varied in different immune and molecular subtypes of cancers. Additionally, IGF2BP3 is critically associated with genetic markers of immunomodulators in various cancers. Finally, we validated that IGF2BP3 protein expression was significantly higher in glioma than in normal tissue, especially in GBM. Conclusions IGF2BP3 may be a potential molecular biomarker for diagnosis and prognosis in pan-cancer, especially for glioma. It could become a novel therapeutic target for various cancers.
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Affiliation(s)
- Pin Chen
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Xu
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zihan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Silin Wu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Xie
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Cancer Center, Shanghai Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaobiao Zhang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Cancer Center, Shanghai Zhongshan Hospital, Fudan University, Shanghai, China.,Digital Medical Research Center, Fudan University, Shanghai, China
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7
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Deb S, Sun J. Endosomal Sorting Protein SNX27 and Its Emerging Roles in Human Cancers. Cancers (Basel) 2022; 15:cancers15010070. [PMID: 36612066 PMCID: PMC9818000 DOI: 10.3390/cancers15010070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
SNX27 belongs to the sorting nexin (SNX) family of proteins that play a critical role in protein sorting and trafficking in the endocytosis pathway. This protein family is characterized by the presence of a Phox (PX) domain; however, SNX27 is unique in containing an additional PDZ domain. Recently, SNX27 has gained popularity as an important sorting protein that is associated with the retromer complex and mediates the recycling of internalized proteins from endosomes to the plasma membrane in a PDZ domain-dependent manner. Over 100 cell surface proteins have been identified as binding partners of the SNX27-retromer complex. However, the roles and underlying mechanisms governed by SNX27 in tumorigenesis remains to be poorly understood. Many of its known binding partners include several G-protein coupled receptors, such as β2-andrenergic receptor and parathyroid hormone receptor, are associated with multiple pathways implicated in oncogenic signaling and tumorigenesis. Additionally, SNX27 mediates the recycling of GLUT1 and the activation of mTORC1, both of which can regulate intracellular energy balance and promote cell survival and proliferation under conditions of nutrient deprivation. In this review, we summarize the structure and fundamental roles of SNX proteins, with a focus on SNX27, and provide the current evidence indicating towards the role of SNX27 in human cancers. We also discuss the gap in the field and future direction of SNX27 research. Insights into the emerging roles and mechanism of SNX27 in cancers will provide better development strategies to prevent and treat tumorigenesis.
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Affiliation(s)
- Shreya Deb
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Jun Sun
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60612, USA
- University of Illinois at Chicago (UIC) Cancer Center, University of Illinois at Chicago, Chicago, IL 60612, USA
- Jesse Brown VA Medical Center, Chicago, IL 60612, USA
- Correspondence: ; Tel.: +1-312-996-5020
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8
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Mall R, Bynigeri RR, Karki R, Malireddi RKS, Sharma B, Kanneganti TD. Pancancer transcriptomic profiling identifies key PANoptosis markers as therapeutic targets for oncology. NAR Cancer 2022; 4:zcac033. [PMID: 36329783 PMCID: PMC9623737 DOI: 10.1093/narcan/zcac033] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/03/2022] [Accepted: 10/28/2022] [Indexed: 11/24/2022] Open
Abstract
Resistance to programmed cell death (PCD) is a hallmark of cancer. While some PCD components are prognostic in cancer, the roles of many molecules can be masked by redundancies and crosstalks between PCD pathways, impeding the development of targeted therapeutics. Recent studies characterizing these redundancies have identified PANoptosis, a unique innate immune-mediated inflammatory PCD pathway that integrates components from other PCD pathways. Here, we designed a systematic computational framework to determine the pancancer clinical significance of PANoptosis and identify targetable biomarkers. We found that high expression of PANoptosis genes was detrimental in low grade glioma (LGG) and kidney renal cell carcinoma (KIRC). ZBP1, ADAR, CASP2, CASP3, CASP4, CASP8 and GSDMD expression consistently had negative effects on prognosis in LGG across multiple survival models, while AIM2, CASP3, CASP4 and TNFRSF10 expression had negative effects for KIRC. Conversely, high expression of PANoptosis genes was beneficial in skin cutaneous melanoma (SKCM), with ZBP1, NLRP1, CASP8 and GSDMD expression consistently having positive prognostic effects. As a therapeutic proof-of-concept, we treated melanoma cells with combination therapy that activates ZBP1 and showed that this treatment induced PANoptosis. Overall, through our systematic framework, we identified and validated key innate immune biomarkers from PANoptosis which can be targeted to improve patient outcomes in cancers.
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Affiliation(s)
- Raghvendra Mall
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ratnakar R Bynigeri
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Rajendra Karki
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | | | - Bhesh Raj Sharma
- Department of Immunology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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9
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Song JK, Zhang Y, Fei XY, Chen YR, Luo Y, Jiang JS, Ru Y, Xiang YW, Li B, Luo Y, Kuai L. Classification and biomarker gene selection of pyroptosis-related gene expression in psoriasis using a random forest algorithm. Front Genet 2022; 13:850108. [PMID: 36110207 PMCID: PMC9468882 DOI: 10.3389/fgene.2022.850108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 07/04/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Psoriasis is a chronic and immune-mediated skin disorder that currently has no cure. Pyroptosis has been proved to be involved in the pathogenesis and progression of psoriasis. However, the role pyroptosis plays in psoriasis remains elusive. Methods: RNA-sequencing data of psoriasis patients were obtained from the Gene Expression Omnibus (GEO) database, and differentially expressed pyroptosis-related genes (PRGs) between psoriasis patients and normal individuals were obtained. A principal component analysis (PCA) was conducted to determine whether PRGs could be used to distinguish the samples. PRG and immune cell correlation was also investigated. Subsequently, a novel diagnostic model comprising PRGs for psoriasis was constructed using a random forest algorithm (ntree = 400). A receiver operating characteristic (ROC) analysis was used to evaluate the classification performance through both internal and external validation. Consensus clustering analysis was used to investigate whether there was a difference in biological functions within PRG-based subtypes. Finally, the expression of the kernel PRGs were validated in vivo by qRT-PCR. Results: We identified a total of 39 PRGs, which could distinguish psoriasis samples from normal samples. The process of T cell CD4 memory activated and mast cells resting were correlated with PRGs. Ten PRGs, IL-1β, AIM2, CASP5, DHX9, CASP4, CYCS, CASP1, GZMB, CHMP2B, and CASP8, were subsequently screened using a random forest diagnostic model. ROC analysis revealed that our model has good diagnostic performance in both internal validation (area under the curve [AUC] = 0.930 [95% CI 0.877–0.984]) and external validation (mean AUC = 0.852). PRG subtypes indicated differences in metabolic processes and the MAPK signaling pathway. Finally, the qRT-PCR results demonstrated the apparent dysregulation of PRGs in psoriasis, especially AIM2 and GZMB. Conclusion: Pyroptosis may play a crucial role in psoriasis and could provide new insights into the diagnosis and underlying mechanisms of psoriasis.
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Affiliation(s)
- Jian-Kun Song
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Ying Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Xiao-Ya Fei
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yi-Ran Chen
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Jing-Si Jiang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yan-Wei Xiang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Bin Li
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
| | - Yue Luo
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Yue Luo, ; Le Kuai,
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- Institute of Dermatology, Shanghai Academy of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yue Luo, ; Le Kuai,
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10
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Li Z, Shen L, Li Y, Shen L, Li N. Identification of pyroptosis-related gene prognostic signature in head and neck squamous cell carcinoma. Cancer Med 2022; 11:5129-5144. [PMID: 35574984 PMCID: PMC9761089 DOI: 10.1002/cam4.4825] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 03/02/2022] [Accepted: 05/04/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is a life-threatening disease with poor prognosis. Pyroptosis has been recently disclosed as a programmed cell death triggered by invasive infection, involved in cancer development. However, the prognosis role of pyroptosis-related genes in HNSCC has not been discussed. METHODS The RNA sequence data of pyroptosis-related genes were obtained from The Cancer Genome Atlas (TCGA) database. Cox regression and the least absolute shrinkage and selection operator (LASSO) analysis were performed to screen the HNSCC survival-related signature genes. We established a HNSCC risk model with the identified prognostic genes, then divided the HNSCC patients into low- and high-risk subgroups according to median risk score. Moreover, we utilized Gene Expression Omnibus (GEO) dataset to validate the risk model. Go and KEGG analyses were conducted to reveal the potential function of differential expression of genes that identified between low- and high-risk subgroups. ESTIMATE algorithm was performed to investigate the immune infiltration of tumors. Correlation between signature gene expression and drug-sensitivity was disclosed by Spearman's analysis. RESULTS We constructed a HNSCC risk model with identified seven pyroptosis-related genes (CASP1, GSDME, IL6, NLRP1, NLRP2, NLRP6, and NOD2) as prognostic signature genes. High-risk subgroup of HNSCC patients in TCGA cohort correlated with lower survival probability than patients from low-risk subgroup (p < .001), and the result is verified with GEO dataset. In addition, 161 genes were identified differentially expressed between the low- and high-risk subgroups in the TCGA cohort, mainly related to immune response. Higher PD-L1 expression level was found in the high-risk subgroup that indicated the possible employment of immune checkpoint inhibitors. IL6 was positively correlated with WZ3105 and MPS-1-IN-1 in the cancer therapeutics response portal database. CONCLUSION We built and verified a risk model for HNSCC prognosis using seven pyroptosis-related signature genes, which could predict the overall survival of HNSCC patients and facilitate treatment.
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Affiliation(s)
- Zhanzhan Li
- Department of OncologyXiangya Hospital, Central South UniversityChina
| | - Lin Shen
- Department of OncologyXiangya Hospital, Central South UniversityChina
| | - Yanyan Li
- Department of NursingXiangya Hospital, Central South UniversityChina
| | - Liangfang Shen
- Department of OncologyXiangya Hospital, Central South UniversityChina
| | - Na Li
- Department of OncologyXiangya Hospital, Central South UniversityChina,National Clinical Research Center for Geriatric DisordersXiangya Hospital, Central South UniversityChina
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11
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Yang Z, Chen Z, Wang Y, Wang Z, Zhang D, Yue X, Zheng Y, Li L, Bian E, Zhao B. A Novel Defined Pyroptosis-Related Gene Signature for Predicting Prognosis and Treatment of Glioma. Front Oncol 2022; 12:717926. [PMID: 35433410 PMCID: PMC9008739 DOI: 10.3389/fonc.2022.717926] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 03/07/2022] [Indexed: 12/23/2022] Open
Abstract
Pyroptosis, a form of programmed cell death, that plays a significant role in the occurrence and progression of tumors, has been frequently investigated recently. However, the prognostic significance and therapeutic value of pyroptosis in glioma remain undetermined. In this research, we revealed the relationship of pyroptosis-related genes to glioma by analyzing whole transcriptome data from The Cancer Genome Atlas (TCGA) dataset serving as the training set and the Chinese Glioma Genome Atlas (CGGA) dataset serving as the validation set. We identified two subgroups of glioma patients with disparate prognostic and clinical features by performing consensus clustering analysis on nineteen pyroptosis-related genes that were differentially expressed between glioma and normal brain tissues. We further derived a risk signature, using eleven pyroptosis-related genes, that was demonstrated to be an independent prognostic factor for glioma. Furthermore, we used Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) to implement functional analysis of our gene set, and the results were closely related to immune and inflammatory responses in accordance with the characteristics of pyroptosis. Moreover, Gene Set Enrichment Analysis (GSEA) results showed that that the high-risk group exhibited enriched characteristics of malignant tumors in accordance with its poor prognosis. Next, we analyzed different immune cell infiltration between the two risk groups using ssGSEA. Finally, CASP1 was identified as a core gene, so we subsequently selected an inhibitor targeting CASP1 and simulated molecular docking. In addition, the inhibitory effect of belnacasan on glioma was verified at the cellular level. In conclusion, pyroptosis-related genes are of great significance for performing prognostic stratification and developing treatment strategies for glioma.
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Affiliation(s)
- Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yu Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhiwei Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Deran Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
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12
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Hao S, Huang M, Xu X, Wang X, Huo L, Wang L, Gu J. MDN1 Mutation Is Associated With High Tumor Mutation Burden and Unfavorable Prognosis in Breast Cancer. Front Genet 2022; 13:857836. [PMID: 35386280 PMCID: PMC8978890 DOI: 10.3389/fgene.2022.857836] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/28/2022] [Indexed: 11/15/2022] Open
Abstract
Background: Breast cancer (BRCA) is the most common cancer worldwide and a serious threat to human health. MDN1 mutations have been observed in several cancers. However, the associations of MDN1 mutation with tumor mutation burden (TMB) and prognosis of BRCA have not been investigated. Methods: Genomic, transcriptomic, and clinical data of 973 patients with BRCA from The Cancer Genome Atlas (TCGA) database were analyzed. The clinical attributes of BRCA based on the MDN1 mutation status were assessed by comparing TMB and tumor infiltrating immune cells. Gene ontology analysis and gene set enrichment analysis (GSEA) were conducted to identify the key signaling pathways associated with MDN1 mutation. Moreover, univariate and multivariate Cox regression analyses were performed to assess the association between prognostic factors and survival outcomes. Finally, nomograms were used to determine the predictive value of MDN1 mutation on clinical outcomes in patients with BRCA. Results: MDN1 was found to have a relatively high mutation rate (2.77%). Compared to the MDN1 wild-type patients, the TMB value was significantly higher in MDN1 mutant patients (p < 0.001). Prognostic analysis revealed that MDN1 mutant patients had a worse survival probability than MDN1 wild-type patients (hazard ratio = 2.91; 95% CI:1.07–7.92; p = 0.036). GSEA revealed samples with MDN1 mutation enriched in retinol metabolism, drug metabolism cytochrome P450, glucuronidation, miscellaneous transport, and binding event pathways. Conclusion: MDN1 mutation was found to be associated with high TMB and inferior prognosis, suggesting that MDN1 mutation may play a potential role in prognosis prediction and immunotherapy guidance in BRCA.
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Affiliation(s)
- Shuai Hao
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Miao Huang
- Nursing School, Chongqing Medical University, Chongqing, China
| | - Xiaofan Xu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Xulin Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Liqun Huo
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Lu Wang
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Jun Gu
- Department of General Surgery, Jinling Hospital, Medical School of Nanjing University, Nanjing, China
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13
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Liu S, Liu W, Jia X, Yang Z, Liu R, Xu N. The association between the CASP5 rs7939842 polymorphism and the risk of rheumatoid arthritis in Chinese Han individuals. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2021.103667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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14
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Wang H, Shao R, Lu S, Bai S, Fu B, Lai R, Lu Y. Integrative Analysis of a Pyroptosis-Related Signature of Clinical and Biological Value in Multiple Myeloma. Front Oncol 2022; 12:845074. [PMID: 35296025 PMCID: PMC8918477 DOI: 10.3389/fonc.2022.845074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/04/2022] [Indexed: 12/12/2022] Open
Abstract
Purpose Pyroptosis is an inflammation-based programmed cell death that holds great potential as a novel cancer therapeutic target in patients with multiple myeloma (MM). However, thus far, the function of pyroptosis-related genes (PRGs) in MM and their prognostic relevance remains undetermined. Methods The model was established by the LASSO analysis, based on the Gene Expression Omnibus (GEO) dabatase, and its efficacy was verified using two external datasets. The model’s predictive ability was assessed by the Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) curves. Finally, a nomogram was established for clinical application. We also confirmed the validity of our model using specimens and in vitro experiments. Results We established an 11-PRG signature profile, and verified its efficacy using two validation cohorts (VCs). In both cohorts, patients were separated into two subpopulations, according to their median risk scores (RS). Our analysis revealed that high-risk (HR) patients experienced considerably lower overall survival (OS), compared to the low-risk (LR) patients. Using functional enrichment and immune infiltration analyses, we demonstrated that the immunologic status was strongly related to RS. Furthermore, using a pyroptosis inhibitor Q-VD-OPh, we revealed that MM cell proliferation and progression was drastically suppressed and the doxorubicin (DOX)-induced apoptosis was reversed. Conclusion Based on our analysis, pyroptosis not only serves as a measure of MM treatment efficiency and patient prognosis, but is also a possible target for anti-MM therapy.
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Affiliation(s)
- Huizhong Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruonan Shao
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shujing Lu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shenrui Bai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Bibo Fu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Renchun Lai
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Yue Lu, ; Renchun Lai,
| | - Yue Lu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Hematologic Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
- *Correspondence: Yue Lu, ; Renchun Lai,
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15
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Niu Z, Xu Y, Li Y, Chen Y, Han Y. Construction and validation of a novel pyroptosis-related signature to predict prognosis in patients with cutaneous melanoma. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:688-706. [PMID: 34903008 DOI: 10.3934/mbe.2022031] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Skin cutaneous melanoma (SKCM) is one of the most malignant skin cancers and remains a health concern worldwide. Pyroptosis is a newly recognized form of programmed cell death and plays a vital role in cancer progression. We aim to construct a prognostic model for SKCM patients based on pyroptosis-related genes (PRGs). SKCM patients from The Cancer Genome Atlas (TCGA) were divided into training and validation cohorts. We used GSE65904 downloaded from GEO database as an external validation cohort. We performed Cox regression and the least absolute shrinkage and selection operator (LASSO) regression to identify prognostic genes and built a risk score. Patients were divided into high- and low-risk groups based on the risk score. Differently expressed genes (DEGs), immune cell infiltration and immune-related pathways activation were compared between the two groups. We established a model containing 4 PRGs, i.e., GSDMA, GSDMC, AIM2 and NOD2. The overall survival (OS) time was significantly different between the 2 groups. The risk score was an independent predictor for prognosis in both the uni- and multi-variable Cox regressions. Gene ontology (GO) and Kyoto Encylopedia of Genes and Genomes (KEGG) analyses showed that DEGs were enriched in immune-related pathways. Most types of immune cells were highly expressed in the low risk group. All immune pathways were significantly up-regulated in the low-risk group. In addition, low-risk patients had a better response to immune checkpoint inhibitors. Our novel pyroptosis-related gene signature could predict the prognosis of SKCM patients and their response to immune checkpoint inhibitors.
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Affiliation(s)
- Zehao Niu
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yujian Xu
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan Li
- Medical School of Chinese PLA, Beijing 100853, China
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Youbai Chen
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Yan Han
- Department of Plastic and Reconstructive Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
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16
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Niu X, Cheng R, Wang Y, Chen J, Wang C, Ji H. Development of a Prognostic Model of Glioma Based on Pyroptosis-Related Genes. World Neurosurg 2021; 158:e929-e945. [PMID: 34861452 DOI: 10.1016/j.wneu.2021.11.112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND Glioma is the most malignant tumor of the central nervous system, with a poor prognosis. Pyroptosis is known to regulate the malignant phenotype of tumor cells, thus affecting the prognosis of patients. However, the role of pyroptosis-related genes (PRGs) in glioma remains unclear. METHODS We used the Cancer Genome Atlas (TCGA), Chinese Glioma Genome Atlas (CGGA), and Rembrandt database of patients with glioma to construct a PRG-based prognostic model and analyzed the relationship between the prognostic model and tumor immune microenvironment. The Wilcox test was used to compare the expression of PRGs in glioma and normal tissues based on TCGA. Univariate Cox and LASSO regression were used to construct the prognostic model. The CGGA and Rembrandt database were used as validation sets to validate the model. RESULTS Five genes were included in the model (BAX, CASP1, CASP3, CASP6, and NOD1). The survival of patients in the high-risk group was lower than that in the low-risk group. The receiver operating characteristic curve showed that the model had good prognostic evaluation ability and accuracy in all 3 cohorts of patients with glioma. The correlation analysis between the prognostic model and immune infiltration showed that the degree of immune cell infiltration, immune response process, and the expression level of immune checkpoints in the high-risk group were higher than those in the low-risk group. CONCLUSIONS We have constructed a reliable PRG-related prognostic model, which can provide reference for the prognostic evaluation of patients with glioma.
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Affiliation(s)
- Xiaochen Niu
- The Fifth Clinical Medical College of Shanxi Medical University, Tai Yuan, China
| | - Rui Cheng
- The Fifth Clinical Medical College of Shanxi Medical University, Tai Yuan, China; Department of Neurosurgery, Shanxi Provincial People's Hospital, Tai Yuan, China
| | - Yongqi Wang
- The Second Clinical Medical College of Shanxi Medical University, Tai Yuan, China
| | - Juanjuan Chen
- The Second Clinical Medical College of Shanxi Medical University, Tai Yuan, China
| | - Chunhong Wang
- The Fifth Clinical Medical College of Shanxi Medical University, Tai Yuan, China; Department of Neurosurgery, Shanxi Provincial People's Hospital, Tai Yuan, China
| | - Hongming Ji
- The Fifth Clinical Medical College of Shanxi Medical University, Tai Yuan, China; Department of Neurosurgery, Shanxi Provincial People's Hospital, Tai Yuan, China.
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17
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Zhao C, Liu Y, Ju S, Wang X. Pan-Cancer Analysis of the N6-Methyladenosine Eraser FTO as a Potential Prognostic and Immunological Biomarker. Int J Gen Med 2021; 14:7411-7422. [PMID: 34744452 PMCID: PMC8565892 DOI: 10.2147/ijgm.s331752] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 09/10/2021] [Indexed: 12/11/2022] Open
Abstract
Background Fat mass and obesity-associated protein (FTO) is a critical N6-methyladenosine (m6A) demethylase that participates in tumorigenesis and is associated with the prognosis of patients in some cancers. However, the key roles of FTO in pan-cancer are still largely obscure. Methods FTO expression levels in pan-cancer were estimated via the Genotype-Tissue Expression (GTEx), Cancer Cell Line Encyclopedia (CCLE), and The Cancer Genome Atlas (TCGA) databases. Univariate survival analysis was used to estimate the effects of FTO on prognosis. In addition, we used the Tumor Immune Evaluation Resource (TIMER) to assess the immune cell infiltration of FTO gene across cancers. The association of FTO expression with immune checkpoint genes expression, DNA mismatch repair (MMR) gene mutation, DNA methyltransferases, microsatellite instability (MSI), and tumor mutational burden (TMB) was investigated using Spearman’s correlation analysis. Moreover, Gene Set Enrichment Analysis (GSEA) was utilized to identify critical pathways in cancers. The STRING website was used to reveal the protein–protein interaction (PPI) network of FTO. Results FTO was aberrantly expressed across cancers and survival analysis demonstrated that its expression was associated with clinical prognosis of many cancer patients. Specifically, FTO expression was significantly associated with immune infiltrating cells in colon adenocarcinoma, kidney renal clear cell carcinoma, and liver hepatocellular carcinoma. In addition, FTO expression was significantly associated with immune checkpoint genes expression, MMR, DNA methyltransferases levels, TMB, and MSI in multiple cancers. Moreover, the GSEA unveiled that FTO was involved in the regulation of tumors and immune-related signaling pathways. In addition, several m6A related genes were implicated in the PPI network of FTO. Conclusion FTO was related to patients’ prognosis and tumor immune infiltrates in various cancers, and may serve as a novel and potential prognostic and immune biomarker in human pan-cancer.
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Affiliation(s)
- Chengwen Zhao
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Yonghui Liu
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China.,Department of Public Health, Nantong University, Nantong, Jiangsu, People's Republic of China
| | - Xudong Wang
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, People's Republic of China.,Department of Public Health, Nantong University, Nantong, Jiangsu, People's Republic of China
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18
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Xu D, Ji Z, Qiang L. Molecular Characteristics, Clinical Implication, and Cancer Immunity Interactions of Pyroptosis-Related Genes in Breast Cancer. Front Med (Lausanne) 2021; 8:702638. [PMID: 34589498 PMCID: PMC8473741 DOI: 10.3389/fmed.2021.702638] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022] Open
Abstract
Objective: Pyroptosis represents an emerging inflammatory form of programmed cell death. Herein, specific functions and clinical implications of pyroptosis-related genes were systematically characterized in breast cancer. Methods: Expression, somatic mutation and copy number variation of 33 pyroptosis-related genes were assessed in breast cancer from TCGA dataset. Their interactions, biological functions and prognostic values were then observed. By stepwise Cox regression analysis, a pyroptosis-related gene signature was generated. The predictive efficacy in survival was examined by survival analyses, ROCs, univariate and multivariate analyses and subgroup analyses. Associations between risk score (RS) and cancer immunity cycle, HLA, immune cell infiltrations, and immune checkpoints were analyzed. Results: Most of pyroptosis-related genes were abnormally expressed in breast cancer. CASP8, NLRC4, NLRP3, NLRP2, PLCG1, NLRP1, NLRP7, SCAF11, GSDMC, and NOD1 occurred somatic mutations as well as most of them had high frequency of CNV. There were closely interactions between them. These genes were distinctly enriched in immune-related processes. A three-gene signature was generated, containing IL-18, GSDMC, and TIRAP. High RS predicted poorer overall survival, progression, and recurrence. After verification, this RS was an independent and sensitive predictive index. This RS was negatively correlated to cancer immunity cycle. Also, low RS was characterized by high HLA, immune cell infiltrations and immune checkpoints. A nomogram including age and RS was generated for accurately predicting 5-, 8-, and 10-year survival probabilities. Conclusion: Pyroptosis-related genes exert key roles in cancer immunity and might be applied as a prognostic factor of breast cancer.
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Affiliation(s)
- Dandan Xu
- Internal Medicine II, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
| | - Zhipeng Ji
- Department of Gastrointestinal Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Ling Qiang
- Department of Medical Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
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19
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Deng L, Wang P, Qu Z, Liu N. The Construction and Analysis of ceRNA Network and Immune Infiltration in Kidney Renal Clear Cell Carcinoma. Front Genet 2021; 12:667610. [PMID: 34567057 PMCID: PMC8455958 DOI: 10.3389/fgene.2021.667610] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 08/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background: Kidney renal clear cell carcinoma (KIRC) has the highest invasion, mortality and metastasis of the renal cell carcinomas and seriously affects patient’s quality of life. However, the composition of the immune microenvironment and regulatory mechanisms at transcriptomic level such as ceRNA of KIRC are still unclear. Methods: We constructed a ceRNA network associated with KIRC by analyzing the long non-coding RNA (lncRNA), miRNA and mRNA expression data of 506 tumor tissue samples and 71 normal adjacent tissue samples downloaded from The Cancer Genome Atlas (TCGA) database. In addition, we estimated the proportion of 22 immune cell types in these samples through “The Cell Type Identification by Estimating Relative Subsets of RNA Transcripts.” Based on the ceRNA network and immune cells screened by univariate Cox analysis and Lasso regression, two nomograms were constructed to predict the prognosis of patients with KIRC. Receiver operating characteristic curves (ROC) and calibration curves were employed to assess the discrimination and accuracy of the nomograms. Consequently, co-expression analysis was carried out to explore the relationship between each prognostic gene in a Cox proportional hazards regression model of ceRNA and each survival-related immune cell in a Cox proportional hazards regression model of immune cell types to reveal the potential regulatory mechanism. Results: We established a ceRNA network consisting of 12 lncRNAs, 25 miRNAs and 136 mRNAs. Two nomograms containing seven prognostic genes and two immune cells, respectively, were successfully constructed. Both ROC [area under curves (AUCs) of 1, 3, and 5-year survival in the nomogram based on ceRNA network: 0.779, 0.747, and 0.772; AUCs of 1, 3, and 5-year survivals in nomogram based on immune cells: 0.603, 0.642, and 0.607] and calibration curves indicated good accuracy and clinical application value of both models. Through co-correlation analysis between ceRNA and immune cells, we found both LINC00894 and KIAA1324 were positively correlated with follicular helper T (Tfh) cells and negatively correlated with resting mast cells. Conclusion: Based on the ceRNA network and tumor-infiltrating immune cells, we constructed two nomograms to predict the survival of KIRC patients and demonstrated their value in improving the personalized management of KIRC.
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Affiliation(s)
- Lugang Deng
- School of Public Health, Guangzhou Medical University, Guangzhou, China.,South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China
| | - Peixi Wang
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, China
| | - Zhi Qu
- Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, China
| | - Nan Liu
- South China Hospital, Health Science Center, Shenzhen University, Shenzhen, China.,Institute of Chronic Disease Risks Assessment, School of Nursing and Health, Henan University, Kaifeng, China
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20
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Xia T, Liu M, Zhao Q, Ouyang J, Xu P, Chen B. PRMT5 regulates cell pyroptosis by silencing CASP1 in multiple myeloma. Cell Death Dis 2021; 12:851. [PMID: 34531375 PMCID: PMC8445991 DOI: 10.1038/s41419-021-04125-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 07/30/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023]
Abstract
Protein arginine methyltransferase 5 (PRMT5), a histone methyltransferase responsible for the symmetric dimethylation of histone H4 on Arg 3 (H4R3me2s), is an enzyme that participates in tumor cell progression in a variety of hematological malignancies. However, the biological functions of PRMT5 in multiple myeloma (MM) and the underlying molecular mechanisms remain unclear. In this study, we conducted a bioinformatics analysis and found that PRMT5 expression was significantly upregulated in MM. In vitro and in vivo phenotypic experiments revealed that knockdown of PRMT5 expression enhanced cell pyroptosis in MM. Moreover, we found that CASP1 expression was negatively correlated with PRMT5 expression, and repressing PRMT5 expression rescued both the phenotype and expression markers (N-GSDMD, IL-1b, and IL-18). Inhibition of PRMT5 activity increased CASP1 expression and promoted MM cell pyroptosis. Finally, high expression of PRMT5 or low expression of CASP1 was correlated with poor overall survival in MM. Collectively, our results provide a mechanism by which PRMT5 regulates cell pyroptosis by silencing CASP1 in MM.
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Affiliation(s)
- Tian Xia
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China
| | - Ming Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210008, People's Republic of China
| | - Quan Zhao
- The State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University, Nanjing, 210008, People's Republic of China
| | - Jian Ouyang
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China.
| | - Peipei Xu
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China.
- Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, 210008, Jiangsu, People's Republic of China.
| | - Bing Chen
- Department of Hematology, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, 210008, Jiangsu, People's Republic of China.
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21
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Chen J, Mai H, Chen H, Zhou B, Hou J, Jiang DK. Pan-Cancer Analysis Identified C1ORF112 as a Potential Biomarker for Multiple Tumor Types. Front Mol Biosci 2021; 8:693651. [PMID: 34490347 PMCID: PMC8416665 DOI: 10.3389/fmolb.2021.693651] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/26/2021] [Indexed: 02/03/2023] Open
Abstract
C1ORF112 is an evolutionarily conserved gene across vertebrates. Over the last decade, studies have suggested that C1ORF112 may play a role in tumorigenesis. Using The Cancer Genome Atlas datasets, we explored the role of C1ORF112 across various tumor types in this study. In most tumor types, C1ORF112 expression was increased in tumor tissues compared to corresponding non-tumor tissues. In patients with certain tumor types, higher C1ORF112 expression was correlated with shorter overall survival, disease-free survival, and progression-free survival. Further analyses of C1ORF112 genetic alteration data showed that C1ORF112 amplification and mutations may have an impact on liver hepatocellular carcinoma and uterine corpus endometrial carcinoma prognosis. In cancers including lower grade glioma and adrenocortical carcinoma, C1ORF112 expression was linked to cancer-associated fibroblast infiltration. Gene Ontology analysis showed that C1ORF112 was co-expressed with genes involved in biological processes such as cell cycle and mitotic regulation. The protein interaction network demonstrated that C1ORF112 physically interacted with RAD51, DMC1, and FIGNL1, which have well characterized functions in DNA repair and cell cycle regulation. This pan-cancer study revealed the prognostic value and oncogenic role of C1ORF112 across multiple tumor types.
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Affiliation(s)
- Jiaxuan Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haoming Mai
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haitao Chen
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bin Zhou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jinlin Hou
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - De-Ke Jiang
- State Key Laboratory of Organ Failure Research, Guangdong Key Laboratory of Viral Hepatitis Research, Guangdong Institute of Liver Diseases, Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical University, Guangzhou, China
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22
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Al-Fatlawi A, Malekian N, García S, Henschel A, Kim I, Dahl A, Jahnke B, Bailey P, Bolz SN, Poetsch AR, Mahler S, Grützmann R, Pilarsky C, Schroeder M. Deep Learning Improves Pancreatic Cancer Diagnosis Using RNA-Based Variants. Cancers (Basel) 2021; 13:2654. [PMID: 34071263 PMCID: PMC8199344 DOI: 10.3390/cancers13112654] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 11/30/2022] Open
Abstract
For optimal pancreatic cancer treatment, early and accurate diagnosis is vital. Blood-derived biomarkers and genetic predispositions can contribute to early diagnosis, but they often have limited accuracy or applicability. Here, we seek to exploit the synergy between them by combining the biomarker CA19-9 with RNA-based variants. We use deep sequencing and deep learning to improve differentiating pancreatic cancer and chronic pancreatitis. We obtained samples of nucleated cells found in peripheral blood from 268 patients suffering from resectable, non-resectable pancreatic cancer, and chronic pancreatitis. We sequenced RNA with high coverage and obtained millions of variants. The high-quality variants served as input together with CA19-9 values to deep learning models. Our model achieved an area under the curve (AUC) of 96% in differentiating resectable cancer from pancreatitis using a test cohort. Moreover, we identified variants to estimate survival in resectable cancer. We show that the blood transcriptome harbours variants, which can substantially improve noninvasive clinical diagnosis.
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Affiliation(s)
- Ali Al-Fatlawi
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
| | - Negin Malekian
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
| | - Sebastián García
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.G.); (B.J.)
| | - Andreas Henschel
- Department of Electrical Engineering and Computer Science, Khalifa University of Science and Technology, Abu Dhabi 127788, United Arab Emirates;
| | - Ilwook Kim
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
| | - Andreas Dahl
- DRESDEN-Concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307 Dresden, Germany;
| | - Beatrix Jahnke
- Department of Visceral, Thoracic and Vascular Surgery, University Hospital and Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany; (S.G.); (B.J.)
| | - Peter Bailey
- Department of Surgical Research, Universitätsklinikum Erlangen, Maximiliansplatz 2, 91054 Erlangen, Germany; (P.B.); (R.G.); (C.P.)
| | - Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
| | - Anna R. Poetsch
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
- National Center for Tumor Diseases (NCT), 01307 Dresden, Germany
| | - Sandra Mahler
- Department of Medical Oncology, Universitätsklinikum Dresden, 01307 Dresden, Germany;
| | - Robert Grützmann
- Department of Surgical Research, Universitätsklinikum Erlangen, Maximiliansplatz 2, 91054 Erlangen, Germany; (P.B.); (R.G.); (C.P.)
| | - Christian Pilarsky
- Department of Surgical Research, Universitätsklinikum Erlangen, Maximiliansplatz 2, 91054 Erlangen, Germany; (P.B.); (R.G.); (C.P.)
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-49, 01307 Dresden, Germany; (A.A.-F.); (N.M.); (I.K.); (S.N.B.); (A.R.P.)
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23
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Jiang S, Jiang Y, Cao Y, Zhao Y, Liu H, Wang X, He Z, Song Z, Wang X, Liu G, Cui R. The use of pan-cancer analysis of ADAMTS9 expression in various cancer types. Epigenomics 2021; 13:253-256. [PMID: 33502246 DOI: 10.2217/epi-2020-0406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Shijun Jiang
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China.,Department of Clinical Laboratory, Daqing Medical College, Daqing, Heilongjiang 163311, PR China
| | - Ying Jiang
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Yingli Cao
- Department of pathology, Heilongjiang Nursing College, Harbin, Heilongjiang 150000, PR China
| | - Yiyang Zhao
- The 1st Clinical Medical College, Southern Medical University, Guangzhou, Guangdong 510000, PR China
| | - Hongfeng Liu
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Xiuli Wang
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Zikang He
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Zheyao Song
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Xingyun Wang
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Gang Liu
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
| | - Rongjun Cui
- Department of Biochemistry & Molecular Biology, Mudanjiang Medical University, Mudanjiang, Heilongjiang 157011, PR China
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