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Kuttiyarthu Veetil N, Henschen AE, Hawley DM, Melepat B, Dalloul RA, Beneš V, Adelman JS, Vinkler M. Varying conjunctival immune response adaptations of house finch populations to a rapidly evolving bacterial pathogen. Front Immunol 2024; 15:1250818. [PMID: 38370402 PMCID: PMC10869556 DOI: 10.3389/fimmu.2024.1250818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 01/11/2024] [Indexed: 02/20/2024] Open
Abstract
Pathogen adaptations during host-pathogen co-evolution can cause the host balance between immunity and immunopathology to rapidly shift. However, little is known in natural disease systems about the immunological pathways optimised through the trade-off between immunity and self-damage. The evolutionary interaction between the conjunctival bacterial infection Mycoplasma gallisepticum (MG) and its avian host, the house finch (Haemorhous mexicanus), can provide insights into such adaptations in immune regulation. Here we use experimental infections to reveal immune variation in conjunctival tissue for house finches captured from four distinct populations differing in the length of their co-evolutionary histories with MG and their disease tolerance (defined as disease severity per pathogen load) in controlled infection studies. To differentiate contributions of host versus pathogen evolution, we compared house finch responses to one of two MG isolates: the original VA1994 isolate and a more evolutionarily derived one, VA2013. To identify differential gene expression involved in initiation of the immune response to MG, we performed 3'-end transcriptomic sequencing (QuantSeq) of samples from the infection site, conjunctiva, collected 3-days post-infection. In response to MG, we observed an increase in general pro-inflammatory signalling, as well as T-cell activation and IL17 pathway differentiation, associated with a decrease in the IL12/IL23 pathway signalling. The immune response was stronger in response to the evolutionarily derived MG isolate compared to the original one, consistent with known increases in MG virulence over time. The host populations differed namely in pre-activation immune gene expression, suggesting population-specific adaptations. Compared to other populations, finches from Virginia, which have the longest co-evolutionary history with MG, showed significantly higher expression of anti-inflammatory genes and Th1 mediators. This may explain the evolution of disease tolerance to MG infection in VA birds. We also show a potential modulating role of BCL10, a positive B- and T-cell regulator activating the NFKB signalling. Our results illuminate potential mechanisms of house finch adaptation to MG-induced immunopathology, contributing to understanding of the host evolutionary responses to pathogen-driven shifts in immunity-immunopathology trade-offs.
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Affiliation(s)
| | - Amberleigh E. Henschen
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States
| | - Dana M. Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Balraj Melepat
- Department of Zoology, Charles University, Faculty of Science, Prague, Czechia
| | - Rami A. Dalloul
- Department of Poultry Science, The University of Georgia, Athens, GA, United States
| | - Vladimír Beneš
- European Molecular Biology Laboratory (EMBL), Genomics Core Facility, Heidelberg, Germany
| | - James S. Adelman
- Department of Biological Sciences, The University of Memphis, Memphis, TN, United States
| | - Michal Vinkler
- Department of Zoology, Charles University, Faculty of Science, Prague, Czechia
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Chen Y, Xu H, Yu P, Wang Q, Li S, Ji F, Wu C, Lan Q. Interferon-γ inducible protein 30 promotes the epithelial-mesenchymal transition-like phenotype and chemoresistance by activating EGFR/AKT/GSK3β/β-catenin pathway in glioma. CNS Neurosci Ther 2023; 29:4124-4138. [PMID: 37408388 PMCID: PMC10651985 DOI: 10.1111/cns.14334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 07/07/2023] Open
Abstract
AIMS Previous studies have indicated that IFI30 plays a protective role in human cancers. However, its potential roles in regulating glioma development are not fully understood. METHODS Public datasets, immunohistochemistry, and western blotting (WB) were used to evaluate the expression of IFI30 in glioma. The potential functions and mechanisms of IFI30 were examined by public dataset analysis; quantitative real-time PCR; WB; limiting dilution analysis; xenograft tumor assays; CCK-8, colony formation, wound healing, and transwell assays; and immunofluorescence microscopy and flow cytometry. RESULTS IFI30 was significantly upregulated in glioma tissues and cell lines compared with corresponding controls, and the expression level of IFI30 was positively associated with tumor grade. Functionally, both in vivo and in vitro evidence showed that IFI30 regulated the migration and invasion of glioma cells. Mechanistically, we found that IFI30 dramatically promoted the epithelial-mesenchymal transition (EMT)-like process by activating the EGFR/AKT/GSK3β/β-catenin pathway. In addition, IFI30 regulated the chemoresistance of glioma cells to temozolomide directly via the expression of the transcription factor Slug, a key regulator of the EMT-like process. CONCLUSION The present study suggests that IFI30 is a regulator of the EMT-like phenotype and acts not only as a prognostic marker but also as a potential therapeutic target for temozolomide-resistant glioma.
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Affiliation(s)
- Ying Chen
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Hui Xu
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Pei Yu
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Qing Wang
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Shenggang Li
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Fufu Ji
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Chunwang Wu
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
| | - Qing Lan
- Department of NeurosurgeryThe Second Affiliated Hospital of Soochow UniversitySuzhouJiangsuP.R. China
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Liang T, Wang X, Wang Y, Ma W. IFN-γ Triggered IFITM2 Expression to Induce Malignant Phenotype in Elderly GBM. J Mol Neurosci 2023; 73:946-955. [PMID: 37889394 DOI: 10.1007/s12031-023-02156-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/07/2023] [Indexed: 10/28/2023]
Abstract
Advanced age is an important risk factor for the worse clinical presentation of gliomas, especially glioblastoma (GBM). The tumor microenvironment (TME) in elderly GBM (eGBM) patients is considerably different from that in young ones, which causes the inferior clinical outcome. Based on the data from the Chinese Glioma Genome Atlas RNA sequence (CGGA RNA-seq), the Cancer Genome Atlas RNA array (TCGA RNA-array), and gene set enrichment (GSE) 16011 array sets, the differential genes and function between eGBM (≥ 60 years old) and young GBM (yGBM, 20-60 years old) groups were explored. Immunohistochemistry (IHC) was utilized to depict the abundance of CD8+ cells (the main resource of IFN-γ) and IFITM2 protein expression in GBM samples. Furthermore, reverse transcription-polymerase chain reaction (RT-PCR) and Western blotting (WB) were performed to verify the link between IFN-γ and IFITM2. Moreover, the small-interfering RNA (siRNA) of IFITM2 was used to explore the function of IFITM2 in GBM. Characterized by inflammatory TME and higher IFITM2 expression, eGBM harbored a shorter survival time. Chemotaxis and inflammatory cytokine-related genes were enriched in the eGBM group, with more infiltrative CD8+ T cells. The IHC of CD8 and IFITM2-staining could demonstrate these results. In addition, the IFN-γ response pathway was activated in eGBM and resulted in a dismal outcome. Next, it was found that IFITM2 triggered by IFN-γ played a key role in IFN-γ-induced malignant phenotype in eGBM.
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Affiliation(s)
- Tingyu Liang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoxuan Wang
- Department of Pathology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yu Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Wenbin Ma
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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Amin A, Koul AM, Wani UM, Farooq F, Amin B, Wani Z, Lone A, Qadri A, Qadri RA. Dissection of paracrine/autocrine interplay in lung tumor microenvironment mimicking cancer cell-monocyte co-culture models reveals proteins that promote inflammation and metastasis. BMC Cancer 2023; 23:926. [PMID: 37784035 PMCID: PMC10544320 DOI: 10.1186/s12885-023-11428-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Tumor cell-monocyte interactions play crucial roles in shaping up the pro-tumorigenic phenotype and functional output of tumor-associated macrophages. Within the tumor microenvironment, such heterotypic cell-cell interactions are known to occur via secretory proteins. Secretory proteins establish a diabolic liaison between tumor cells and monocytes, leading to their recruitment, subsequent polarization and consequent tumor progression. METHODS We co-cultured model lung adenocarcinoma cell line A549 with model monocytes, THP-1 to delineate the interactions between them. The levels of prototypical pro-inflammatory cytokines like TNF-𝛼, IL-6 and anti-inflammatory cytokines like IL-10 were measured by ELISA. Migration, invasion and attachment independence of lung cancer cells was assessed by wound healing, transwell invasion and colony formation assays respectively. The status of EMT was evaluated by immunofluorescence. Identification of secretory proteins differentially expressed in monocultures and co-culture was carried out using SILAC LC-MS/MS. Various insilico tools like Cytoscape, Reacfoam, CHAT and Kaplan-Meier plotter were utilized for association studies, pathway analysis, functional classification, cancer hallmark relevance and predicting the prognostic potential of the candidate secretory proteins respectively. RESULTS Co-culture of A549 and THP-1 cells in 1:10 ratio showed early release of prototypical pro-inflammatory cytokines TNF-𝛼 and IL-6, however anti-inflammatory cytokine, IL-10 was observed to be released at the highest time point. The conditioned medium obtained from this co-culture ratio promoted the migration, invasion and colony formation as well as the EMT of A549 cells. Co-culturing of A549 with THP-1 cells modulated the secretion of proteins involved in cell proliferation, migration, invasion, EMT, inflammation, angiogenesis and inhibition of apoptosis. Among these proteins Versican, Tetranectin, IGFBP2, TUBB4B, C2 and IFI30 were found to correlate with the inflammatory and pro-metastatic milieu observed in our experimental setup. Furthermore, dysregulated expression of these proteins was found to be associated with poor prognosis and negative disease outcomes in lung adenocarcinoma compared to other cancer types. Pharmacological interventions targeting these proteins may serve as useful therapeutic approaches in lung adenocarcinoma. CONCLUSION In this study, we have demonstrated that the lung cancer cell-monocyte cross-talk modulates the secretion of IFI30, RNH1, CLEC3B, VCAN, IGFBP2, C2 and TUBB4B favoring tumor growth and metastasis.
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Affiliation(s)
- Asif Amin
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Aabid Mustafa Koul
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Umer Majeed Wani
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Faizah Farooq
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Basit Amin
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Zubair Wani
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India
| | - Asif Lone
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi, 110608, India
| | - Ayub Qadri
- Abdul Kalam Chair for Translational Research, Islamic University of Science and Technology, Awantipora, J&K, 192122, India
| | - Raies A Qadri
- Immunobiology Lab, Department of Biotechnology, University of Kashmir, Srinagar, J&K, 190006, India.
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Li S, Li Z, Wang X, Zhong J, Yu D, Chen H, Ma W, Liu L, Ye M, Shen R, Jiang C, Meng X, Cai J. HK3 stimulates immune cell infiltration to promote glioma deterioration. Cancer Cell Int 2023; 23:227. [PMID: 37779195 PMCID: PMC10543879 DOI: 10.1186/s12935-023-03039-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND Glioma is the most common and lethal type of brain tumor, and it is characterized by unfavorable prognosis and high recurrence rates. The reprogramming of energy metabolism and an immunosuppressive tumor microenvironment (TME) are two hallmarks of tumors. Complex and dynamic interactions between neoplastic cells and the surrounding microenvironment can generate an immunosuppressive TME, which can accelerate the malignant progression of glioma. Therefore, it is crucial to explore associations between energy metabolism and the immunosuppressive TME and to identify new biomarkers for glioma prognosis. METHODS In our work, we analyzed the co-expression relationship between glycolytic genes and immune checkpoints based on the transcriptomic data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA) and found the correlation between HK3 expression and glioma tumor immune status. To investigate the biological role of HK3 in glioma, we performed bioinformatics analysis and established a mouse glioblastoma (GBM) xenograft model. RESULTS Our study showed that HK3 significantly stimulated immune cell infiltration into the glioma TME. Tissue samples with higher HK3 expressive level showed increasing levels of immune cells infiltration, including M2 macrophages, neutrophils, and various subtypes of activated memory CD4+ T cells. Furthermore, HK3 expression was significantly increasing along with the elevated tumor grade, had a higher level in the mesenchymal subtype compared with those in other subtypes of GBM and could independently predict poor outcomes of GBM patients. CONCLUSION The present work mainly concentrated on the biological role of HK3 in glioma and offered a novel insight of HK3 regulating the activation of immune cells in the glioma microenvironment. These findings could provide a new theoretical evidence for understanding the metabolic molecular within the glioma microenvironment and identifying new therapeutic targets.
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Affiliation(s)
- Shupeng Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Department of Neurosurgery, The Dalian Municipal Central Hospital, Dalian, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ziwei Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Tiantan Hospital, Capital Medical University, Beijing, China
| | - Xinyu Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Junzhe Zhong
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Daohan Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Wenbin Ma
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lingling Liu
- Department of Clinical Medical Record, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Minghuang Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ruofei Shen
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chuanlu Jiang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
- The Sixth Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Xiangqi Meng
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
| | - Jinquan Cai
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
- Future Medical Laboratory, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.
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Chuang YH, Lin CY, Lee JC, Lee CH, Liu CL, Huang SH, Lee JY, Lai WS, Yang JM. Identification of the HNSC88 Molecular Signature for Predicting Subtypes of Head and Neck Cancer. Int J Mol Sci 2023; 24:13068. [PMID: 37685875 PMCID: PMC10487792 DOI: 10.3390/ijms241713068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/14/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSC) exhibits genetic heterogeneity in etiologies, tumor sites, and biological processes, which significantly impact therapeutic strategies and prognosis. While the influence of human papillomavirus on clinical outcomes is established, the molecular subtypes determining additional treatment options for HNSC remain unclear and inconsistent. This study aims to identify distinct HNSC molecular subtypes to enhance diagnosis and prognosis accuracy. In this study, we collected three HNSC microarrays (n = 306) from the Gene Expression Omnibus (GEO), and HNSC RNA-Seq data (n = 566) from The Cancer Genome Atlas (TCGA) to identify differentially expressed genes (DEGs) and validate our results. Two scoring methods, representative score (RS) and perturbative score (PS), were developed for DEGs to summarize their possible activation functions and influence in tumorigenesis. Based on the RS and PS scoring, we selected candidate genes to cluster TCGA samples for the identification of molecular subtypes in HNSC. We have identified 289 up-regulated DEGs and selected 88 genes (called HNSC88) using the RS and PS scoring methods. Based on HNSC88 and TCGA samples, we determined three HNSC subtypes, including one HPV-associated subtype, and two HPV-negative subtypes. One of the HPV-negative subtypes showed a relationship to smoking behavior, while the other exhibited high expression in tumor immune response. The Kaplan-Meier method was used to compare overall survival among the three subtypes. The HPV-associated subtype showed a better prognosis compared to the other two HPV-negative subtypes (log rank, p = 0.0092 and 0.0001; hazard ratio, 1.36 and 1.39). Additionally, within the HPV-negative group, the smoking-related subgroup exhibited worse prognosis compared to the subgroup with high expression in immune response (log rank, p = 0.039; hazard ratio, 1.53). The HNSC88 not only enables the identification of HPV-associated subtypes, but also proposes two potential HPV-negative subtypes with distinct prognoses and molecular signatures. This study provides valuable strategies for summarizing the roles and influences of genes in tumorigenesis for identifying molecular signatures and subtypes of HNSC.
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Affiliation(s)
- Yi-Hsuan Chuang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Chun-Yu Lin
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Jih-Chin Lee
- Department of Otolaryngology—Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan
| | - Chia-Hwa Lee
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
- Ph.D. Program in Medicine Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan
| | - Chia-Lin Liu
- Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan
| | - Sing-Han Huang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Jung-Yu Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
| | - Wen-Sen Lai
- Department of Otolaryngology—Head and Neck Surgery, Taichung Armed Forces General Hospital, Taichung 404, Taiwan
| | - Jinn-Moon Yang
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices, National Yang Ming Chiao Tung University, Hsinchu 300, Taiwan
- Center of Excellence for Metabolic Associated Fatty Liver Disease, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
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Bonnett SA, Rosenbloom AB, Ong GT, Conner M, Rininger AB, Newhouse D, New F, Phan CQ, Ilcisin S, Sato H, Lyssand JS, Geiss G, Beechem JM. Ultra High-plex Spatial Proteogenomic Investigation of Giant Cell Glioblastoma Multiforme Immune Infiltrates Reveals Distinct Protein and RNA Expression Profiles. Cancer Res Commun 2023; 3:763-779. [PMID: 37377888 PMCID: PMC10155752 DOI: 10.1158/2767-9764.crc-22-0396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/20/2023] [Accepted: 04/04/2023] [Indexed: 06/29/2023]
Abstract
A deeper understanding of complex biological processes, including tumor development and immune response, requires ultra high-plex, spatial interrogation of multiple "omes". Here we present the development and implementation of a novel spatial proteogenomic (SPG) assay on the GeoMx Digital Spatial Profiler platform with next-generation sequencing readout that enables ultra high-plex digital quantitation of proteins (>100-plex) and RNA (whole transcriptome, >18,000-plex) from a single formalin-fixed paraffin-embedded (FFPE) sample. This study highlighted the high concordance, R > 0.85 and <15% change in sensitivity between the SPG assay and the single-analyte assays on various cell lines and tissues from human and mouse. Furthermore, we demonstrate that the SPG assay was reproducible across multiple users. When used in conjunction with advanced cellular neighborhood segmentation, distinct immune or tumor RNA and protein targets were spatially resolved within individual cell subpopulations in human colorectal cancer and non-small cell lung cancer. We used the SPG assay to interrogate 23 different glioblastoma multiforme (GBM) samples across four pathologies. The study revealed distinct clustering of both RNA and protein based on pathology and anatomic location. The in-depth investigation of giant cell glioblastoma multiforme (gcGBM) revealed distinct protein and RNA expression profiles compared with that of the more common GBM. More importantly, the use of spatial proteogenomics allowed simultaneous interrogation of critical protein posttranslational modifications alongside whole transcriptomic profiles within the same distinct cellular neighborhoods. Significance We describe ultra high-plex spatial proteogenomics; profiling whole transcriptome and high-plex proteomics on a single FFPE tissue section with spatial resolution. Investigation of gcGBM versus GBM revealed distinct protein and RNA expression profiles.
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Affiliation(s)
| | | | | | - Mark Conner
- NanoString Technologies, Seattle, Washington
| | | | | | - Felicia New
- NanoString Technologies, Seattle, Washington
| | - Chi Q. Phan
- NanoString Technologies, Seattle, Washington
| | | | - Hiromi Sato
- NanoString Technologies, Seattle, Washington
| | | | - Gary Geiss
- NanoString Technologies, Seattle, Washington
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Li Y, Liu Y, Zhang J, Li J, Shu Y. Propofol Suppresses Glioma Tumorigenesis by Regulating circ_0047688/miR-516b-5p/IFI30 Axis. Biochem Genet 2023; 61:151-69. [PMID: 35763173 DOI: 10.1007/s10528-022-10243-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 06/07/2022] [Indexed: 01/24/2023]
Abstract
Propofol has recently attracted increasing attention for its anti-tumor property in cancers, including glioma. Circular RNAs (circRNAs) can act as key regulators in various cancers. However, the relationship between propofol and circ_0047688 in glioma is still unclear. Cell proliferation was evaluated by Cell Counting Kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU), and colony formation assays. Cell migration and invasion were determined using transwell assay. Cell apoptosis was detected by flow cytometry. Protein levels and RNA levels were detected by western blot assay and real-time quantitative polymerase chain reaction (RT‑qPCR), respectively. The intermolecular interaction was predicted by bioinformatics analysis and verified by dual-luciferase reporter assay. A mouse xenograft model was established for in vivo experiments. Propofol inhibited cell proliferation, migration, and invasion and accelerated apoptosis in glioma cells. Circ_0047688 was upregulated in glioma tissues and cells, and propofol downregulated circ_0047688 in a dose-dependent manner. Circ_0047688 knockdown inhibited glioma cell progression and its overexpression abated the anti-tumor role of propofol in glioma cells. Moreover, miR-516b-5p was a direct target of circ_0047688, and circ_0047688 promoted glioma cell progression by sponging miR-516b-5p. In addition, IFI30 was a direct target of miR-516b-5p, and miR-516b-5p inhibited glioma cell malignant behaviors by targeting IFI30 in propofol-treated cells. Furthermore, circ_0047688 overexpression could weaken the anti-tumor role of propofol in vivo. Propofol inhibited glioma progression via modulating circ_0047688/miR-516b-5p/IFI30 axis, providing a potential therapeutic strategy for treatment of glioma.
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Liu C, Zhang W, Xu G, Zhang D, Zhang C, Qiao S, Wang Z, Wang H. Deep multilayer brain omics identifies the potential involvement of menopause molecular networks in Gliomas' disease progression. FASEB J 2022; 36:e22570. [PMID: 36165217 DOI: 10.1096/fj.202200427rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/15/2022] [Accepted: 09/15/2022] [Indexed: 11/11/2022]
Abstract
The risk of high-grade gliomas is lower in young females, however, its incidence enhances after menopause, suggesting potential protective roles of female sex hormones. Hormone oscillations after menopause have received attention as a possible risk factor. Little is known about risk factors for adult gliomas. We examined the association of the aging brain after menopause, determining the risk of gliomas with proteomics and the MALDI-MSI experiment. Menopause caused low neurotransmitter levels such as GABA and ACH, high inflammatory factor levels like il-1β, and increased lipid metabolism-related levels like triglycerides in the brain. Upregulated and downregulated proteins after menopause were correlated with differentially expressed glioma genes, such as ACTA2, CAMK2D, FNBPIL, ARL1, HEBP1, CAST, CLIC1, LPCAT4, MAST3, and DOCK9. Furthermore, differential gene expression analysis of monocytes showed that the downregulated gene LPCAT4 could be used as a marker to prevent menopausal gliomas in women. Our findings regarding the association of menopause with the risk of gliomas are consistent with several extensive cohort studies. In view of the available evidence, postmenopausal status is likely to represent a significant risk factor for gliomas.
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Affiliation(s)
- Chunhua Liu
- Department of Physiology and Neurobiology, Shandong First Medical University, Jinan, China
| | - Wei Zhang
- School of Medicine, Southeast University, Nanjing, China
| | - Guozheng Xu
- Department of Physiology and Neurobiology, Shandong First Medical University, Jinan, China
| | - Daolai Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Cheng Zhang
- School of Pharmacy, Binzhou Medical University, Yantai, China
| | - Sen Qiao
- Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, Homburg, Germany
| | - Zhimei Wang
- Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, and School of Chemistry and Chemical Engineering, Southeast University, Nanjing, China
| | - Hongmei Wang
- School of Medicine, Southeast University, Nanjing, China.,School of Pharmacy, Binzhou Medical University, Yantai, China
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Yin X, Wu Q, Hao Z, Chen L. Identification of novel prognostic targets in glioblastoma using bioinformatics analysis. Biomed Eng Online 2022; 21:26. [PMID: 35436915 PMCID: PMC9014588 DOI: 10.1186/s12938-022-00995-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Background Glioblastoma (GBM) is the most malignant grade of glioma. Highly aggressive characteristics of GBM and poor prognosis cause GBM-related deaths. The potential prognostic biomarkers remain to be demonstrated. This research builds up predictive gene targets of expression alterations in GBM utilizing bioinformatics analysis. Methods and results The microarray datasets (GSE15824 and GSE16011) associated with GBM were obtained from Gene Expression Omnibus (GEO) database to identify the differentially expressed genes (DEGs) between GBM and non-tumor tissues. In total, 719 DEGs were obtained and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for function enrichment analysis. Furthermore, we constructed protein–protein Interaction (PPI) network among DEGs utilizing Search Tool for the Retrieval of Interacting Genes (STRING) online tool and Cytoscape software. The DEGs of degree > 10 was selected as hub genes, including 73 upregulated genes and 21 downregulated genes. Moreover, MCODE application in Cytoscape software was employed to identify three key modules involved in GBM development and prognosis. Additionally, we used the Gene expression profiling and interactive analyses (GEPIA) online tool to further confirm four genes involving in poor prognosis of GBM patients, including interferon-gamma-inducible protein 30 (IFI30), major histocompatibility complex class II-DM alpha (HLA-DMA), Prolyl 4-hydroxylase beta polypeptide (P4HB) and reticulocalbin-1 (RCN1). Furthermore, the correlation analysis indicated that the expression of IFI30, an acknowledged biomarker in glioma, was positively correlated with HLA-DMA, P4HB and RCN1. RCN1 expression was positively correlated with P4HB and HLA-DMA. Moreover, qRT-PCR and immunohistochemistry analysis further validated the upregulation of four prognostic markers in GBM tissues. Conclusions Analysis of multiple datasets combined with global network information and experimental verification presents a successful approach to uncover the risk hub genes and prognostic markers of GBM. Our study identified four risk- and prognostic-related gene signatures, including IFI30, HLA-DMA, P4HB and RCN1. This gene sets contribute a new perspective to improve the diagnostic, prognostic, and therapeutic outcomes of GBM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Quansheng Wu
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Zheng Hao
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Laizhao Chen
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China.
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11
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Zhou GX, Liu WB, Dai LM, Zhu HL, Xiong YW, Li DX, Xu DX, Wang H. Environmental cadmium impairs blood-testis barrier via activating HRI-responsive mitochondrial stress in mice. Sci Total Environ 2022; 810:152247. [PMID: 34896485 DOI: 10.1016/j.scitotenv.2021.152247] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 11/13/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
Cadmium (Cd) is a well-known testicular toxicant. Blood-testis barrier (BTB), a vital part of testes, which has been reported to be damaged upon Cd exposure. However, the detailed mechanism about Cd-mediated disruption of BTB remains unclear. This study aims to investigate the role of Heme-Regulated Inhibitor (HRI)-responsive mitochondrial stress in Cd-mediated disruption of BTB. Male mice are intraperitoneally injected (i.p.) with melatonin (Mel, a cellular stress antagonist, 5.0 mg/kg) before Cd treatment (i.p., 2.0 mg/kg) for 8 h, and then treated with Cd for 0-48 h. Mouse Sertoli cells are pretreated with Mel (10 μM) for 1 h, and then treated with Cd (10 μM) for 0-24 h. We find that Cd damages the BTB and reduces the Occludin protein, a crucial BTB-related protein via activating p38/matrix metalloproteinase-2 (p38/MMP2) pathway and Integrated Stress Response (ISR). Further experiments reveal that the Heme-Regulated Inhibitor (HRI)-responsive mitochondrial stress is triggered in Cd-treated Sertoli cells. Most importantly, Cd-activated p38 signaling and ISR are regulated by HRI-responsive mitochondrial stress in Sertoli cells. Unexpectedly, we find that melatonin rescues the Cd-mediated disruption of BTB through blocking HRI-responsive mitochondrial stress in testes. Overall, these data indicate that environmental cadmium exposure impairs the BTB through activating HRI-responsive mitochondrial stress in Sertoli cells.
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Affiliation(s)
- Guo-Xiang Zhou
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Wei-Bo Liu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Li-Min Dai
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua-Long Zhu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Yong-Wei Xiong
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Dai-Xin Li
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - De-Xiang Xu
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China
| | - Hua Wang
- Department of Toxicology, School of Public Health, Anhui Medical University, China; Key Laboratory of Environmental Toxicology of Anhui Higher Education Institutes, China.
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12
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Liu T, Zhu C, Chen X, Wu J, Guan G, Zou C, Shen S, Chen L, Cheng P, Cheng W, Wu A. Dual role of ARPC1B in regulating the network between tumor-associated macrophages and tumor cells in glioblastoma. Oncoimmunology 2022; 11:2031499. [PMID: 35111386 PMCID: PMC8803105 DOI: 10.1080/2162402x.2022.2031499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Tianqi Liu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xin Chen
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianqi Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Cunyi Zou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Shuai Shen
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ling Chen
- Department of Neurosurgery, Chinese People’s Liberation Army of China (Pla) General Hospital, Medical School of Chinese Pla, Institute of Neurosurgery of Chinese Pla, Beijing, China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wen Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
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13
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Sørensen MD, Kristensen BW. TUMOUR-ASSOCIATED CD204+ MICROGLIA/MACROPHAGES ACCUMULATE IN PERIVASCULAR AND PERINECROTIC NICHES AND CORRELATE WITH AN INTERLEUKIN-6 ENRICHED INFLAMMATORY PROFILE IN GLIOBLASTOMA. Neuropathol Appl Neurobiol 2021; 48:e12772. [PMID: 34713474 PMCID: PMC9306597 DOI: 10.1111/nan.12772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 09/30/2021] [Accepted: 10/25/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Mia Dahl Sørensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Bjarne Winther Kristensen
- Department of Pathology, Odense University Hospital, Odense, Denmark.,Department of Clinical Research, University of Southern Denmark, Odense, Denmark.,Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine and Biotech Research and Innovation Center (BRIC), University of Copenhagen, Copenhagen, Denmark
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14
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Ye C, Zhou W, Wang F, Yin G, Zhang X, Kong L, Gao Z, Feng M, Zhou C, Sun D, Wang L, Liu L, Zheng C, Xiang Y, Guo M, Huang S, Yu Z. Prognostic value of gamma-interferon-inducible lysosomal thiol reductase expression in female patients diagnosed with breast cancer. Int J Cancer 2021; 150:705-717. [PMID: 34648659 DOI: 10.1002/ijc.33843] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/01/2021] [Indexed: 12/25/2022]
Abstract
Because of the high heterogeneity of breast cancer outcome, identification of novel prognostic biomarkers is critical to improve patient stratification and guide precise treatment. We examined the prognostic value of gamma-interferon-inducible lysosomal thiol reductase (GILT) expression in a training set of 416 breast cancer patients and a validation set of 210 patients, and performed functional studies to investigate the functions and underlying mechanisms of GILT on breast cancer prognosis. Our results indicated that high GILT expression in breast cancer cells was associated with improved disease-free survival (DFS; hazard ratio [HR] = 0.189, 95% confidence interval [CI]: 0.099-0.361) and breast cancer-specific survival (BCSS; HR = 0.187, 95% CI: 0.080-0.437) of breast cancer patients both in the training set and the external validation set (HR = 0.453, 95% CI: 0.235-0.873 for DFS, HR = 0.488, 95% CI: 0.245-0.970 for BCSS). In vitro and in vivo studies showed that GILT overexpression inhibited breast cancer cells proliferation, invasion, migration and tumor formation in nude mice and increased sensitivity of breast cancer cells to standard treatment. Proteomics analysis indicated that GILT inhibited reactive oxygen species (ROS) and autophagy activation in breast cancer cells, and GILT overexpression-mediated tumor growth was further enhanced in the presence of autophagy or ROS inhibitors. Our results demonstrate that GILT expression can be effectively used to predict the prognosis and guide treatment strategies of breast cancer patients.
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Affiliation(s)
- Chunmiao Ye
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Wenzhong Zhou
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fei Wang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Gengshen Yin
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoxia Zhang
- Department of Thyroid and Breast Surgery, Linyi People's Hospital, Linyi, China
| | - Lingyu Kong
- Department of Breast Surgery, Linyi Cancer Hospital, Linyi, China
| | - Zhongcheng Gao
- Department of Thyroid and Breast Surgery, Linyi People's Hospital, Linyi, China
| | - Man Feng
- Department of Pathology, The Third Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Chengjun Zhou
- Department of Pathology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dianshui Sun
- Cancer Center, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Lei Wang
- Department of Oncology, Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Liyuan Liu
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chao Zheng
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yujuan Xiang
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Mingming Guo
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Shuya Huang
- School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Zhigang Yu
- Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.,Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.,Shandong Provincial Engineering Laboratory of Translational Research on Prevention and Treatment of Breast Disease, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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15
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Cheng Q, Duan W, He S, Li C, Cao H, Liu K, Ye W, Yuan B, Xia Z. Multi-Omics Data Integration Analysis of an Immune-Related Gene Signature in LGG Patients With Epilepsy. Front Cell Dev Biol 2021; 9:686909. [PMID: 34336837 PMCID: PMC8322853 DOI: 10.3389/fcell.2021.686909] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background The tumor immune microenvironment significantly affects tumor occurrence, progression, and prognosis, but its impact on the prognosis of low-grade glioma (LGG) patients with epilepsy has not been reported. Hence, the purpose of this study is to explore its effect on LGG patients with epilepsy. Methods The data of LGG patients derived from the TCGA database. The level of immune cell infiltration and the proportion of 22 immune cells were evaluated by ESTIMATE and CIBERSORT algorithms, respectively. The Cox and LASSO regression analysis was adopted to determine the DEGs, and further established the clustering and risk score models. The association between genomic alterations and risk score was investigated using CNV and somatic mutation data. GSVA was adopted to identify the immunological pathways, immune infiltration and inflammatory profiles related to the signature genes. The Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and GDSC database were used to predict the patient’s response to immunotherapy and chemotherapy, respectively. Results The prognosis of LGG patients with epilepsy was associated with the immune score. Three prognostic DEGs (ABCC3, PDPN, and INA) were screened out. The expression of signature genes was regulated by DNA methylation. The clustering and risk score models could stratify glioma patients into distinct prognosis groups. The risk score was an independent predictor in prognosis, with a high risk-score indicating a poor prognosis, more malignant clinicopathological and genomic aberration features. The nomogram had the better predictive ability. Patients at high risk had a higher level of macrophage infiltration and increased inflammatory activities associated with T cells and macrophages. While the higher percentage of NK CD56bright cell and more active inflammatory activity associated with B cell were present in the low-risk patients. The signature genes participated in the regulation of immune-related pathways, such as IL6-JAK-STAT3 signaling, IFN-α response, IFN-γ response, and TNFA-signaling-via-NFKB pathways. The high-risk patients were more likely to benefit from anti-PD1 and temozolomide (TMZ) treatment. Conclusion An immune-related gene signature was established based on ABCC3, PDPN, and INA, which can be used to predict the prognosis, immune infiltration status, immunotherapy and chemotherapy response of LGG patients with epilepsy.
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Affiliation(s)
- Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Weiwei Duan
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Shiqing He
- Department of Neurosurgery, Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, China
| | - Chen Li
- Department of Rehabilitation Medicine, Hunan Provincial People's Hospital, Hunan Normal University, Changsha, China
| | - Hui Cao
- Department of Psychiatry, The Second People's Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Kun Liu
- Department of Cerebrovascular Surgery, The Second People's Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Weijie Ye
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Bo Yuan
- Department of Cerebrovascular Surgery, The Second People's Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Zhiwei Xia
- Department of Neurology, Hunan Aerospace Hospital, Changsha Medical University, Changsha, China
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16
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Niu LT, Wang YQ, Wong CCL, Gao SX, Mo XD, Huang XJ. Targeting IFN-γ-inducible lysosomal thiol reductase overcomes chemoresistance in AML through regulating the ROS-mediated mitochondrial damage. Transl Oncol 2021; 14:101159. [PMID: 34252711 PMCID: PMC8319687 DOI: 10.1016/j.tranon.2021.101159] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 06/14/2021] [Indexed: 12/13/2022] Open
Abstract
GILT is upregulated in chemoresistant LSC-enriched CD34+ progenitor cells. Inhibition of GILT in AML cells sensitized them to Ara-C treatment through ROS-mediated mitochondrial damage and apoptosis. PI3K/Akt/NRF2 pathway inhibition is critical for the intracellular oxidative state in GILT-suppression AML cells after Ara-C treatment. GILT expression is related to a poor prognosis in AML patients.
The persistence of leukemia stem cells (LSCs) is one of the leading causes of chemoresistance in acute myeloid leukemia (AML). To explore the factors important in LSC-mediated resistance, we use mass spectrometry to screen the factors related to LSC chemoresistance and defined IFN-γ-inducible lysosomal thiol reductase (GILT) as a candidate. We found that the GILT expression was upregulated in chemoresistant CD34+ AML cells. Loss of function studies demonstrated that silencing of GILT in AML cells sensitized them to Ara-C treatment both in vitro and in vivo. Further mechanistic findings revealed that the ROS-mediated mitochondrial damage plays a pivotal role in inducing apoptosis of GILT-inhibited AML cells after Ara-C treatment. The inactivation of PI3K/Akt/ nuclear factor erythroid 2-related factor 2 (NRF2) pathway, causing reduced generation of antioxidants such as SOD2 and leading to a shifted ratio of GSH/GSSG to the oxidized form, contributed to the over-physiological oxidative status in the absence of GILT. The prognostic value of GILT was also validated in AML patients. Taken together, our work demonstrated that the inhibition of GILT increases AML chemo-sensitivity through elevating ROS level and induce oxidative mitochondrial damage-mediated apoptosis, and inhibition of the PI3K/Akt/NRF2 pathway enhances the intracellular oxidative state by disrupting redox homeostasis, providing a potentially effective way to overcome chemoresistance of AML.
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Affiliation(s)
- Li-Ting Niu
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, 100044, China
| | - Yu-Qing Wang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, 100044, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871
| | - Catherine C L Wong
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871,; Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China.; School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China; Peking University First Hospital, Beijing, 100034, China
| | - Shuai-Xin Gao
- Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center, Peking University, Beijing 100191, China
| | - Xiao-Dong Mo
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, 100044, China
| | - Xiao-Jun Huang
- Peking University People's Hospital, Peking University Institute of Hematology, National Clinical Research Center for Hematologic Disease, Beijing Key Laboratory of Hematopoietic Stem Cell Transplantation, Beijing, 100044, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871,.
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17
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Wei D, Shen S, Lin K, Lu F, Zheng P, Wu S, Kang D. NPC2 as a Prognostic Biomarker for Glioblastoma Based on Integrated Bioinformatics Analysis and Cytological Experiments. Front Genet 2021; 12:611442. [PMID: 33777094 PMCID: PMC7990766 DOI: 10.3389/fgene.2021.611442] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/08/2021] [Indexed: 12/31/2022] Open
Abstract
Glioblastoma (GBM) is one of the most common and fatal malignancies worldwide, while its prognostic biomarkers are still being explored. This study aims to identify potential genes with clinical and prognostic significance by integrating bioinformatics analysis and investigating their function in HNSCC. Based on the Single-cell RNA sequencing (scRNA-seq) results of H3K27M-glioma cells, computational bioinformatics methods were employed for selecting prognostic biomarker for GBM. The protein NPC2 (NPC Intracellular Cholesterol Transporter 2), which has been shown to be related to lipoprotein metabolism and innate immune system, was identified to be upregulated in GBM. NPC2 showed a relatively higher expression in GBM samples, and a negative correlation with tumor purity and tumor infiltrating immune cells. Additionally, NPC2 was knocked down in U87-MG and U251 cells line, and cell proliferation and migration capability were evaluated with CCK-8, scratch and transwell assay, respectively. Cytological experiments has shown that NPC2 overexpression inhibited GBM cells proliferation and migration, indicating its important role in GBM progression. This is the first investigation into the prognostic value of NPC2 interact with GBM. The potential molecular factor NPC2 have been identified as a prognostic biomarker for GBM.
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Affiliation(s)
- De Wei
- Department of Neurosurgery, Fujian Provincial Hospital South Branch, Fuzhou, China.,Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China.,Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shanghang Shen
- Department of Neurosurgery, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kun Lin
- Department of Neurosurgery, Fujian Provincial Hospital South Branch, Fuzhou, China.,Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Feng Lu
- Department of Neurosurgery, Fujian Provincial Hospital South Branch, Fuzhou, China.,Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Pengfeng Zheng
- Department of Neurosurgery, Fujian Provincial Hospital South Branch, Fuzhou, China.,Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Shizhong Wu
- Department of Neurosurgery, Fujian Provincial Hospital South Branch, Fuzhou, China.,Department of Neurosurgery, Shengli Clinical Medical College of Fujian Medical University, Fuzhou, China
| | - Dezhi Kang
- Department of Neurosurgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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18
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Yu K, Yang H, Lv QL, Wang LC, Tan ZL, Zhang Z, Ji YL, Lin QX, Chen JJ, He W, Chen Z, Shen XL. Construction of a competitive endogenous RNA network and analysis of potential regulatory axis targets in glioblastoma. Cancer Cell Int 2021; 21:102. [PMID: 33579282 PMCID: PMC7881621 DOI: 10.1186/s12935-021-01789-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 01/27/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Glioblastoma is the most common primary malignant brain tumor. Because of the limited understanding of its pathogenesis, the prognosis of glioblastoma remains poor. This study was conducted to explore potential competing endogenous RNA (ceRNA) network chains and biomarkers in glioblastoma by performing integrated bioinformatics analysis. METHODS Transcriptome expression data from The Cancer Genome Atlas database and Gene Expression Omnibus were analyzed to identify differentially expressed genes between glioblastoma and normal tissues. Biological pathways potentially associated with the differentially expressed genes were explored by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, and a protein-protein interaction network was established using the STRING database and Cytoscape. Survival analysis using Gene Expression Profiling Interactive Analysis was based on the Kaplan-Meier curve method. A ceRNA network chain was established using the intersection method to align data from four databases (miRTarBase, miRcode, TargetScan, and lncBace2.0), and expression differences and correlations were verified by quantitative reverse-transcription polymerase chain reaction analysis and by determining the Pearson correlation coefficient. Additionally, an MTS assay and the wound-healing and transwell assays were performed to evaluate the effects of complement C1s (C1S) on the viability and migration and invasion abilities of glioblastoma cells, respectively. RESULTS We detected 2842 differentially expressed (DE) mRNAs, 2577 DE long non-coding RNAs (lncRNAs), and 309 DE microRNAs (miRNAs) that were dysregulated in glioblastoma. The final ceRNA network consisted of six specific lncRNAs, four miRNAs, and four mRNAs. Among them, four DE mRNAs and one DE lncRNA were correlated with overall survival (p < 0.05). C1S was significantly correlated with overall survival (p= 0.015). In functional assays, knockdown of C1S inhibited the proliferation and invasion of glioblastoma cell lines. CONCLUSIONS We established four ceRNA networks that may influence the occurrence and development of glioblastoma. Among them, the MIR155HG/has-miR-129-5p/C1S axis is a potential marker and therapeutic target for glioblastoma. Knockdown of C1S inhibited the proliferation, migration, and invasion of glioblastoma cells. These findings clarify the role of the ceRNA regulatory network in glioblastoma and provide a foundation for further research.
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Affiliation(s)
- Kai Yu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Huan Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Qiao-Li Lv
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi, Nanchang, People's Republic of China
| | - Li-Chong Wang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zi-Long Tan
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zhe Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Yu-Long Ji
- Jiangxi University of Traditional Chinese Medicine, Jiangxi, Nanchang, People's Republic of China
| | - Qian-Xia Lin
- Jiangxi University of Traditional Chinese Medicine, Jiangxi, Nanchang, People's Republic of China
| | - Jun-Jun Chen
- Jiangxi Key Laboratory of Translational Cancer Research, Jiangxi Cancer Hospital, Jiangxi, Nanchang, People's Republic of China
| | - Wei He
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Zhen Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China
| | - Xiao-Li Shen
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Donghu District, Jiangxi, 330006, Nanchang, People's Republic of China.
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19
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Sun N, Gao P, Li Y, Yan Z, Peng Z, Zhang Y, Han F, Qi X. Screening and Identification of Key Common and Specific Genes and Their Prognostic Roles in Different Molecular Subtypes of Breast Cancer. Front Mol Biosci 2021; 8:619110. [PMID: 33644115 PMCID: PMC7905399 DOI: 10.3389/fmolb.2021.619110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 01/08/2021] [Indexed: 01/27/2023] Open
Abstract
Breast cancer is one of the most common cancers. Although the present molecular classification improves the treatment effect and prognosis of breast cancer, the heterogeneity of the molecular subtype remains very complex, and the applicability and effectiveness of treatment methods are still limited leading to poorer patient prognosis than expected. Further identification of more refined molecular typing based on gene expression profile will yield better understanding of the heterogeneity, improving treatment effects and prolonging prognosis of patients. Here, we downloaded the mRNA expression profiles and corresponding clinical data of patients with breast cancer from public databases and performed typical molecular typing using PAM50 (Prediction Analysis of Microarray 50) method. Comparative analyses were performed to screen the common and specific differentially expressed genes (DEGs) between cancer and corresponding para-cancerous tissues in each breast cancer subtype. The GO and KEGG analyses of the DEGs were performed to enrich the common and specific functional progress and signaling pathway involved in breast cancer subtypes. A total of 38 key common and specific DEGs were identified and selected based on the validated results, GO/KEGG enrichments, and the priority of expression, including four common DEGs and 34 specific DEGs in different subtypes. The prognostic value of these key common and specific DEGs was further analyzed to obtain useful potential markers in clinic. Finally, the potential roles and the specific prognostic values of the common and specific DEGs were speculated and summarized in total breast cancer and different subtype breast cancer based on the results of these analyses. The findings of our study provide the basis of more refined molecular typing of breast cancer, potential new therapeutic targets and prognostic markers for different breast cancer subtypes
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Affiliation(s)
- Na Sun
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Pingping Gao
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yanling Li
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zexuan Yan
- Institute of Pathology and Southwest Cancer Center, Key Laboratory of the Ministry of Education, Southwest Hospital, Army Medical University, Chongqing, China
| | - Zaihui Peng
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Yi Zhang
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
| | - Fei Han
- Institute of Toxicology, College of Preventive Medicine, Army Medical University, Chongqing, China
| | - Xiaowei Qi
- Department of Breast and Thyroid Surgery, Southwest Hospital, Army Medical University, Chongqing, China
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20
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Fan Y, Wang X, Li Y. IFI30 expression predicts patient prognosis in breast cancer and dictates breast cancer cells proliferation via regulating autophagy. Int J Med Sci 2021; 18:3342-3352. [PMID: 34400904 PMCID: PMC8364447 DOI: 10.7150/ijms.62870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction: Incidence and mortality rates of breast cancer are increasing in women worldwide. Immunotherapy is a relatively popular treatment modality for all malignant tumors including breast cancer in recent years. Interferon γ-inducible protein 30 (IFI30) could catalyze the reduction of disulfide bonds and enhance major histocompatibility complex (MHC) class II-restricted antigen processing. Recent studies showed that IFI30 played an important role in the immune response of malignant tumors. Methods: The Cancer Genome Atlas (TCGA) database and clinical proteomic tumor Analysis consortium (CPTAC) database were applied to predict the role of IFI30 in breast cancer and the relationship between IFI30 and prognosis of breast cancer patients. Then we detected the expression of IFI30 in clinical samples of breast cancer patients, and analyzed the relationship between IFI30 and the prognosis of breast cancer patients. We used lentivirus infection method to construct a stable IFI30 knockdown cell line, and detected the effect of IFI30 in breast cancer cells. Nude mice tumor bearing experiment was performed to investigate the effect of IFI30 on breast cancer cells in vivo. Western blot was used to verify the regulation of autophagy related protein LC3 and p62 by IFI30. Results: We found that IFI30 was highly expressed in breast cancer tissues and was associated with poor outcome of patients. The knockdown of IFI30 could inhibit the proliferation, migration and invasion of breast cancer cells and significantly inhibit tumor growth in vivo. Increased accumulation of LC3-II and p62 suggested impaired autophagy in IFI30 knockdown cells. Discussion: As a result, we suggested that IFI30 might play a key role in the initiation and progression of human breast cancer and might be a new therapeutic target in breast cancer.
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Affiliation(s)
- Yan Fan
- Department of Pediatrics, The First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang , Liaoning, 110001 China
| | - Xu Wang
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang , Liaoning, 110001 China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC, and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC, China Medical University, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning,110122 China
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