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Tariq A, Piontkivska H. Reovirus infection induces transcriptome-wide unique A-to-I editing changes in the murine fibroblasts. Virus Res 2024; 346:199413. [PMID: 38848818 PMCID: PMC11225029 DOI: 10.1016/j.virusres.2024.199413] [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: 02/20/2024] [Revised: 05/26/2024] [Accepted: 06/02/2024] [Indexed: 06/09/2024]
Abstract
The conversion of Adenosine (A) to Inosine (I), by Adenosine Deaminases Acting on RNA or ADARs, is an essential post-transcriptional modification that contributes to proteome diversity and regulation in metazoans including humans. In addition to its transcriptome-regulating role, ADARs also play a major part in immune response to viral infection, where an interferon response activates interferon-stimulated genes, such as ADARp150, in turn dynamically regulating host-virus interactions. A previous report has shown that infection from reoviruses, despite strong activation of ADARp150, does not influence the editing of some of the major known editing targets, while likely editing others, suggesting a potentially nuanced editing pattern that may depend on different factors. However, the results were based on a handful of selected editing sites and did not cover the entire transcriptome. Thus, to determine whether and how reovirus infection specifically affects host ADAR editing patterns, we analyzed a publicly available deep-sequenced RNA-seq dataset, from murine fibroblasts infected with wild-type and mutant reovirus strains that allowed us to examine changes in editing patterns on a transcriptome-wide scale. To the best of our knowledge, this is the first transcriptome-wide report on host editing changes after reovirus infection. Our results demonstrate that reovirus infection induces unique nuanced editing changes in the host, including introducing sites uniquely edited in infected samples. Genes with edited sites are overrepresented in pathways related to immune regulation, cellular signaling, metabolism, and growth. Moreover, a shift in editing targets has also been observed, where the same genes are edited in infection and control conditions but at different sites, or where the editing rate is increased for some and decreased for other differential targets, supporting the hypothesis of dynamic and condition-specific editing by ADARs.
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Affiliation(s)
- Ayesha Tariq
- Department of Biological Sciences, Kent State University, Kent, OH, USA
| | - Helen Piontkivska
- Department of Biological Sciences, Kent State University, Kent, OH, USA; Brain Health Research Institute, Kent State University, Kent, OH, USA; Healthy Communities Research Institute, Kent State University, Kent, OH, USA.
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Zhang X, Li J, Yang L, Zhu Y, Gao R, Zhang T, Chen X, Fu J, He G, Shi H, Peng S, Wu X. Targeted proteomics-determined multi-biomarker profiles developed classifier for prognosis and immunotherapy responses of advanced cervical cancer. Front Immunol 2024; 15:1391524. [PMID: 38835778 PMCID: PMC11148239 DOI: 10.3389/fimmu.2024.1391524] [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: 02/26/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
Background Cervical cancer (CC) poses a global health challenge, with a particularly poor prognosis in cases of recurrence, metastasis, or advanced stages. A single biomarker is inadequate to predict CC prognosis or identify CC patients likely to benefit from immunotherapy, presumably owing to tumor complexity and heterogeneity. Methods Using advanced Olink proteomics, we analyzed 92 oncology-related proteins in plasma from CC patients receiving immunotherapy, based upon the comparison of protein expression levels of pre-therapy with those of therapy-Cycle 6 in the partial response (PR) group and progressive disease (PD) group, respectively. Results 55 proteins were identified to exhibit differential expression trends across pre-therapy and post-therapy in both PR and PD groups. Enriched GO terms and KEGG pathways were associated with vital oncological and immunological processes. A logistic regression model, using 5 proteins (ITGB5, TGF-α, TLR3, WIF-1, and ERBB3) with highest AUC values, demonstrated good predictive performance for prognosis of CC patients undergoing immunotherapy and showed potential across different cancer types. The effectiveness of these proteins in prognosis prediction was further validated using TCGA-CESC datasets. A negative correlation and previously unidentified roles of WIF-1 in CC immunotherapy was also first determined. Conclusion Our findings reveal multi-biomarker profiles effectively predicting CC prognosis and identifying patients benefitting most from immunotherapy, especially for those with limited treatment options and traditionally poor prognosis, paving the way for personalized immunotherapeutic treatments and improved clinical strategies.
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Affiliation(s)
- Xu Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Jin Li
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Liuke Yang
- College of Plant Protection, Nanjing Agricultural University, Nanjing, China
| | - Youwei Zhu
- Clinical Center of Bio-Therapy at Zhongshan Hospital & Institutes of Biomedical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Rongrong Gao
- Clinical Center for Biotherapy at Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tiancheng Zhang
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Xuwen Chen
- Shanghai Kelin Clinical Bioinformatics Institute, Shanghai, China
| | - Jun Fu
- LC-Bio Technology Co., Ltd, Hangzhou, China
| | - Gaoyang He
- LC-Bio Technology Co., Ltd, Hangzhou, China
| | - Huijuan Shi
- NHC Key Laboratory of Reproduction Regulation, Shanghai Engineering Research Center of Reproductive Health Drug and Devices, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, NHC Key Laboratory of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Shenjie Peng
- Shanghai Medical College of Fudan University, Fudan University, Shanghai, China
| | - XiaoHua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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Sakurai S, Ishida Y, Shintani T, Yamasaki S, Matsui K, Hamana T, Nobumoto T, Yanamoto S, Hayashido Y. Clinical significance of integrin αV and β superfamily members and focal adhesion kinase activity in oral squamous cell carcinoma: a retrospective observational study. Pathol Oncol Res 2024; 30:1611571. [PMID: 38312516 PMCID: PMC10830843 DOI: 10.3389/pore.2024.1611571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 01/09/2024] [Indexed: 02/06/2024]
Abstract
Objectives: Integrins are heterodimeric transmembrane plasma membrane proteins composed of α- and β-chains. They bind to extracellular matrix (ECM) and cytoskeletal proteins as ECM protein receptors. Upon ECM protein binding, integrins activate focal adhesion kinase (FAK) and transduce various signals. Despite their importance, integrin and FAK expression in oral squamous cell carcinoma (OSCC) tissue and the prognosis of patients with OSCC remains elusive. Methods: In a retrospective observational study, we immunohistochemically evaluated integrin αV, β1, β3, β5, β6, FAK, and phosphorylated-FAK (pFAK) expressions as prognostic predictors in 96 patients with OSCC. Patients were classified as positive or negative based on staining intensity, and clinicopathologic characteristics and survival rates of the two groups were compared. The association between above integrin-related proteins and PD-1 or PD-L1 in OSCC tissues was investigated. Results: We observed immunohistochemical integrin αV, β1, β6, β8, and FAK expressions in the cell membrane and cytoplasm but not integrin β3 and β5 in the OSCC tissues. pFAK was expressed in the cytoplasm of OSCC cells. The overall survival rate significantly decreased in pFAK-positive OSCC patients compared to the negative group, and cervical lymph node metastasis significantly increased in integrin β8-positive patients with OSCC (p < 0.05). No association between integrin-related proteins and PD-1 or PD-L1 in OSCC tissues was observed. Conclusion: Our results indicate that pFAK and integrin β8 are prognostic factors for OSCC. Therefore, pFAK- and integrin β8-targeting new oral cancer diagnostic and therapeutic methods hold a promising potential.
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Affiliation(s)
- Shigeru Sakurai
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Yasutaka Ishida
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Tomoaki Shintani
- Center of Oral Clinical Examination, Hiroshima University Hospital, Hiroshima, Japan
| | - Sachiko Yamasaki
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Kensaku Matsui
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Tomoaki Hamana
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Tadayoshi Nobumoto
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Souichi Yanamoto
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
| | - Yasutaka Hayashido
- Department of Oral Oncology, Graduate School of Biomedical and Health Science, Hiroshima University, Hiroshima, Japan
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Fu Q, Gao H, Liu K, Su J, Zhang J, Guo X, Yang F. Identification of circRNA-miRNA-mRNA Network Regulated by Hsp90 in Human Melanoma A375 Cells. Comb Chem High Throughput Screen 2024; 27:307-316. [PMID: 37303182 DOI: 10.2174/1386207326666230609145247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND Melanoma is the deadliest form of skin cancer. Heat shock protein 90 (Hsp90) is highly expressed in human melanoma. Hsp90 inhibitors can suppress the growth of human melanoma A375 cells; however, the underlying mechanism remains unclear. METHODS A375 cells were treated with SNX-2112, an Hsp90 inhibitor, for 48 h, and wholetranscriptome sequencing was performed. RESULTS A total of 2,528 differentially expressed genes were identified, including 895 upregulated and 1,633 downregulated genes. Pathway enrichment analyses of differentially expressed mRNAs identified the extracellular matrix (ECM)-receptor interaction pathway as the most significantly enriched pathway. The ECM receptor family mainly comprises integrins (ITGs) and collagens (COLs), wherein ITGs function as the major cell receptors for COLs. 19 upregulated miRNAs were found to interact with 6 downregulated ITG genes and 8 upregulated miRNAs were found to interact with 3 downregulated COL genes. 9 differentially expressed circRNAs in SNX-2112- treated A375 cells were identified as targets of the ITG- and COL-related miRNAs. Based on the differentially expressed circRNAs, miRNAs, and mRNAs, ITGs- and COL-based circRNAmiRNA- mRNA regulatory networks were mapped, revealing a novel regulatory mechanism of Hsp90-regulated melanoma. CONCLUSION Targeting the ITG-COL network is a promising approach to the treatment of melanoma.
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Affiliation(s)
- Qiang Fu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Hengyuan Gao
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Kaisheng Liu
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Juan Su
- Department of Dermatology, Xiangya Hospital, Central South University, Changsha, China
| | - Jianglin Zhang
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
- Candidate Branch of the National Clinical Research Center for Skin Diseases, Shenzhen, 518020, Guangdong, China
| | - Xiaojing Guo
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
| | - Fang Yang
- Guangdong Provincial Clinical Research Center for Geriatrics, Shenzhen Clinical Research Center for Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
- Candidate Branch of the National Clinical Research Center for Skin Diseases, Shenzhen, 518020, Guangdong, China
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Ma L, Song K, Zang J. Integrin β5 is an independent prognostic marker for intrahepatic cholangiocarcinoma in a Chinese population. Exp Ther Med 2023; 26:532. [PMID: 37869645 PMCID: PMC10587877 DOI: 10.3892/etm.2023.12231] [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: 01/13/2023] [Accepted: 06/21/2023] [Indexed: 10/24/2023] Open
Abstract
Intrahepatic cholangiocarcinoma (ICC) is the second most common primary liver tumor and a major cause of cancer mortality worldwide. Integrin β5 (ITGB5) is considered to be involved in the intercellular signal transduction and regulation of tumorigenesis and development. The present study investigated the association between ITGB5 expression levels and the prognosis of ICC, as well as the effects of ITGB5 on the proliferation and invasion of ICC cells. RNA-sequencing transcriptomic profiling data of ICC samples were retrieved from The Cancer Genome Atlas (TCGA) and the Gene Expression Omnibus (GEO) databases. Tissue specimens from patients with ICC treated at Taizhou People's Hospital were collected and the ITGB5 expression levels were evaluated using immunohistochemical staining. The biological function of ITGB5 in ICC was investigated using Gene Ontology (GO), Gene Set Enrichment Analysis (GSEA) and in vitro experiments using HuCCT1 cells. After knocking down ITGB5 expression, cell proliferation was detected using Cell Counting Kit-8 assay, while cell invasion was assessed using Transwell assays. According to TCGA dataset, ITGB5 was highly expressed in ICC; however, there was no significant difference in prognosis between patients with high and low ITGB5 expression levels. High expression of ITGB5 was present in the tissues of patients with ICC from the GEO database, which was associated with poor prognosis. Survival analyses of the clinical data obtained in the present study revealed that high expression levels of ITGB5 in patients with ICC were associated with a reduced overall survival. GO and GSEA indicated that genes associated with ITGB5 were enriched in the extracellular matrix-receptor interaction and focal adhesion signaling pathways. Silencing ITGB5 inhibited the proliferation and invasion of ICC cells. In conclusion, ITGB5 may act as an essential regulator of ICC development and progression by influencing the proliferation and invasion of ICC cells. However, future studies with larger sample sizes are required to validate the role of ITGB5 in the prognosis of patients with ICC.
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Affiliation(s)
- Lixing Ma
- Department of Surgery, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Kang Song
- Department of Hepatobiliary Surgery, Taixing People's Hospital, The Affiliated Taixing People's Hospital of Yangzhou University, Taixing, Jiangsu 225400, P.R. China
| | - Jinfeng Zang
- Department of Hepatobiliary Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, Jiangsu 225300, P.R. China
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Zhang Q, Yu B, Zhang Y, Tian Y, Yang S, Chen Y, Wu H. Combination of single-cell and bulk RNA seq reveals the immune infiltration landscape and targeted therapeutic drugs in spinal cord injury. Front Immunol 2023; 14:1068359. [PMID: 36742334 PMCID: PMC9894719 DOI: 10.3389/fimmu.2023.1068359] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Background In secondary spinal cord injury (SCI), the immune microenvironment of the injured spinal cord plays an important role in spinal regeneration. Among the immune microenvironment components, macrophages/microglia play a dual role of pro-inflammation and anti-inflammation in the subacute stage of SCI. Therefore, discovering the immune hub genes and targeted therapeutic drugs of macrophages/microglia after SCI has crucial implications in neuroregeneration. This study aimed to identify immune hub genes and targeted therapeutic drugs for the subacute phase of SCI. Methods Bulk RNA sequencing (bulk-RNA seq) datasets (GSE5296 and GSE47681) and single-cell RNA sequencing (scRNA-seq) dataset (GSE189070) were obtained from the Gene Expression Omnibus database. In the bulk RNA-seq, the R package 'limma,' 'WGCNA,' and 'CIBERSORT' were used to jointly screen key immune genes. Subsequently, the R package 'Seurat' and the R package 'celldex' were used to divide and annotate the cell clusters, respectively. After using the Autodock software to dock immune hub genes and drugs that may be combined, the effectiveness of the drug was verified using an in vivo experiment with the T9 SCI mouse model. Results In the bulk-RNA seq, B2m, Itgb5, and Vav1 were identified as immune hub genes. Ten cell clusters were identified in scRNA-seq, and B2m and Itgb5 were mainly located in the microglia, while Vav1 was mainly located in macrophages. Molecular docking results showed that the proteins corresponding to these immune genes could accurately bind to decitabine. In decitabine-treated mice, the pro-inflammatory factor (TNF-α, IL-1β) levels were decreased while anti-inflammatory factor (IL-4, IL-10) levels were increased at 2 weeks post-SCI, and macrophages/microglia transformed from M1 to M2. At 6 weeks post-SCI, the neurological function score and electromyography of the decitabine treatment group were also improved. Conclusion In the subacute phase of SCI, B2m, Itgb5, and Vav1 in macrophages/microglia may be key therapeutic targets to promote nerve regeneration. In addition, low-dose decitabine may promote spinal cord regeneration by regulating the polarization state of macrophages/microglia.
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Affiliation(s)
- Qing Zhang
- Key laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Beibei Yu
- Department of Neurourgery, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Yongfeng Zhang
- Department of Neurourgery, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Yunze Tian
- Department of Neurourgery, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Shijie Yang
- Department of Neurourgery, the Second Affiliated Hospital of Xi'an Jiao Tong University, Xi'an, China
| | - Yongfeng Chen
- Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Haining Wu
- Department of Orthopaedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
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Sossa-Rojas H, Franco-Maz PG, Zapata-Acevedo C, Gutierrez-Castañeda LD, Guerrero C. Preclinical evaluation of oncolytic potential human rotavirus Wt 1-5 in gastric adenocarcinoma. PLoS One 2023; 18:e0285543. [PMID: 37186587 PMCID: PMC10184912 DOI: 10.1371/journal.pone.0285543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023] Open
Abstract
Despite advances in biomedical research, gastric cancer remains the leading cause of morbidity and mortality worldwide due to the limited efficacy of conventional therapies. In recent decades, oncolytic viruses have emerged as a biological therapeutic alternative to cancer due to their selectivity, effectiveness, and low toxicity. However, clinical trials have shown that developing a virus with selectivity for multiple tumor receptors and the ability to penetrate and diffuse through the tumor microenvironment to reactivate the immune system remains challenging. This study aimed to examine the oncolytic potential of tumor cell-adapted rotavirus Wt1-5 in gastric adenocarcinoma samples. This study focused on determining the propagation capacity of the RV Wt1-5 through the tumor and the importance of the expression of cell surface co-receptors, including integrin β3, protein disulfide isomerase (PDI), and heat shock proteins (Hsp-90, -70, -60, -40, and Hsc 70), during infection of tumor cells. These proteins were found to be differentially expressed in tumor cells compared to adjacent non-tumor cells. Preincubation of gastric tumor cells with antibodies against these proteins decreased rotavirus infections, validating their importance in the binding and entry of RV Wt1-5 into tumor cells, as previously reported. Upon RV infection, apoptosis was one of the types of death that was observed. This was evidenced by evaluating the expression of CASP-3, -9, PARP, cytochrome C, Bax, Bid, p53, and Bcl-2, as well as observing morphological changes such as chromatin margination, nuclear condensation, and fragmentation. Finally, at 60 h.p.i, histological analysis revealed that oncolysis compromised the entire thickness of the tumor. Therefore, the results suggest that RV Wt1-5 could be a novel therapeutic agent co-adjuvant agent for conventional and targeted therapies in managing GC. Ex vivo infection of the tumor tissue model showed characteristics of an immune response that could be explored in future studies.
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Affiliation(s)
- Henry Sossa-Rojas
- Departamento de Ciencias Básicas y Medicina Oral, Facultad de Odontología, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, D.C., Colombia
| | - Pedro Gabriel Franco-Maz
- Departamento de Morfología, Facultad de Medicina, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, D.C., Colombia
- Servicio de Patología, Hospital Universitario La Samaritana, Bogotá, D.C., Colombia
| | - Carlos Zapata-Acevedo
- Departamento de Cirugía, Facultad de Medicina, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, D.C., Colombia
- Servicio de Cirugía General, Hospital Universitario La Samaritana, Bogoté, D.C., Colombia
| | - Luz Dary Gutierrez-Castañeda
- Research Institute, Grupos Ciencias Básicas en Salud - CBS-FUCS, Fundación Universitaria de Ciencias de la Salud, Hospital Infantil Universitario de San Josá, Bogotá, D.C., Colombia
| | - Carlos Guerrero
- Departamento de Ciencias Fisiológicas, Facultad de Medicina, Universidad Nacional de Colombia, Sede Bogotá, Bogotá, D.C., Colombia
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Liao Y, Liu Q, Xiao C, Zhou J. Machine learning and experimental validation to construct a metastasis-related gene signature and ceRNA network for predicting osteosarcoma prognosis. J Orthop Surg Res 2022; 17:516. [PMID: 36457129 PMCID: PMC9713963 DOI: 10.1186/s13018-022-03386-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/05/2022] [Indexed: 12/03/2022] Open
Abstract
OBJECTIVE Osteosarcoma (OS) is more common in adolescents and significantly harmful, and the survival rate is considerably low, especially in patients with metastatic OS. The identification of effective biomarkers and associated regulatory mechanisms, which predict OS occurrence and development as well as improve prognostic accuracy, will help develop more refined protocols for OS treatment. METHODS In this study, genes showing differential expression in metastatic and non-metastatic types of OS were identified, and the ones affecting OS prognosis were screened from among these. Following this, the functions and pathways associated with the genes were explored via enrichment analysis, and an effective predictive signature was constructed using Cox regression based on the machine learning algorithm, least absolute shrinkage and selection operator (LASSO). Next, a correlative competing endogenous RNA (ceRNA) regulatory axis was constructed after verification by bioinformatics analysis and luciferase reporter gene experiments conducted based on the prognostic signature. RESULTS Overall, 251 differentially expressed genes were identified and screened using bioinformatics and double luciferase reporter gene experiments. An effective prognostic signature was constructed based on 15 genes associated with OS metastasis, and upstream non-coding RNAs were identified to construct the "NBR2/miR-129-5p/FKBP11" regulatory axis based on the ceRNA networks, which helped identify candidate biomarkers for the OS clinical diagnosis and treatment, drug research, and prognostic prediction, among other applications. The findings of this study provide a novel strategy for determining the mechanism underlying OS occurrence and development and the appropriate treatment.
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Affiliation(s)
- Yong Liao
- grid.513391.c0000 0004 8339 0314Department of Pharmacy, Maoming People’s Hospital, Maoming, 525000 China
| | - Qingsong Liu
- grid.411304.30000 0001 0376 205XChengdu University of Traditional Chinese Medicine Affiliated Hospital, Chengdu, 610000 Sichuan China
| | - Chunxia Xiao
- grid.263785.d0000 0004 0368 7397The Affiliated Dianbai School of South China Normal University, Maoming, 525000 China
| | - Jihui Zhou
- grid.513391.c0000 0004 8339 0314Department of Traumatic Orthopedics, Maoming People’s Hospital, No. 101 Weimin Road, Maoming, 525000 Guangdong Province China
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Xiao C, Dong T, Yang L, Jin L, Lin W, Zhang F, Han Y, Huang Z. Identification of Novel Immune Ferropotosis-Related Genes Associated With Clinical and Prognostic Features in Gastric Cancer. Front Oncol 2022; 12:904304. [PMID: 35664744 PMCID: PMC9157572 DOI: 10.3389/fonc.2022.904304] [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: 03/25/2022] [Accepted: 04/19/2022] [Indexed: 12/08/2022] Open
Abstract
Background Gastric cancer (GC) is the fifth commonest cancer and the third commonest reason of death causing by cancer worldwide. Currently, tumor immunology and ferropotosis develop rapidly that has made gastric cancer be treated in new directions. So, finding the potential targets and prognostic biomarkers for immunotherapy combined with ferropotosis is urgent. Methods By mining TCGA, immune-related genes, ferropotosis-related genes and immune-ferropotosis-related differentially expressed genes (IFR-DEGs) were identified. The independent prognostic value of IFR-DEGs was determined by differential expression analysis, prognostic analysis, and univariate and lasso regression analysis. Then, based on the prognostic risk model, the correlation between IFR-DEGs and immune scores, immune checkpoints were evaluated. Besides, we predicted the response of high and low risk groups to drugs. Results A 15-gene prognostic feature was constructed. The high-risk group had a poorer prognosis than the low-risk group. High-risk group had higher level of Treg immune cell infiltration compared with that in the low-risk group, and the tumor purity, immune checkpoint PD-1 and CTLA4, and immunity in the high-risk group were higher than those in the low-risk group. These results indicate that immune ferropotosis-related genes migh be potential predictors of STAD's response to ICI immunotherapy biomarkers. In addition, the response of small molecule drugs such as Nilotini, Sunitinib, Imatinib, etc. for high and low risk groups was predicted. Conclusion IFRSig can be regarded as an independent prognostic feature and may estimate OS and clinical treatment response in patients with STAD. IFRSig also has important correlation with immune microenvironment. A new understanding of the immune-ferropotosis-related genes during the occurrence and development of STAD is provided in this study.
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Affiliation(s)
- Chen Xiao
- Department of Gastroenterology, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Tao Dong
- Department of Digestion, Yidu Central Hospital of Weifang, Weifang, China
| | - Linhui Yang
- Graduate School of Fujian Medical University, Fuzhou, China
| | - Liangzi Jin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Weiguo Lin
- Department of Gastroenterology, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Faqin Zhang
- Department of Gastroenterology, Fuzhou Second Hospital Affiliated to Xiamen University, Fuzhou, China
| | - Yuanyuan Han
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming, China
| | - Zhijian Huang
- Department of Breast Surgical Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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