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Kori M, Arga KY. HPV16 status predicts potential protein biomarkers and therapeutics in head and neck squamous cell carcinoma. Virology 2023; 582:90-99. [PMID: 37031657 DOI: 10.1016/j.virol.2023.03.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/11/2023]
Abstract
Human papillomavirus (HPV) infection, especially HPV16, is one of the causative factors for the development of head and neck squamous cell (HNSC) carcinoma. HPV-positive and HPV-negative HNSC patients differ significantly in their molecular profiles and clinical features, so they should be evaluated differently depending on their HPV status. Given the tremendous variation in HNSC cancers depending on HPV, our goal in this study was to present biomarkers and treatment options tailored to the patient's HPV status. Gene expression levels of HPV16-positive and -negative patients were used as proxies, and the differential interactome algorithm was employed to identify the differential interacting proteins (DIPs). By assessing the prognostic capabilities and druggabilities of DIPs and their interacting partners (DIP-centered modules), we introduce eight modules as potential biomarkers specialized for either positive or negative phenotype. Finally, raloxifene was repositioned for the first time as a drug candidate for the treatment of HPV16-positive HNSC patients.
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Affiliation(s)
- Medi Kori
- Department of Bioengineering, Marmara University, Istanbul, Turkey.
| | - Kazim Yalcin Arga
- Department of Bioengineering, Marmara University, Istanbul, Turkey; Genetic and Metabolic Diseases Research and Investigation Center, Marmara University, Istanbul, Turkey.
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Jiang C, He L, Xiao S, Wu W, Zhao Q, Liu F. E3 Ubiquitin Ligase RNF125 Suppresses Immune Escape in Head and Neck Squamous Cell Carcinoma by Regulating PD-L1 Expression. Mol Biotechnol 2022; 65:891-903. [DOI: 10.1007/s12033-022-00587-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
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Huang R, Liao X, Li Q. Integrative genomic analysis of a novel small nucleolar RNAs prognostic signature in patients with acute myelocytic leukemia. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:2424-2452. [PMID: 35240791 DOI: 10.3934/mbe.2022112] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study mainly used The Cancer Genome Atlas (TCGA) RNA sequencing dataset to screen prognostic snoRNAs of acute myeloid leukemia (AML), and used for the construction of prognostic snoRNAs signature for AML. A total of 130 AML patients with RNA sequencing dataset were used for prognostic snoRNAs screenning. SnoRNAs co-expressed genes and differentially expressed genes (DEGs) were used for functional annotation, as well as gene set enrichment analysis (GSEA). Connectivity Map (CMap) also used for potential targeted drugs screening. Through genome-wide screening, we identified 30 snoRNAs that were significantly associated with the prognosis of AML. Then we used the step function to screen a prognostic signature composed of 14 snoRNAs (SNORD72, SNORD38, U3, SNORA73B, SNORD79, SNORA73, SNORD12B, SNORA74, SNORD116-12, SNORA65, SNORA14, snoU13, SNORA75, SNORA31), which can significantly divide AML patients into high- and low-risk groups. Through GSEA, snoRNAs co-expressed genes and DEGs functional enrichment analysis, we screened a large number of potential functional mechanisms of this prognostic signature in AML, such as phosphatidylinositol 3-kinase-Akt, Wnt, epithelial to mesenchymal transition, T cell receptors, NF-kappa B, mTOR and other classic cancer-related signaling pathways. In the subsequent targeted drug screening using CMap, we also identified six drugs that can be used for AML targeted therapy, they were alimemazine, MG-262, fluoxetine, quipazine, naltrexone and oxybenzone. In conclusion, our current study was constructed an AML prognostic signature based on the 14 prognostic snoRNAs, which may serve as a novel prognostic biomarker for AML.
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Affiliation(s)
- Rui Huang
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
| | - Qiaochuan Li
- Department of Hematology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China
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Deng T, Gong Y, Liao X, Wang X, Zhou X, Zhu G, Mo L. Integrative Analysis of a Novel Eleven-Small Nucleolar RNA Prognostic Signature in Patients With Lower Grade Glioma. Front Oncol 2021; 11:650828. [PMID: 34164339 PMCID: PMC8215672 DOI: 10.3389/fonc.2021.650828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/12/2021] [Indexed: 12/13/2022] Open
Abstract
Objective The present study used the RNA sequencing (RNA-seq) dataset to identify prognostic snoRNAs and construct a prognostic signature of The Cancer Genome Atla (TCGA) lower grade glioma (LGG) cohort, and comprehensive analysis of this signature. Methods RNA-seq dataset of 488 patients from TCGA LGG cohort were included in this study. Comprehensive analysis including function enrichment, gene set enrichment analysis (GSEA), immune infiltration, cancer immune microenvironment, and connectivity map (CMap) were used to evaluate the snoRNAs prognostic signature. Results We identified 21 LGG prognostic snoRNAs and constructed a novel eleven-snoRNA prognostic signature for LGG patients. Survival analysis suggests that this signature is an independent prognostic risk factor for LGG, and the prognosis of LGG patients with a high-risk phenotype is poor (adjusted P = 0.003, adjusted hazard ratio = 2.076, 95% confidence interval = 1.290–3.340). GSEA and functional enrichment analysis suggest that this signature may be involved in the following biological processes and signaling pathways: such as cell cycle, Wnt, mitogen-activated protein kinase, janus kinase/signal transducer and activator of tran-ions, T cell receptor, nuclear factor-kappa B signaling pathway. CMap analysis screened out ten targeted therapy drugs for this signature: 15-delta prostaglandin J2, MG-262, vorinostat, 5155877, puromycin, anisomycin, withaferin A, ciclopirox, chloropyrazine and megestrol. We also found that high- and low-risk score phenotypes of LGG patients have significant differences in immune infiltration and cancer immune microenvironment. Conclusions The present study identified a novel eleven-snoRNA prognostic signature of LGG and performed a integrative analysis of its molecular mechanisms and relationship with tumor immunity.
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Affiliation(s)
- Teng Deng
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Yizhen Gong
- Evidence-based Medicine Teaching and Research Section, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Xiwen Liao
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xiangkun Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xin Zhou
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guangzhi Zhu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Ligen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, China
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Cabrera-Andrade A, López-Cortés A, Jaramillo-Koupermann G, González-Díaz H, Pazos A, Munteanu CR, Pérez-Castillo Y, Tejera E. A Multi-Objective Approach for Anti-Osteosarcoma Cancer Agents Discovery through Drug Repurposing. Pharmaceuticals (Basel) 2020; 13:ph13110409. [PMID: 33266378 PMCID: PMC7700154 DOI: 10.3390/ph13110409] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 02/08/2023] Open
Abstract
Osteosarcoma is the most common type of primary malignant bone tumor. Although nowadays 5-year survival rates can reach up to 60–70%, acute complications and late effects of osteosarcoma therapy are two of the limiting factors in treatments. We developed a multi-objective algorithm for the repurposing of new anti-osteosarcoma drugs, based on the modeling of molecules with described activity for HOS, MG63, SAOS2, and U2OS cell lines in the ChEMBL database. Several predictive models were obtained for each cell line and those with accuracy greater than 0.8 were integrated into a desirability function for the final multi-objective model. An exhaustive exploration of model combinations was carried out to obtain the best multi-objective model in virtual screening. For the top 1% of the screened list, the final model showed a BEDROC = 0.562, EF = 27.6, and AUC = 0.653. The repositioning was performed on 2218 molecules described in DrugBank. Within the top-ranked drugs, we found: temsirolimus, paclitaxel, sirolimus, everolimus, and cabazitaxel, which are antineoplastic drugs described in clinical trials for cancer in general. Interestingly, we found several broad-spectrum antibiotics and antiretroviral agents. This powerful model predicts several drugs that should be studied in depth to find new chemotherapy regimens and to propose new strategies for osteosarcoma treatment.
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Affiliation(s)
- Alejandro Cabrera-Andrade
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador;
- Carrera de Enfermería, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito 170125, Ecuador
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071 A Coruña, Spain; (A.L.-C.); (A.P.); (C.R.M.)
- Correspondence: (A.C.-A.); (E.T.)
| | - Andrés López-Cortés
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071 A Coruña, Spain; (A.L.-C.); (A.P.); (C.R.M.)
- Centro de Investigación Genética y Genómica, Facultad de Ciencias de la Salud Eugenio Espejo, Universidad UTE, Quito 170129, Ecuador
- Latin American Network for Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), 28029 Madrid, Spain
| | - Gabriela Jaramillo-Koupermann
- Laboratorio de Biología Molecular, Subproceso de Anatomía Patológica, Hospital de Especialidades Eugenio Espejo, Quito 170403, Ecuador;
| | - Humberto González-Díaz
- Department of Organic and Inorganic Chemistry, and Basque Center for Biophysics CSIC-UPV/EHU, University of the Basque Country UPV/EHU, 48940 Leioa, Spain;
- IKERBASQUE, Basque Foundation for Science, 48011 Bilbao, Spain
| | - Alejandro Pazos
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071 A Coruña, Spain; (A.L.-C.); (A.P.); (C.R.M.)
- Biomedical Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Cristian R. Munteanu
- Department of Computer Science and Information Technologies, Faculty of Computer Science, University of A Coruña, CITIC, Campus Elviña s/n, 15071 A Coruña, Spain; (A.L.-C.); (A.P.); (C.R.M.)
- Biomedical Research Institute of A Coruña (INIBIC), University Hospital Complex of A Coruña (CHUAC), 15006 A Coruña, Spain
| | - Yunierkis Pérez-Castillo
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador;
- Escuela de Ciencias Físicas y Matemáticas, Universidad de Las Américas, Quito 170125, Ecuador
| | - Eduardo Tejera
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito 170125, Ecuador;
- Facultad de Ingeniería y Ciencias Agropecuarias, Universidad de Las Américas, Quito 170125, Ecuador
- Correspondence: (A.C.-A.); (E.T.)
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Low ZY, Farouk IA, Lal SK. Drug Repositioning: New Approaches and Future Prospects for Life-Debilitating Diseases and the COVID-19 Pandemic Outbreak. Viruses 2020; 12:E1058. [PMID: 32972027 PMCID: PMC7551028 DOI: 10.3390/v12091058] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 08/02/2020] [Accepted: 08/21/2020] [Indexed: 02/06/2023] Open
Abstract
Traditionally, drug discovery utilises a de novo design approach, which requires high cost and many years of drug development before it reaches the market. Novel drug development does not always account for orphan diseases, which have low demand and hence low-profit margins for drug developers. Recently, drug repositioning has gained recognition as an alternative approach that explores new avenues for pre-existing commercially approved or rejected drugs to treat diseases aside from the intended ones. Drug repositioning results in lower overall developmental expenses and risk assessments, as the efficacy and safety of the original drug have already been well accessed and approved by regulatory authorities. The greatest advantage of drug repositioning is that it breathes new life into the novel, rare, orphan, and resistant diseases, such as Cushing's syndrome, HIV infection, and pandemic outbreaks such as COVID-19. Repositioning existing drugs such as Hydroxychloroquine, Remdesivir, Ivermectin and Baricitinib shows good potential for COVID-19 treatment. This can crucially aid in resolving outbreaks in urgent times of need. This review discusses the past success in drug repositioning, the current technological advancement in the field, drug repositioning for personalised medicine and the ongoing research on newly emerging drugs under consideration for the COVID-19 treatment.
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Affiliation(s)
- Zheng Yao Low
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
| | - Isra Ahmad Farouk
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
| | - Sunil Kumar Lal
- School of Science, Monash University, Bandar Sunway, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia; (Z.Y.L.); (I.A.F.)
- Tropical Medicine & Biology Platform, Monash University, Subang Jaya 47500, Selangor Darul Ehsan, Malaysia
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Yu D, Liu X, Han G, Liu Y, Zhao X, Wang D, Bian X, Gu T, Wen L. The let-7 family of microRNAs suppresses immune evasion in head and neck squamous cell carcinoma by promoting PD-L1 degradation. Cell Commun Signal 2019; 17:173. [PMID: 31881947 PMCID: PMC6935121 DOI: 10.1186/s12964-019-0490-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Background Accumulation of immunosuppressive protein programmed death-ligand 1 (PD-L1) has been documented in several cancers and contributes to the evasion of the host immune system. However, cancer cell-intrinsic signaling-dependent control of PD-L1 expression remains to be elucidated. Herein, we aimed to identify the let-7 family of microRNAs as candidates that up-regulate tumor cell PD-L1 expression and mediates immune evasion of head and neck squamous cell carcinoma (HNSCC). Methods The expression of let-7 family and PD-L1 was quantified in HNSCC tissues and adjacent normal tissues. PD-L1 degradation was evaluated in HNSCC cells in response to elevated expressions of let-7a or let-7b. The regulation of let-7 family on PD-L1 degradation through a mechanism involving T-cell factor-4 (TCF-4) control of β-catenin/STT3 pathway was evaluated. Immune recognition of HNSCC in vivo was examined in subcutaneous tumor-bearing C3H mice in the presence of let-7a/b and/or CTLA-4 antibody. Results The let-7 family were significantly down-regulated in the context of HNSCC, sharing a negative correlation with PD-L1 expression. Glycosylated PD-L1 was detected in HNSCC cells, which was reduced by let-7a/b over-expression. TCF-4, the target of let-7a/b, activated the β-catenin/STT3 pathway and promoted PD-L1 degradation. In vivo analysis demonstrated that let-7a/b over-expression potentiated anticancer immunotherapy by CTLA-4 blockade. Conclusions Taken together, our findings highlight targeting let-7 family as a potential strategy to enhance immune checkpoint therapy for HNSCC.
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Affiliation(s)
- Dan Yu
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Xueshibojie Liu
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Guanghong Han
- Department of Oral Geriatrics, School and Hospital of Stomatology, Jilin University, Changchun, 130021, People's Republic of China
| | - Yan Liu
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Xue Zhao
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Di Wang
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Xiaomin Bian
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Tingting Gu
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China
| | - Lianji Wen
- Department of Otolaryngology Head and Neck Surgery, the Second Hospital, Jilin University, No. 218, Ziqiang Street, Nanguan District, Changchun, 130041, Jilin Province, People's Republic of China.
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