1
|
Lu Z, Chen Y, Chen S, Zhu X, Wang C, Wang Z, Yao Q. Comprehensive Prognostic Analysis of Immune Implication Value and Oxidative Stress Significance of NECAP2 in Low-Grade Glioma. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:1494520. [PMID: 36531205 PMCID: PMC9750773 DOI: 10.1155/2022/1494520] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 12/07/2023]
Abstract
Adaptin ear-binding coat-associated protein 2 (NECAP2) belongs to the family of proteins encoding adaptin-ear-binding coat-associated proteins. However, its immune effect on tumors and its microenvironment are still unclear. Here, we systematically evaluated the differences (variations) in NECAP2 expression for low-grade glioma (LGG) and pan-cancer in the LGG dataset of The Cancer Genome Atlas (TCGA) utilizing bioinformatics methods. We found for the first time that NECAP2 level was elevated in gliomas and that this upregulation increased as the tumor grade increased. In addition, Pearson correlations of NECAP2 with five immune pathways and significant gene mutations associated with NECAP2 were also analyzed. Univariate survival and multivariate Cox analyses were used to compare the clinical characteristics and survival of the patients. Glioma patients with NECAP2 overexpression have a remarkably higher risk of developing malignant behavior and a worse prognosis. The correlation between the expression levels of NECAP2 and the prognosis of glioma patients was identified. Kaplan-Meier curves showed that patients with upregulated NECAP2 expression exhibited an unfavorable prognosis. Western blotting showed that NECAP2 was overexpressed in glioma patients. IHC staining results illustrated an elevation in the NECAP2 protein expression level with the development of tumor malignancy. Additionally, qRT-PCR verified that oxidative stress in glioma tissues reduced the expression of stress-related genes and oxidative stress capacity compared to normal tissues, which may be associated with tumor evasion of immune surveillance and tumor progression. In vitro wound-healing and Transwell assay confirmed that NECAP2 promotes glioma cell migration and invasion. Our study also thoroughly examined the immune significance of NECAP2 in the TCGA-LGG samples, using CIBERSORT and ESTIMATE to explore the correlation between NECAP2 and cancer immune infiltration. The NECAP2 expression levels were correlated with the infiltration degree of immune cells such as neutrophils, CD4+ T cells, macrophages, CD8+ T cells, and B cells. Therefore, our results indicate that NECAP2 strongly correlates with the overall immune infiltration level of glioma and could independently serve as a prognostic biological marker for glioma patients.
Collapse
Affiliation(s)
- Zhichao Lu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Yixun Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Siqi Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Xingjia Zhu
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Chenxing Wang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| | - Ziheng Wang
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Department of Clinical Biobank & Institute of Oncology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Qi Yao
- Department of Neurosurgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, China
| |
Collapse
|
2
|
Huang B, Pan W, Wang W, Wang Y, Liu P, Geng W. Overexpression of Pleckstrin Homology Domain-Containing Family A Member 4 Is Correlated with Poor Prognostic Outcomes and Immune Infiltration in Lower-Grade Glioma. DISEASE MARKERS 2022; 2022:1292648. [PMID: 36408463 PMCID: PMC9674417 DOI: 10.1155/2022/1292648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 09/28/2022] [Accepted: 10/22/2022] [Indexed: 10/12/2023]
Abstract
INTRODUCTION The global incidence of brain tumors, the most common of which is lower grade glioma (LGG), remains high. Pleckstrin homology domain-containing family A member 4 (PLEKHA4) has been reported to be related to tumor invasion and growth. However, its role and correlation with immunity in LGG remain elusive. METHODS We evaluated the expression pattern, prognostic value, biological functions, and immune effects of PLEKHA4 in LGG. We also analyzed the association between PLEKHA4 levels in different tumors, patient prognosis, and its role in tumor immunity. Depending on the type of research data, we used statistical methods such as Student's t-tests, Mann-Whitney U tests one-way ANOVA tests Kruskal-Wallis tests Pearson's or Spearman's correlation analysis Chi-square and Fisher's exact tests in this paper. Results and Conclusions. The results revealed that PLEKHA4 levels were markedly elevated in most tumors (such as LGG). High PLEKHA4 levels are associated with poor overall survival (OS), progression-free interval (PFI) rates, and disease-specific survival (DSS) in LGG patients. Cox regression analysis and nomograms showed that PLEKHA4 levels are independent prognostic factors for LGG patients. According to functional enrichment analysis, PLEKHA4 levels in LGG are associated with immune infiltration and immunotherapy. In conclusion, PLEKHA4 is a potential prognostic marker and immunotherapy target for LGG.
Collapse
Affiliation(s)
- Baojun Huang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Weijun Pan
- Southern Medical University, Guangzhou, Guangdong, China
| | - Wenchao Wang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yijian Wang
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Pan Liu
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Wujun Geng
- Department of Anaesthesiology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
- Wenzhou Key Laboratory of Perioperative Medicine, Wenzhou, Zhejiang, China
| |
Collapse
|
3
|
Fahmy SA, Dawoud A, Zeinelabdeen YA, Kiriacos CJ, Daniel KA, Eltahtawy O, Abdelhalim MM, Braoudaki M, Youness RA. Molecular Engines, Therapeutic Targets, and Challenges in Pediatric Brain Tumors: A Special Emphasis on Hydrogen Sulfide and RNA-Based Nano-Delivery. Cancers (Basel) 2022; 14:5244. [PMID: 36358663 PMCID: PMC9657918 DOI: 10.3390/cancers14215244] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/20/2022] [Accepted: 10/22/2022] [Indexed: 09/11/2023] Open
Abstract
Pediatric primary brain tumors represent a real challenge in the oncology arena. Besides the psychosocial burden, brain tumors are considered one of the most difficult-to-treat malignancies due to their sophisticated cellular and molecular pathophysiology. Notwithstanding the advances in research and the substantial efforts to develop a suitable therapy, a full understanding of the molecular pathways involved in primary brain tumors is still demanded. On the other hand, the physiological nature of the blood-brain barrier (BBB) limits the efficiency of many available treatments, including molecular therapeutic approaches. Hydrogen Sulfide (H2S), as a member of the gasotransmitters family, and its synthesizing machinery have represented promising molecular targets for plentiful cancer types. However, its role in primary brain tumors, generally, and pediatric types, particularly, is barely investigated. In this review, the authors shed the light on the novel role of hydrogen sulfide (H2S) as a prominent player in pediatric brain tumor pathophysiology and its potential as a therapeutic avenue for brain tumors. In addition, the review also focuses on the challenges and opportunities of several molecular targeting approaches and proposes promising brain-delivery strategies for the sake of achieving better therapeutic results for brain tumor patients.
Collapse
Affiliation(s)
- Sherif Ashraf Fahmy
- Chemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, R5 New Capital City, Cairo 11835, Egypt
| | - Alyaa Dawoud
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
- Biochemistry Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Yousra Ahmed Zeinelabdeen
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
- Faculty of Medical Sciences/UMCG, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Caroline Joseph Kiriacos
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Kerolos Ashraf Daniel
- Biology and Biochemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo 11835, Egypt
| | - Omar Eltahtawy
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Miriam Mokhtar Abdelhalim
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
| | - Maria Braoudaki
- Clinical, Pharmaceutical, and Biological Science Department, School of Life and Medical Sciences, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - Rana A. Youness
- Molecular Genetics Research Team (MGRT), Pharmaceutical Biology Department, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo 11835, Egypt
- Biology and Biochemistry Department, School of Life and Medical Sciences, University of Hertfordshire Hosted by Global Academic Foundation, Cairo 11835, Egypt
| |
Collapse
|
4
|
Guo X, Zhang Y, Jiao H, Miao X. The prognostic significance of PD-L1 expression in patients with glioblastoma: A meta-analysis. Front Oncol 2022; 12:925560. [PMID: 36313683 PMCID: PMC9596987 DOI: 10.3389/fonc.2022.925560] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/19/2022] [Indexed: 11/13/2022] Open
Abstract
Background Glioblastoma (GBM) is a malignant brain tumor associated with high morbidity and mortality rates with a poor prognosis. In recent years, studies on prognostic markers such as programmed death ligand 1 (PD-L1) have increased; however, their conclusions remain controversial. Here, relevant literature was reviewed and a meta-analysis was performed to clarify the correlation between PD-L1 expression and overall survival (OS) in GBM. Methods The non-foundational literature on PD-L1 expression associated with OS in GBM up to February 2022 was searched in the PubMed, Metstr, Cochrane, and Web of Science databases. Literature was rigorously screened according to inclusion and exclusion criteria, the total hazard ratio (HR), and corresponding 95% confidence intervals (CIs). Results Calculating the combined HR value and corresponding 95% CI of HR=1.124 (95% CI: 1.047–1.201, P=0.000, I2 (I-squared)=48.8%), it was shown that PD-L1 expression was significantly associated with low OS in GBM patients. Although I2 = 48.8% < 50%, to make the results more credible, in the cutoff values ≥10% subgroup HR=1.37 (95% CI: 1.07–1.67, P=0.000, I2 = 0%), which was also the result found in the first meta-analysis. In contrast, in the cutoff value ≥5% subgroup HR=1.14 (95% CI: 0.98–1.30, P=0.000, I2 = 59.8%) and in the cutoff value median PD-L1 expression levels subgroup HR=1.05 (95% CI: 0.92–1.18, P=0.000, I2 = 0%), indicating that PD-L1 expression was not associated with low OS in GBM. Furthermore, in four studies, we found no significant correlation between PD-L1 expression and the progression-free survival of GBM (HR=1.14, 95% CI:0.40–1.88, P=0.03, I2 = 29.3%). Conclusion PD-L1 expression was significantly associated with low OS in GBM patients; however, this result needs to be interpreted with caution and requires a large, multicenter clinical study in patients with similar baseline data for further evaluation.
Collapse
Affiliation(s)
- Xin Guo
- Department of Neurosurgery, Shaanxi Provincial People's Hospital, Xi’an, China
- Department of Graduate Work, Hanguang Campus of Xi’an Medical University, Xi’an, China
| | - Yuelin Zhang
- Department of Graduate Work, Hanguang Campus of Xi’an Medical University, Xi’an, China
| | - Hengxing Jiao
- Department of Neurosurgery, Shaanxi Provincial People's Hospital, Xi’an, China
- Department of Graduate Work, Hanguang Campus of Xi’an Medical University, Xi’an, China
| | - Xingyu Miao
- Department of Neurosurgery, Shaanxi Provincial People's Hospital, Xi’an, China
- *Correspondence: Xingyu Miao,
| |
Collapse
|
5
|
Fabrizio FP, Castellana S, Centra F, Sparaneo A, Mastroianno M, Mazza T, Coco M, Trombetta D, Cingolani N, Centonza A, Graziano P, Maiello E, Fazio VM, Muscarella LA. Design and experimental validation of OPERA_MET-A panel for deep methylation analysis by next generation sequencing. Front Oncol 2022; 12:968804. [PMID: 36033501 PMCID: PMC9404304 DOI: 10.3389/fonc.2022.968804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is the most recognized epigenetic mark that leads to a massive distortion in cancer cells. It has been observed that a large number of DNA aberrant methylation events occur simultaneously in a group of genes, thus providing a growth advantage to the cell in promoting cell differentiation and neoplastic transformation. Due to this reason, methylation profiles have been suggested as promising cancer biomarkers. Here, we designed and performed a first step of validation of a novel targeted next generation sequencing (NGS) panel for methylation analysis, which can simultaneously evaluate the methylation levels at CpG sites of multiple cancer-related genes. The OPERA_MET-A methylation panel was designed using the Ion AmpliSeq™ technology to amplify 155 regions with 125-175 bp mean length and covers a total of 1107 CpGs of 18 cancer-related genes. The performance of the panel was assessed by running commercially available fully methylated and unmethylated control human genomic DNA (gDNA) samples and a variable mixture of them. The libraries were run on Ion Torrent platform and the sequencing output was analyzed using the “methylation_analysis” plugin. DNA methylation calls on both Watson (W) and Crick (C) strands and methylated:unmethylated ratio for each CpG site were obtained. Cell lines, fresh frozen and formalin-fixed paraffin-embedded (FFPE) lung cancer tissues were tested. The OPERA_MET-A panel allows to run a minimum of 6 samples/530 chip to reach an observed mean target depth ≥2,500X (W and C strands) and an average number of mapped reads >750,000/sample. The conversion efficiency, determined by spiking-in unmethylated Lambda DNA into each sample before the bisulfite conversion process, was >97% for all samples. The observed percentage of global methylation for all CpGs was >95% and <5% for fully methylated and unmethylated gDNA samples, respectively, and the observed results for the variable mixtures were in agreement with what was expected. Methylation-specific NGS analysis represents a feasible method for a fast and multiplexed screening of cancer patients by a high-throughput approach. Moreover, it offers the opportunity to construct a more robust algorithm for disease prediction in cancer patients having a low quantity of biological material available.
Collapse
Affiliation(s)
- Federico Pio Fabrizio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
| | - Stefano Castellana
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Flavia Centra
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Angelo Sparaneo
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Mario Mastroianno
- Scientific Direction, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Tommaso Mazza
- Unit of Bioinformatics, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Michelina Coco
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Domenico Trombetta
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Nicola Cingolani
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Antonella Centonza
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paolo Graziano
- Unit of Pathology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Evaristo Maiello
- Unit of Oncology, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- Laboratory of Molecular Medicine and Biotechnology, University Campus Bio-Medico of Rome, Rome, Italy
- Institute of Translational Pharmacology, National Research Council of Italy (CNR), Rome, Italy
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione IRCCS, Scientific Institute for Research and Health Care Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
- *Correspondence: Federico Pio Fabrizio, ; Lucia Anna Muscarella,
| |
Collapse
|