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Kumari A, Kashyap D, Garg VK. Osteopontin in cancer. Adv Clin Chem 2024; 118:87-110. [PMID: 38280808 DOI: 10.1016/bs.acc.2023.11.002] [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] [Indexed: 01/29/2024]
Abstract
Osteopontin (OPN) is a heavily post-translationally modified protein with a molecular weight of 44-70 kDa, depending on the degree of glycosylation. OPN is involved in various biological processes, including bone remodeling, immune response, cell adhesion, migration, and survival. It is essential for controlling osteoclast and osteoblast activity for maintaining bone mass and bone strength. Additionally, OPN has been linked to cardiovascular, inflammatory illnesses, as well as the onset and progression of cancer. OPN is a multifunctional protein that can interact with a variety of cell surface receptors, such as integrins, CD44, the urokinase-type plasminogen activator receptor (uPAR), as well as extracellular matrix (ECM) components (e.g. collagen and hydroxyapatite). These interactions contribute to its wide range of biological functions in general and has significant implications for bone biology, immunology and cancer, specifically. In this chapter, we summarize the structure of OPN with a focus on its molecular mechanisms of action in various cancers.
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Affiliation(s)
- Alpana Kumari
- Department of Optometry, University Institute of Allied Health Sciences, Chandigarh University, Gharuan, Mohali, Punjab, India
| | - Dharambir Kashyap
- Department of Medicine, The Brown Centre for Immunotherapy, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Vivek Kumar Garg
- Department of Medical Lab Technology, University Institute of Allied Health Sciences, Chandigarh University, Gharuan, Mohali, Punjab, India.
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2
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Marković L, Bukovac A, Varošanec AM, Šlaus N, Pećina-Šlaus N. Genetics in ophthalmology: molecular blueprints of retinoblastoma. Hum Genomics 2023; 17:82. [PMID: 37658463 PMCID: PMC10474694 DOI: 10.1186/s40246-023-00529-w] [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: 04/18/2023] [Accepted: 08/25/2023] [Indexed: 09/03/2023] Open
Abstract
This review presents current knowledge on the molecular biology of retinoblastoma (RB). Retinoblastoma is an intraocular tumor with hereditary and sporadic forms. 8,000 new cases of this ocular malignancy of the developing retina are diagnosed each year worldwide. The major gene responsible for retinoblastoma is RB1, and it harbors a large spectrum of pathogenic variants. Tumorigenesis begins with mutations that cause RB1 biallelic inactivation preventing the production of functional pRB proteins. Depending on the type of mutation the penetrance of RB is different. However, in small percent of tumors additional genes may be required, such as MYCN, BCOR and CREBBP. Additionally, epigenetic changes contribute to the progression of retinoblastoma as well. Besides its role in the cell cycle, pRB plays many additional roles, it regulates the nucleosome structure, participates in apoptosis, DNA replication, cellular senescence, differentiation, DNA repair and angiogenesis. Notably, pRB has an important role as a modulator of chromatin remodeling. In recent years high-throughput techniques are becoming essential for credible biomarker identification and patient management improvement. In spite of remarkable advances in retinoblastoma therapy, primarily in high-income countries, our understanding of retinoblastoma and its specific genetics still needs further clarification in order to predict the course of this disease and improve therapy. One such approach is the tumor free DNA that can be obtained from the anterior segment of the eye and be useful in diagnostics and prognostics.
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Affiliation(s)
- Leon Marković
- Department of Ophthalmology, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital "Sveti Duh", Zagreb, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Anja Bukovac
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000, Zagreb, Croatia
| | - Ana Maria Varošanec
- Department of Ophthalmology, Reference Center of the Ministry of Health of the Republic of Croatia for Pediatric Ophthalmology and Strabismus, University Hospital "Sveti Duh", Zagreb, Croatia
- Faculty of Dental Medicine and Health Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Nika Šlaus
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia
| | - Nives Pećina-Šlaus
- Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000, Zagreb, Croatia.
- Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000, Zagreb, Croatia.
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Aldughayfiq B, Ashfaq F, Jhanjhi NZ, Humayun M. Explainable AI for Retinoblastoma Diagnosis: Interpreting Deep Learning Models with LIME and SHAP. Diagnostics (Basel) 2023; 13:diagnostics13111932. [PMID: 37296784 DOI: 10.3390/diagnostics13111932] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Retinoblastoma is a rare and aggressive form of childhood eye cancer that requires prompt diagnosis and treatment to prevent vision loss and even death. Deep learning models have shown promising results in detecting retinoblastoma from fundus images, but their decision-making process is often considered a "black box" that lacks transparency and interpretability. In this project, we explore the use of LIME and SHAP, two popular explainable AI techniques, to generate local and global explanations for a deep learning model based on InceptionV3 architecture trained on retinoblastoma and non-retinoblastoma fundus images. We collected and labeled a dataset of 400 retinoblastoma and 400 non-retinoblastoma images, split it into training, validation, and test sets, and trained the model using transfer learning from the pre-trained InceptionV3 model. We then applied LIME and SHAP to generate explanations for the model's predictions on the validation and test sets. Our results demonstrate that LIME and SHAP can effectively identify the regions and features in the input images that contribute the most to the model's predictions, providing valuable insights into the decision-making process of the deep learning model. In addition, the use of InceptionV3 architecture with spatial attention mechanism achieved high accuracy of 97% on the test set, indicating the potential of combining deep learning and explainable AI for improving retinoblastoma diagnosis and treatment.
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Affiliation(s)
- Bader Aldughayfiq
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia
| | - Farzeen Ashfaq
- School of Computer Science, SCS, Taylor's University, Subang Jaya 47500, Malaysia
| | - N Z Jhanjhi
- School of Computer Science, SCS, Taylor's University, Subang Jaya 47500, Malaysia
| | - Mamoona Humayun
- Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka 72388, Saudi Arabia
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4
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Nucleic acid therapy in pediatric cancer. Pharmacol Res 2022; 184:106441. [PMID: 36096420 DOI: 10.1016/j.phrs.2022.106441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/02/2022] [Accepted: 09/07/2022] [Indexed: 12/24/2022]
Abstract
The overall survival, progress free survival, and life quality of cancer patients have improved due to the advance in minimally invasive surgery, precision radiotherapy, and various combined chemotherapy in the last decade. Furthermore, the discovery of new types of therapeutics, such as immune checkpoint inhibitors and immune cell therapies have facilitated both patients and doctors to fight with cancers. Moreover, in the context of the development in biocompatible and cell type targeting nano-carriers as well as nucleic acid-based drugs for initiating and enhancing the anti-tumor response have come to the age. The treatment paradigms utilization of nucleic acids, including short interfering RNA (siRNA), antisense oligonucleotides (ASO), and messenger RNA (mRNA), can target specific protein expression to achieve the therapeutic effects. Over ten nucleic acid therapeutics have been approved by the FDA and EMA in rare diseases and genetic diseases as well as dozens of registered clinical trails for varies cancers. Though generally less dangerous of pediatric cancers than adult cancers was observed during the past decades, yet pediatric cancers accounted for a significant proportion of child deaths which hurt those family very deeply. Therefore, it is necessary to pay more attention for improving the treatment of pediatric cancer and discovering new nucleic acid therapeutics which may help to improve the therapeutic effect and prognoses in turns to ameliorate the survival period and quality of life for children patient. In this review, we focus on the nucleic acid therapy in pediatric cancers.
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Liu JC, Zhang CL, Dong KY, Li MJ, Sun SG, Li CR. Advances in the research of plant-derived natural products against retinoblastoma. Int J Ophthalmol 2022; 15:1391-1400. [PMID: 36017045 DOI: 10.18240/ijo.2022.08.24] [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: 06/01/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022] Open
Abstract
Retinoblastoma (RB) is a highly aggressive ocular tumor, and due to socioeconomic and medical constraints, many children receive treatment only in the metaphase and advanced clinical stages, resulting in high rates of blindness and disability. Although several approaches exist in the treatment of RB, some children with the disease do not have satisfactory results because of various factors. Plant-derived natural products have shown definite therapeutic effects in the treatment of various tumors and are also widely used in the study of RB. We review plant-derived natural products used in the study of anti-RB to provide ideas for the clinical application of these drugs and the development of new therapeutic drugs.
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Affiliation(s)
- Jing-Chen Liu
- Department of Ophthalmology, Jiangxi Provincial Hospital of Integrated Traditional Chinese and Western Medicine, the Fourth Affiliated Hospital of Jiangxi University of Traditional Chinese Medicine, Nanchang 330003, Jiangxi Province, China.,School of Clinical Medicine, Dali University, Dali 671000, Yunnan Province, China.,School of Clinical Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, Jiangxi Province, China
| | - Chun-Li Zhang
- Department of Ophthalmology, General Hospital of Southern Theatre Command, Guangzhou 510010, Guangdong Province, China
| | - Kai-Ye Dong
- Department of Ophthalmology, the First Affiliated Hospital of Dali University, Dali 671000, Yunnan Province, China
| | - Ming-Jun Li
- School of Clinical Medicine, Dali University, Dali 671000, Yunnan Province, China
| | - Shu-Guang Sun
- School of Clinical Medicine, Dali University, Dali 671000, Yunnan Province, China.,Department of Endocrinology, the First Affiliated Hospital of Dali University, Dali 671000, Yunnan Province, China
| | - Cai-Rui Li
- School of Clinical Medicine, Dali University, Dali 671000, Yunnan Province, China.,Department of Ophthalmology, the First Affiliated Hospital of Dali University, Dali 671000, Yunnan Province, China
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Application Progress of High-Throughput Sequencing in Ocular Diseases. J Clin Med 2022; 11:jcm11123485. [PMID: 35743555 PMCID: PMC9225376 DOI: 10.3390/jcm11123485] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 06/11/2022] [Accepted: 06/16/2022] [Indexed: 02/01/2023] Open
Abstract
Ocular diseases affect multiple eye parts and can be caused by pathogenic infections, complications of systemic diseases, genetics, environment, and old age. Understanding the etiology and pathogenesis of eye diseases and improving their diagnosis and treatment are critical for preventing any adverse consequences of these diseases. Recently, the advancement of high-throughput sequencing (HTS) technology has paved wide prospects for identifying the pathogenesis, signaling pathways, and biomarkers involved in eye diseases. Due to the advantages of HTS in nucleic acid sequence recognition, HTS has not only identified several normal ocular surface microorganisms but has also discovered many pathogenic bacteria, fungi, parasites, and viruses associated with eye diseases, including rare pathogens that were previously difficult to identify. At present, HTS can directly sequence RNA, which will promote research on the occurrence, development, and underlying mechanism of eye diseases. Although HTS has certain limitations, including low effectiveness, contamination, and high cost, it is still superior to traditional diagnostic methods for its efficient and comprehensive diagnosis of ocular diseases. This review summarizes the progress of the application of HTS in ocular diseases, intending to explore the pathogenesis of eye diseases and improve their diagnosis.
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Surgical Antimicrobial Prophylaxis in Patients of Neonatal and Pediatric Age Subjected to Eye Surgery: A RAND/UCLA Appropriateness Method Consensus Study. Antibiotics (Basel) 2022; 11:antibiotics11050561. [PMID: 35625205 PMCID: PMC9137626 DOI: 10.3390/antibiotics11050561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 01/25/2023] Open
Abstract
Ocular surgery encompasses a wide range of procedures, including surgery of the tear ducts, eyelid, cornea and conjunctiva, lens, ocular muscle, and vitreoretinal and iris surgery. Operations are also performed for the removal of tumors, repairs of ocular trauma and, finally, corneal transplantation. Antibiotic prophylaxis for the prevention of surgical site infections (SSIs) in ocular surgery is a complex field in which shared lines of action are absent. In light of the scarcity of shared evidence in the use of ocular antimicrobial prophylaxis for the pediatric population, this consensus document aims to provide clinicians with a series of recommendations on antimicrobial prophylaxis for patients of neonatal and pediatric age undergoing eye surgery. The following scenarios are considered: (1) intraocular surgery; (2) extraocular surgery; (3) ocular trauma; (4) ocular neoplasm; (5) ocular surface transplantations; (6) corneal grafts. This work has been made possible by the multidisciplinary contribution of experts belonging to the most important Italian scientific societies and represents, in our opinion, the most complete and up-to-date collection of recommendations regarding clinical actions in the peri-operative environment in eye surgery. The application of uniform and shared protocols aims to improve surgical practice, through the standardization of procedures, with a consequent reduction of SSIs, also limiting the phenomenon of antimicrobial resistance.
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Shi K, Zhu X, Wu J, Chen Y, Zhang J, Sun X. Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma. Bioengineered 2021; 12:5950-5970. [PMID: 34482803 PMCID: PMC8806431 DOI: 10.1080/21655979.2021.1972080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Retinoblastoma is the most common intraocular malignancy during childhood. Currently, there is no effective treatment for metastatic retinoblastoma. We investigated potential biomarkers of retinoblastoma by utilizing three datasets from a public database. Functional enrichment analysis, including gene ontology, Kyoto encyclopedia of genes and genomes, gene set enrichment analysis and variation analysis, suggested that differentially expressed genes in retinoblastoma were enriched in accelerated cell cycle events. Protein-protein interaction analysis constructed a network consisting of six hub genes, including benzimidazoles 1 (BUB1), cyclin dependent kinase 1 (CDK1), centromere protein E (CENPE), kinesin family member 20A (KIF20A), PDZ binding kinase (PBK), and targeting protein for xklp2 (TPX2). Drug sensitivity analysis showed that nelarabine was positively correlated with five hub genes. All six genes were expressed differently in six immune subtypes and were positively correlated with stemness indices in most human cancer types. Since CENPE is the least known hub gene in retinoblastoma, we further analyzed the potential non-coding RNAs and transcription factors that regulate CENPE and built interaction networks of competing endogenous RNA and transcription factors. Immune cell infiltration, especially by plasma and B cells, was enhanced in samples with high CENPE expression. Pan-cancer analysis illustrated that CENPE was highly expressed in a wide range of human tumors. In vitro validation revealed that CENPE was significantly upregulated at both the mRNA and protein levels in retinoblastoma cells. In conclusion, CENPE, along with other hub genes, could serve as a potential biomarker and intervention target for retinoblastoma.
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Affiliation(s)
- Ke Shi
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xinyue Zhu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jiali Wu
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yuhong Chen
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jingfa Zhang
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaodong Sun
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.,National Clinical Research Center for Eye Diseases, Shanghai, China.,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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Sun S, Wang R, Yi S, Li S, Wang L, Wang J. Roles of the microRNA‑338‑3p/NOVA1 axis in retinoblastoma. Mol Med Rep 2021; 23:394. [PMID: 33760207 PMCID: PMC8008220 DOI: 10.3892/mmr.2021.12033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Retinoblastoma (RB) is an intraocular malignancy that mainly affects young children. Previous reports have demonstrated that mutations or the inactivation of the RB1 gene were the main cause of RB; however, disruption of the intracellular signaling pathways following deficiency of RB1 requires further investigation. Based on the Gene Expression Omnibus data and bioinformatics prediction, the present study aimed to investigate the microRNA (miR)-338-3p/neuro-oncological ventral antigen 1 (NOVA1) axis in RB. Subsequently, overexpression and knockdown of miR-338-3p and NOVA1, respectively, were performed to study the role of miR-338-3p/NOVA1 in the progression of the RB cells. The results demonstrated that overexpression of miR-338-3p significantly inhibited cell proliferation, migration and invasion, and promoted apoptosis of the RB cells. Moreover, knockdown of NOVA1 showed similar results. A dual-luciferase reporter assay and rescue experiments further confirmed the direct binding between miR-338-3p and NOVA1. Taken together, the results indicated that miR-338-3p acted as tumor suppressor by targeting the oncogene of NOVA1 in RB, which may serve as potential therapeutic targets in RB.
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Affiliation(s)
- Shoubin Sun
- Department of Ophthalmology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Runze Wang
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Sisi Yi
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Sijia Li
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Lei Wang
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jianwen Wang
- Department of Ophthalmology, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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