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Patiyal S, Tiwari P, Ghai M, Dhapola A, Dhall A, Raghava GPS. A hybrid approach for predicting transcription factors. FRONTIERS IN BIOINFORMATICS 2024; 4:1425419. [PMID: 39119181 PMCID: PMC11306938 DOI: 10.3389/fbinf.2024.1425419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 07/03/2024] [Indexed: 08/10/2024] Open
Abstract
Transcription factors are essential DNA-binding proteins that regulate the transcription rate of several genes and control the expression of genes inside a cell. The prediction of transcription factors with high precision is important for understanding biological processes such as cell differentiation, intracellular signaling, and cell-cycle control. In this study, we developed a hybrid method that combines alignment-based and alignment-free methods for predicting transcription factors with higher accuracy. All models have been trained, tested, and evaluated on a large dataset that contains 19,406 transcription factors and 523,560 non-transcription factor protein sequences. To avoid biases in evaluation, the datasets were divided into training and validation/independent datasets, where 80% of the data was used for training, and the remaining 20% was used for external validation. In the case of alignment-free methods, models were developed using machine learning techniques and the composition-based features of a protein. Our best alignment-free model obtained an AUC of 0.97 on an independent dataset. In the case of the alignment-based method, we used BLAST at different cut-offs to predict the transcription factors. Although the alignment-based method demonstrated excellent performance, it was unable to cover all transcription factors due to instances of no hits. To combine the strengths of both methods, we developed a hybrid method that combines alignment-free and alignment-based methods. In the hybrid method, we added the scores of the alignment-free and alignment-based methods and achieved a maximum AUC of 0.99 on the independent dataset. The method proposed in this study performs better than existing methods. We incorporated the best models in the webserver/Python Package Index/standalone package of "TransFacPred" (https://webs.iiitd.edu.in/raghava/transfacpred).
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Affiliation(s)
| | | | | | | | | | - Gajendra P. S. Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, New Delhi, India
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Mojumdar A, B S U, Packirisamy G. A simple and effective method for smartphone-based detection of polyamines in oral cancer. Biomed Mater 2024; 19:045044. [PMID: 38871001 DOI: 10.1088/1748-605x/ad581a] [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: 09/17/2023] [Accepted: 06/13/2024] [Indexed: 06/15/2024]
Abstract
Oral cancer accounts for 50%-70% of all cancer-related deaths in India and ranks sixth among the most frequent cancers globally. Roughly 90% of oral malignancies are histologically arise from squamous cells and are therefore called oral squamous cell carcinoma. Organic polycations known as biogenic polyamines, for example, putrescine (Put), spermidine (Spd), and spermine (Spm), are vital for cell proliferation, including gene expression control, regulation of endonuclease-mediated fragmentation of DNA, and DNA damage inhibition. Higher Spm and Spd levels have been identified as cancer biomarkers for detecting tumour development in various cancers. The current study utilises tannic acid, a polyphenolic compound, as a reducing and capping agent to fabricate AuNPs via a one-step microwave-assisted synthesis. The fabricated TA@AuNPs were utilised as a nanoprobe for colourimetric sensing of polyamines in PBS. When TA@AuNPs are added to the polyamine, the amine groups in polyamines interact with the phenolic groups of TA@AuNPs via hydrogen bonding or electrostatic interactions. These interactions cause the aggregation of TA@AuNPs, resulting in a red shift of the Surface Plasmon Resonance band of TA@AuNPs from 530 nm to 560 nm. The nanoprobe was found to be highly specific for Spm at low concentrations. TA@AuNPs were able to detect Spm successfully in artificial saliva samples. On recording the RGB values of the sensing process using a smartphone app, it was found that as the nanoparticles aggregated due to the presence of Spm, the intensity of theR-value decreased, indicating the aggregation of TA@AuNPs due to interaction with the polyamine.
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Affiliation(s)
- Asmita Mojumdar
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Unnikrishnan B S
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
| | - Gopinath Packirisamy
- Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand 247667, India
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Shetty MG, Pai P, Dey B, Satyamoorthy K, Shil S, Nayak UY, T A, Sundara BK. Evaluation of 1,10-phenanthroline-based hydroxamate derivative as dual histone deacetylases/ribonucleotide reductase inhibitor with antitumor activities. Daru 2024; 32:263-278. [PMID: 38683491 PMCID: PMC11087398 DOI: 10.1007/s40199-024-00514-1] [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: 08/22/2023] [Accepted: 04/07/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Aberrant expression of histone deacetylases (HDACs) and ribonucleotide reductase (RR) enzymes are commonly observed in various cancers. Researchers are focusing on these enzymes in cancer studies with the aim of developing effective chemotherapeutic drugs for cancer treatment. Targeting both HDAC and RR simultaneously with a dual HDAC/RR inhibitor has exhibited enhanced effectiveness compared to monotherapy in cancer treatment, making it a promising strategy. OBJECTIVES The objective of the study is to synthesize and assess the anti-cancer properties of a 1,10-phenanthroline-based hydroxamate derivative, characterizing it as a novel dual HDAC/RR inhibitor. METHODS The N1-hydroxy-N8-(1,10-phenanthrolin-5-yl)octanediamide (PA), a 1,10-phenanthroline-based hydroxamate derivative, was synthesized and structurally characterized. The compound was subjected to in vitro assessments of its anti-cancer, HDAC, and RR inhibitory activities. In silico docking and molecular dynamics simulations were further studied to explore its interactions with HDACs and RRM2. RESULTS The structurally confirmed PA exhibited antiproliferative activity in SiHa cells with an IC50 of 16.43 μM. It displayed potent inhibitory activity against HDAC and RR with IC50 values of 10.80 μM and 9.34 μM, respectively. Co-inhibition of HDAC and RR resulted in apoptosis-induced cell death in SiHa cells, mediated by the accumulation of reactive oxygen species (ROS). In silico docking studies demonstrated that PA can effectively bind to the active sites of HDAC isoforms and RRM2. Furthermore, PA demonstrated a more favorable interaction with HDAC7, displaying a docking score of -9.633 kcal/mol, as compared to the standard HDAC inhibitor suberoylanilide hydroxamic acid (SAHA), which exhibited a docking score of -8.244 kcal/mol against HDAC7. CONCLUSION The present study emphasizes the prospect of designing a potential 1,10-phenanthroline hydroxamic acid derivative as a novel dual HDAC and RR-inhibiting anti-cancer molecule.
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Affiliation(s)
- Manasa Gangadhar Shetty
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Padmini Pai
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Bipasa Dey
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Shri Dharmasthala Manjunatheshwara (SDM) University, Manjushree Nagar, Sattur, Dharwad, 580009, Karnataka, India
| | - Suranjan Shil
- Department of Chemistry, Manipal Centre for Natural Sciences (Centre of Excellence), Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Usha Yogendra Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Ashwini T
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Babitha Kampa Sundara
- Department of Biophysics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
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Lin C, Teng W, Tian Y, Li S, Xia N, Huang C. Immune landscape and response to oncolytic virus-based immunotherapy. Front Med 2024; 18:411-429. [PMID: 38453818 DOI: 10.1007/s11684-023-1048-0] [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: 07/19/2023] [Accepted: 11/15/2023] [Indexed: 03/09/2024]
Abstract
Oncolytic virus (OV)-based immunotherapy has emerged as a promising strategy for cancer treatment, offering a unique potential to selectively target malignant cells while sparing normal tissues. However, the immunosuppressive nature of tumor microenvironment (TME) poses a substantial hurdle to the development of OVs as effective immunotherapeutic agents, as it restricts the activation and recruitment of immune cells. This review elucidates the potential of OV-based immunotherapy in modulating the immune landscape within the TME to overcome immune resistance and enhance antitumor immune responses. We examine the role of OVs in targeting specific immune cell populations, including dendritic cells, T cells, natural killer cells, and macrophages, and their ability to alter the TME by inhibiting angiogenesis and reducing tumor fibrosis. Additionally, we explore strategies to optimize OV-based drug delivery and improve the efficiency of OV-mediated immunotherapy. In conclusion, this review offers a concise and comprehensive synopsis of the current status and future prospects of OV-based immunotherapy, underscoring its remarkable potential as an effective immunotherapeutic agent for cancer treatment.
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Affiliation(s)
- Chaolong Lin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Wenzhong Teng
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Yang Tian
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Shaopeng Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China
| | - Ningshao Xia
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China.
| | - Chenghao Huang
- State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, Department of Laboratory Medicine, School of Public Health, Xiamen University, Xiamen, 361102, China.
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, 361102, China.
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Zhang Y, Xiang Z, Chen L, Deng X, Liu H, Peng X. PSMA2 promotes glioma proliferation and migration via EMT. Pathol Res Pract 2024; 256:155278. [PMID: 38574629 DOI: 10.1016/j.prp.2024.155278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/15/2024] [Accepted: 03/26/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Gliomas advance rapidly and are associated with a poor prognosis. Epithelial-mesenchymal transition (EMT) accelerates the progression of gliomas, exerting a pivotal role in glioma development. Proteasome subunit alpha type-2 (PSMA2) exhibits high expression levels in gliomas. however, its specific involvement in glioma progression and its correlation with EMT remain elusive. This study aims to elucidate the role of PSMA2 in glioma progression and its potential association with EMT. METHODS Online tools were employed to analyze the expression patterns and survival curves of PSMA2 in gliomas. The relationship between PSMA2 and various characteristics of glioma patients was investigated using data from the TCGA and CGGA databases. In vitro, cell proliferation and migration were assessed through CCK-8, colony formation, and transwell assays. Furthermore, a tumor xenograft model in nude mice was established to evaluate in vivo tumorigenesis. Protein binding to PSMA2 was scrutinized using co-immunoprecipitation MS (co-IP MS). The potential biological functions and molecular pathways associated with PSMA2 were explored through GO analysis and KEGG analysis, and the correlation between PSMA2 and EMT was validated through correlation analysis and Western blot experiments. RESULTS Bioinformatics analysis revealed a significant upregulation of PSMA2 across various cancers, with particularly heightened expression in gliomas. Moreover, elevated PSMA2 levels were correlated with advanced tumor stages and diminished survival rates among glioma patients. Inhibition of PSMA2 demonstrated a pronounced suppressive effect on glioma cell proliferation, both in vitro and in vivo. Knockdown of PSMA2 also impeded the migratory capacity of glioma cells. GO and KEGG enrichment analyses indicated that PSMA2-binding proteins (identified through Co-IP-MS) were associated with cell adhesion molecule binding and cadherin binding. Western blot results further confirmed the role of PSMA2 in promoting epithelial-mesenchymal transition (EMT) in glioma cells. CONCLUSION Our study provides evidence supporting the role of PSMA2 as a regulatory factor in EMT and suggests its potential as a prognostic biomarker for glioma progression.
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Affiliation(s)
- Yujun Zhang
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Zijin Xiang
- Department of Pharmacy, Shaodong People's Hospital, Shaodong, Hunan 422800, China
| | - Le Chen
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Xingyan Deng
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Huaizheng Liu
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha 410013, China.
| | - Xiangdong Peng
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China.
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Lee JY, Bhandare RR, Boddu SHS, Shaik AB, Saktivel LP, Gupta G, Negi P, Barakat M, Singh SK, Dua K, Chellappan DK. Molecular mechanisms underlying the regulation of tumour suppressor genes in lung cancer. Biomed Pharmacother 2024; 173:116275. [PMID: 38394846 DOI: 10.1016/j.biopha.2024.116275] [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: 11/24/2023] [Revised: 01/30/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Tumour suppressor genes play a cardinal role in the development of a large array of human cancers, including lung cancer, which is one of the most frequently diagnosed cancers worldwide. Therefore, extensive studies have been committed to deciphering the underlying mechanisms of alterations of tumour suppressor genes in governing tumourigenesis, as well as resistance to cancer therapies. In spite of the encouraging clinical outcomes demonstrated by lung cancer patients on initial treatment, the subsequent unresponsiveness to first-line treatments manifested by virtually all the patients is inherently a contentious issue. In light of the aforementioned concerns, this review compiles the current knowledge on the molecular mechanisms of some of the tumour suppressor genes implicated in lung cancer that are either frequently mutated and/or are located on the chromosomal arms having high LOH rates (1p, 3p, 9p, 10q, 13q, and 17p). Our study identifies specific genomic loci prone to LOH, revealing a recurrent pattern in lung cancer cases. These loci, including 3p14.2 (FHIT), 9p21.3 (p16INK4a), 10q23 (PTEN), 17p13 (TP53), exhibit a higher susceptibility to LOH due to environmental factors such as exposure to DNA-damaging agents (carcinogens in cigarette smoke) and genetic factors such as chromosomal instability, genetic mutations, DNA replication errors, and genetic predisposition. Furthermore, this review summarizes the current treatment landscape and advancements for lung cancers, including the challenges and endeavours to overcome it. This review envisages inspired researchers to embark on a journey of discovery to add to the list of what was known in hopes of prompting the development of effective therapeutic strategies for lung cancer.
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Affiliation(s)
- Jia Yee Lee
- School of Health Sciences, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia
| | - Richie R Bhandare
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates.
| | - Sai H S Boddu
- Department of Pharmaceutical Sciences, College of Pharmacy & Health Sciences, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates
| | - Afzal B Shaik
- St. Mary's College of Pharmacy, St. Mary's Group of Institutions Guntur, Affiliated to Jawaharlal Nehru Technological University Kakinada, Chebrolu, Guntur, Andhra Pradesh 522212, India; Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, India
| | - Lakshmana Prabu Saktivel
- Department of Pharmaceutical Technology, University College of Engineering (BIT Campus), Anna University, Tiruchirappalli 620024, India
| | - Gaurav Gupta
- Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Al-Jurf, P.O. Box 346, Ajman, United Arab Emirates; School of Pharmacy, Suresh Gyan Vihar University, Jaipur, Rajasthan 302017, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University, PO Box 9, Solan, Himachal Pradesh 173229, India
| | - Muna Barakat
- Department of Clinical Pharmacy & Therapeutics, Applied Science Private University, Amman-11937, Jordan
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T Road, Phagwara 144411, India; Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Kamal Dua
- Australian Research Centre in Complementary and Integrative Medicine, Faculty of Health, University of Technology Sydney, Sydney 2007, Australia; Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia.
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Ma Y, Huang X, Wang Y, Lei Y, Yu J, Yu S, Gao Y, Yang J, Zhao F, Yu H, Zeng J, Chu Y, Yang M, Li G, Xie X, Zhang J. NNMT/1-MNA Promote Cell-Cycle Progression of Breast Cancer by Targeting UBC12/Cullin-1-Mediated Degradation of P27 Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305907. [PMID: 38126621 PMCID: PMC10916551 DOI: 10.1002/advs.202305907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/17/2023] [Indexed: 12/23/2023]
Abstract
Cell cycle dysregulation is a defining feature of breast cancer. Here, 1-methyl-nicotinamide (1-MNA), metabolite of nicotinamide N-methyltransferase(NNMT) is identified, as a novel driver of cell-cycle progression in breast cancer. NNMT, highly expressed in breast cancer tissues, positively correlates with tumor grade, TNM stage, Ki-67 index, and tumor size. Ablation of NNMT expression dramatically suppresses cell proliferation and causes cell-cycle arrest in G0/G1 phase. This phenomenon predominantly stems from the targeted action of 1-MNA, resulting in a specific down-regulation of p27 protein expression. Mechanistically, 1-MNA expedites the degradation of p27 proteins by enhancing cullin-1 neddylation, crucial for the activation of Cullin-1-RING E3 ubiquitin ligase(CRL1)-an E3 ubiquitin ligase targeting p27 proteins. NNMT/1-MNA specifically up-regulates the expression of UBC12, an E2 NEDD8-conjugating enzyme required for cullin-1 neddylation. 1-MNA showes high binding affinity to UBC12, extending the half-life of UBC12 proteins via preventing their localization to lysosome for degradation. Therefore, 1-MNA is a bioactive metabolite that promotes breast cancer progression by reinforcing neddylation pathway-mediated p27 degradation. The study unveils the link between NNMT enzymatic activity with cell-cycle progression, indicating that 1-MNA may be involved in the remodeling of tumor microenvironment.
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Affiliation(s)
- Yilei Ma
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Xucheng Huang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yanzhong Wang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yinjiao Lei
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
- Department of PathologySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
| | - Jinwei Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Shaobo Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yuzhen Gao
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jun Yang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Department of CytopathologyNingbo Diagnostic Pathology CenterNingboZhejiang315046P. R. China
| | - Feng Zhao
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Haitao Yu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jin Zeng
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Yadong Chu
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
- Department of Clinical LaboratoryZhejiang Armed Police Corps HospitalHangzhouZhejiang310051P. R. China
| | - Min Yang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Guoli Li
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Xinyou Xie
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
| | - Jun Zhang
- Department of Clinical LaboratorySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiang310016P. R. China
- Key Laboratory of Precision Medicine in Diagnosis and Monitoring Research of Zhejiang ProvinceHangzhouZhejiang310016P. R. China
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Meyer OS, Andersen MM, Børsting C, Morling N, Wulf HC, Philipsen PA, Lerche CM, Dyrberg Andersen J. Comparison of global DNA methylation analysis by whole genome bisulfite sequencing and the Infinium Mouse Methylation BeadChip using fresh and fresh-frozen mouse epidermis. Epigenetics 2023; 18:2144574. [PMID: 36373380 PMCID: PMC9980693 DOI: 10.1080/15592294.2022.2144574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Until recently, studying the murine methylome was restricted to sequencing-based methods. In this study we compared the global DNA methylation levels of hairless mouse epidermis using the recently released Infinium Mouse Methylation BeadChip from Illumina and whole genome bisulphite sequencing (WGBS). We also studied the effect of sample storage conditions by using fresh and fresh-frozen epidermis. The DNA methylation levels of 123,851 CpG sites covered by both the BeadChip and WGBS were compared. DNA methylation levels obtained with WGBS and the BeadChip were strongly correlated (Pearson correlation r = 0.984). We applied a threshold of 15 reads for the WGBS methylation analysis. Even at a threshold of 10 reads, we observed no substantial difference in DNA methylation levels compared with that obtained with the BeadChip. The DNA methylation levels from the fresh and the fresh-frozen samples were strongly correlated when analysed with both the BeadChip (r = 0.999) and WGBS (r = 0.994). We conclude that the two methods of analysis generally work equally well for studies of DNA methylation of mouse epidermis and find that fresh and fresh-frozen epidermis can generally be used equally well. The choice of method will depend on the specific study's aims and the available resources in the laboratory.
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Affiliation(s)
- Olivia Strunge Meyer
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,CONTACT Olivia Strunge Meyer Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Heafth and Medical Sciences, University of Copenhagen. Frederik V's vej 11, 2100 Copenhagen, Denmark
| | - Mikkel Meyer Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
| | - Niels Morling
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark,Department of Mathematical Sciences, Aalborg University, 9220Aalborg, Denmark
| | - Hans Christian Wulf
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Peter Alshede Philipsen
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark
| | - Catharina Margrethe Lerche
- Department of Dermatology, Copenhagen University Hospital - Bispebjerg and Frederiksberg, 2400Copenhagen, Denmark,Department of Pharmacy, University of Copenhagen, 2100Copenhagen, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, 2100Copenhagen, Denmark
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9
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Liang Y, Wang L, Ma P, Ju D, Zhao M, Shi Y. Enhancing anti-tumor immune responses through combination therapies: epigenetic drugs and immune checkpoint inhibitors. Front Immunol 2023; 14:1308264. [PMID: 38077327 PMCID: PMC10704038 DOI: 10.3389/fimmu.2023.1308264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Epigenetic mechanisms are processes that affect gene expression and cellular functions without involving changes in the DNA sequence. This abnormal or unstable expression of genes regulated by epigenetics can trigger cancer and other various diseases. The immune cells involved in anti-tumor responses and the immunogenicity of tumors may also be affected by epigenomic changes. This holds significant implications for the development and application of cancer immunotherapy, epigenetic therapy, and their combined treatments in the fight against cancer. We provide an overview of recent research literature focusing on how epigenomic changes in immune cells influence immune cell behavior and function, as well as the immunogenicity of cancer cells. And the combined utilization of epigenetic medications with immune checkpoint inhibitors that focus on immune checkpoint molecules [e.g., Programmed Death 1 (PD-1), Cytotoxic T-Lymphocyte-Associated Protein 4 (CTLA-4), T cell Immunoglobulin and Mucin Domain (TIM-3), Lymphocyte Activation Gene-3 (LAG-3)] present in immune cells and stromal cells associated with tumors. We highlight the potential of small-molecule inhibitors targeting epigenetic regulators to amplify anti-tumor immune responses. Moreover, we discuss how to leverage the intricate relationship between cancer epigenetics and cancer immunology to create treatment regimens that integrate epigenetic therapies with immunotherapies.
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Affiliation(s)
- Ying Liang
- Precision Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Lingling Wang
- Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan Wuchang Hospital, Wuhan, China
| | - Peijun Ma
- Clinical Laboratory, Shanghai Mental Health Center, Shanghai, China
| | - Dongen Ju
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Minggao Zhao
- Precision Pharmacy and Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi’an, Shaanxi, China
| | - Yun Shi
- Department of Immunology and Theranostics, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of the City of Hope, Duarte, CA, United States
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10
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Wang L, Ma Y, Han W, Yang Q, Jamil M. Whole Exome Sequencing reveals clinically important pathogenic mutations in DNA repair genes across lung cancer patients. Am J Cancer Res 2023; 13:4989-5004. [PMID: 37970346 PMCID: PMC10636674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 09/24/2023] [Indexed: 11/17/2023] Open
Abstract
Lung cancer remains a substantial health challenge, with distinct genetic factors influencing disease susceptibility and progression. This study aimed to decipher the landscape of DNA repair gene mutations in Pakistani lung cancer patients using Whole Exome Sequencing (WES) and to investigate their potential functional implications through downstream analyses. WES analysis of genomic DNA from 15 lung cancer patients identified clinically important pathogenic mutations in 6 DNA repair genes, including, BReast CAncer gene 1 (BRCA1), BReast CAncer gene 2 (BRCA2), Excision Repair Cross Complementing rodent repair deficiency, complementation group 6 (ERCC6), Checkpoint Kinase 1 (CHEK1), mutY DNA glycosylase (MUTYH), and RAD51D (RAD51 Paralog D). Kaplan-Meier (KM) analysis showed that pathogenic mutations in BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D genes were the prognostic biomarkers of worse OS in lung cancer patients. To explore the functional impact of these mutations, we performed Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and Immunohistochemistry (IHC) analyses. Our results revealed a down-regulation in the expression of the mutated genes, indicating a potential link between the identified mutations and reduced gene activity. This down-regulation could contribute to compromised DNA repair efficiency, thereby fostering genomic instability in lung cancer cells. Furthermore, targeted bisulfite sequencing analysis was employed to assess the DNA methylation status of the mutated genes. Strikingly, hypermethylation in the promoters of BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D was observed across lung cancer samples harboring pathogenic mutations, suggesting the involvement of epigenetic mechanism underlying the altered gene expression. In conclusion, this study provides insights into the genetic landscape of DNA repair gene mutations in Pakistani lung cancer patients. The observed pathogenic mutations in BRCA1, BRCA2, ERCC6, CHEK1, MUTYH, and RAD51D, coupled with their down-regulation and hypermethylation, suggest a potential convergence of genetic and epigenetic factors driving genomic instability in lung cancer cells. These findings contribute to our understanding of lung cancer susceptibility and highlight potential avenues for targeted therapeutic interventions in Pakistani lung cancer patients.
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Affiliation(s)
- Lanlan Wang
- Department of Medicine, The First People’s Hospital of ShangqiuShangqiu 476100, Henan, China
| | - Yali Ma
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Wenjie Han
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Qiumin Yang
- Department of Oncology, Shangqiu First People’s HospitalShangqiu 476000, Henan, China
| | - Muhammad Jamil
- PARC Arid Zone Research CenterDera Ismail Khan 29050, Pakistan
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11
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Nada H, Gul AR, Elkamhawy A, Kim S, Kim M, Choi Y, Park TJ, Lee K. Machine Learning-Based Approach to Developing Potent EGFR Inhibitors for Breast Cancer-Design, Synthesis, and In Vitro Evaluation. ACS OMEGA 2023; 8:31784-31800. [PMID: 37692247 PMCID: PMC10483653 DOI: 10.1021/acsomega.3c02799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 08/11/2023] [Indexed: 09/12/2023]
Abstract
The epidermal growth factor receptor (EGFR) is vital for regulating cellular functions, including cell division, migration, survival, apoptosis, angiogenesis, and cancer. EGFR overexpression is an ideal target for anticancer drug development as it is absent from normal tissues, marking it as tumor-specific. Unfortunately, the development of medication resistance limits the therapeutic efficacy of the currently approved EGFR inhibitors, indicating the need for further development. Herein, a machine learning-based application that predicts the bioactivity of novel EGFR inhibitors is presented. Clustering of the EGFR small-molecule inhibitor (∼9000 compounds) library showed that N-substituted quinazolin-4-amine-based compounds made up the largest cluster of EGFR inhibitors (∼2500 compounds). Taking advantage of this finding, rational drug design was used to design a novel series of 4-anilinoquinazoline-based EGFR inhibitors, which were first tested by the developed artificial intelligence application, and only the compounds which were predicted to be active were then chosen to be synthesized. This led to the synthesis of 18 novel compounds, which were subsequently evaluated for cytotoxicity and EGFR inhibitory activity. Among the tested compounds, compound 9 demonstrated the most potent antiproliferative activity, with 2.50 and 1.96 μM activity over MCF-7 and MDA-MB-231 cancer cell lines, respectively. Moreover, compound 9 displayed an EGFR inhibitory activity of 2.53 nM and promising apoptotic results, marking it a potential candidate for breast cancer therapy.
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Affiliation(s)
- Hossam Nada
- BK21
FOUR Team and Integrated Research Institute for Drug Development,
College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Anam Rana Gul
- Department
of Chemistry, Chung-Ang University, 84 Heukseok-ro, Seoul 06974, South Korea
| | - Ahmed Elkamhawy
- BK21
FOUR Team and Integrated Research Institute for Drug Development,
College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Sungdo Kim
- BK21
FOUR Team and Integrated Research Institute for Drug Development,
College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Minkyoung Kim
- BK21
FOUR Team and Integrated Research Institute for Drug Development,
College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Yongseok Choi
- College
of Life Sciences and Biotechnology, Korea
University, Seoul 02841, Republic of Korea
| | - Tae Jung Park
- Department
of Chemistry, Chung-Ang University, 84 Heukseok-ro, Seoul 06974, South Korea
| | - Kyeong Lee
- BK21
FOUR Team and Integrated Research Institute for Drug Development,
College of Pharmacy, Dongguk University-Seoul, Goyang 10326, Republic of Korea
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12
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Natan Y, Blum YD, Arav A, Poliansky Y, Neuman S, Ecker Cohen O, Ben Y. Amorphous Calcium Carbonate Shows Anti-Cancer Properties That are Attributed to Its Buffering Capacity. Cancers (Basel) 2023; 15:3785. [PMID: 37568601 PMCID: PMC10417113 DOI: 10.3390/cancers15153785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/03/2023] [Accepted: 07/15/2023] [Indexed: 08/13/2023] Open
Abstract
AIM Amorphous calcium carbonate (ACC) is a non-crystalline form of calcium carbonate, and it is composed of aggregated nano-size primary particles. Here, we evaluated its anti-cancer effect postulated relative to its buffering capabilities in lung cancer. METHODS Tumors were evaluated in vivo using the Lewis lung carcinoma (LLC) mouse cell line and A549 human lung cancer carcinoma cell line. LLC and A549 cells were injected subcutaneously into the right hind leg of mice. Treatments (ACC, cisplatin, vehicle, and ACC with cisplatin, all given via daily IP injections) started once tumors reached a measurable size. Treatments were carried out for 14 days in the LLC model and for 22 and 24 days in the xenograft model (two experiments). LLC tumors were resected from ACC at the end of the study, and vehicle groups were evaluated for cathepsin B activity. Differential gene expression was carried out on A549 cells following 8 weeks of in vitro culture in the presence or absence of ACC in a culture medium. RESULTS The ACC treatment decelerated tumor growth rates in both models. When tumor volumes were compared on the last day of each study, the ACC-treated animal tumor volume was reduced by 44.83% compared to vehicle-treated animals in the LLC model. In the xenograft model, the tumor volume was reduced by 51.6% in ACC-treated animals compared to vehicle-treated animals. A more substantial reduction of 74.75% occurred in the combined treatment of ACC and cisplatin compared to the vehicle (carried out only in the LLC model). Cathepsin B activity was significantly reduced in ACC-treated LLC tumors compared to control tumors. Differential gene expression results showed a shift towards anti-tumorigenic pathways in the ACC-treated A549 cells. CONCLUSION This study supports the ACC anti-malignant buffering hypothesis by demonstrating decelerated tumor growth, reduced cathepsin B activity, and altered gene expressions to produce anti-cancerous effects.
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Affiliation(s)
- Yehudit Natan
- Amorphical Ltd., 11 HaHarash st., Nes-Ziona 7403118, Israel
| | - Yigal Dov Blum
- Amorphical Ltd., 11 HaHarash st., Nes-Ziona 7403118, Israel
| | - Amir Arav
- A.A. Cash Technology Ltd., 59 Shlomzion Hamalka st., Tel-Aviv 6226618, Israel
| | | | - Sara Neuman
- Amorphical Ltd., 11 HaHarash st., Nes-Ziona 7403118, Israel
| | | | - Yossi Ben
- Amorphical Ltd., 11 HaHarash st., Nes-Ziona 7403118, Israel
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13
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Iyer M, Anand U, Thiruvenkataswamy S, Babu HWS, Narayanasamy A, Prajapati VK, Tiwari CK, Gopalakrishnan AV, Bontempi E, Sonne C, Barceló D, Vellingiri B. A review of chromium (Cr) epigenetic toxicity and health hazards. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 882:163483. [PMID: 37075992 DOI: 10.1016/j.scitotenv.2023.163483] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/13/2023] [Accepted: 04/09/2023] [Indexed: 05/03/2023]
Abstract
Carcinogenic metals affect a variety of cellular processes, causing oxidative stress and cancer. The widespread distribution of these metals caused by industrial, residential, agricultural, medical, and technical activities raises concern for adverse environmental and human health effects. Of these metals, chromium (Cr) and its derivatives, including Cr(VI)-induced, are of a public health concern as they cause DNA epigenetic alterations resulting in heritable changes in gene expression. Here, we review and discuss the role of Cr(VI) in epigenetic changes, including DNA methylation, histone modifications, micro-RNA changes, biomarkers of exposure and toxicity, and highlight prevention and intervention strategies to protect susceptible populations from exposure and adverse occupational health effects. Cr(VI) is a ubiquitous toxin linked to cardiovascular, developmental, neurological, and endocrine diseases as well as immunologic disorders and a high number of cancer types in humans following inhalation and skin contact. Cr alters DNA methylation levels as well as global and gene-specific histone posttranslational modifications, emphasizing the importance of considering epigenetics as a possible mechanism underlying Cr(VI) toxicity and cell-transforming ability. Our review shows that determining the levels of Cr(VI) in occupational workers is a crucial first step in shielding health problems, including cancer and other disorders. More clinical and preventative measures are therefore needed to better understand the toxicity and safeguard employees against cancer.
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Affiliation(s)
- Mahalaxmi Iyer
- Department of Biotechnology, Karpagam Academy of Higher Education (Deemed to be University), Coimbatore 641021, India
| | - Uttpal Anand
- Zuckerberg Institute for Water Research, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Midreshet Ben-Gurion 8499000, Israel
| | - Saranya Thiruvenkataswamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India; Department of Zoology (PG-SF), PSG college of arts and science, Coimbatore 641014, Tamil Nadu, India
| | - Harysh Winster Suresh Babu
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore 641 046, Tamil Nadu, India
| | - Arul Narayanasamy
- Disease Proteomics Laboratory, Department of Zoology, Bharathiar University, Coimbatore 641046, Tamil Nadu, India.
| | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, India
| | - Chandan Kumar Tiwari
- Research and Development section, Carestream Health Inc., Oakdale, MN 55128, United States of America
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore 632 014, India
| | - Elza Bontempi
- INSTM and Chemistry for Technologies Laboratory, University of Brescia, via Branze 38, 25123 Brescia, Italy
| | - Christian Sonne
- Department of Ecoscience, Arctic Research Centre, Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, 4000 Roskilde, Denmark
| | - Damià Barceló
- Catalan Institute for Water Research (ICRA-CERCA), H(2)O Building, Scientific and Technological Park of the University of Girona, Emili Grahit 101, Girona 17003, Spain; Water and Soil Quality Research Group, Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA-CSIC), Jordi Girona 1826, Barcelona 08034, Spain
| | - Balachandar Vellingiri
- Stem cell and Regenerative Medicine/Translational Research, North block, Department of Zoology, School of Basic Sciences, Central University of Punjab, Bathinda, Punjab 151401, India.
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14
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Rasuleva K, Jangili KP, Akinlalu A, Guo A, Borowicz P, Li CZ, Sun D. EvIPqPCR, Target Circulating Tumorous Extracellular Vesicles for Detection of Pancreatic Cancer. Anal Chem 2023; 95:10353-10361. [PMID: 37339258 DOI: 10.1021/acs.analchem.3c01218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023]
Abstract
Pancreatic cancer patients predominantly present with advanced disease at diagnosis, contributing to its high mortality. A noninvasive, fast screening method to detect this disease is an unmet need. Tumor-derived extracellular vesicles (tdEVs) bearing information from parental cells have emerged as a promising cancer diagnostic biomarker. However, most tdEV-based assays have impractical sample volumes and time-consuming, complex, and costly techniques. To overcome these limitations, we developed a novel diagnostic method for pancreatic cancer screening. Our approach utilizes the mitochondrial DNA to nuclear DNA ratio of EVs as a collective cell-specific characteristic. We introduce EvIPqPCR, a fast method that combines immunoprecipitation (IP) and qPCR quantification to detect tumor-derived EVs directly from serum. Importantly, our method employs DNA isolation-free and duplexing probes for qPCR, saving at least 3 h. This technique has the potential to serve as a translational assay for cancer screening with a weak correlation to prognosis biomarkers and sufficient discriminatory power among healthy controls, pancreatitis, and pancreatic cancer cases.
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Affiliation(s)
- Komila Rasuleva
- Biomedical Engineering Program, North Dakota State University, 1401 Centennial Blvd, Engineering Administration, Room 203, Fargo, North Dakota 58102, United States
| | - Keerthi Priya Jangili
- Biomedical Engineering Program, North Dakota State University, 1401 Centennial Blvd, Engineering Administration, Room 203, Fargo, North Dakota 58102, United States
| | - Alfred Akinlalu
- Biomedical Engineering Program, North Dakota State University, 1401 Centennial Blvd, Engineering Administration, Room 203, Fargo, North Dakota 58102, United States
| | - Ang Guo
- Department of Pharmaceutical Sciences, North Dakota State University, 1401 Albrecht Blvd., Fargo, North Dakota 58102, United States
| | - Pawel Borowicz
- Advanced Imaging and Microscopy Core Lab, Department of Animal Sciences, Center for Nutrition and Pregnancy, North Dakota State University, NDSU Department 7630, Fargo, North Dakota 58108-6050, United States
| | - Chen-Zhong Li
- Bioelectronics and Biosensors Center, Biomedical Engineering, The Chinese University of Hong Kong, Shenzhen, Medical School Start Building, Room 307 2001 Longxiang Avenue, Longgang District, Shenzhen 518172, China
| | - Dali Sun
- Biomedical Engineering Program, North Dakota State University, 1401 Centennial Blvd, Engineering Administration, Room 203, Fargo, North Dakota 58102, United States
- Department of Electrical and Computer Engineering, North Dakota State University, 1411 Centennial Blvd., 101S, Fargo, North Dakota 58102, United States
- Department of Electrical & Computer Engineering, University of Denver, 2155 E. Wesley Ave., Denver, Colorado 80210, United States
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15
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Herdiana Y, Sriwidodo S, Sofian FF, Wilar G, Diantini A. Nanoparticle-Based Antioxidants in Stress Signaling and Programmed Cell Death in Breast Cancer Treatment. Molecules 2023; 28:5305. [PMID: 37513179 PMCID: PMC10384004 DOI: 10.3390/molecules28145305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/04/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Breast cancer (BC) is a complex and heterogeneous disease, and oxidative stress is a hallmark of BC. Oxidative stress is characterized by an imbalance between the production of reactive oxygen species (ROS) and antioxidant defense mechanisms. ROS has been implicated in BC development and progression by inducing DNA damage, inflammation, and angiogenesis. Antioxidants have been shown to scavenge ROS and protect cells from oxidative damage, thereby regulating signaling pathways involved in cell growth, survival, and death. Plants contain antioxidants like ascorbic acid, tocopherols, carotenoids, and flavonoids, which have been found to regulate stress signaling and PCD in BC. Combining different antioxidants has shown promise in enhancing the effectiveness of BC treatment. Antioxidant nanoparticles, when loaded with antioxidants, can effectively target breast cancer cells and enhance their cellular uptake. Notably, these nanoparticles have shown promising results in inducing PCD and sensitizing breast cancer cells to chemotherapy, even in cases where resistance is observed. This review aims to explore how nanotechnology can modulate stress signaling and PCD in breast cancer. By summarizing current research, it underscores the potential of nanotechnology in enhancing antioxidant properties for the treatment of breast cancer.
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Affiliation(s)
- Yedi Herdiana
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Sriwidodo Sriwidodo
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Ferry Ferdiansyah Sofian
- Department of Pharmaceutical Biology, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Gofarana Wilar
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
| | - Ajeng Diantini
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Sumedang 45363, Indonesia
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16
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Aghiorghiesei O, Irimie AI, Braicu C, Raduly L, Nutu A, Balint E, Mehterov N, Vladimirov B, Sarafian V, Lucaciu O, Campian R, Berindan-Neagoe I. Epigenetic methylation changes: implication as biomarkers in oral and maxillofacial area cancers. Med Pharm Rep 2023; 96:310-317. [PMID: 37577021 PMCID: PMC10419680 DOI: 10.15386/mpr-2570] [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: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 08/15/2023] Open
Abstract
Background/Aim Squamous cell carcinoma (SCC) is the most frequent cancer of the head and neck area in the oral cavity. Epigenetic alterations in oral and maxillofacial area cancers are urgently needed to be investigated, as the observed changes might have crucial diagnostic value for personalized medicine. Methods Our study aimed to identify the most frequently hypermethylated tumor suppressor gene promoters in OSCC, followed by correlation analysis with the patients' survival. We evaluated the methylation status of the promoters in a panel of 22 tumor suppressor genes in Romanian (n=9) and Bulgarian (n=12) patient groups suffering from oral and maxillofacial area cancers. The extracted DNA was further digested through EpiTect Methyl II PCR Array System containing methylation-sensitive and methylation-dependent restriction enzymes, followed by specific amplification of the products obtained by qPCR and data analysis using the online platform provided by the producer. Results Different methylation patterns were observed in the tumor suppressor genes' promoters. Among them, the methylation profile of Cccnd2, Chd1, Cdh13, Cdkn1c, Neurog1, Gstp1, and Runx3 genes further correlated with overall survival rates. Conclusions Our data emphasize that epigenetic alterations are responsible for the clinical heterogeneity of oral and maxillofacial area cancers and significantly impact on patient survival. Additional investigation on a larger patient cohort should validate these potential biomarkers.
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Affiliation(s)
- Ovidiu Aghiorghiesei
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Emilia Balint
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Nikolay Mehterov
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, Plovdiv, Bulgaria
- Clinic of Maxillofacial Surgery, University Hospital St. George, Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Ondine Lucaciu
- Department of Preventive Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Campian
- Department of Oral Rehabilitation, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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17
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Subramani P, Nagarajan N, Mariaraj S, Vilwanathan R. Knockdown of sirtuin6 positively regulates acetylation of DNMT1 to inhibit NOTCH signaling pathway in non-small cell lung cancer cell lines. Cell Signal 2023; 105:110629. [PMID: 36813148 DOI: 10.1016/j.cellsig.2023.110629] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 02/22/2023]
Abstract
BACKGROUND AND AIM Sirtuin proteins (1-7) are nicotinamide adenine dinucleotide (NAD)-dependent deacetylases and ADP-ribosyl transferases (class III histone deacetylase enzymes (HDAC)) mainly involved in the removal of the acetyl group from histone proteins. SIRT6, one of the sirtuins, plays a major role in cancer progression in many types of cancer conditions. We recently reported that SIRT6 acts as an oncogene in NSCLC; thus, silencing of SIRT6 inhibits cell proliferation and induces apoptosis in NSCLC cell lines. NOTCH signaling has been reported to be involved in cell survival and regulates cell proliferation and differentiation. However, recent studies from different groups have converged on the notion that NOTCH1 may be an important oncogene in NSCLC. The abnormal expression of NOTCH signaling pathway members is a relatively frequent event in patients with NSCLC. SIRT6 and the NOTCH signaling pathway might play a critical role in tumorigenesis since they are highly expressed in NSCLC. This study has been performed to explore the exact mechanism by which SIRT6 inhibits cell proliferation and induces the apoptosis of NSCLC cell lines and its correlation with NOTCH signaling. MAIN METHODS In vitro experiments with human NSCLC cells have been performed. Immunocytochemistry study was used to analyze the expression of NOTCH1 and DNMT1 in A549 and NCI-H460 cell lines. RT-qPCR, Western Blot, Methylated DNA specific PCR, and Co-Immunoprecipitation were performed to explore the key events in the regulation of NOTCH signaling by silencing SIRT6 in NSCLC cell lines. KEY FINDINGS The findings of this study suggest that silencing of SIRT6 significantly promotes the acetylation status of DNMT1 and stabilizes it. Consequently, acetylated DNMT1 translocates into the nucleus and methylates the NOTCH1 promoter region, resulting in the hindering of NOTCH1-mediated NOTCH signaling.
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Affiliation(s)
- Prabhu Subramani
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Nanthakumar Nagarajan
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Sagayamercy Mariaraj
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India
| | - Ravikumar Vilwanathan
- Cancer Biology Laboratory, Department of Biochemistry, School of Life Sciences, Bharathidasan University, Tiruchirappalli 620 024, Tamil Nadu, India.
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Balakittnen J, Weeramange CE, Wallace DF, Duijf PHG, Cristino AS, Kenny L, Vasani S, Punyadeera C. Noncoding RNAs in oral cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1754. [PMID: 35959932 PMCID: PMC10909450 DOI: 10.1002/wrna.1754] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/09/2022] [Accepted: 07/05/2022] [Indexed: 05/13/2023]
Abstract
Oral cancer (OC) is the most prevalent subtype of cancer arising in the head and neck region. OC risk is mainly attributed to behavioral risk factors such as exposure to tobacco and excessive alcohol consumption, and a lesser extent to viral infections such as human papillomaviruses and Epstein-Barr viruses. In addition to these acquired risk factors, heritable genetic factors have shown to be associated with OC risk. Despite the high incidence, biomarkers for OC diagnosis are lacking and consequently, patients are often diagnosed in advanced stages. This delay in diagnosis is reflected by poor overall outcomes of OC patients, where 5-year overall survival is around 50%. Among the biomarkers proposed for cancer detection, noncoding RNA (ncRNA) can be considered as one of the most promising categories of biomarkers due to their role in virtually all cellular processes. Similar to other cancer types, changes in expressions of ncRNAs have been reported in OC and a number of ncRNAs have diagnostic, prognostic, and therapeutic potential. Moreover, some ncRNAs are capable of regulating gene expression by various mechanisms. Therefore, elucidating the current literature on the four main types of ncRNAs namely, microRNA, lncRNA, snoRNA, piwi-RNA, and circular RNA in the context of OC pathogenesis is timely and would enable further improvements and innovations in diagnosis, prognosis, and treatment of OC. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jaikrishna Balakittnen
- The Centre for Biomedical Technologies, The School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyKelvin GroveQueenslandAustralia
- Saliva & Liquid Biopsy Translational Laboratory, Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
- Department of Medical Laboratory Sciences, Faculty of Allied Health SciencesUniversity of JaffnaJaffnaSri Lanka
| | - Chameera Ekanayake Weeramange
- Saliva & Liquid Biopsy Translational Laboratory, Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
| | - Daniel F. Wallace
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
| | - Pascal H. G. Duijf
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQueenslandAustralia
- Queensland University of Technology, School of Biomedical SciencesFaculty of Health at the Translational Research InstituteWoolloongabbaQueenslandAustralia
- Centre for Data Science, Queensland University of Queensland, TechnologyBrisbaneQueenslandAustralia
- Institute of Clinical Medicine, Faculty of Medicine, HerstonUniversity of OsloOsloNorway
- Department of Medical GeneticsOslo University HospitalOsloNorway
- University of Queensland Diamantina InstituteThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Liz Kenny
- Royal Brisbane and Women's Hospital, Cancer Care ServicesHerstonQueenslandAustralia
- Faculty of MedicineThe University of QueenslandBrisbaneQueenslandAustralia
| | - Sarju Vasani
- Royal Brisbane and Women's Hospital, Cancer Care ServicesHerstonQueenslandAustralia
- Department of OtolaryngologyRoyal Brisbane and Women's HospitalHerstonQueenslandAustralia
| | - Chamindie Punyadeera
- Saliva & Liquid Biopsy Translational Laboratory, Griffith Institute for Drug DiscoveryGriffith UniversityNathanQueenslandAustralia
- Queensland University of Technology, School of Biomedical SciencesFaculty of Health at the Translational Research InstituteWoolloongabbaQueenslandAustralia
- Menzies Health InstituteGriffith UniversityGold CoastQueenslandAustralia
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19
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Maryam S, Krukiewicz K, Haq IU, Khan AA, Yahya G, Cavalu S. Interleukins (Cytokines) as Biomarkers in Colorectal Cancer: Progression, Detection, and Monitoring. J Clin Med 2023; 12:jcm12093127. [PMID: 37176567 PMCID: PMC10179696 DOI: 10.3390/jcm12093127] [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: 03/18/2023] [Revised: 04/18/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Cancer is the primary cause of death in economically developed countries and the second leading cause in developing countries. Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide. Risk factors for CRC include obesity, a diet low in fruits and vegetables, physical inactivity, and smoking. CRC has a poor prognosis, and there is a critical need for new diagnostic and prognostic biomarkers to reduce related deaths. Recently, studies have focused more on molecular testing to guide targeted treatments for CRC patients. The most crucial feature of activated immune cells is the production and release of growth factors and cytokines that modulate the inflammatory conditions in tumor tissues. The cytokine network is valuable for the prognosis and pathogenesis of colorectal cancer as they can aid in the cost-effective and non-invasive detection of cancer. A large number of interleukins (IL) released by the immune system at various stages of CRC can act as "biomarkers". They play diverse functions in colorectal cancer, and include IL-4, IL-6, IL-8, IL-11, IL-17A, IL-22, IL-23, IL-33, TNF, TGF-β, and vascular endothelial growth factor (VEGF), which are pro-tumorigenic genes. However, there are an inadequate number of studies in this area considering its correlation with cytokine profiles that are clinically useful in diagnosing cancer. A better understanding of cytokine levels to establish diagnostic pathways entails an understanding of cytokine interactions and the regulation of their various biochemical signaling pathways in healthy individuals. This review provides a comprehensive summary of some interleukins as immunological biomarkers of CRC.
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Affiliation(s)
- Sajida Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
| | - Katarzyna Krukiewicz
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Centre for Organic and Nanohybrid Electronics, Silesian University of Technology, Konarskiego 22B, 44-100 Gliwice, Poland
| | - Ihtisham Ul Haq
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
- Department of Physical Chemistry and Technology of Polymers, Silesian University of Technology, M. Strzody 9, 44-100 Gliwice, Poland
- Joint Doctoral School, Silesian University of Technology, Akademicka 2A, 44-100 Gliwice, Poland
| | - Awal Ayaz Khan
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad 44000, Pakistan
| | - Galal Yahya
- Department of Microbiology and Immunology, Faculty of Pharmacy, Zagazig University, Zagazig 44519, Al Sharqia, Egypt
- Department of Molecular Genetics, Faculty of Biology, Technical University of Kaiserslautern, Paul-Ehrlich Str. 24, 67663 Kaiserslautern, Germany
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, P-ta 1 Decembrie 10, 410087 Oradea, Romania
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20
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Nickel GA, Diehl KL. Chemical Biology Approaches to Identify and Profile Interactors of Chromatin Modifications. ACS Chem Biol 2023; 18:1014-1026. [PMID: 35238546 PMCID: PMC9440160 DOI: 10.1021/acschembio.1c00794] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In eukaryotes, DNA is packaged with histone proteins in a complex known as chromatin. Both the DNA and histone components of chromatin can be chemically modified in a wide variety of ways, resulting in a complex landscape often referred to as the "epigenetic code". These modifications are recognized by effector proteins that remodel chromatin and modulate transcription, translation, and repair of the underlying DNA. In this Review, we examine the development of methods for characterizing proteins that interact with these histone and DNA modifications. "Mark first" approaches utilize chemical, peptide, nucleosome, or oligonucleotide probes to discover interactors of a specific modification. "Reader first" approaches employ arrays of peptides, nucleosomes, or oligonucleotides to profile the binding preferences of interactors. These complementary strategies have greatly enhanced our understanding of how chromatin modifications effect changes in genomic regulation, bringing us ever closer to deciphering this complex language.
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Affiliation(s)
- Garrison A. Nickel
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
| | - Katharine L. Diehl
- Department of Medicinal Chemistry, University of Utah, Salt Lake City, UT 84112, United States
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21
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Finetti F, Paradisi L, Bernardi C, Pannini M, Trabalzini L. Cooperation between Prostaglandin E2 and Epidermal Growth Factor Receptor in Cancer Progression: A Dual Target for Cancer Therapy. Cancers (Basel) 2023; 15:cancers15082374. [PMID: 37190301 DOI: 10.3390/cancers15082374] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/15/2023] [Accepted: 04/17/2023] [Indexed: 05/17/2023] Open
Abstract
It is recognized that prostaglandin E2 (PGE2) is one key lipid mediator involved in chronic inflammation, and it is directly implicated in tumor development by regulating cancer cell growth and migration, apoptosis, epithelial-mesenchymal transition, angiogenesis, and immune escape. In addition, the expression of the enzymes involved in PGE2 synthesis, cyclooxygenase 2 (COX-2) and microsomal prostaglandin E synthase 1 (mPGES1), positively correlates with tumor progression and aggressiveness, clearly indicating the crucial role of the entire pathway in cancer. Moreover, several lines of evidence suggest that the COX2/mPGES1/PGE2 inflammatory axis is involved in the modulation of epidermal growth factor receptor (EGFR) signaling to reinforce the oncogenic drive of EGFR activation. Similarly, EGFR activation promotes the induction of COX2/mPGES1 expression and PGE2 production. In this review, we describe the interplay between COX2/mPGES1/PGE2 and EGFR in cancer, and new therapeutic strategies that target this signaling pathway, to outline the importance of the modulation of the inflammatory process in cancer fighting.
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Affiliation(s)
- Federica Finetti
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Lucrezia Paradisi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Clizia Bernardi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Margherita Pannini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Lorenza Trabalzini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
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22
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Conte M, Di Mauro A, Capasso L, Montella L, De Simone M, Nebbioso A, Altucci L. Targeting HDAC2-Mediated Immune Regulation to Overcome Therapeutic Resistance in Mutant Colorectal Cancer. Cancers (Basel) 2023; 15:cancers15071960. [PMID: 37046620 PMCID: PMC10093005 DOI: 10.3390/cancers15071960] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/08/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
A large body of clinical and experimental evidence indicates that colorectal cancer is one of the most common multifactorial diseases. Although some useful prognostic biomarkers for clinical therapy have already been identified, it is still difficult to characterize a therapeutic signature that is able to define the most appropriate treatment. Gene expression levels of the epigenetic regulator histone deacetylase 2 (HDAC2) are deregulated in colorectal cancer, and this deregulation is tightly associated with immune dysfunction. By interrogating bioinformatic databases, we identified patients who presented simultaneous alterations in HDAC2, class II major histocompatibility complex transactivator (CIITA), and beta-2 microglobulin (B2M) genes based on mutation levels, structural variants, and RNA expression levels. We found that B2M plays an important role in these alterations and that mutations in this gene are potentially oncogenic. The dysregulated mRNA expression levels of HDAC2 were reported in about 5% of the profiled patients, while other specific alterations were described for CIITA. By analyzing immune infiltrates, we then identified correlations among these three genes in colorectal cancer patients and differential infiltration levels of genetic variants, suggesting that HDAC2 may have an indirect immune-related role in specific subgroups of immune infiltrates. Using this approach to carry out extensive immunological signature studies could provide further clinical information that is relevant to more resistant forms of colorectal cancer.
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Affiliation(s)
- Mariarosaria Conte
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- Correspondence: ; Tel.: +39-081-5667564
| | - Annabella Di Mauro
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- Pathology Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Lucia Capasso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
| | - Liliana Montella
- ASL NA2 NORD, Oncology Operative Unit, “Santa Maria delle Grazie” Hospital, 80078 Pozzuoli, Italy;
| | - Mariacarla De Simone
- Stem Cell Transplantation Unit, Division of Hematology, Cardarelli Hospital, 80131 Naples, Italy;
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.D.M.); (L.C.); (A.N.); (L.A.)
- BIOGEM, Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy
- IEOS, Institute for Endocrinology and Experimental Oncology, CNRs, 80131 Napoli, Italy
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23
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Mishra D, Mishra A, Nand Rai S, Vamanu E, Singh MP. Demystifying the Role of Prognostic Biomarkers in Breast Cancer through Integrated Transcriptome and Pathway Enrichment Analyses. Diagnostics (Basel) 2023; 13:diagnostics13061142. [PMID: 36980449 PMCID: PMC10046968 DOI: 10.3390/diagnostics13061142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023] Open
Abstract
Breast cancer (BC) is the most commonly diagnosed cancer and the leading cause of death in women. Researchers have discovered an increasing number of molecular targets for BC prognosis and therapy. However, it is still urgent to identify new biomarkers. Therefore, we evaluated biomarkers that may contribute to the diagnosis and treatment of BC. We searched TCGA datasets and identified differentially expressed genes (DEGs) by comparing tumor (100 samples) and non-tumor (100 samples) tissues using the Deseq2 package. Pathway and functional enrichment analysis of the DEGs was performed using the DAVID (Database for Annotation, Visualization, and Integrated Discovery) database. The protein–protein interaction (PPI) network was identified using the STRING database and visualized through Cytoscape software. Hub gene analysis of the PPI network was completed using cytohubba plugins. The associations between the identified genes and overall survival (OS) were analyzed using a Kaplan–Meier plot. Finally, we have identified hub genes at the transcriptome level. A total of 824 DEGs were identified, which were mostly enriched in cell proliferation, signal transduction, and cell division. The PPI network comprised 822 nodes and 12,145 edges. Elevated expression of the five hub genes AURKA, BUB1B, CCNA2, CCNB2, and PBK are related to poor OS in breast cancer patients. A promoter methylation study showed these genes to be hypomethylated. Validation through genetic alteration and missense mutations resulted in chromosomal instability, leading to improper chromosome segregation causing aneuploidy. The enriched functions and pathways included the cell cycle, oocyte meiosis, and the p53 signaling pathway. The identified five hub genes in breast cancer have the potential to become useful targets for the diagnosis and treatment of breast cancer.
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Affiliation(s)
- Divya Mishra
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj 211002, India
| | - Ashish Mishra
- Centre of Bioinformatics, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj 211002, India
| | - Sachchida Nand Rai
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania
| | - Emanuel Vamanu
- Centre of Biotechnology, Institute of Interdisciplinary Studies, University of Allahabad, Prayagraj 211002, India
- Correspondence: (E.V.); (M.P.S.)
| | - Mohan P. Singh
- Faculty of Biotechnology, University of Agricultural Sciences and Veterinary Medicine, 011464 Bucharest, Romania
- Correspondence: (E.V.); (M.P.S.)
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24
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Tanti GK, Pandey P, Shreya S, Jain BP. Striatin family proteins: The neglected scaffolds. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2023; 1870:119430. [PMID: 36638846 DOI: 10.1016/j.bbamcr.2023.119430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 12/19/2022] [Accepted: 12/31/2022] [Indexed: 01/12/2023]
Abstract
The Striatin family of proteins constitutes Striatin, SG2NA, and Zinedin. Members of this family of proteins act as a signaling scaffold due to the presence of multiple protein-protein interaction domains. At least two members of this family, namely Zinedin and SG2NA, have a proven role in cancer cell proliferation. SG2NA, the second member of this family, undergoes alternative splicing and gives rise to several isoforms which are differentially regulated in a tissue-dependent manner. SG2NA evolved earlier than the other two members of the family, and SG2NA undergoes not only alternative splicing but also other posttranscriptional gene regulation. Striatin also undergoes alternative splicing, and as a result, it gives rise to multiple isoforms. It has been shown that this family of proteins plays a significant role in estrogen signaling, neuroprotection, cancer as well as in cell cycle regulation. Members of the striatin family form a complex network of signaling hubs with different kinases and phosphatases, and other signaling proteins named STRIPAK. Here, in the present manuscript, we thoroughly reviewed the findings on striatin family members to elaborate on the overall structural and functional idea of this family of proteins. We also commented on the involvement of these proteins in STRIPAK complexes and their functional relevance.
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Affiliation(s)
- Goutam Kumar Tanti
- Department of Neurology, School of Medicine, Technical University of Munich, Germany.
| | - Prachi Pandey
- National Institute of Plant Genome Research, New Delhi, India
| | - Smriti Shreya
- Department of Zoology, Mahatma Gandhi Central University, Motihari, Bihar, India
| | - Buddhi Prakash Jain
- Department of Zoology, Mahatma Gandhi Central University, Motihari, Bihar, India.
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25
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Soscia R, Della Starza I, De Novi LA, Ilari C, Ansuinelli M, Cavalli M, Bellomarino V, Cafforio L, Di Trani M, Cazzaniga G, Fazio G, Santoro A, Salemi D, Spinelli O, Tosi M, Terragna C, Robustelli V, Bellissimo T, Colafigli G, Breccia M, Chiaretti S, Di Rocco A, Martelli M, Guarini A, Del Giudice I, Foà R. Circulating cell-free DNA for target quantification in hematologic malignancies: Validation of a protocol to overcome pre-analytical biases. Hematol Oncol 2023; 41:50-60. [PMID: 36251440 DOI: 10.1002/hon.3087] [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: 07/11/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 02/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has become the most investigated analyte in blood. It is shed from the tumor into the circulation and represents a subset of the total cell-free DNA (cfDNA) pool released into the peripheral blood. In order to define if ctDNA could represent a useful tool to monitor hematologic malignancies, we analyzed 81 plasma samples from patients affected by different diseases. The results showed that: (i) the comparison between two different extraction methods Qiagen (Hilden, Germany) and Promega (Madison, WI) showed no significant differences in cfDNA yield, though the first recovered higher amounts of larger DNA fragments; (ii) cfDNA concentrations showed a notable inter-patient variability and differed among diseases: acute lymphoblastic leukemia and chronic myeloid leukemia released higher amounts of cfDNA than chronic lymphocytic leukemia, and diffuse large B-cell lymphoma released higher cfDNA quantities than localized and advanced follicular lymphoma; (iii) focusing on the tumor fraction of cfDNA, the quantity of ctDNA released was insufficient for an adequate target quantification for minimal residual disease monitoring; (iv) an amplification system proved to be free of analytical biases and efficient in increasing ctDNA amounts at diagnosis and in follow-up samples as shown by droplet digital PCR target quantification. The protocol has been validated by quality control rounds involving external laboratories. To conclusively document the feasibility of a ctDNA-based monitoring of patients with hematologic malignancies, more post-treatment samples need to be evaluated. This will open new possibilities for ctDNA use in the clinical practice.
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Affiliation(s)
- Roberta Soscia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Irene Della Starza
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,GIMEMA Foundation, Rome, Italy
| | - Lucia Anna De Novi
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Caterina Ilari
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Michela Ansuinelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Marzia Cavalli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Vittorio Bellomarino
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Luciana Cafforio
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Mariangela Di Trani
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Grazia Fazio
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Alessandra Santoro
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Domenico Salemi
- Division of Hematology and Bone Marrow Transplantation, Ospedali Riuniti Villa Sofia-Cervello, Palermo, Italy
| | - Orietta Spinelli
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Manuela Tosi
- Hematology and Bone Marrow Transplant Unit, Ospedale Papa Giovanni XXIII, Bergamo, Italy
| | - Carolina Terragna
- Seràgnoli Institute of Hematology, Azienda Ospedaliero-Universitaria Sant'Orsola-Malpighi, Bologna, Italy
| | - Valentina Robustelli
- Dipartimento di Medicina Specialistica Diagnostica e Sperimentale, Università di Bologna, Bologna, Italy
| | - Teresa Bellissimo
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Gioia Colafigli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Massimo Breccia
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Sabina Chiaretti
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Alice Di Rocco
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Maurizio Martelli
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Anna Guarini
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy.,Department of Molecular Medicine, Sapienza University, Rome, Italy
| | - Ilaria Del Giudice
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
| | - Robin Foà
- Hematology, Department of Translational and Precision Medicine, Sapienza University, Rome, Italy
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A novel prognostic model of methylation-associated genes in acute myeloid leukemia. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:1719-1728. [PMID: 36715873 DOI: 10.1007/s12094-022-03069-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/29/2022] [Indexed: 01/31/2023]
Abstract
BACKGROUND There is growing evidence that methylation-associated genes (MAGs) play an important role in the prognosis of acute myeloid leukemia (AML) patients. Thus, the aim of this research was to investigate the impact of MAGs in predicting the outcomes of AML patients. METHODS The expression profile and clinical information of patients were downloaded from public databases. A novel prognostic model based on 7 MAGs was established in the TCGA training cohort and validated in the GSE71014 dataset. To validate the clinical implications, the correlation between MAGs signature and drug sensitivity was further investigated. RESULTS 76 genes were screened out by the univariate Cox regression and significantly enriched in multiple methylation-related pathways. After filtering variables using LASSO regression analysis, 7 MAGs were introduced to construct the predictive model. The survival analysis showed overall survival of patients with the high-risk score was considerably poorer than that with the low-risk score in both the training and validating cohorts (p < 0.01). Furthermore, the risk score system as a prognostic factor also worked in the intermediate-risk patients based on ELN-2017 classification. Importantly, the risk score was demonstrated to be an independent prognostic factor for AML in the univariate and multivariate Cox regression analysis. Interestingly, GSEA analysis revealed that multiple metabolism-related pathways were significantly enriched in the high-risk group. Drug sensitivity analysis showed there was a significant difference in sensitivity of some drugs between the two groups. CONCLUSION We developed a robust and accurate prognostic model with 7 MAGs. Our findings might provide a reference for the clinical prognosis and management of AML.
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27
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Pilcher W, Thomas BE, Bhasin SS, Jayasinghe RG, Yao L, Gonzalez-Kozlova E, Dasari S, Kim-Schulze S, Rahman A, Patton J, Fiala M, Cheloni G, Kourelis T, Dhodapkar MV, Vij R, Mehr S, Hamilton M, Cho HJ, Auclair D, Avigan DE, Kumar SK, Gnjatic S, Ding L, Bhasin M. Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma. NPJ Genom Med 2023; 8:3. [PMID: 36702834 PMCID: PMC9879959 DOI: 10.1038/s41525-022-00340-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 11/18/2022] [Indexed: 01/27/2023] Open
Abstract
Despite advancements in understanding the pathophysiology of Multiple Myeloma (MM), the cause of rapid progressing disease in a subset of patients is still unclear. MM's progression is facilitated by complex interactions with the surrounding bone marrow (BM) cells, forming a microenvironment that supports tumor growth and drug resistance. Understanding the immune microenvironment is key to identifying factors that promote rapid progression of MM. To accomplish this, we performed a multi-center single-cell RNA sequencing (scRNA-seq) study on 102,207 cells from 48 CD138- BM samples collected at the time of disease diagnosis from 18 patients with either rapid progressing (progression-free survival (PFS) < 18 months) or non-progressing (PFS > 4 years) disease. Comparative analysis of data from three centers demonstrated similar transcriptome profiles and cell type distributions, indicating subtle technical variation in scRNA-seq, opening avenues for an expanded multicenter trial. Rapid progressors depicted significantly higher enrichment of GZMK+ and TIGIT+ exhausted CD8+ T-cells (P = 0.022) along with decreased expression of cytolytic markers (PRF1, GZMB, GNLY). We also observed a significantly higher enrichment of M2 tolerogenic macrophages in rapid progressors and activation of pro-proliferative signaling pathways, such as BAFF, CCL, and IL16. On the other hand, non-progressive patients depicted higher enrichment for immature B Cells (i.e., Pre/Pro B cells), with elevated expression for markers of B cell development (IGLL1, SOX4, DNTT). This multi-center study identifies the enrichment of various pro-tumorigenic cell populations and pathways in those with rapid progressing disease and further validates the robustness of scRNA-seq data generated at different study centers.
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Affiliation(s)
- William Pilcher
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
| | - Beena E Thomas
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Swati S Bhasin
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA
| | - Reyka G Jayasinghe
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Lijun Yao
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Edgar Gonzalez-Kozlova
- Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Surendra Dasari
- Division of Biomedical Statistics & Informatics, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adeeb Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Mark Fiala
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Giulia Cheloni
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | | | - Madhav V Dhodapkar
- Department of Hematology/Medical Oncology Emory University School of Medicine, Atlanta, GA, USA
- Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Ravi Vij
- Washington University School of Medicine, St Louis, MO, USA
| | - Shaadi Mehr
- Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - Mark Hamilton
- Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - Hearn Jay Cho
- Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - Daniel Auclair
- Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - David E Avigan
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Shaji K Kumar
- Mayo Clinic Rochester, Division of Hematology, Rochester, MN, USA
| | - Sacha Gnjatic
- Human Immune Monitoring Center, Icahn School of Medicine at Mt. Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Li Ding
- Department of Medicine, Washington University School of Medicine, Saint Louis, MO, USA
| | - Manoj Bhasin
- Aflac Cancer and Blood Disorders Center, Atlanta, GA, USA.
- Coulter Department of Biomedical Engineering, Emory University, Atlanta, GA, USA.
- Department of Pediatrics, Emory School of Medicine, Atlanta, GA, USA.
- Winship Cancer Institute, Emory University, Atlanta, GA, USA.
- Department of Biomedical Informatics, Emory School of Medicine, Atlanta, GA, USA.
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28
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Li Y, Chen M, Chen Q, Yuan M, Zeng X, Zeng Y, He M, Wang B, Han B. Bioinformatics Identification of Therapeutic Gene Targets for Gastric Cancer. Adv Ther 2023; 40:1456-1473. [PMID: 36694099 DOI: 10.1007/s12325-023-02428-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023]
Abstract
INTRODUCTION The global prevalence of gastric cancer (GC) is increasing, and novel chemotherapeutic targets are needed. METHODS We searched for potential biomarkers for GC in three microarray data sets within the Gene Expression Omnibus (GEO) database. FunRich (v3.1.3) was used to perform Gene Ontology (GO) analyses and STRUN and Cytoscape (v3.6.0) were employed to construct a protein-protein interaction (PPI) network. To explore hub gene expression and survival, we used Gene Expression Profiling Interactive Analysis (GEPIA) and Kaplan-Meier (KM) plotter. Drugs that were closely related to key genes were screened by the Gene Set Cancer Analysis (GSCA), and relevant correlations were verified experimentally. We validated that the sensitivity of a GC cell line to these drugs was correlated with fibrillin 1 (FBN1) mRNA expression levels. RESULTS We identified 83 upregulated and 133 downregulated differentially expressed genes (DEGs) and these were enriched with regards to their cellular component (extracellular and exosomes), molecular function (extracellular matrix structural constituent and catalytic activity), and biological process (cell growth and/or maintenance and metabolism). The biological pathways most prominently involved were epithelial-to-mesenchymal transition (EMT) and β3 integrin cell surface interactions. For the PPI network, we selected 10 hub genes, and 70% of these were significantly connected to poor overall survival (OS) in patients with GC. We found a significant link between the expression of FBN1 and two small molecule drugs (PAC-1 and PHA-793887). CONCLUSIONS Overall, we suggest that these hub genes can be used as biomarkers and novel targets for GC. FBN1 may be associated with drug resistance in gastric cancer.
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Affiliation(s)
- Yuanting Li
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Minghao Chen
- Department of Nuclear Medicine, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Qing Chen
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Min Yuan
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Xi Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Yan Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Meibo He
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Baiqiang Wang
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
| | - Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
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29
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Li S. Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns. Cancer Treat Res 2023; 190:375-393. [PMID: 38113008 DOI: 10.1007/978-3-031-45654-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
Tumor cells evolve through space and time, generating genetically and phenotypically diverse cancer cell populations that are continually subjected to the selection pressures of their microenvironment and cancer treatment.
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Affiliation(s)
- Sheng Li
- The Jackson Laboratory for Genomic Medicine and Cancer Center, Farmington, USA.
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30
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Jin D, Loh KL, Shamekhi T, Ting YT, Lim Kam Sian TCC, Roest J, Ooi JD, Vivian JP, Faridi P. Engineering Cell Lines for Specific Human Leukocyte Antigen Presentation. Methods Mol Biol 2023; 2691:351-369. [PMID: 37355557 DOI: 10.1007/978-1-0716-3331-1_25] [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: 06/26/2023]
Abstract
Epitope-specific immunotherapies have enabled the targeted treatment of a variety of diseases, ranging from cancer, infection, and autoimmune disorders. For CD8+ T cell-based therapies, the precise identification of immunogenic peptides presented by human leukocyte antigen (HLA) class I is essential which can be achieved by immunopeptidomics. Here, using lentivirus-mediated transduction and cell sorting approaches, we present a method to engineer a cell line that does not express its native HLA but instead expresses an HLA of interest (in this instance HLA-A*02:01). This technique can be used to elucidate the immunopeptidome of cell lines expressing different HLAs.
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Affiliation(s)
- Dongbin Jin
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
| | - Khai Lee Loh
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Tima Shamekhi
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
| | - Yi Tian Ting
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Terry C C Lim Kam Sian
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - James Roest
- St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Joshua D Ooi
- Centre for Inflammatory Diseases, Department of Medicine, Monash University, Monash Medical Centre, Clayton, VIC, Australia
| | - Julian P Vivian
- St Vincent's Institute of Medical Research, Fitzroy, VIC, Australia.
- Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia.
| | - Pouya Faridi
- Department of Medicine, School of Clinical Sciences, Monash Univesity, Clayton, VIC, Australia
- Monash Proteomics & Metabolomics Facility, Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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31
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Faltus T. The applicability of the European GMO legislation to epigenetically modified organisms. Front Bioeng Biotechnol 2023; 11:1124131. [PMID: 36923460 PMCID: PMC10009104 DOI: 10.3389/fbioe.2023.1124131] [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: 12/16/2022] [Accepted: 02/16/2023] [Indexed: 03/03/2023] Open
Abstract
In addition to classic genetic engineering for the targeted modification of the base sequence of the DNA, epigenetic methods for the targeted modification of the genetic material without base changes are increasingly being used. Such epigenetic techniques can be used, for example, to influence stress tolerance to heat or aridity in plants. The regulatory handling of organisms generated by means of epigenetic techniques on the grounds of genetic engineering law has not yet been clarified. This paper critically reviews the legal classification of epigenetically modified organisms as GMOs as expressed in the study on New Genomic Techniques published in April 2021 by the European Commission. The paper shows that there are reasons to assume that epigenetically modified organisms are not covered by the European GMO legislation. In addition, the paper provides an introductory overview of the significance of epigenetics and the methods used to intentionally influence epigenetic traits and illustrates the possibility for a consistent, risk-based regulation of epigenetic modifications.
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Affiliation(s)
- Timo Faltus
- Faculty of Law, Economics and Business, Martin-Luther-University Halle-Wittenberg, Halle an der Saale, Germany
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32
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El azzouzi M, El ahanidi H, Hafidi Alaoui C, Chaoui I, Benbacer L, Tetou M, Hassan I, Bensaid M, Oukabli M, Ameur A, Al bouzidi A, El mzibri M, Attaleb M. Exploring urine sediments as a non-invasive method for DNA methylation detection in bladder cancer. AFRICAN JOURNAL OF UROLOGY 2022. [DOI: 10.1186/s12301-022-00298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
The main epigenetic event occurring during the bladder carcinogenesis process is DNA methylation, affecting genes involved in various metabolic pathways and cell regulation. The use of biological fluids such as urine sediments could be used as a non-invasive approach to enhance bladder cancer management. In this study, we aim to determine the promoter methylation status of a panel of genes in bladder cancer on tumor biopsies and urine sediments to evaluate the usefulness of urine samples as a non-invasive approach for methylation status assessment.
Methods
Using the methylation-specific PCR technique, we explored the promoter methylation status of hTERT, TWIST1, VIM and NID2 genes in 40 tumor biopsies and their paired urine samples from Moroccan bladder cancer patients.
Results
In this study, bladder tumors showed promoter hypermethylation frequency of individual genes as 90%, 85%, 62.5% and 72.5% in TWIST1, hTERT, NID2 and VIM genes, respectively.
Interestingly, the specificity of methylation detection in urine samples was 100% and the sensitivity to detect hypermethylation of TWIST1, hTERT, NID2 and VIM genes reached 91.7%; 97.1%; 84% and 82.8%, respectively.
Conclusions
Our results clearly show that the assessment of promoter hypermethylation in urine samples is highly specific and has high sensitivity. Furthermore, urine sediments would be a useful approach to detect the DNA methylation status of genes and its potential association with bladder cancer development.
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33
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Ku SC, Liu HL, Su CY, Yeh IJ, Yen MC, Anuraga G, Ta HDK, Chiao CC, Xuan DTM, Prayugo FB, Wang WJ, Wang CY. Comprehensive analysis of prognostic significance of cadherin (CDH) gene family in breast cancer. Aging (Albany NY) 2022; 14:8498-8567. [PMID: 36315446 PMCID: PMC9648792 DOI: 10.18632/aging.204357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 09/23/2022] [Indexed: 11/07/2022]
Abstract
Breast cancer is one of the leading deaths in all kinds of malignancies; therefore, it is important for early detection. At the primary tumor site, tumor cells could take on mesenchymal properties, termed the epithelial-to-mesenchymal transition (EMT). This process is partly regulated by members of the cadherin (CDH) family of genes, and it is an essential step in the formation of metastases. There has been a lot of study of the roles of some of the CDH family genes in cancer; however, a holistic approach examining the roles of distinct CDH family genes in the development of breast cancer remains largely unexplored. In the present study, we used a bioinformatics approach to examine expression profiles of CDH family genes using the Oncomine, Gene Expression Profiling Interactive Analysis 2 (GEPIA2), cBioPortal, MetaCore, and Tumor IMmune Estimation Resource (TIMER) platforms. We revealed that CDH1/2/4/11/12/13 messenger (m)RNA levels are overexpressed in breast cancer cells compared to normal cells and were correlated with poor prognoses in breast cancer patients’ distant metastasis-free survival. An enrichment analysis showed that high expressions of CDH1/2/4/11/12/13 were significantly correlated with cell adhesion, the extracellular matrix remodeling process, the EMT, WNT/beta-catenin, and interleukin-mediated immune responses. Collectively, CDH1/2/4/11/12/13 are thought to be potential biomarkers for breast cancer progression and metastasis.
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Affiliation(s)
- Su-Chi Ku
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of General Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan
| | - Hsin-Liang Liu
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Che-Yu Su
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - I-Jeng Yeh
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Meng-Chi Yen
- Department of Emergency Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia
| | - Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Chung-Chieh Chiao
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Fidelia Berenice Prayugo
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- International Master/PhD Program in Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Wei-Jan Wang
- Department of Biological Science and Technology, Research Center for Cancer Biology, China Medical University, Taichung 406040, Taiwan
- Research Center for Cancer Biology, China Medical University, Taichung 40676, Taiwan
| | - Chih-Yang Wang
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 11031, Taiwan
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34
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Phosphorylated Proteins from Serum: A Promising Potential Diagnostic Biomarker of Cancer. Int J Mol Sci 2022; 23:ijms232012359. [PMID: 36293212 PMCID: PMC9604268 DOI: 10.3390/ijms232012359] [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: 09/22/2022] [Revised: 10/07/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Cancer is a fatal disease worldwide. Each year ten million people are diagnosed around the world, and more than half of patients eventually die from it in many countries. A majority of cancer remains asymptomatic in the earlier stages, with specific symptoms appearing in the advanced stages when the chances of adequate treatment are low. Cancer screening is generally executed by different imaging techniques like ultrasonography (USG), mammography, CT-scan, and magnetic resonance imaging (MRI). Imaging techniques, however, fail to distinguish between cancerous and non-cancerous cells for early diagnosis. To confirm the imaging result, solid and liquid biopsies are done which have certain limitations such as invasive (in case of solid biopsy) or missed early diagnosis due to extremely low concentrations of circulating tumor DNA (in case of liquid biopsy). Therefore, it is essential to detect certain biomarkers by a noninvasive approach. One approach is a proteomic or glycoproteomic study which mostly identifies proteins and glycoproteins present in tissues and serum. Some of these studies are approved by the Food and Drug Administration (FDA). Another non-expensive and comparatively easier method to detect glycoprotein biomarkers is by ELISA, which uses lectins of diverse specificities. Several of the FDA approved proteins used as cancer biomarkers do not show optimal sensitivities for precise diagnosis of the diseases. In this regard, expression of phosphoproteins is associated with a more specific stage of a particular disease with high sensitivity and specificity. In this review, we discuss the expression of different serum phosphoproteins in various cancers. These phosphoproteins are detected either by phosphoprotein enrichment by immunoprecipitation using phosphospecific antibody and metal oxide affinity chromatography followed by LC-MS/MS or by 2D gel electrophoresis followed by MALDI-ToF/MS analysis. The updated knowledge on phosphorylated proteins in clinical samples from various cancer patients would help to develop these serum phophoproteins as potential diagnostic/prognostic biomarkers of cancer.
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35
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Nam SE, Jin T, Park KS, Saindane M, Noh WC, Yoo YB, Park WS, Yun IJ. Vitamin D receptor ( VDR) mRNA overexpression is associated with poor prognosis in breast carcinoma. Ann Surg Treat Res 2022; 103:183-194. [PMID: 36304189 PMCID: PMC9582618 DOI: 10.4174/astr.2022.103.4.183] [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: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 11/30/2022] Open
Abstract
Purpose The prognostic value of vitamin D receptor gene (VDR) expression in breast cancer development is unclear. Here, we aimed to investigate whether VDR expression can be used as a prognostic indicator of breast cancer. Methods We used various public bioinformatics platforms: Oncomine, GEPIA, UALCAN, Kaplan-Meier plotter, UCSC XENA, bc-GenExMiner, WebGestalt, and STRING database. Results We found that VDR was upregulated in breast cancer in comparison to normal tissues. Overexpression of VDR was significantly associated with worse overall survival in breast cancer. The expression of VDR was related to age, TNM stages, estrogen receptor status, progesterone receptor status, human epidermal growth factor receptor 2 status, basal-like (PAM 50) status, triple-negative breast cancer (TNBC) status, and basal-like (PAM 50) & TNBC status (P < 0.05). Increased VDR expression in breast cancer was significantly associated with older age. The 5 hub genes for VDR were NCOA1, EP300, CREBBP, and RXRA. Conclusion Our investigation offers hints about the prognostic role of VDR in breast cancer. The findings suggest that VDR expression might be used as a marker to determine a breast cancer patient's prognosis. Nevertheless, further validation is warranted.
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Affiliation(s)
- Sang Eun Nam
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.,Department of Surgery, Konkuk University Medical Center, Seoul, Korea
| | - TongYi Jin
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea
| | - Kyoung Sik Park
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.,Department of Surgery, Konkuk University Medical Center, Seoul, Korea
| | - Madhuri Saindane
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea
| | - Woo Chul Noh
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea
| | - Young Bum Yoo
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.,Department of Surgery, Konkuk University Medical Center, Seoul, Korea
| | - Won Seo Park
- Department of Surgery, Kyung Hee University School of Medicine, Seoul, Korea
| | - Ik Jin Yun
- Department of Surgery, Konkuk University School of Medicine, Seoul, Korea.,Research Institute of Medical Science, Konkuk University School of Medicine, Seoul, Korea.,Department of Surgery, Konkuk University Medical Center, Seoul, Korea
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36
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Ahmed YW, Alemu BA, Bekele SA, Gizaw ST, Zerihun MF, Wabalo EK, Teklemariam MD, Mihrete TK, Hanurry EY, Amogne TG, Gebrehiwot AD, Berga TN, Haile EA, Edo DO, Alemu BD. Epigenetic tumor heterogeneity in the era of single-cell profiling with nanopore sequencing. Clin Epigenetics 2022; 14:107. [PMID: 36030244 PMCID: PMC9419648 DOI: 10.1186/s13148-022-01323-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Nanopore sequencing has brought the technology to the next generation in the science of sequencing. This is achieved through research advancing on: pore efficiency, creating mechanisms to control DNA translocation, enhancing signal-to-noise ratio, and expanding to long-read ranges. Heterogeneity regarding epigenetics would be broad as mutations in the epigenome are sensitive to cause new challenges in cancer research. Epigenetic enzymes which catalyze DNA methylation and histone modification are dysregulated in cancer cells and cause numerous heterogeneous clones to evolve. Detection of this heterogeneity in these clones plays an indispensable role in the treatment of various cancer types. With single-cell profiling, the nanopore sequencing technology could provide a simple sequence at long reads and is expected to be used soon at the bedside or doctor's office. Here, we review the advancements of nanopore sequencing and its use in the detection of epigenetic heterogeneity in cancer.
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Affiliation(s)
- Yohannis Wondwosen Ahmed
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia.
| | - Berhan Ababaw Alemu
- Department of Medical Biochemistry, School of Medicine, St. Paul's Hospital, Millennium Medical College, Addis Ababa, Ethiopia
| | - Sisay Addisu Bekele
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Solomon Tebeje Gizaw
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Muluken Fekadie Zerihun
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endriyas Kelta Wabalo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Maria Degef Teklemariam
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tsehayneh Kelemu Mihrete
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Endris Yibru Hanurry
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Tensae Gebru Amogne
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Assaye Desalegne Gebrehiwot
- Department of Medical Anatomy, School of Medicine, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Tamirat Nida Berga
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Ebsitu Abate Haile
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Dessiet Oma Edo
- Department of Medical Biochemistry, School of Medicine, College of Health Sciences, Addis Ababa University, P.O. Box: 9086, Addis Ababa, Ethiopia
| | - Bizuwork Derebew Alemu
- Department of Statistics, College of Natural and Computational Sciences, Mizan Tepi University, Tepi, Ethiopia
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Mosleh-Shirazi S, Abbasi M, Moaddeli MR, Vaez A, Shafiee M, Kasaee SR, Amani AM, Hatam S. Nanotechnology Advances in the Detection and Treatment of Cancer: An Overview. Nanotheranostics 2022; 6:400-423. [PMID: 36051855 PMCID: PMC9428923 DOI: 10.7150/ntno.74613] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 07/25/2022] [Indexed: 12/01/2022] Open
Abstract
Over the last few years, progress has been made across the nanomedicine landscape, in particular, the invention of contemporary nanostructures for cancer diagnosis and overcoming complexities in the clinical treatment of cancerous tissues. Thanks to their small diameter and large surface-to-volume proportions, nanomaterials have special physicochemical properties that empower them to bind, absorb and transport high-efficiency substances, such as small molecular drugs, DNA, proteins, RNAs, and probes. They also have excellent durability, high carrier potential, the ability to integrate both hydrophobic and hydrophilic compounds, and compatibility with various transport routes, making them especially appealing over a wide range of oncology fields. This is also due to their configurable scale, structure, and surface properties. This review paper discusses how nanostructures can function as therapeutic vectors to enhance the therapeutic value of molecules; how nanomaterials can be used as medicinal products in gene therapy, photodynamics, and thermal treatment; and finally, the application of nanomaterials in the form of molecular imaging agents to diagnose and map tumor growth.
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Affiliation(s)
- Sareh Mosleh-Shirazi
- Department of Materials Science and Engineering, Shiraz University of Technology, Shiraz, Iran
| | - Milad Abbasi
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad reza Moaddeli
- Assistant Professor, Department of Oral and Maxillofacial Surgery, School of Dentistry, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Ahmad Vaez
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mostafa Shafiee
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyed Reza Kasaee
- Shiraz Endocrinology and Metabolism Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Mohammad Amani
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeid Hatam
- Assistant Lecturer, Azad University, Zarghan Branch, Shiraz, Iran
- ExirBitanic, Science and Technology Park of Fars, Shiraz, Iran
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Function of the Long Noncoding RNAs in Hepatocellular Carcinoma: Classification, Molecular Mechanisms, and Significant Therapeutic Potentials. Bioengineering (Basel) 2022; 9:bioengineering9080406. [PMID: 36004931 PMCID: PMC9405066 DOI: 10.3390/bioengineering9080406] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/15/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common and serious type of primary liver cancer. HCC patients have a high death rate and poor prognosis due to the lack of clear signs and inadequate treatment interventions. However, the molecular pathways that underpin HCC pathogenesis remain unclear. Long non-coding RNAs (lncRNAs), a new type of RNAs, have been found to play important roles in HCC. LncRNAs have the ability to influence gene expression and protein activity. Dysregulation of lncRNAs has been linked to a growing number of liver disorders, including HCC. As a result, improved understanding of lncRNAs could lead to new insights into HCC etiology, as well as new approaches for the early detection and treatment of HCC. The latest results with respect to the role of lncRNAs in controlling multiple pathways of HCC were summarized in this study. The processes by which lncRNAs influence HCC advancement by interacting with chromatin, RNAs, and proteins at the epigenetic, transcriptional, and post-transcriptional levels were examined. This critical review also highlights recent breakthroughs in lncRNA signaling pathways in HCC progression, shedding light on the potential applications of lncRNAs for HCC diagnosis and therapy.
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Zhang X, Guo Y, Xiao T, Li J, Guo A, Lei L, Jin C, Long Q, Su J, Yin M, Liu H, Chen C, Zhou Z, Zhu S, Tao J, Hu S, Chen X, Peng C. CD147 mediates epidermal malignant transformation through the RSK2/AP-1 pathway. J Exp Clin Cancer Res 2022; 41:246. [PMID: 35964097 PMCID: PMC9375950 DOI: 10.1186/s13046-022-02427-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/01/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Malignant transformation of the epidermis is an essential process in the pathogenesis of cutaneous squamous-cell carcinoma (cSCC). Although evidence has demonstrated that CD147 plays key roles in various tumors, the role of CD147 in epidermal malignant transformation in vivo remains unclear.
Methods
Epidermal CD147-overexpression or knockout (EpiCD147-OE or EpiCD147-KO) transgenic mouse models were generated for in vivo study. RNA-sequencing and q-PCR were performed to identify the differentially expressed genes. Immunohistochemistry and flow cytometry were performed to investigate the role of CD147 in regulating myeloid-derived suppressor cells (MDSCs). Immunoprecipitation, EMSA and ChIP assays were performed to investigate the mechanism of CD147 in cell transformation.
Results
We found that specific overexpression of CD147 in the epidermis (EpiCD147-OE) induces spontaneous tumor formation; moreover, a set of chemokines and cytokines including CXCL1, which play essential function in MDSC recruitment, were significantly upregulated in EpiCD147-OE transgenic mice. As expected, overexpression of CD147 in the epidermis remarkably facilitated tumorigenesis by increasing the rate of tumor initiation and the number and size of tumors in the DMBA/TPA mouse model. Interestingly, the expression of CXCL1 and the infiltration of MDSCs were dramatically increased in EpiCD147-OE transgenic mice. Our findings also showed that knockdown of CD147 attenuated EGF-induced malignant transformation as well as CXCL1 expression in HaCaT cells. Consistently, CD147 was found overexpressed in cutaneous squamous cell carcinoma (cSCC), and positively related with the expression of CD33, a myeloid-associated marker. We further identified RSK2, a serine/threonine kinase, as an interacting partner of CD147 at the binding site of CD147D207-230. The interaction of CD147 and RSK2 activated RSK2, thus enhancing AP-1 transcriptional activation. Furthermore, EMSAs and ChIP assays showed that AP-1 could associate with the CXCL1 promoter. Importantly, RSK2 inhibitor suppressed the tumor growth in DMBA/TPA mouse model by inhibiting the recruitment of MDSCs.
Conclusion
Our findings demonstrate that CD147 exerts a key function in epidermal malignant transformation in vivo by activating keratinocytes and recruiting MDSCs via the RSK2/AP-1 pathway.
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Involvement of Phytochemical-Encapsulated Nanoparticles' Interaction with Cellular Signalling in the Amelioration of Benign and Malignant Brain Tumours. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27113561. [PMID: 35684498 PMCID: PMC9182026 DOI: 10.3390/molecules27113561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/24/2022] [Indexed: 12/05/2022]
Abstract
Brain tumours have unresolved challenges that include delay prognosis and lower patient survival rate. The increased understanding of the molecular pathways underlying cancer progression has aided in developing various anticancer medications. Brain cancer is the most malignant and invasive type of cancer, with several subtypes. According to the WHO, they are classified as ependymal tumours, chordomas, gangliocytomas, medulloblastomas, oligodendroglial tumours, diffuse astrocytomas, and other astrocytic tumours on the basis of their heterogeneity and molecular mechanisms. The present study is based on the most recent research trends, emphasising glioblastoma cells classified as astrocytoma. Brain cancer treatment is hindered by the failure of drugs to cross the blood–brain barrier (BBB), which is highly impregnableto foreign molecule entry. Moreover, currently available medications frequently fail to cross the BBB, whereas chemotherapy and radiotherapy are too expensive to be afforded by an average incomeperson and have many associated side effects. When compared to our current understanding of molecularly targeted chemotherapeutic agents, it appears that investigating the efficacy of specific phytochemicals in cancer treatment may be beneficial. Plants and their derivatives are game changers because they are efficacious, affordable, environmentally friendly, faster, and less toxic for the treatment of benign and malignant tumours. Over the past few years, nanotechnology has made a steady progress in diagnosing and treating cancers, particularly brain tumours. This article discusses the effects of phytochemicals encapsulated in nanoparticles on molecular targets in brain tumours, along with their limitations and potential challenges.
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Tang X, Chen F, Xie LC, Liu SX, Mai HR. Targeting metabolism: A potential strategy for hematological cancer therapy. World J Clin Cases 2022; 10:2990-3004. [PMID: 35647127 PMCID: PMC9082716 DOI: 10.12998/wjcc.v10.i10.2990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 11/01/2021] [Accepted: 02/27/2022] [Indexed: 02/06/2023] Open
Abstract
Most hematological cancer-related relapses and deaths are caused by metastasis; thus, the importance of this process as a target of therapy should be considered. Hematological cancer is a type of cancer in which metabolism plays an essential role in progression. Therefore, we are required to block fundamental metastatic processes and develop specific preclinical and clinical strategies against those biomarkers involved in the metabolic regulation of hematological cancer cells, which do not rely on primary tumor responses. To understand progress in this field, we provide a summary of recent developments in the understanding of metabolism in hematological cancer and a general understanding of biomarkers currently used and under investigation for clinical and preclinical applications involving drug development. The signaling pathways involved in cancer cell metabolism are highlighted and shed light on how we could identify novel biomarkers involved in cancer development and treatment. This review provides new insights into biomolecular carriers that could be targeted as anticancer biomarkers.
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Affiliation(s)
- Xue Tang
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Fen Chen
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Li-Chun Xie
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Si-Xi Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
| | - Hui-Rong Mai
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong Province, China
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Prediction of Metabolic Profiles from Transcriptomics Data in Human Cancer Cell Lines. Int J Mol Sci 2022; 23:ijms23073867. [PMID: 35409231 PMCID: PMC8998886 DOI: 10.3390/ijms23073867] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/24/2022] [Accepted: 03/29/2022] [Indexed: 02/01/2023] Open
Abstract
The Metabolome and Transcriptome are mutually communicating within cancer cells, and this interplay is translated into the existence of quantifiable correlation structures between gene expression and metabolite abundance levels. Studying these correlations could provide a novel venue of understanding cancer and the discovery of novel biomarkers and pharmacological strategies, as well as laying the foundation for the prediction of metabolite quantities by leveraging information from the more widespread transcriptomics data. In the current paper, we investigate the correlation between gene expression and metabolite levels in the Cancer Cell Line Encyclopedia dataset, building a direct correlation network between the two molecular ensembles. We show that a metabolite/transcript correlation network can be used to predict metabolite levels in different samples and datasets, such as the NCI-60 cancer cell line dataset, both on a sample-by-sample basis and in differential contrasts. We also show that metabolite levels can be predicted in principle on any sample and dataset for which transcriptomics data are available, such as the Cancer Genome Atlas (TCGA).
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Zambonin C, Aresta A. MALDI-TOF/MS Analysis of Non-Invasive Human Urine and Saliva Samples for the Identification of New Cancer Biomarkers. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27061925. [PMID: 35335287 PMCID: PMC8951187 DOI: 10.3390/molecules27061925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/06/2022] [Accepted: 03/14/2022] [Indexed: 01/22/2023]
Abstract
Cancer represents a group of heterogeneous diseases that are a leading global cause of death. Even though mortality has decreased in the past thirty years for different reasons, most patients are still diagnosed at the advanced stage, with limited therapeutic choices and poor outcomes. Moreover, the majority of cancers are detected using invasive painful methods, such as endoscopic biopsy, making the development of non-invasive or minimally invasive methods for the discovery and fast detection of specific biomarkers a crucial need. Among body fluids, a valuable non-invasive alternative to tissue biopsy, the most accessible and least invasive are undoubtedly urine and saliva. They are easily retrievable complex fluids containing a large variety of endogenous compounds that may provide information on the physiological condition of the body. The combined analysis of these fluids with matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI-TOF/MS), a reliable and easy-to-use instrumentation that provides information with relatively simple sample pretreatments, could represent the ideal option to rapidly achieve fast early stage diagnosis of tumors and their real-time monitoring. On this basis, the present review summarizes the recently reported applications relevant to the MALDI analysis of human urine and saliva samples.
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Dvoriantchikova G, Lypka KR, Ivanov D. The Potential Role of Epigenetic Mechanisms in the Development of Retinitis Pigmentosa and Related Photoreceptor Dystrophies. Front Genet 2022; 13:827274. [PMID: 35360866 PMCID: PMC8961674 DOI: 10.3389/fgene.2022.827274] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa and related photoreceptor dystrophies (RPRPD) are rare retinal diseases caused by hereditary gene mutations resulting in photoreceptor death, followed by vision loss. While numerous genes involved in these diseases have been identified, many cases have still not been associated with any gene, indicating that new mechanisms may be involved in the pathogenesis of these photoreceptor dystrophies. Many genes associated with RPRPD regulate photoreceptor specification and maturation in the developing retina. Since retinal development begins with a population of equivalent, proliferating retinal progenitor cells (RPCs) having a specific “competence” in generating all types of retinal neurons, including cone and rod photoreceptors, we tested the epigenetic changes in promoters of genes required for photoreceptor development and genes associated with RPRPD during RPC differentiation into cone and rod photoreceptors. We found that promoters of many of these genes are epigenetically repressed in RPCs but have no epigenetic restrictions in photoreceptors. Our findings also suggest that DNA methylation as an epigenetic mark, and DNA demethylation as a process, are more important than other epigenetic marks or mechanisms in the pathogenesis of these diseases. Most notably, irregularities in the DNA demethylation process during the RPC-to-photoreceptor transition may significantly contribute to retinitis pigmentosa (RP) pathogenesis since genes with hypermethylated promoters in RPCs account for at least 40% of autosomal recessive RP cases and at least 30% of autosomal dominant RP cases. Thus, we proposed an epigenetic model according to which unsuccessful demethylation of regulatory sequences (e.g., promoters, enhancers) of genes required for photoreceptor development, maturation, and function during the RPC-to-photoreceptor transition may reduce or even eliminate their activity, leading to RPRPD without any inheritable mutations in these genes.
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Affiliation(s)
- Galina Dvoriantchikova
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Karin Rose Lypka
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Dmitry Ivanov
- Department of Ophthalmology, Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- *Correspondence: Dmitry Ivanov,
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El-shaarawy F, Abo ElAzm MM, Mohamed RH, Radwan MI, Abo-Elmatty DM, Mehanna ET. Relation of the methylation state of RUNX3 and p16 gene promoters with hepatocellular carcinoma in Egyptian patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00256-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Hepatocellular carcinoma (HCC) is the most common primary hepatic malignancy of adults. RUNX3 and p16 are tumor suppressor genes that may be inactivated by hypermethylation which is a key epigenetic mechanism that contributes to the initiation and progression of various types of human carcinomas including HCC. The aim of this study was to assess the association of hypermethylation of RUNX3 and p16 gene promoters with the incidence of HCC in Egyptian patients. The study included 120 subjects: 30 HCC patients, 30 patients with hepatitis C virus (HCV) without cirrhosis, 30 cirrhotic patients, and 30 healthy volunteers. Methylation-specific polymerase chain reaction (PCR) was done for detection of hypermethylated p16 and RUNX3. Serum levels of liver enzymes and albumin were detected spectrophotometrically and alpha fetoprotein (AFP) was measured in serum by ELISA.
Results
Methylation of RUNX3 and p16 was detected in 25/30 (83.3%) and 26/30 (86.7%) of HCC patients, respectively. The methylation state of both RUNX3 and p16 genes was significantly higher in HCC patients compared to the control subjects (P = 0.016, OR = 4.38) and (P = 0.014, OR = 4.97), respectively. The methylation of both promoters was associated with higher AFP levels in the serum of all patients.
Conclusions
Hypermethylation of RUNX3 and p16 is significantly associated with the development of HCC and may be implicated in its pathogenesis.
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Song Y, Xu X, Wang N, Zhang T, Hu C. MALDI-TOF-MS analysis in low molecular weight serum peptidome biomarkers for NSCLC. J Clin Lab Anal 2022; 36:e24254. [PMID: 35212031 PMCID: PMC8993654 DOI: 10.1002/jcla.24254] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
Objects Lung cancer is one of the leading causes of death from cancer in the world. Screening new serum biomarkers is important for the early detection of lung cancer. The purpose of this study was to investigate the serum peptide model between non‐small cell lung cancer (NSCLC) patients and healthy controls, as well as between paired pre‐ and postoperative NSCLC patients, and to find the low molecular weight (LMW) potential tumor markers for NSCLC. Methods 56 serum samples from NSCLC patients, 56 controls, and 20 matched pre‐ and postoperative patients were analyzed using magnetic‐bead (MB)‐based purification technique combined with MALDI‐TOF‐MS. To distinguish NSCLC from cancer‐free controls, three models were established. Finally, comparing the three groups of serum protein fingerprints, nano‐liquid chromatography–electrospray ionization tandem mass spectrometry was used to further identify the differential peptides. Results Among the three models constructed, the GA model had the best diagnostic efficacy. Five differential peaks were screened by combining the case group, healthy controls, and postoperative group analysis, which were up‐regulated in the case group and showed a tendency to return to healthy control values after surgery. The protein matching the mass spectrometry peak m/z 2953.73 was identified as fibrinogen α chain. Conclusion This study shows that the application of MALDI‐TOF‐MS is a promising approach for the identification of potential serum biomarkers for NSCLC, which is potentially valuable for establishing a new diagnostic method for lung cancer. In addition, we found that fibrinogen α chain may be an auxiliary diagnostic indicator for NSCLC.
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Affiliation(s)
- Yufan Song
- Departments of Laboratory Medicine, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, China
| | - Xiaoyu Xu
- Departments of Laboratory Medicine, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, China
| | - Nana Wang
- Departments of Laboratory Medicine, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, China
| | - Ting Zhang
- Departments of Laboratory Medicine, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, China
| | - Chengjin Hu
- Departments of Laboratory Medicine, The 960th Hospital of the PLA Joint Logistics Support Force, Jinan, China
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Azzouz A, Hejji L, Kim KH, Kukkar D, Souhail B, Bhardwaj N, Brown RJC, Zhang W. Advances in surface plasmon resonance-based biosensor technologies for cancer biomarker detection. Biosens Bioelectron 2022; 197:113767. [PMID: 34768064 DOI: 10.1016/j.bios.2021.113767] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 01/25/2023]
Abstract
Surface plasmon resonance approach is a highly useful option to offer optical and label-free detection of target bioanalytes with numerous advantages (e.g., low-cost fabrication, appreciable sensitivity, label-free detection, and outstanding accuracy). As such, it allows early diagnosis of cancer biomarkers to monitor tumor progression and to prevent the recurrence of oncogenic tumors. This work highlights the recent progress in SPR biosensing technology for the diagnosis of various cancer types (e.g., lung, breast, prostate, and ovarian). Further, the performance of various SPR biosensors is also evaluated in terms of the basic quality assurance criteria (e.g., limit of detection (LOD), selectivity, sensor response time, and reusability). Finally, the limitations and future challenges associated with SPR biosensors are also discussed with respect to cancer biomarker detection.
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Affiliation(s)
- Abdelmonaim Azzouz
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Lamia Hejji
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul, 04763, South Korea.
| | - Deepak Kukkar
- Department of Nanotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, 140406, Punjab, India
| | - Badredine Souhail
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M'Hannech II, 93002, Tétouan, Morocco
| | - Neha Bhardwaj
- Department of Biotechnology, University Institute of Engineering Technology (UIET), Panjab University, Chandigarh, India
| | - Richard J C Brown
- Environment Department, National Physical Laboratory, Teddington, TW11 0LW, UK
| | - Wei Zhang
- School of Ecology and Environmental Science, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan, 450001, PR China
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Novel prognostic value and potential utility of opioid receptor gene methylation in liquid biopsy for oral cavity cancer. Curr Probl Cancer 2022; 46:100834. [DOI: 10.1016/j.currproblcancer.2021.100834] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/18/2021] [Accepted: 12/22/2021] [Indexed: 11/15/2022]
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Ta HDK, Minh Xuan DT, Tang WC, Anuraga G, Ni YC, Pan SR, Wu YF, Fitriani F, Putri Hermanto EM, Athoillah M, Andriani V, Ajiningrum PS, Wang CY, Lee KH. Novel Insights into the Prognosis and Immunological Value of the SLC35A (Solute Carrier 35A) Family Genes in Human Breast Cancer. Biomedicines 2021; 9:1804. [PMID: 34944621 PMCID: PMC8698499 DOI: 10.3390/biomedicines9121804] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/17/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
According to statistics 2020, female breast cancer (BRCA) became the most commonly diagnosed malignancy worldwide. Prognosis of BRCA patients is still poor, especially in population with advanced or metastatic. Particular functions of each members of the solute carrier 35A (SLC35A) gene family in human BRCA are still unknown regardless of awareness that they play critical roles in tumorigenesis and progression. Using integrated bioinformatics analyses to identify therapeutic targets for specific cancers based on transcriptomics, proteomics, and high-throughput sequencing, we obtained new information and a better understanding of potential underlying molecular mechanisms. Leveraging BRCA dataset that belongs to The Cancer Genome Atlas (TCGA), which were employed to clarify SLC35A gene expression levels. Then we used a bioinformatics approach to investigate biological processes connected to SLC35A family genes in BRCA development. Beside that, the Kaplan-Meier estimator was leveraged to explore predictive values of SLC35A family genes in BCRA patients. Among individuals of this family gene, expression levels of SLC35A2 were substantially related to poor prognostic values, result from a hazard ratio of 1.3 (with 95 percent confidence interval (95% CI: 1.18-1.44), the p for trend (ptrend) is 3.1 × 10-7). Furthermore, a functional enrichment analysis showed that SLC35A2 was correlated with hypoxia-inducible factor 1A (HIF1A), heat shock protein (HSP), E2 transcription factor (E2F), DNA damage, and cell cycle-related signaling. Infiltration levels observed in specific types of immune cell, especially the cluster of differentiation found on macrophages and neutrophils, were positively linked with SLC35A2 expression in multiple BRCA subclasses (luminal A, luminal B, basal, and human epidermal growth factor receptor 2). Collectively, SLC35A2 expression was associated with a lower recurrence-free survival rate, suggesting that it could be used as a biomarker in treating BRCA.
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Affiliation(s)
- Hoang Dang Khoa Ta
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Do Thi Minh Xuan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Wan-Chun Tang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan;
| | - Gangga Anuraga
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Yi-Chun Ni
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Syu-Ruei Pan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Yung-Fu Wu
- National Defense Medical Center, School of Medicine, Department of Medical Research, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Fenny Fitriani
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Elvira Mustikawati Putri Hermanto
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Muhammad Athoillah
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (F.F.); (E.M.P.H.); (M.A.)
| | - Vivin Andriani
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Purity Sabila Ajiningrum
- Department of Biological Science, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, Indonesia; (V.A.); (P.S.A.)
| | - Chih-Yang Wang
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
| | - Kuen-Haur Lee
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Academia Sinica, Taipei 11031, Taiwan; (H.D.K.T.); (G.A.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (D.T.M.X.); (Y.-C.N.); (S.-R.P.)
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei 11031, Taiwan
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Natu A, Singh A, Gupta S. Hepatocellular carcinoma: Understanding molecular mechanisms for defining potential clinical modalities. World J Hepatol 2021; 13:1568-1583. [PMID: 34904030 PMCID: PMC8637668 DOI: 10.4254/wjh.v13.i11.1568] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 05/12/2021] [Accepted: 09/08/2021] [Indexed: 02/06/2023] Open
Abstract
Liver cancer is the sixth most commonly occurring cancer and costs millions of lives per year. The diagnosis of hepatocellular carcinoma (HCC) has relied on scanning techniques and serum-based markers such as α-fetoprotein. These measures have limitations due to their detection limits and asymptomatic conditions during the early stages, resulting in late-stage cancer diagnosis where targeted chemotherapy or systemic treatment with sorafenib is offered. However, the aid of conventional therapy for patients in the advanced stage of HCC has limited outcomes. Thus, it is essential to seek a new treatment strategy and improve the diagnostic techniques to manage the disease. Researchers have used the omics profile of HCC patients for sub-classification of tissues into different groups, which has helped us with prognosis. Despite these efforts, a promising target for treatment has not been identified. The hurdle in this situation is genetic and epigenetic variations in the tumor, leading to disparities in response to treatment. Understanding reversible epigenetic changes along with clinical traits help to define new markers for patient categorization and design personalized therapy. Many clinical trials of inhibitors of epigenetic modifiers (also known as epi-drugs) are in progress. Epi-drugs like azacytidine or belinostat are already approved for other cancer treatments. Furthermore, epigenetic changes have also been observed in drug-resistant HCC tumors. In such cases, combinatorial treatment of epi-drugs with systemic therapy or trans-arterial chemoembolization might re-sensitize resistant cells.
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Affiliation(s)
- Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
| | - Anjali Singh
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai 410210, Maharashtra, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400085, Maharashtra, India
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