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Khasawneh AI, Himsawi N, Sammour A, Al Shboul S, Alorjani M, Al-Momani H, Shahin U, Al-Momani H, Alotaibi MR, Saleh T. Association of Human Papilloma Virus, Cytomegalovirus, and Epstein-Barr Virus with Breast Cancer in Jordanian Women. MEDICINA (KAUNAS, LITHUANIA) 2024; 60:699. [PMID: 38792882 PMCID: PMC11122978 DOI: 10.3390/medicina60050699] [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: 03/22/2024] [Revised: 04/09/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
Background and Objectives: The investigation of oncogenic viruses and their potential association with breast cancer (BC) remains an intriguing area of study. The current work aims to assess evidence of three specific viruses, human papillomavirus (HPV), cytomegalovirus (CMV), and Epstein-Barr virus (EBV) in BC samples and to explore their relationship with relevant clinicopathological variables. Materials and Methods: The analysis involved BC samples from 110 Jordanian female patients diagnosed with BC and breast tissue samples from 30 control patients with no evidence of breast malignancy, investigated using real-time PCR. The findings were then correlated with various clinico-pathological characteristics of BC. Results: HPV was detected in 27 (24.5%), CMV in 15 (13.6%), and EBV in 18 (16.4%) BC patients. None of the control samples was positive for HPV or CMV while EBV was detected in only one (3.3%) sample. While (HPV/EBV), (HPV/CMV), and (EBV/CMV) co-infections were reported in 1.8%, 2.7%, and 5.5%, respectively, coinfection with the three viruses (HPV/CMV/EBV) was not reported in our cohort. A statistically significant association was observed between HPV status and age (p = 0.047), and between clinical stage and CMV infection (p = 0.015). Conclusions: Our findings indicate the presence or co-presence of HPV, CMV, and EBV in the BC subpopulation, suggesting a potential role in its development and/or progression. Further investigation is required to elucidate the underlying mechanisms that account for the exact role of oncoviruses in breast carcinogenesis.
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Affiliation(s)
- Ashraf I. Khasawneh
- Department of Microbiology, Pathology, and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan (H.A.-M.)
| | - Nisreen Himsawi
- Department of Microbiology, Pathology, and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan (H.A.-M.)
| | - Ashraf Sammour
- Department of Anatomy, Physiology & Biochemistry, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Sofian Al Shboul
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Mohammed Alorjani
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Hadeel Al-Momani
- Department of Pathology and Microbiology, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Uruk Shahin
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
| | - Hafez Al-Momani
- Department of Microbiology, Pathology, and Forensic Medicine, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan (H.A.-M.)
| | - Moureq R. Alotaibi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia
| | - Tareq Saleh
- Department of Pharmacology and Public Health, Faculty of Medicine, The Hashemite University, Zarqa 13133, Jordan
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Fernandes Q, Inchakalody VP, Bedhiafi T, Mestiri S, Taib N, Uddin S, Merhi M, Dermime S. Chronic inflammation and cancer; the two sides of a coin. Life Sci 2024; 338:122390. [PMID: 38160787 DOI: 10.1016/j.lfs.2023.122390] [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: 10/22/2023] [Revised: 12/21/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
The correlation between chronic inflammation and cancer was initially identified in the 19th century. Biomolecules like interleukins, chemokines, tumor necrosis factors, growth factors, and adhesion molecules, which regulate inflammation, are recognized contributors to neoplastic transformation through various mechanisms, including oncogenic mutations, resistance to apoptosis, and adaptive responses like angiogenesis. This review aims to establish connections between the intricate and complex mechanisms of chronic inflammation and cancer. We illuminate implicit signaling mechanisms that drive the association between chronic inflammation and the initiation/progression of cancer, exploring potential impacts on other diseases. Additionally, we discuss the modalities of currently available therapeutic options for chronic inflammation and cancer, emphasizing the dual nature of such therapies. A thorough understanding of the molecular basis of chronic inflammation is crucial for developing novel approaches in the prevention and treatment of cancer.
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Affiliation(s)
- Queenie Fernandes
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Medicine, Qatar University, Doha, Qatar
| | - Varghese Philipose Inchakalody
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Takwa Bedhiafi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Sarra Mestiri
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Nassiba Taib
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Shahab Uddin
- Translational Research Institute and Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar; Laboratory Animal Research Center, Qatar University, Doha, Qatar
| | - Maysaloun Merhi
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar.
| | - Said Dermime
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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Jafari Maskouni E, Jamalvandi T, Tabatabaei F, Bourenjan Shirazi S, Saadati H, Letafati A, Hosseini M, Motlaghzadeh S, Khalesi Z, Moradi P, Saeb S, Sheikh N, Fozouni E, Khatami A, Baker AH, Keyvanlou Z, Tamrchi V, Tavakoli A, Ghorbani S. Association between Epstein-Bar virus and colorectal cancer: A systematic review and meta-analysis. Microb Pathog 2023; 179:106087. [PMID: 37003501 DOI: 10.1016/j.micpath.2023.106087] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]
Abstract
AIM This study aimed to investigate the prevalence and any potential association between Epstein-Barr virus (EBV) infection and colorectal cancer (CRC). METHODS A systematic literature search was performed by finding relevant cross-sectional and case-control studies from main online databases. Heterogeneity, odds ratio (OR), and corresponding 95% confidence interval (CI) were applied to all studies through meta-analysis and forest plots. The analysis was performed using STATA Software v.14.1. RESULTS Twenty-three articles were included in the meta-analysis, eight of them were case/control and 15 were cross-sectional. The pooled prevalence of EBV among 1954 CRC patients was 18% (95% CI: 12%-26%; I2 = 93.14%). Furthermore, in geographical regions, the highest and lowest prevalence of EBV was observed in South America 30% (95% CI: 18%-43%) and Africa 0% (95% CI: 0%-5%), respectively. An association was found between EBV infection and CRC [OR = 3.4 (95% CI (1.13-10.27); I2 = 72.3%)]. CONCLUSION EBV infection is associated with CRC and can be considered a potential risk factor for the development of CRC. Although the exact molecular mechanism of EBV infection in the development of CRC is still unknown, it seems that latent infection by EBV, intestinal damage, and inflammation can be important factors in the induction of CRC.
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Affiliation(s)
- Elham Jafari Maskouni
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Tasnim Jamalvandi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farbod Tabatabaei
- Faculty of Converting Sciences and Technologies, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Sepideh Bourenjan Shirazi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Hasan Saadati
- Department of Epidemiology and Biostatistics, School of Health, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Arash Letafati
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdiyeh Hosseini
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeed Motlaghzadeh
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zohreh Khalesi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Pouya Moradi
- Department of Virology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Sepideh Saeb
- Department of Virology, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Najmeh Sheikh
- Department of Virology, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Elaheh Fozouni
- Department of Microbiology and Virology, School of Medicine, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Khatami
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Zahra Keyvanlou
- Department of Virology, Faculty of Medical Science, Tarbiat Modares University, Tehran, Iran
| | - Vahid Tamrchi
- Department of Microbiology of Golestan University of Medical Sciences, Golesatn, Iran
| | - Ahmad Tavakoli
- Research Center of Pediatric Infectious Diseases, Institute of Immunology and Infectious Diseases, Iran University of Medical Sciences, Tehran, Iran.
| | - Saied Ghorbani
- Department of Virology, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.
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Fernandes Q, Gupta I, Murshed K, Abo Samra H, Al-Thawadi H, Vranic S, Petkar M, Babu GR, Al Moustafa AE. Coinfection of HPVs Is Associated with Advanced Stage in Colorectal Cancer Patients from Qatar. Pathogens 2023; 12:pathogens12030424. [PMID: 36986346 PMCID: PMC10053117 DOI: 10.3390/pathogens12030424] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/11/2023] Open
Abstract
High-risk human papillomaviruses (HPVs) are considered risk factors in the origin of several human malignancies, such as breast, cervical, head and neck, as well as colorectal cancers. However, there are no data reported on the HPV status in colorectal cancer in the State of Qatar. Therefore, we herein examined the presence of high-risk HPVs (16, 18, 31, 33, 35, 45, 51, 52, and 59), using polymerase chain reaction (PCR) in a cohort of 100 Qatari colorectal cancer patients, and their association with tumor phenotype. We found that high-risk HPV types 16, 18, 31, 35, 45, 51, 52, and 59 were present in 4, 36, 14, 5, 14, 6, 41, and 17% of our samples, respectively. Overall, 69 (69%) of the 100 samples were HPV positive; among these, 34/100 (34%) were positive for single HPV subtypes, while 35/100 (35%) of the samples were positive for two or more HPV subtypes. No significant association was noted between the presence of HPV and tumor grade, stage, or location. However, the presence of coinfection of HPV subtypes strongly correlated with advanced stage (stage 3 and 4) colorectal cancer, indicating that the copresence of more than one HPV subtype can significantly worsen the prognosis of colorectal cancer. The results from this study imply that coinfection with high-risk HPV subtypes is associated with the development of colorectal cancer in the Qatari population.
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Affiliation(s)
- Queenie Fernandes
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
- Translational Cancer Research Facility, National Center for Cancer Care and Research, Translational Research Institute, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Ishita Gupta
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
| | - Khaled Murshed
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Hayan Abo Samra
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | - Hamda Al-Thawadi
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
| | - Mahir Petkar
- Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, Doha P.O. Box 3050, Qatar
| | | | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
- Biomedical Research Center, QU Health, Qatar University, Doha P.O. Box 2713, Qatar
- Oncology Department, McGill University, Montreal, QC H3A 0G4, Canada
- Correspondence: ; Tel.: +974-4403-7817
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Shen D, Hong Y, Feng Z, Chen X, Cai Y, Peng Q, Tu J. Development of dynamical network biomarkers for regulation in Epstein-Barr virus positive peripheral T cell lymphoma unspecified type. Front Genet 2022; 13:966247. [PMID: 36544484 PMCID: PMC9760704 DOI: 10.3389/fgene.2022.966247] [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: 06/10/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: This study was performed to identify key regulatory network biomarkers including transcription factors (TFs), miRNAs and lncRNAs that may affect the oncogenesis of EBV positive PTCL-U. Methods: GSE34143 dataset was downloaded and analyzed to identify differentially expressed genes (DEGs) between EBV positive PTCL-U and normal samples. Gene ontology and pathway enrichment analyses were performed to illustrate the potential function of the DEGs. Then, key regulators including TFs, miRNAs and lncRNAs involved in EBV positive PTCL-U were identified by constructing TF-mRNA, lncRNA-miRNA-mRNA, and EBV encoded miRNA-mRNA regulatory networks. Results: A total of 96 DEGs were identified between EBV positive PTCL-U and normal tissues, which were related to immune responses, B cell receptor signaling pathway, chemokine activity. Pathway analysis indicated that the DEGs were mainly enriched in cytokine-cytokine receptor interaction and chemokine signaling pathway. Based on the TF network, hub TFs were identified regulate the target DEGs. Afterwards, a ceRNA network was constructed, in which miR-181(a/b/c/d) and lncRNA LINC01744 were found. According to the EBV-related miRNA regulatory network, CXCL10 and CXCL11 were found to be regulated by EBV-miR-BART1-3p and EBV-miR-BHRF1-3, respectively. By integrating the three networks, some key regulators were found and may serve as potential network biomarkers in the regulation of EBV positive PTCL-U. Conclusion: The network-based approach of the present study identified potential biomarkers including transcription factors, miRNAs, lncRNAs and EBV-related miRNAs involved in EBV positive PTCL-U, assisting us in understanding the molecular mechanisms that underlie the carcinogenesis and progression of EBV positive PTCL-U.
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Affiliation(s)
- Dan Shen
- Department of Oncology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yin Hong
- Department of Cardiothoracic Surgery, Suzhou BenQ Hospital, Suzhou, China
| | - Zhengyang Feng
- Department of Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangying Chen
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuxing Cai
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Qiliang Peng
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
| | - Jian Tu
- Department of Pathology, The Second Affiliated Hospital of Soochow University, Suzhou, China,*Correspondence: Jian Tu, ; Qiliang Peng,
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Wang Z, Guo K, Liu Y, Huang C, Wu M. Dynamic impact of virome on colitis and colorectal cancer: Immunity, inflammation, prevention and treatment. Semin Cancer Biol 2022; 86:943-954. [PMID: 34656791 PMCID: PMC9008076 DOI: 10.1016/j.semcancer.2021.10.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 09/20/2021] [Accepted: 10/08/2021] [Indexed: 02/05/2023]
Abstract
The gut microbiome includes a series of microorganism genomes, such as bacteriome, virome, mycobiome, etc. The gut microbiota is critically involved in intestine immunity and diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC); however, the underlying mechanism remains incompletely understood. Clarifying the relationship between microbiota and inflammation may profoundly improve our understanding of etiology, disease progression, patient management, and the development of prevention and treatment. In this review, we discuss the latest studies of the influence of enteric viruses (i.e., commensal viruses, pathogenic viruses, and bacteriophages) in the initiation, progression, and complication of colitis and colorectal cancer, and their potential for novel preventative approaches and therapeutic application. We explore the interplay between gut viruses and host immune systems for its effects on the severity of inflammatory diseases and cancer, including both direct and indirect interactions between enteric viruses with other microbes and microbial products. Furthermore, the underlying mechanisms of the virome's roles in gut inflammatory response have been explained to infer potential therapeutic targets with examples in specific clinical trials. Given that very limited literature has thus far discussed these various topics with the gut virome, we believe these extensive analyses may provide insight into the understanding of the molecular pathogenesis of IBD and CRC, which could help add the design of improved therapies for these important human diseases.
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Affiliation(s)
- Zhihan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Kai Guo
- Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yingying Liu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China.
| | - Min Wu
- Department of Biomedical Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND, 58202, USA.
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7
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PCR Detection of Epstein-Barr Virus (EBV) DNA in Patients with Head and Neck Squamous Cell Carcinoma, in Patients with Chronic Tonsillitis, and in Healthy Individuals. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8506242. [PMID: 35993047 PMCID: PMC9381848 DOI: 10.1155/2022/8506242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
Epstein-Barr virus (EBV) is a common virus worldwide that is an etiologic agent in the development of many diseases, including cancer. Recent reports have shown the association of EBV with tumorigenesis in head and neck squamous cell carcinoma (HNSCC). Moreover, EBV has been reported to be present in tonsillar tissues, which suggests a close relationship between viral infections and tonsillar diseases, including chronic tonsillitis. The aim of the study was to analyze the prevalence of EBV DNA in 86 patients with HNSCC, in 70 patients with chronic tonsillitis, and in 144 healthy individuals (control group) and the associations between EBV infection and clinicopathological and demographic characteristics and the use of stimulants in all study groups. The objective of this study was also to analyze the prevalence of coinfection with human papillomavirus (HPV). After prior DNA isolation, EBV detection was performed using an EBV kit by real-time polymerase chain reaction. The prevalence of EBV infection in patients with HNSCC, patients with chronic tonsillitis, and the control group was 47.7%, 60%, and 24.3%, respectively. Compared to controls, a significantly higher prevalence of EBV in patients with chronic tonsillitis and HNSCC may suggest that EBV is a potential risk factor. No association was found between EBV infection and demographic or clinical data. Further studies are warranted due to inconclusive reports that were mainly related to geographic distribution, sample type, and detection technique. Considering the prevalence of the virus and the risk of serious diseases, attention should be paid to screening diagnosis and prevention of the infection.
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Cordeiro Silva AT, Santos N, Bezerra Tocantins P, Bernardes Leão-Cordeiro J, Ataides F, Rosa Marques LO. The human papillomavirus in colorectal cancer. JOURNAL OF MEDICAL SCIENCES 2022. [DOI: 10.4103/jmedsci.jmedsci_194_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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9
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Bourdakou MM, Spyrou GM, Kolios G. Colon Cancer Progression Is Reflected to Monotonic Differentiation in Gene Expression and Pathway Deregulation Facilitating Stage-specific Drug Repurposing. Cancer Genomics Proteomics 2021; 18:757-769. [PMID: 34697067 DOI: 10.21873/cgp.20295] [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: 07/16/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM Colon cancer is one of the most common cancer types and the second leading cause of death due to cancer. Many efforts have been performed towards the investigation of molecular alterations during colon cancer progression. However, the identification of stage-specific molecular markers remains a challenge. The aim of this study was to develop a novel computational methodology for the analysis of alterations in differential gene expression and pathway deregulation across colon cancer stages in order to reveal stage-specific biomarkers and reinforce drug repurposing investigation. MATERIALS AND METHODS Transcriptomic datasets of colon cancer were used to identify (a) differentially expressed genes with monotonicity in their fold changes (MEGs) and (b) perturbed pathways with ascending monotonic enrichment (MEPs) related to the number of the participating differentially expressed genes (DEGs), across the four colon cancer stages. Through an in silico drug repurposing pipeline we identified drugs that regulate the expression of MEGs and also target the resulting MEPs. RESULTS Our methodology highlighted 15 MEGs and 32 candidate repurposed drugs that affect their expression. We also found 51 MEPs divided into two groups according to their rate of DEG content alteration across colon cancer stages. Focusing on the target MEPs of the highlighted repurposed drugs, we found that one of them, the neuroactive ligand-receptor interaction, was targeted by the majority of the candidate drugs. Moreover, we observed that two of the drugs (PIK-75 and troglitazone) target the majority of the resulting MEPs. CONCLUSION These findings highlight significant genes and pathways that can be used as stage-specific biomarkers and facilitate the discovery of new potential repurposed drugs for colon cancer. We expect that the computational methodology presented can be applied in a similar way to the analysis of any progressive disease.
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Affiliation(s)
- Marilena M Bourdakou
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George M Spyrou
- The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus.,The Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - George Kolios
- Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Alexandroupolis, Greece;
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10
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Oleynikova NA, Danilova NV, Grimuta MO, Malkov PG. Epstein-Barr Virus in the Development of Colorectal Cancer (Review). Sovrem Tekhnologii Med 2021; 13:82-91. [PMID: 34603767 PMCID: PMC8482827 DOI: 10.17691/stm2021.13.4.09] [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: 12/04/2020] [Indexed: 12/03/2022] Open
Abstract
The study of the influence of the Epstein–Barr virus (EBV) on the development of colorectal cancer is of current interest, particularly in light of the active discussion of the participation of this virus in the carcinogenesis of stomach cancer. In this review, aimed at a fundamental understanding of the processes associated with the impact of EBV on the human body, attention is paid to the issues of the life cycle of the virus, its phases (latent and lytic), as well as proteins that may be detected in each of the phases. The papers reporting on the role of EBV in the development of colorectal cancer have been analyzed. A summary table indicating the population under study, the number of samples, the method, and the result obtained is provided. Given that the primary cells affected by EBV are lymphocytes, it is logical to assume the involvement of this virus in the development of inflammatory bowel diseases. The review cites studies which confirm the presence of virus DNA in tissues in the inflammatory diseases of the colon, including microscopic and ulcerative colitis. To confirm the direct impact of EBV on the development of colorectal cancer, large studies with applying various methods for detecting the virus and the mandatory description of its localization are required. Besides, it is necessary to correlate these data with the clinical and morphological characteristics of EBV.
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Affiliation(s)
- N A Oleynikova
- Researcher, Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
| | - N V Danilova
- Senior Researcher, Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
| | - M O Grimuta
- Student; I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya St., Moscow, 119991, Russia
| | - P G Malkov
- Head of the Department of Clinical Pathology; Medical Scientific and Educational Center, Lomonosov Moscow State University, 27/10 Lomonosov Prospect, Moscow, 119192, Russia
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11
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Agapito G, Cannataro M. Using BioPAX-Parser (BiP) to enrich lists of genes or proteins with pathway data. BMC Bioinformatics 2021; 22:376. [PMID: 34592927 PMCID: PMC8482563 DOI: 10.1186/s12859-021-04297-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/06/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pathway enrichment analysis (PEA) is a well-established methodology for interpreting a list of genes and proteins of interest related to a condition under investigation. This paper aims to extend our previous work in which we introduced a preliminary comparative analysis of pathway enrichment analysis tools. We extended the earlier work by providing more case studies, comparing BiP enrichment performance with other well-known PEA software tools. METHODS PEA uses pathway information to discover connections between a list of genes and proteins as well as biological mechanisms, helping researchers to overcome the problem of explaining biological entity lists of interest disconnected from the biological context. RESULTS We compared the results of BiP with some existing pathway enrichment analysis tools comprising Centrality-based Pathway Enrichment, pathDIP, and Signaling Pathway Impact Analysis, considering three cancer types (colorectal, endometrial, and thyroid), for a total of six datasets (that is, two datasets per cancer type) obtained from the The Cancer Genome Atlas and Gene Expression Omnibus databases. We measured the similarities between the overlap of the enrichment results obtained using each couple of cancer datasets related to the same cancer. CONCLUSION As a result, BiP identified some well-known pathways related to the investigated cancer type, validated by the available literature. We also used the Jaccard and meet-min indices to evaluate the stability and the similarity between the enrichment results obtained from each couple of cancer datasets. The obtained results show that BiP provides more stable enrichment results than other tools.
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Affiliation(s)
- Giuseppe Agapito
- Department of Legal, Economic and Social Sciences, University "Magna Graecia", Catanzaro, Italy. .,Data Analytics Research Center, University "Magna Graecia", Catanzaro, Italy.
| | - Mario Cannataro
- Department of Medical and Surgical Sciences, University "Magna Graecia", Catanzaro, Italy. .,Data Analytics Research Center, University "Magna Graecia", Catanzaro, Italy.
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12
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Copresence of High-Risk Human Papillomaviruses and Epstein-Barr Virus in Colorectal Cancer: A Tissue Microarray and Molecular Study from Lebanon. Int J Mol Sci 2021; 22:ijms22158118. [PMID: 34360884 PMCID: PMC8347509 DOI: 10.3390/ijms22158118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/14/2021] [Accepted: 06/28/2021] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) is the third most common cause of cancer-related deaths worldwide. Human papillomaviruses (HPVs) and Epstein-Barr virus (EBV) have been reported to be present in different types of human cancers, including CRCs, where they can play a key role in the onset and/or progression of these cancers. Thus, we herein explored the prevalence of high-risk HPVs and EBV in a cohort of 94 CRC tissue samples and 13 colorectal normal tissues from the Lebanese population using polymerase chain reaction, immunohistochemistry, and tissue microarray methodologies. We found that high-risk HPVs are present in 64%, while EBV is present in 29% of our CRC samples. Additionally, our data showed that high-risk HPV types (16, 18, 35, 58, 51, 45, 52, 31, and 33) are the most frequent in CRC in the Lebanese cohort, respectively. Our data point out that HPVs and EBV are copresent in 28% of the samples. Thus, this study clearly suggests that high-risk HPVs and EBV are present/copresent in CRCs, where they could play an important role in colorectal carcinogenesis. Nevertheless, further investigations using a larger cohort are needed to elucidate the possible cooperation between these oncoviruses in the development of CRC.
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13
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Establishment of a Patient-Derived Xenograft Model of Colorectal Cancer in CIEA NOG Mice and Exploring Smartfish Liquid Diet as a Source of Omega-3 Fatty Acids. Biomedicines 2021; 9:biomedicines9030282. [PMID: 33802022 PMCID: PMC8000445 DOI: 10.3390/biomedicines9030282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/20/2021] [Accepted: 03/07/2021] [Indexed: 01/10/2023] Open
Abstract
Cancer patient-derived xenografts (PDXs) better preserve tumor characteristics and microenvironment than traditional cancer cell line derived xenografts and are becoming a valuable model in translational cancer research and personalized medicine. We have established a PDX model for colorectal cancer (CRC) in CIEA NOG mice with a 50% engraftment rate. Tumor fragments from patients with CRC (n = 5) were engrafted in four mice per tumor (n = 20). Mice with established PDXs received a liquid diet enriched with fish oil or placebo, and fatty acid profiling was performed to measure fatty acid content in whole blood. Moreover, a biobank consisting of tissue and blood samples from patients was established. Histology, immunohistochemistry and in situ hybridization procedures were used for staining of tumor and xenograft tissue slides. Results demonstrate that key histological characteristics of the patients’ tumors were retained in the established PDXs, and the liquid diets were consumed as intended by the mice. Some of the older mice developed lymphomas that originated from human Ki67+, CD45+, and EBV+ lymphoid cells. We present a detailed description of the process and methodology, as well as possible issues that may arise, to refine the method and improve PDX engraftment rate for future studies. The established PDX model for CRC can be used for exploring different cancer treatment regimes, and liquid diets enriched with fish oil may be successfully delivered to the mice through the drinking flasks.
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14
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Turkington CJR, Varadan AC, Grenier SF, Grasis JA. The Viral Janus: Viruses as Aetiological Agents and Treatment Options in Colorectal Cancer. Front Cell Infect Microbiol 2021; 10:601573. [PMID: 33489934 PMCID: PMC7817644 DOI: 10.3389/fcimb.2020.601573] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/23/2020] [Indexed: 12/24/2022] Open
Abstract
In recent years, our understanding of the importance of microorganisms on and within our bodies has been revolutionized by the ability to characterize entire microbial communities. No more so is this true than in cases of disease. Community studies have revealed strong associations between microbial populations and disease states where such concomitance was previously absent from aetiology: including in cancers. The study of viruses, in particular, has benefited from the development of new community profiling techniques and we are now realising that their prominence within our physiology is nearly as broad as the diversity of the organisms themselves. Here, we examine the relationship between viruses and colorectal cancer (CRC), the leading cause of gastrointestinal cancer-related death worldwide. In CRC, viruses have been suggested to be involved in oncogenesis both directly, through infection of our cells, and indirectly, through modulating the composition of bacterial communities. Interestingly though, these characteristics have also led to their examination from another perspective—as options for treatment. Advances in our understanding of molecular and viral biology have caused many to look at viruses as potential modular biotherapeutics, where deleterious characteristics can be tamed and desirable characteristics exploited. In this article, we will explore both of these perspectives, covering how viral infections and involvement in microbiome dynamics may contribute to CRC, and examine ways in which viruses themselves could be harnessed to treat the very condition their contemporaries may have had a hand in creating.
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Affiliation(s)
| | - Ambarish C Varadan
- School of Natural Sciences, University of California Merced, Merced, CA, United States
| | - Shea F Grenier
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Juris A Grasis
- School of Natural Sciences, University of California Merced, Merced, CA, United States
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15
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Gupta I, Al Farsi H, Jabeen A, Skenderi F, Al-Thawadi H, AlAhmad YM, Abdelhafez I, Al Moustafa AE, Vranic S. High-Risk Human Papillomaviruses and Epstein-Barr Virus in Colorectal Cancer and Their Association with Clinicopathological Status. Pathogens 2020; 9:E452. [PMID: 32521661 PMCID: PMC7350373 DOI: 10.3390/pathogens9060452] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is a common malignancy with a high mortality rate worldwide. It is a complex, multifactorial disease that is strongly impacted by both hereditary and environmental factors. The role of microbes (e.g., viruses) in the pathogenesis of CRC is poorly understood. In the current study, we explored the status of high-risk human papillomaviruses (HPV) and Epstein-Barr virus (EBV) in a well-defined CRC cohort using immunohistochemistry and polymerase chain reaction assays. Our data showed that high-risk HPVs were common (~80%) and EBV had a low presence (14-25%) in the CRC samples. The most common high-risk HPVs are HPV16, 31, 18, 51, 52 and 45 genotypes. The co-presence of high-risk HPV and EBV was observed in ~16% of the sample population without any significant association with the clinicopathological variables. We conclude that high-risk HPVs are very prevalent in CRC samples while EBV positivity is relatively low. The co-expression of the two viruses was observed in a minority of cases and without any correlation with the studied parameters. Further studies are necessary to confirm the clinical relevance and potential therapeutic (preventive) effects of the observations reported herein.
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Affiliation(s)
- Ishita Gupta
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Halema Al Farsi
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Ayesha Jabeen
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Faruk Skenderi
- Department of Pathology, Clinical Center, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina;
| | - Hamda Al-Thawadi
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Yaman M. AlAhmad
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Ibrahim Abdelhafez
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
| | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
- Biomedical Research Centre, Qatar University, 2713 Doha, Qatar
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, 2713 Doha, Qatar; (I.G.); (H.A.F.); (A.J.); (H.A.-T.); (Y.M.A.); (I.A.)
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