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Hu X, Li Y, Cao Y, Shi F, Shang L. The role of nitric oxide synthase/ nitric oxide in infection-related cancers: Beyond antimicrobial activity. Biochim Biophys Acta Rev Cancer 2024; 1879:189156. [PMID: 39032540 DOI: 10.1016/j.bbcan.2024.189156] [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: 12/01/2023] [Revised: 07/11/2024] [Accepted: 07/14/2024] [Indexed: 07/23/2024]
Abstract
As a free radical and endogenous effector molecule, mammalian endogenous nitric oxide (NO) is mainly derived from nitric oxide synthase (NOS) via L-arginine. NO participates in normal physiological reactions and provides immune responses to prevent the invasion of foreign bacteria. However, NO also has complex and contradictory biological effects. Abnormal NO signaling is involved in the progression of many diseases, such as cancer. In the past decades, cancer research has been closely linked with NOS/ NO, and many tumors with poor prognosis are associated with high expression of NOS. In this review, we give a overview of the biological effects of NOS/ NO. Then we focus on the oncogenic role of iNOS/ NO in HPV, HBV, EBV and H. pylori related tumors. In fact, there is growing evidence that iNOS could be used as a potential therapeutic target in cancer therapy. We emphasize that the pro-tumor effect of NOS/ NO is greater than the anti-tumor effect.
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Affiliation(s)
- Xudong Hu
- Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, XiangYa Hospital, Central South University, Changsha 410078, China; Department of Pathology, National Clinical Research Center for Geriatric Disorders/ XiangYa Hospital, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Yueshuo Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, XiangYa Hospital, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, XiangYa Hospital, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Feng Shi
- Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, XiangYa Hospital, Central South University, Changsha 410078, China; Department of Pathology, National Clinical Research Center for Geriatric Disorders/ XiangYa Hospital, Central South University, Changsha 410078, China; Key Laboratory of Carcinogenesis of National Health Commission, Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, Changsha 410078, China
| | - Li Shang
- Key Laboratory of Carcinogenesis and Cancer Invasion of Chinese Ministry of Education, XiangYa Hospital, Central South University, Changsha 410078, China; Department of Pathology, National Clinical Research Center for Geriatric Disorders/ XiangYa Hospital, Central South University, Changsha 410078, China.
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Chatterjee S, Starrett GJ. Microhomology-mediated repair machinery and its relationship with HPV-mediated oncogenesis. J Med Virol 2024; 96:e29674. [PMID: 38757834 DOI: 10.1002/jmv.29674] [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: 12/30/2023] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/18/2024]
Abstract
Human Papillomaviruses (HPV) are a diverse family of non-enveloped dsDNA viruses that infect the skin and mucosal epithelia. Persistent HPV infections can lead to cancer frequently involving integration of the virus into the host genome, leading to sustained oncogene expression and loss of capsid and genome maintenance proteins. Microhomology-mediated double-strand break repair, a DNA double-stranded breaks repair pathway present in many organisms, was initially thought to be a backup but it's now seen as vital, especially in homologous recombination-deficient contexts. Increasing evidence has identified microhomology (MH) near HPV integration junctions, suggesting MH-mediated repair pathways drive integration. In this comprehensive review, we present a detailed summary of both the mechanisms underlying MH-mediated repair and the evidence for its involvement in HPV integration in cancer. Lastly, we highlight the involvement of these processes in the integration of other DNA viruses and the broader implications on virus lifecycles and host innate immune response.
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Affiliation(s)
- Subhajit Chatterjee
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Gabriel J Starrett
- Laboratory of Cellular Oncology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Šimičić P, Batović M, Stojanović Marković A, Židovec-Lepej S. Deciphering the Role of Epstein-Barr Virus Latent Membrane Protein 1 in Immune Modulation: A Multifaced Signalling Perspective. Viruses 2024; 16:564. [PMID: 38675906 PMCID: PMC11054855 DOI: 10.3390/v16040564] [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: 01/29/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
The disruption of antiviral sensors and the evasion of immune defences by various tactics are hallmarks of EBV infection. One of the EBV latent gene products, LMP1, was shown to induce the activation of signalling pathways, such as NF-κB, MAPK (JNK, ERK1/2, p38), JAK/STAT and PI3K/Akt, via three subdomains of its C-terminal domain, regulating the expression of several cytokines responsible for modulation of the immune response and therefore promoting viral persistence. The aim of this review is to summarise the current knowledge on the EBV-mediated induction of immunomodulatory molecules by the activation of signal transduction pathways with a particular focus on LMP1-mediated mechanisms. A more detailed understanding of the cytokine biology molecular landscape in EBV infections could contribute to the more complete understanding of diseases associated with this virus.
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Affiliation(s)
- Petra Šimičić
- Department of Oncology and Nuclear Medicine, Sestre Milosrdnice University Hospital Center, Vinogradska cesta 29, 10 000 Zagreb, Croatia;
| | - Margarita Batović
- Department of Clinical Microbiology and Hospital Infections, Dubrava University Hospital, Avenija Gojka Šuška 6, 10 000 Zagreb, Croatia;
| | - Anita Stojanović Marković
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Snjezana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, Mirogojska 8, 10 000 Zagreb, Croatia
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Quek ZBR, Ng SH. Hybrid-Capture Target Enrichment in Human Pathogens: Identification, Evolution, Biosurveillance, and Genomic Epidemiology. Pathogens 2024; 13:275. [PMID: 38668230 PMCID: PMC11054155 DOI: 10.3390/pathogens13040275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 04/29/2024] Open
Abstract
High-throughput sequencing (HTS) has revolutionised the field of pathogen genomics, enabling the direct recovery of pathogen genomes from clinical and environmental samples. However, pathogen nucleic acids are often overwhelmed by those of the host, requiring deep metagenomic sequencing to recover sufficient sequences for downstream analyses (e.g., identification and genome characterisation). To circumvent this, hybrid-capture target enrichment (HC) is able to enrich pathogen nucleic acids across multiple scales of divergences and taxa, depending on the panel used. In this review, we outline the applications of HC in human pathogens-bacteria, fungi, parasites and viruses-including identification, genomic epidemiology, antimicrobial resistance genotyping, and evolution. Importantly, we explored the applicability of HC to clinical metagenomics, which ultimately requires more work before it is a reliable and accurate tool for clinical diagnosis. Relatedly, the utility of HC was exemplified by COVID-19, which was used as a case study to illustrate the maturity of HC for recovering pathogen sequences. As we unravel the origins of COVID-19, zoonoses remain more relevant than ever. Therefore, the role of HC in biosurveillance studies is also highlighted in this review, which is critical in preparing us for the next pandemic. We also found that while HC is a popular tool to study viruses, it remains underutilised in parasites and fungi and, to a lesser extent, bacteria. Finally, weevaluated the future of HC with respect to bait design in the eukaryotic groups and the prospect of combining HC with long-read HTS.
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Affiliation(s)
- Z. B. Randolph Quek
- Defence Medical & Environmental Research Institute, DSO National Laboratories, Singapore 117510, Singapore
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5
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Dash SR, Kundu A, Kundu CN. The role of viruses in cancer progression versus cancer treatment: A dual paradigm. Life Sci 2024; 341:122506. [PMID: 38373620 DOI: 10.1016/j.lfs.2024.122506] [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: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/13/2024] [Indexed: 02/21/2024]
Abstract
Most human malignancies are attributed to exposure to infectious organisms such as viruses. Certain infections that can induce cancer can evade the immune system, leading to persistent inflammation that facilitates uncontrolled cell growth. Moreover, these pathogens can increase the likelihood of oncogenic transformation, leading to cancer development. Despite significant advancements in medicine, oncological research continues to seek innovative treatment techniques in light of the constraints imposed by traditional therapeutic agents. Virus-based therapy is a novel treatment method that has garnered significant interest due to its broad range of applications. Virotherapy employs oncolytic viruses that are genetically modified to target tumor cells specifically, undergo replication inside them and destroy the malignant cells. Additionally, this therapeutic approach elicits an anticancer response by boosting the patient's immune system. In addition, viruses are commonly employed as targeted delivery vectors for the precise transportation of various genes, medicinal compounds and immune-stimulating substances. Furthermore, virotherapy offers more excellent anticancer activity in combination with established treatment modalities such as immune therapy, chemotherapy and radiation therapy. This review presents a concise overview of the roles played by infectious agents, such as viruses in cancer progression. In addition, we have thoroughly summarized the advancements in utilizing viruses for their oncolytic properties in conjunction with established cancer treatment modalities such as chemotherapy, radiation and immunotherapy.
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Affiliation(s)
- Somya Ranjan Dash
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Anushka Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, Odisha, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar 751024, Odisha, India.
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Sattar AA, Qaiser A, Kausar H, Aqil S, Mudassar R, Manzoor S, Ashraf J. The potential of IFN-λ, IL-32γ, IL-6, and IL-22 as safeguards against human viruses: a systematic review and a meta-analysis. Front Immunol 2024; 15:1303115. [PMID: 38420119 PMCID: PMC10899505 DOI: 10.3389/fimmu.2024.1303115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 01/17/2024] [Indexed: 03/02/2024] Open
Abstract
Many studies have investigated the antiviral activity of cytokines, including interleukin-6 (IL-6), interleukin-22 (IL-22), interleukin-32 gamma (IL-32γ), and interferon-lambda (IFN-λ) in diverse populations. This study aims to evaluate the role of these cytokines in inhibition of various human and animal viruses when administered exogenously. A comprehensive meta-analysis and systematic review were conducted on all the relevant studies from three databases. Standard mean differences (SMDs) of overall viral inhibition were used to generate the difference in the antiviral efficacy of these cytokines between control and experimental groups. A total of 4,618 abstracts for IL-6, 3,517 abstracts for IL-22, 2,160 abstracts for IL-32γ, and 1,026 abstracts for IFN-λ were identified, and 7, 4, 8, and 35 studies were included, respectively, for each cytokine. IFN-λ (SMD = 0.9540; 95% CI: 0.69-0.22) and IL-32γ (SMD = 0.459; 95% CI: 0.02-0.90) showed the highest influence followed by IL-6 (SMD = 0.456; CI: -0.04-0.95) and IL-22 (SMD = 0.244; 95% CI: -0.33-0.81). None of the cytokines represented heterogeneity (tau² > 0), but only IFN-λ indicated the funnel plot asymmetry (p = 0.0097). Results also indicated that IFN-λ and IL-32γ are more potent antivirals than IL-6 and IL-22. The collective findings of this study emphasize that exogenously administered pro-inflammatory cytokines, specifically IFN-λ and IL-32, exhibit a significant antiviral activity, thereby underscoring them as potent antiviral agents. Nonetheless, additional research is required to ascertain their clinical utility and potential for integration into combinatorial therapeutic regimens against viral infections.
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Affiliation(s)
- Areej A Sattar
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Ariba Qaiser
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Hina Kausar
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Sarah Aqil
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Rida Mudassar
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Sobia Manzoor
- Molecular Virology Lab, Atta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Javed Ashraf
- Department of Community Dentistry, Islamabad Medical and Dental College (IMDC), Islamabad, Pakistan
- Institute of Dentistry, University of Eastern Finland (UEF), Kuopio, Finland
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7
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Xu S, Shi C, Zhou R, Han Y, Li N, Qu C, Xia R, Zhang C, Hu Y, Tian Z, Liu S, Wang L, Li J, Zhang Z. Mapping the landscape of HPV integration and characterising virus and host genome interactions in HPV-positive oropharyngeal squamous cell carcinoma. Clin Transl Med 2024; 14:e1556. [PMID: 38279874 PMCID: PMC10819103 DOI: 10.1002/ctm2.1556] [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: 05/31/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Human papillomavirus (HPV) integration into the host genome is an important factor in HPV(+)OPSCC carcinogenesis, in conjunction with HPV oncoproteins E6/E7. However, a well-studied investigation about virus-host interaction still needs to be completed. Our objective is to characterise HPV integration to investigate potential mechanisms of tumourigenesis independent of E6/E7 oncoproteins. MATERIALS AND METHODS High-throughput viral integration detection was performed on 109 HPV(+)OPSCC tumours with relevant clinicopathological information. Of these tumours, 38 tumours underwent targeted gene sequencing, 29 underwent whole exome sequencing and 26 underwent RNA sequencing. RESULTS HPV integration was detected in 94% of tumours (with a mean integration count of 337). Tumours occurring at the tonsil/oropharyngeal wall that exhibit higher PD-L1 expression demonstrated increased integration sites (p = .024). HPV exhibited a propensity for integration at genomic sites located within specific fragile sites (FRA19A) or genes associated with functional roles such as cell proliferation and differentiation (PTEN, AR), immune evasion (CD274) and glycoprotein biosynthesis process (FUT8). The viral oncogenes E2, E4, E6 and E7 tended to remain intact. HPV fragments displayed enrichment within host copy number variation (CNV) regions. However, insertions into genes related to altered homologous recombination repair were infrequent. Genes with integration had distinct expression levels. Fifty-nine genes whose expression level was affected by viral integration were identified, for example, EPHB1, which was reported to be involved in cellular protein metabolic process. CONCLUSIONS HPV can promote oncogenesis through recurrent integration into functional host genome regions, leading to subsequent genomic aberrations and gene expression disruption. This study characterises viral integrations and virus-host interactions, enhancing our understanding of HPV-related carcinogenesis mechanisms.
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Affiliation(s)
- Shengming Xu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Chaoji Shi
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Rong Zhou
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Yong Han
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - NianNian Li
- Department of BioinfomaticsSequantaShanghaiChina
| | - Chuxiang Qu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Ronghui Xia
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Chunye Zhang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Yuhua Hu
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhen Tian
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Shuli Liu
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
| | - Lizhen Wang
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Jiang Li
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
- Department of Oral PathologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of Medicine
ShanghaiChina
| | - Zhiyuan Zhang
- Department of Oral and Maxillofacial‐Head Neck OncologyShanghai Ninth People's HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
- College of StomatologyShanghai Jiao Tong UniversityShanghaiChina
- National Center for StomatologyShanghaiChina
- National Clinical Research Center for Oral DiseasesShanghaiChina
- Shanghai Key Laboratory of Stomatology, Shanghai Research Institute of StomatologyShanghaiChina
- Research Unit of Oral and Maxillofacial Regenerative MedicineChinese Academy of Medical SciencesShanghaiChina
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Hu J, Zhao J, Wang C, Jia M, Su M, Li S. Epstein-Barr virus reactivation correlates with worse outcomes for patients exposed to hepatitis B virus after haploidentical hematopoietic stem cell transplantation. Ann Hematol 2023; 102:3593-3601. [PMID: 37831153 DOI: 10.1007/s00277-023-05492-z] [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: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023]
Abstract
Hepatitis B virus (HBV)has a high, chronic infection rate in Asian populations, but only few studies have analyzed the effect of Epstein-Barr virus (EBV) or Cytomegalovirus (CMV) reactivation in patients exposed to HBV after haploidentical hematopoietic stem cell transplantation (haplo-HSCT). This study aimed to assess the clinical outcomes of these patients. We conducted a retrospective research including 61 patients exposed to HBV after undergoing haplo-HSCT. The patients were classified into two groups: the CMV reactivation group and no CMV reactivation group. The results were compared between the two groups using the K-W test for continuous variables, Pearson's chi-square test for categorical variables, Kaplan-Meier curves to estimate overall survival (OS) and leukemia-free survival (LFS), and a Cox proportional hazards model to analyze multivariable influences. The 3-year cumulative HBV reactivation rate was 8.2%. The median duration of HBV reactivation was 16 months (16-22 months) after haplo-HSCT. The CMV reactivation group had a higher cumulative incidence of HBV reactivation than the group without CMV reactivation. The EBV reactivation was substantially higher in the CMV reactivation group compared to that in the no CMV reactivation group (37.0% vs.5.9% respectively; P = 0.002). Furthermore, EBV reactivation was a risk factor for 1-year LFS and 1-year OS. Based on our data, EBV reactivation was related to worse outcomes in patients exposed to HBV after haplo-HSCT, whereas CMV reactivation was not.
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Affiliation(s)
- Jiajia Hu
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Jie Zhao
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Chunyan Wang
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Mei Jia
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China
| | - Ming Su
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China.
| | - Shanshan Li
- Department of Clinical Laboratory, Peking University People's Hospital, No. 11 Xizhimen South Street, Xicheng District, Beijing, 100044, People's Republic of China.
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9
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Sinegubova MV, Orlova NA, Vorobiev II. Promoter from Chinese hamster elongation factor-1a gene and Epstein-Barr virus terminal repeats concatemer fragment maintain stable high-level expression of recombinant proteins. PeerJ 2023; 11:e16287. [PMID: 37901457 PMCID: PMC10607201 DOI: 10.7717/peerj.16287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023] Open
Abstract
Background The Chinese hamster ovary (CHO) cell line is the main host for the high-titer production of therapeutic and diagnostic proteins in the biopharmaceutical industry. In most cases, plasmids for efficient protein expression in CHO cells are based on the cytomegalovirus (CMV) promoter. The autologous Chinese hamster eukaryotic translation elongation factor 1α (EEF1A1) promoter is a viable alternative to the CMV promoter in industrial applications. The EEF1A1 promoter and its surrounding DNA regions proved to be effective at maintaining high-level and stable expression of recombinant proteins in CHO cells. EEF1A1-based plasmids' large size can lead to low transfection efficiency and hamper target gene amplification. We hypothesized that an efficient EEF1A1-based expression vector with a long terminal repeat fragment from the Epstein-Barr virus (EBVTR) could be truncated without affecting promoter strength or the long-term stability of target gene expression. Methods We made a series of deletions in the downstream flanking region of the EEF1A1 gene, and then in its upstream flanking region. The resulting plasmids, which coded for the enhanced green fluorescent protein (eGFP), were tested for the level of eGFP expression in the populations of stably transfected CHO DG44 cells and the stability of eGFP expression in the long-term culture in the absence of selection agents. Results It was shown that in the presence of the EBVTR fragment, the entire downstream flanking region of the EEF1A1 gene could be excluded from the plasmid vector. Shortening of the upstream flanking region of the EEF1A1 gene to a length of 2.5 kbp also had no significant effect on the level of eGFP expression or long-term stability. The EBVTR fragment significantly increased expression stability for both the CMV and EEF1A1 promoter-based plasmids, and the expression level drop during the two-month culture was more significant for both CMV promoter-based plasmids. Conclusion Target protein expression stability for the truncated plasmid, based on the EEF1A1 gene and EBVTR fragment, is sufficient for common biopharmaceutical applications, making these plasmid vectors a viable alternative to conventional CMV promoter-based vectors.
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Affiliation(s)
- Maria V. Sinegubova
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Nadezhda A. Orlova
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Ivan I. Vorobiev
- Laboratory of Mammalian Cell Bioengineering, Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
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Smirnova KV, Lubenskaya AK, Senyuta NB, Dushenkina TE, Gurtsevitch VE. [Epstein-Barr virus (Herpesviridae: Lymphocryptovirus) types 1 and 2 and other viral markers in patients with nasopharyngeal carcinoma in two geographically and ethnically distinct regions of Russia]. Vopr Virusol 2023; 68:291-301. [PMID: 38156586 DOI: 10.36233/0507-4088-181] [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: 07/25/2023] [Indexed: 12/30/2023]
Abstract
INTRODUCTION The discovery of two types of Epstein-Barr virus (EBV) (EBV-1 and EBV-2) that have different biological properties stimulated the search for neoplasms associated with each type of the virus. The aim of the work is to study the nature of the association of nasopharyngeal cancer (NPC) with EBV-1 and EBV-2, serological activity for each viral type and the concentration of EBV DNA in the blood plasma of two gender, age and ethnic groups of NPC patients that represent geographically and climatically different regions of Russia,. MATERIALS AND METHODS In the blood plasma of patients with NPC and other non- EBV associated tumors of oral cavity (OTOCEBV-) from the North Caucasian (NCFD) and Central (CFD) Federal Districts of Russia, the types of EBV and the concentration of viral DNA were determined using respectively «nested» and real time PCR; titers of IgG and IgA antibodies to viral capsid antigen (VCA) were measured in indirect immunofluorescence assay. RESULTS The blood plasma samples testing showed that NPC and OTOCEBV- patients were infected with both types of EBV in approximately equal proportions. In two groups of NPC patients infected with one of the virus types only, EBV-1 or EBV-2, respectively, no statistically significant differences were found between the geometric mean values of IgG and IgA anti-EBV antibody titers and viral DNA concentrations in blood plasma. The distribution of virus types was not affected by either patient gender or ethnogeographic origin. The difference was found only between age groups: EBV-2 dominated in NPC patients up to 60 years, and EBV-1 was prevalent in patients over 60 years. CONCLUSION The lack of the predominance of one of EBV types in NPC patients that are the representatives of different ethnic groups from geographically and climatically different regions, suggests that none of these factors play an important role in the NPC carcinogenesis. Evidently, each type of EBV, EBV-1 or EBV-2, if the necessary conditions arise, are able to exhibit its oncogenic potential to initiate tumor development.
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Affiliation(s)
- K V Smirnova
- N.N. Blokhin National Medical Research Center of Oncology
- Peoples' Friendship University of Russia named after Patrice Lumumba
- N.I. Pirogov National Research Medical University
| | - A K Lubenskaya
- N.N. Blokhin National Medical Research Center of Oncology
| | - N B Senyuta
- N.N. Blokhin National Medical Research Center of Oncology
| | - T E Dushenkina
- N.N. Blokhin National Medical Research Center of Oncology
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11
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Hedges EC, Cocks G, Shaw CE, Nishimura AL. Generation of an Open-Access Patient-Derived iPSC Biobank for Amyotrophic Lateral Sclerosis Disease Modelling. Genes (Basel) 2023; 14:genes14051108. [PMID: 37239468 DOI: 10.3390/genes14051108] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 05/15/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease affecting the upper and lower motor neurons, causing patients to lose control over voluntary movement, and leading to gradual paralysis and death. There is no cure for ALS, and the development of viable therapeutics has proved challenging, demonstrated by a lack of positive results from clinical trials. One strategy to address this is to improve the tool kit available for pre-clinical research. Here, we describe the creation of an open-access ALS iPSC biobank generated from patients carrying mutations in the TARDBP, FUS, ANXA11, ARPP21, and C9ORF72 genes, alongside healthy controls. To demonstrate the utilisation of these lines for ALS disease modelling, a subset of FUS-ALS iPSCs were differentiated into functionally active motor neurons. Further characterisation revealed an increase in cytoplasmic FUS protein and reduced neurite outgrowth in FUS-ALS motor neurons compared to the control. This proof-of-principle study demonstrates that these novel patient-derived iPSC lines can recapitulate specific and early disease-related ALS phenotypes. This biobank provides a disease-relevant platform for discovery of ALS-associated cellular phenotypes to aid the development of novel treatment strategies.
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Affiliation(s)
- Erin C Hedges
- United Kingdom Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Rd., London SE5 9RT, UK
| | - Graham Cocks
- Genome Editing and Embryology Core, King's College London, London SE1 1UL, UK
| | - Christopher E Shaw
- United Kingdom Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Rd., London SE5 9RT, UK
- Centre for Brain Research, University of Auckland, 85 Park Road, Grafton, Auckland 1023, New Zealand
| | - Agnes L Nishimura
- United Kingdom Dementia Research Institute, Maurice Wohl Clinical Neuroscience Institute, Institute of Psychiatry, Psychology and Neuroscience, King's College London, 5 Cutcombe Rd., London SE5 9RT, UK
- Blizard Institute, Neuroscience, Surgery and Trauma, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
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12
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Chen Y, Wang Y, Zhou P, Huang H, Li R, Zeng Z, Cui Z, Tian R, Jin Z, Liu J, Huang Z, Li L, Huang Z, Tian X, Yu M, Hu Z. VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:300-310. [PMID: 36804047 PMCID: PMC10626058 DOI: 10.1016/j.gpb.2023.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023]
Abstract
Integration of oncogenic DNA viruses into the human genome is a key step in most virus-induced carcinogenesis. Here, we constructed a virus integration site (VIS) Atlas database, an extensive collection of integration breakpoints for three most prevalent oncoviruses, human papillomavirus, hepatitis B virus, and Epstein-Barr virus based on the next-generation sequencing (NGS) data, literature, and experimental data. There are 63,179 breakpoints and 47,411 junctional sequences with full annotations deposited in the VIS Atlas database, comprising 47 virus genotypes and 17 disease types. The VIS Atlas database provides (1) a genome browser for NGS breakpoint quality check, visualization of VISs, and the local genomic context; (2) a novel platform to discover integration patterns; and (3) a statistics interface for a comprehensive investigation of genotype-specific integration features. Data collected in the VIS Atlas aid to provide insights into virus pathogenic mechanisms and the development of novel antitumor drugs. The VIS Atlas database is available at https://www.vis-atlas.tech/.
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Affiliation(s)
- Ye Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Yuyan Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Ping Zhou
- Department of Obstetrics and Gynecology, Dongguan Maternal and Child Health Care Hospital, Dongguan 523000, China
| | - Hao Huang
- Office of Scientific Research & Development, Sun Yat-sen University, Guangzhou 510000, China
| | - Rui Li
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zhen Zeng
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Rui Tian
- Center for Translational Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhuang Jin
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Jiashuo Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zhaoyue Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Lifang Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Zheying Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician Expert Workstation, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China.
| | - Meiying Yu
- Department of Pathology, the Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi 445000, China.
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Zhongnan Hospital of Wuhan University, Wuhan 430062, China; Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510000, China.
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13
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An Integrative Analysis of Nasopharyngeal Carcinoma Genomes Unraveled Unique Processes Driving a Viral-Positive Cancer. Cancers (Basel) 2023; 15:cancers15041243. [PMID: 36831585 PMCID: PMC9953764 DOI: 10.3390/cancers15041243] [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: 01/13/2023] [Revised: 02/03/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
As one of few viral-positive cancers, nasopharyngeal carcinoma (NPC) is extremely rare across the world but very frequent in several regions of the world, including Southern China (known as the Cantonese cancer). Even though several genomic studies have been conducted for NPC, their sample sizes are relatively small and systematic comparison with other cancer types has not been explored. In this study, we collected four-hundred-thirty-one samples from six previous studies and provided the first integrative analysis of NPC genomes. Combining several statistical methods for detecting driver genes, we identified 25 novel drivers for NPC, including ATG14 and NLRC5. Many of these novel drivers are enriched in several important pathways, such as autophagy and immunity. By comparing NPC with many other cancer types, we found NPC is a unique cancer type in which a high proportion of patients (45.2%) do not have any known driver mutations (termed as "missing driver events") but have a preponderance of deletion events, including chromosome 3p deletion. Through signature analysis, we identified many known and novel signatures, including single-base signatures (n = 12), double-base signatures (n = 1), indel signatures (n = 9) and copy number signatures (n = 8). Many of these new signatures are involved in DNA repair and have unknown etiology and genome instability, implying an unprecedented dynamic mutational process possibly driven by complex interactions between viral and host genomes. By combining clinical, molecular and intra-tumor heterogeneity features, we constructed the first integrative survival model for NPC, providing a strong basis for patient prognosis and stratification. Taken together, we have performed one of the first integrative analyses of NPC genomes and brought unique genomic insights into tumorigenesis of a viral-driven cancer.
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14
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Awasthi P, Dwivedi M, Kumar D, Hasan S. Insights into intricacies of the Latent Membrane Protein-1 (LMP-1) in EBV-associated cancers. Life Sci 2023; 313:121261. [PMID: 36493876 DOI: 10.1016/j.lfs.2022.121261] [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: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
Numerous lymphomas, carcinomas, and other disorders have been associated with Epstein-Barr Virus (EBV) infection. EBV's carcinogenic potential can be correlated to latent membrane protein 1 (LMP1), which is essential for fibroblast and primary lymphocyte transformation. LMP1, a transmembrane protein with constitutive activity, belongs to the tumour necrosis factor receptor (TNFR) superfamily. LMP1 performs number of role in the life cycle of EBV and the pathogenesis by interfering with, reprogramming, and influencing a vast range of host cellular activities and functions that are getting well-known but still poorly understood. LMP1, pleiotropically perturbs, reprograms and balances a wide range of various processes of cell such as extracellular vesicles, epigenetics, ubiquitin machinery, metabolism, cell proliferation and survival, and also promotes oncogenic transformation, angiogenesis, anchorage-independent cell growth, metastasis and invasion, tumour microenvironment. By the help of various experiments, it is proven that EBV-encoded LMP1 activates multiple cell signalling pathways which affect antigen presentation, cell-cell interactions, chemokine and cytokine production. Therefore, it is assumed that LMP1 may perform majorly in EBV associated malignancies. For the development of novel techniques toward targeted therapeutic applications, it is essential to have a complete understanding of the LMP1 signalling landscape in order to identify potential targets. The focus of this review is on LMP1-interacting proteins and related signalling processes. We further discuss tactics for using the LMP1 protein as a potential therapeutic for cancers caused by the EBV.
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Affiliation(s)
- Prankur Awasthi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 226028, India
| | - Dhruv Kumar
- School of Health Sciences and Technology, UPES University Dehradun, Uttarakhand, India
| | - Saba Hasan
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow 226028, India.
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15
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Silva JM, Qi W, Pinho AJ, Pratas D. AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. Gigascience 2022; 12:giad101. [PMID: 38091509 PMCID: PMC10716826 DOI: 10.1093/gigascience/giad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC-biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the model's ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances-namely, local, medium, or distant associations. FINDINGS This article addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference and alignment free, providing additional methodologies for testing, including a highly flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar. CONCLUSIONS The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multithreading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.
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Affiliation(s)
- Jorge M Silva
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse, 190, 8057, Zurich, Switzerland
- SIB, Swiss Institute of Bioinformatics, 1202, Geneva, Switzerland
| | - Armando J Pinho
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Diogo Pratas
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
- Department of Virology, University of Helsinki, Haartmaninkatu, 3, 00014 Helsinki, Finland
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16
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Wu B, Shen L, Peng G, Li Y, Zhou Z, Li J, Huang X, Zhou Q, Jiang H, Huang J, Ding Q, Zhang Z, Qin Y, Hong X, Shi L, Zou Z, Yao J, Zhang J, Liu D, Wan C, Wu G, Song L, Chen S, Yi J, Yang K. Molecular characteristics of pediatric nasopharyngeal carcinoma using whole-exome sequencing. Oral Oncol 2022; 135:106218. [DOI: 10.1016/j.oraloncology.2022.106218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/08/2022] [Accepted: 10/14/2022] [Indexed: 11/08/2022]
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17
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EBV persistence in gastric cancer cases conventionally classified as EBER-ISH negative. Infect Agent Cancer 2022; 17:57. [DOI: 10.1186/s13027-022-00469-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
Abstract
Abstract
Background
The Epstein-Barr virus (EBV) causes various B-cell lymphomas and epithelial malignancies, including gastric cancer (GC) at frequencies ranging from 5 to 10% in adenocarcinomas (ADK) to 80% in GC with lymphoid stroma (GCLS). Using high-sensitivity methods, we recently detected EBV traces in a large cohort of EBV-negative B-cell lymphomas, suggesting a hit-and-run mechanism.
Methods
Here, we used routine and higher-sensitivity methods [droplet digital PCR (ddPCR) for EBV segments on microdissected tumour cells and RNAscope for EBNA1 mRNA] to assess EBV infection in a cohort of 40 GCs (28 ADK and 12 GCLS).
Results
ddPCR documented the presence of EBV nucleic acids in rare tumour cells of several cases conventionally classified as EBV-negative (ADK, 8/26; GCLS, 6/7). Similarly, RNAscope confirmed EBNA1 expression in rare tumour cells (ADK, 4/26; GCLS, 3/7). Finally, since EBV induces epigenetic changes that are heritable and retained after complete loss of the virus from the host cell, we studied the methylation pattern of EBV-specifically methylated genes (Timp2, Eya1) as a mark of previous EBV infection. Cases with EBV traces showed a considerable level of methylation in Timp2 and Eya1 genes that was similar to that observed in EBER-ISH positive cases and greater than cases not featuring any EBV traces.
Conclusions
These findings suggest that: (a) EBV may contribute to gastric pathogenesis more widely than currently acknowledged and (b) indicate the methylation changes as a mechanistic framework for how EBV can act in a hit-and-run manner. Finally, we found that the viral state was of prognostic significance in univariate and multivariate analyses.
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18
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Liu Z, He J, Hu X. Ferroptosis regulators related scoring system by Gaussian finite mixture model to predict prognosis and immunotherapy efficacy in nasopharyngeal carcinoma. Front Genet 2022; 13:975190. [PMID: 36118882 PMCID: PMC9479336 DOI: 10.3389/fgene.2022.975190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
The role of ferroptosis in tumor progression and metastasis has been demonstrated. Nonetheless, potential biological function of ferroptosis regulatory pattern in nasopharyngeal carcinoma (NPC) remains unknown. Ferroptosis regulatory patterns of nasopharyngeal carcinoma samples were evaluated based on 113 ferroptosis regulators and three distinct ferroptosis subtypes were determined by unsupervised clustering. The ferroptosis score (FEP score) was identified to quantify ferroptosis patterns within individual tumors by Gaussian finite mixture model and systematically correlated with representative tumor characteristics. Subtype 1 and subtype 3 were consistent with immune activated phenotype, while subtype 2 was consistent with immune suppressed phenotype. High ferroptosis score, characterized by immune activation and suppression of mRNA based stemness index (mRNAsi) and Epstein-Barr virus (EBV) genes, indicated an immune activated tumor microenvironment (TME) phenotype, with better progression free survival (PFS) and lower risk of recurrence and metastasis. Low ferroptosis score, characterized by activation of Wnt and NF-κB signaling pathways and lack of effective immune infiltration, indicated an immune suppressed tumor microenvironment phenotype and poorer survival. High ferroptosis score was also correlated to enhanced response to immunotherapy, and was confirmed to correlate with therapeutic advantages and clinical benefits in an anti-programmed cell death 1 ligand 1 (PD-L1) immunotherapy cohort. As ferroptosis played a crucial role in the tumor microenvironment’s diversity, assessing the ferroptosis pattern within individual tumor with ferroptosis score could enhance our understanding of tumor microenvironment infiltration characterization and help develop more effective immunotherapy.
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Affiliation(s)
- Zijian Liu
- Department of Head and Neck Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jinlan He
- Department of Head and Neck Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaolin Hu
- West China School of Nursing, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Xiaolin Hu,
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19
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Tian R, Wang Y, Li W, Cui Z, Pan T, Jin Z, Huang Z, Li L, Lang B, Wu J, Xie H, Lu Y, Tian X, Hu Z. Genome-wide virus-integration analysis reveals a common insertional mechanism of HPV, HBV and EBV. Clin Transl Med 2022; 12:e971. [PMID: 35968887 PMCID: PMC9376973 DOI: 10.1002/ctm2.971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Rui Tian
- Department of Obstetrics and Gynecology, Academician expert workstation, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China.,Center of Cervical Cancer Precision Prevention and Treatment, Sun Yat-sen University Nanchang Research Institution, Nanchang, Jiangxi, 330200, China
| | - Yuyan Wang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Weiping Li
- Department of Obstetrics and Gynecology, General Hospital of People's Liberation Army, Beijing, 100039, China
| | - Zifeng Cui
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Ting Pan
- Institute of Human Virology, Key Laboratory of Tropical Disease Control of Ministry of Education, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhuang Jin
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhaoyue Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Lifang Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, Macao, 999078, China
| | - Jian Wu
- MyGenostics Inc, Beijing, 101300, China
| | - Hongxian Xie
- Generulor Company Bio-X Lab, Zhuhai, Guangdong, 519000, China
| | - Yiqin Lu
- Department of Gynecology, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Xun Tian
- Department of Obstetrics and Gynecology, Academician expert workstation, the Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430014, China
| | - Zheng Hu
- Center of Cervical Cancer Precision Prevention and Treatment, Sun Yat-sen University Nanchang Research Institution, Nanchang, Jiangxi, 330200, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
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20
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Linden N, Jones RB. Potential multi-modal effects of provirus integration on HIV-1 persistence: lessons from other viruses. Trends Immunol 2022; 43:617-629. [PMID: 35817699 PMCID: PMC9429957 DOI: 10.1016/j.it.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/29/2022]
Abstract
Despite antiretroviral therapy (ART), HIV-1 persists as proviruses integrated into the genomic DNA of CD4+ T cells. The mechanisms underlying the persistence and clonal expansion of these cells remain incompletely understood. Cases have been described in which proviral integration can alter host gene expression to drive cellular proliferation. Here, we review observations from other genome-integrating human viruses to propose additional putative modalities by which HIV-1 integration may alter cellular function to favor persistence, such as by altering susceptibility to cytotoxicity in virus-expressing cells. We propose that signals implicating such mechanisms may have been masked thus far by the preponderance of defective and/or nonreactivatable HIV-1 proviruses, but could be revealed by focusing on the integration sites of intact proviruses with expression potential.
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Affiliation(s)
- Noemi Linden
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R Brad Jones
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Immunology and Microbial Pathogenesis Graduate Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10021, USA; Department of Microbiology and Immunology, Weill Cornell Medicine, New York, NY 10021, USA.
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21
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Javadzadeh S, Rajkumar U, Nguyen N, Sarmashghi S, Luebeck J, Shang J, Bafna V. FastViFi: Fast and accurate detection of (Hybrid) Viral DNA and RNA. NAR Genom Bioinform 2022; 4:lqac032. [PMID: 35493723 PMCID: PMC9041341 DOI: 10.1093/nargab/lqac032] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 11/13/2022] Open
Abstract
DNA viruses are important infectious agents known to mediate a large number of human diseases, including cancer. Viral integration into the host genome and the formation of hybrid transcripts are also associated with increased pathogenicity. The high variability of viral genomes, however requires the use of sensitive ensemble hidden Markov models that add to the computational complexity, often requiring > 40 CPU-hours per sample. Here, we describe FastViFi, a fast 2-stage filtering method that reduces the computational burden. On simulated and cancer genomic data, FastViFi improved the running time by 2 orders of magnitude with comparable accuracy on challenging data sets. Recently published methods have focused on identification of location of viral integration into the human host genome using local assembly, but do not extend to RNA. To identify human viral hybrid transcripts, we additionally developed ensemble Hidden Markov Models for the Epstein Barr virus (EBV) to add to the models for Hepatitis B (HBV), Hepatitis C (HCV) viruses and the Human Papillomavirus (HPV), and used FastViFi to query RNA-seq data from Gastric cancer (EBV) and liver cancer (HBV/HCV). FastViFi ran in <10 minutes per sample and identified multiple hybrids that fuse viral and human genes suggesting new mechanisms for oncoviral pathogenicity. FastViFi is available at https://github.com/sara-javadzadeh/FastViFi.
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Affiliation(s)
- Sara Javadzadeh
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Utkrisht Rajkumar
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Nam Nguyen
- Boundless Bio, Inc. 11099 N Torrey Pines Rd, La Jolla, CA, USA
| | - Shahab Sarmashghi
- Department of Electrical and Computer Engineering, UC San Diego, La Jolla, California, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, UC San Diego, La Jolla, California, USA
| | - Jingbo Shang
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
| | - Vineet Bafna
- Department of Computer Science & Engineering, UC San Diego, La Jolla, California, USA
- Boundless Bio, Inc. 11099 N Torrey Pines Rd, La Jolla, CA, USA
- Moores Cancer Center, UC San Diego, La Jolla, California, USA
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22
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Woerner J, Huang Y, Hutter S, Gurnari C, Sánchez JMH, Wang J, Huang Y, Schnabel D, Aaby M, Xu W, Thorat V, Jiang D, Jha BK, Koyuturk M, Maciejewski JP, Haferlach T, LaFramboise T. Circulating microbial content in myeloid malignancy patients is associated with disease subtypes and patient outcomes. Nat Commun 2022; 13:1038. [PMID: 35210415 PMCID: PMC8873459 DOI: 10.1038/s41467-022-28678-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
Although recent work has described the microbiome in solid tumors, microbial content in hematological malignancies is not well-characterized. Here we analyze existing deep DNA sequence data from the blood and bone marrow of 1870 patients with myeloid malignancies, along with healthy controls, for bacterial, fungal, and viral content. After strict quality filtering, we find evidence for dysbiosis in disease cases, and distinct microbial signatures among disease subtypes. We also find that microbial content is associated with host gene mutations and with myeloblast cell percentages. In patients with low-risk myelodysplastic syndrome, we provide evidence that Epstein-Barr virus status refines risk stratification into more precise categories than the current standard. Motivated by these observations, we construct machine-learning classifiers that can discriminate among disease subtypes based solely on bacterial content. Our study highlights the association between the circulating microbiome and patient outcome, and its relationship with disease subtype.
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Affiliation(s)
- Jakob Woerner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yidi Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | | | - Carmelo Gurnari
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Janet Wang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Daniel Schnabel
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Michael Aaby
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Wanying Xu
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA
| | - Dongxu Jiang
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Babal K Jha
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | - Mehmet Koyuturk
- Department of Computer Science, Case Western Reserve University, Cleveland, USA
| | - Jaroslaw P Maciejewski
- Department of Translational Hematology & Oncology Research, Cleveland Clinic Foundation, Cleveland, USA
| | | | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, USA.
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23
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Janjetovic S, Hinke J, Balachandran S, Akyüz N, Behrmann P, Bokemeyer C, Dierlamm J, Murga Penas EM. Non-Random Pattern of Integration for Epstein-Barr Virus with Preference for Gene-Poor Genomic Chromosomal Regions into the Genome of Burkitt Lymphoma Cell Lines. Viruses 2022; 14:v14010086. [PMID: 35062290 PMCID: PMC8781420 DOI: 10.3390/v14010086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/25/2021] [Accepted: 12/28/2021] [Indexed: 01/27/2023] Open
Abstract
Background: Epstein-Barr virus (EBV) is an oncogenic virus found in about 95% of endemic Burkitt lymphoma (BL) cases. In latently infected cells, EBV DNA is mostly maintained in episomal form, but it can also be integrated into the host genome, or both forms can coexist in the infected cells. Methods: In this study, we mapped the chromosomal integration sites of EBV (EBV-IS) into the genome of 21 EBV+ BL cell lines (BL-CL) using metaphase fluorescence in situ hybridization (FISH). The data were used to investigate the EBV-IS distribution pattern in BL-CL, its relation to the genome instability, and to assess its association to common fragile sites and episomes. Results: We detected a total of 459 EBV-IS integrated into multiple genome localizations with a preference for gene-poor chromosomes. We did not observe any preferential affinity of EBV to integrate into common and rare fragile sites or enrichment of EBV-IS at the chromosomal breakpoints of the BL-CL analyzed here, as other DNA viruses do. Conclusions: We identified a non-random integration pattern into 13 cytobands, of which eight overlap with the EBV-IS in EBV-transformed lymphoblastoid cell lines and with a preference for gene- and CpGs-poor G-positive cytobands. Moreover, it has been demonstrated that the episomal form of EBV interacts in a non-random manner with gene-poor and AT-rich regions in EBV+ cell lines, which may explain the observed affinity for G-positive cytobands in the EBV integration process. Our results provide new insights into the patterns of EBV integration in BL-CL at the chromosomal level, revealing an unexpected connection between the episomal and integrated forms of EBV.
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Affiliation(s)
- Snjezana Janjetovic
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Clinic of Hematology and Stem Cell Transplantation, HELIOS Clinic Berlin-Buch, 13125 Berlin, Germany
| | - Juliane Hinke
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Department for Psychiatry, Albertinen Hospital, 22459 Hamburg, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24118 Kiel, Germany;
| | - Nuray Akyüz
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Petra Behrmann
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Carsten Bokemeyer
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
| | - Judith Dierlamm
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Correspondence: (J.D.); (E.M.M.P.); Tel.: +49-451-500-50438 (E.M.M.P.)
| | - Eva Maria Murga Penas
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section Pneumology, University Clinic Hamburg-Eppendorf, 20251 Hamburg, Germany; (S.J.); (J.H.); (N.A.); (P.B.); (C.B.)
- Institute of Human Genetics, Christian-Albrechts-University of Kiel and University Hospital Schleswig-Holstein, Campus Kiel, 24118 Kiel, Germany;
- Correspondence: (J.D.); (E.M.M.P.); Tel.: +49-451-500-50438 (E.M.M.P.)
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24
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Chakravorty S, Afzali B, Kazemian M. EBV-associated diseases: Current therapeutics and emerging technologies. Front Immunol 2022; 13:1059133. [PMID: 36389670 PMCID: PMC9647127 DOI: 10.3389/fimmu.2022.1059133] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
EBV is a prevalent virus, infecting >90% of the world's population. This is an oncogenic virus that causes ~200,000 cancer-related deaths annually. It is, in addition, a significant contributor to the burden of autoimmune diseases. Thus, EBV represents a significant public health burden. Upon infection, EBV remains dormant in host cells for long periods of time. However, the presence or episodic reactivation of the virus increases the risk of transforming healthy cells to malignant cells that routinely escape host immune surveillance or of producing pathogenic autoantibodies. Cancers caused by EBV display distinct molecular behaviors compared to those of the same tissue type that are not caused by EBV, presenting opportunities for targeted treatments. Despite some encouraging results from exploration of vaccines, antiviral agents and immune- and cell-based treatments, the efficacy and safety of most therapeutics remain unclear. Here, we provide an up-to-date review focusing on underlying immune and environmental mechanisms, current therapeutics and vaccines, animal models and emerging technologies to study EBV-associated diseases that may help provide insights for the development of novel effective treatments.
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Affiliation(s)
- Srishti Chakravorty
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Behdad Afzali
- Immunoregulation Section, Kidney Diseases Branch, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Majid Kazemian
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States.,Department of Computer Science, Purdue University, West Lafayette IN, United States
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25
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Liu Y, Lu Z, Huang H. Genome-Wide Profiling of Epstein-Barr Virus (EBV) Isolated from EBV-Related Malignancies. Infect Dis (Lond) 2021. [DOI: 10.5772/intechopen.93244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Epstein–Barr virus (EBV) is the cause of certain cancers, such as Burkitt lymphoma, Hodgkin lymphoma, NK/T cell lymphoma, nasopharyngeal carcinoma, and a subset of gastric carcinomas. The genome-wide characteristics of EBV are essential to understand the diversity of strains isolated from EBV-related malignancies, provide the first opportunity to test the general validity of the EBV genetic map and explore recombination, geographic variation, and the major features of variation in this virus. Moreover, understanding more about EBV sequence variations isolated from EBV-related malignancies might give important implications for the development of effective prophylactic and therapeutic vaccine approaches targeting the personalized or geographic-specific EBV antigens in these aggressive diseases. In this chapter, we will mainly focus on the EBV genome-wide profiling in three common EBV-related cancers in Asia, including nasopharyngeal carcinoma, EBV-associated gastric carcinoma, and NK/T-cell lymphoma.
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26
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Genomic Landscapes of Epstein-Barr Virus in Pulmonary Lymphoepithelioma-like Carcinoma. J Virol 2021; 96:e0169321. [PMID: 34908446 DOI: 10.1128/jvi.01693-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Epstein-Barr virus (EBV) infection is associated with multiple malignancies, including pulmonary lymphoepithelioma-like carcinoma (pLELC), a particular subtype of primary lung cancer. However, the genomic characteristics of EBV related to pLELC remain unclear. Here, we obtained the whole-genome dataset of EBV isolated from 78 pLELC patients and 37 healthy controls using EBV-captured sequencing. Compared to the reference genome (NC_007605), a total of 3995 variations were detected across pLELC-derived EBV sequences, with the mutational hotspots located in latent genes. Combined with 180 published EBV sequences derived from healthy people in Southern China, we performed a genome-wide association study and identified 32 variations significantly related to pLELC (p < 2.56×10-05, Bonferroni correction), with the top signal of SNP coordinate T7327C (OR = 1.22, p = 2.39×10-15) locating in the origin of plasmid replication (OriP). The results of population structure analysis of EBV isolates in East Asian showed the EBV strains derived from pLELC were more similar to those from nasopharyngeal carcinoma (NPC) than other EBV-associated diseases. In addition, typical latency type-II infection were recognized for EBV of pLELC at both transcription and methylation levels. Taken together, we defined the global view of EBV genomic profiles in pLELC patients for the first time, providing new insights to deepening our understanding of this rare EBV-associated primary lung carcinoma. Importance Pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rarely distinctive subtype of primary lung cancer closely associated with Epstein-Barr virus (EBV) infection. Here, we gave the first overview of pLELC-derived EBV at the level of genome, methylation and transcription. We obtained the EBV sequences dataset from 78 primary pLELC patients, and revealed the sequences diversity across EBV genome and detected variability in known immune epitopes. Genome-wide association analysis combining 217 healthy controls identifies significant variations related to the risk of pLELC. Meanwhile, we characterized the integration landscapes of EBV at the genome-wide level. These results provided new insight for understanding EBV's role in pLELC tumorigenesis.
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27
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Han S, Tay JK, Loh CJL, Chu AJM, Yeong JPS, Lim CM, Toh HC. Epstein–Barr Virus Epithelial Cancers—A Comprehensive Understanding to Drive Novel Therapies. Front Immunol 2021; 12:734293. [PMID: 34956172 PMCID: PMC8702733 DOI: 10.3389/fimmu.2021.734293] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/12/2021] [Indexed: 12/19/2022] Open
Abstract
Epstein–Barr virus (EBV) is a ubiquitous oncovirus associated with specific epithelial and lymphoid cancers. Among the epithelial cancers, nasopharyngeal carcinoma (NPC), lymphoepithelioma-like carcinoma (LELC), and EBV-associated gastric cancers (EBVaGC) are the most common. The role of EBV in the pathogenesis of NPC and in the modulation of its tumour immune microenvironment (TIME) has been increasingly well described. Much less is known about the pathogenesis and tumour–microenvironment interactions in other EBV-associated epithelial cancers. Despite the expression of EBV-related viral oncoproteins and a generally immune-inflamed cancer subtype, EBV-associated epithelial cancers have limited systemic therapeutic options beyond conventional chemotherapy. Immune checkpoint inhibitors are effective only in a minority of these patients and even less efficacious with molecular targeting drugs. Here, we examine the key similarities and differences of NPC, LELC, and EBVaGC and comprehensively describe the clinical, pathological, and molecular characteristics of these cancers. A deeper comparative understanding of these EBV-driven cancers can potentially uncover targets in the tumour, TIME, and stroma, which may guide future drug development and cast light on resistance to immunotherapy.
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Affiliation(s)
- Shuting Han
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
| | - Joshua K. Tay
- Department of Otolaryngology—Head & Neck Surgery, National University of Singapore, Singapore, Singapore
| | | | | | - Joe Poh Sheng Yeong
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Chwee Ming Lim
- Department of Anatomical Pathology, Singapore General Hospital, Singapore, Singapore
| | - Han Chong Toh
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore, Singapore
- *Correspondence: Han Chong Toh,
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28
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Liu H, Dong Z. Cancer Etiology and Prevention Principle: "1 + X". Cancer Res 2021; 81:5377-5395. [PMID: 34470778 DOI: 10.1158/0008-5472.can-21-1862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/16/2021] [Accepted: 08/31/2021] [Indexed: 11/16/2022]
Abstract
Cancer was previously thought to be an inevitable aspect of human health with no effective treatments. However, the results of in-depth cancer research suggest that most types of cancer may be preventable. Therefore, a comprehensive understanding of the disparities in cancer burden caused by different risk factors is essential to inform and improve cancer prevention and control. Here, we propose the cancer etiology and prevention principle "1 + X," where 1 denotes the primary risk factor for a cancer and X represents the secondary contributing risk factors for the cancer. We elaborate upon the "1 + X" principle with respect to risk factors for several different cancer types. The "1 + X" principle can be used for precise prevention of cancer by eliminating the main cause of a cancer and minimizing the contributing factors at the same time.
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Affiliation(s)
- Hui Liu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, China. .,China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
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29
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Liang J, Cui Z, Wu C, Yu Y, Tian R, Xie H, Jin Z, Fan W, Xie W, Huang Z, Xu W, Zhu J, You Z, Guo X, Qiu X, Ye J, Lang B, Li M, Tan S, Hu Z. DeepEBV: A deep learning model to predict Epstein-Barr virus (EBV) integration sites. Bioinformatics 2021; 37:3405-3411. [PMID: 34009299 DOI: 10.1093/bioinformatics/btab388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 03/26/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Epstein-Barr virus (EBV) is one of the most prevalent DNA oncogenic viruses. The integration of EBV into the host genome has been reported to play an important role in cancer development. The preference of EBV integration showed strong dependence on the local genomic environment, which enables the prediction of EBV integration sites. RESULTS An attention-based deep learning model, DeepEBV, was developed to predict EBV integration sites by learning local genomic features automatically. First, DeepEBV was trained and tested using the data from the dsVIS database. The results showed that DeepEBV with EBV integration sequences plus Repeat peaks and 2 fold data augmentation performed the best on the training dataset. Furthermore, the performance of the model was validated in an independent dataset. In addition, the motifs of DNA-binding proteins could influence the selection preference of viral insertional mutagenesis. Furthermore, the results showed that DeepEBV can predict EBV integration hotspot genes accurately. In summary, DeepEBV is a robust, accurate and explainable deep learning model, providing novel insights into EBV integration preferences and mechanisms. AVAILABILITY DeepEBV is available as open-source software and can be downloaded from https://github.com/JiuxingLiang/DeepEBV.gitSupplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Jiuxing Liang
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Zifeng Cui
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Canbiao Wu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Yao Yu
- Department of Urology, The First Medical Center of Chinese PLA General Hospital, Beijing 100853 China.,School of Medicine, Nankai University, Tianjin 300071, China
| | - Rui Tian
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hongxian Xie
- STech Company Bio-X Lab, Zhuhai 519000, Guangdong, China
| | - Zhuang Jin
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiwen Fan
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Weiling Xie
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zhaoyue Huang
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Wei Xu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jingjing Zhu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Zeshan You
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Xiaofang Guo
- Department of Medical Oncology of the Eastern Hospital, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510700, China
| | - Xiaofan Qiu
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China
| | - Jiahao Ye
- Key Laboratory of Brain, Cognition and Education Sciences, Ministry of Education, China; Institute for Brain Research and Rehabilitation, South China Normal University, Guangzhou 510631, China.,School of Computer Science, South China Normal University, Guangzhou 510631, China
| | - Bin Lang
- School of Health Sciences and Sports, Macao Polytechnic Institute, China
| | - Mengyuan Li
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Songwei Tan
- School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zheng Hu
- Department of Gynaecological oncology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China.,Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, Hubei, China
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30
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Rajaby R, Zhou Y, Meng Y, Zeng X, Li G, Wu P, Sung WK. SurVirus: a repeat-aware virus integration caller. Nucleic Acids Res 2021; 49:e33. [PMID: 33444454 PMCID: PMC8034624 DOI: 10.1093/nar/gkaa1237] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 12/01/2020] [Accepted: 01/12/2021] [Indexed: 01/01/2023] Open
Abstract
A significant portion of human cancers are due to viruses integrating into human genomes. Therefore, accurately predicting virus integrations can help uncover the mechanisms that lead to many devastating diseases. Virus integrations can be called by analysing second generation high-throughput sequencing datasets. Unfortunately, existing methods fail to report a significant portion of integrations, while predicting a large number of false positives. We observe that the inaccuracy is caused by incorrect alignment of reads in repetitive regions. False alignments create false positives, while missing alignments create false negatives. This paper proposes SurVirus, an improved virus integration caller that corrects the alignment of reads which are crucial for the discovery of integrations. We use publicly available datasets to show that existing methods predict hundreds of thousands of false positives; SurVirus, on the other hand, is significantly more precise while it also detects many novel integrations previously missed by other tools, most of which are in repetitive regions. We validate a subset of these novel integrations, and find that the majority are correct. Using SurVirus, we find that HPV and HBV integrations are enriched in LINE and Satellite regions which had been overlooked, as well as discover recurrent HBV and HPV breakpoints in human genome-virus fusion transcripts.
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Affiliation(s)
- Ramesh Rajaby
- School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 Medical Drive, 117456, Singapore
| | - Yi Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yifan Meng
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Cancer Biology Research Center (Key laboratory of the ministry of education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Peng Wu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Cancer Biology Research Center (Key laboratory of the ministry of education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wing-Kin Sung
- School of Computing, National University of Singapore, 13 Computing Drive, 117417, Singapore.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.,Genome Institute of Singapore, 60 Biopolis Street, Genome 138672, Singapore
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31
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Xu H, Jia P, Zhao Z. DeepVISP: Deep Learning for Virus Site Integration Prediction and Motif Discovery. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2004958. [PMID: 33977077 PMCID: PMC8097320 DOI: 10.1002/advs.202004958] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Indexed: 05/08/2023]
Abstract
Approximately 15% of human cancers are estimated to be attributed to viruses. Virus sequences can be integrated into the host genome, leading to genomic instability and carcinogenesis. Here, a new deep convolutional neural network (CNN) model is developed with attention architecture, namely DeepVISP, for accurately predicting oncogenic virus integration sites (VISs) in the human genome. Using the curated benchmark integration data of three viruses, hepatitis B virus (HBV), human herpesvirus (HPV), and Epstein-Barr virus (EBV), DeepVISP achieves high accuracy and robust performance for all three viruses through automatically learning informative features and essential genomic positions only from the DNA sequences. In comparison, DeepVISP outperforms conventional machine learning methods by 8.43-34.33% measured by area under curve (AUC) value enhancement in three viruses. Moreover, DeepVISP can decode cis-regulatory factors that are potentially involved in virus integration and tumorigenesis, such as HOXB7, IKZF1, and LHX6. These findings are supported by multiple lines of evidence in literature. The clustering analysis of the informative motifs reveales that the representative k-mers in clusters could help guide virus recognition of the host genes. A user-friendly web server is developed for predicting putative oncogenic VISs in the human genome using DeepVISP.
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Affiliation(s)
- Haodong Xu
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
| | - Peilin Jia
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
| | - Zhongming Zhao
- Center for Precision HealthSchool of Biomedical InformaticsThe University of Texas Health Science Center at Houston (UTHealth)HoustonTX77030USA
- MD Anderson Cancer Center UTHealth Graduate School of Biomedical SciencesHoustonTX77030USA
- Department of Biomedical InformaticsVanderbilt University Medical CenterNashvilleTN37203USA
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32
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Naughton P, Healy M, Enright F, Lucey B. Infectious Mononucleosis: diagnosis and clinical interpretation. Br J Biomed Sci 2021; 78:107-116. [PMID: 33721513 DOI: 10.1080/09674845.2021.1903683] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
EBV is the sole causative agent of the acute illness in humans described either as infectious mononucleosis (IM), or glandular fever. IM, when not clinically silent, can present in patients with at least two of the classic triad of symptoms of fever, pharyngitis, and lymphadenopathy. Challenges for the clinician arise when atypical cases present. Early, accurate and informed laboratory test results are vital for diagnosis, appropriate treatment, and management. A key challenge for the practitioner, particularly in cases where the illness can present atypically, is distinguishing bacterial tonsillitis infections from early acute IM. The ability to draw on timely, clear, and insightful laboratory results to distinguish viral from bacterial infection is vital. Correct and prompt diagnosis of IM can help prevent the unnecessary administration of antibiotics and mitigate the need for other expensive exploratory tests in cases of IM that present with splenomegaly, lymphadenopathy, or suspect haematological conditions. Good communication between the requesting clinician and those carrying out the investigative process, and between the different laboratory departments involved, is good practice and would ultimately benefit the patient. This communication will comprehensively review the aetiology, clinical presentation, and laboratory findings in IM with a view to promoting further research and so derive a standard diagnostic algorithm of the condition.
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Affiliation(s)
- P Naughton
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland.,Department of Haematology, Mercy University Hospital, Cork, Ireland
| | - M Healy
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
| | - F Enright
- Department of Paediatrics, Mercy University Hospital, Cork, Ireland
| | - B Lucey
- Department of Biological Sciences, Munster Technological University, Bishopstown, Cork, Ireland
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Richardson BE. Initial Experience Treating HPV-Related Laryngeal Diseases with Oral Brincidofovir: A Pilot Study. Ann Otol Rhinol Laryngol 2021; 130:1383-1391. [PMID: 33834883 DOI: 10.1177/00034894211007227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
OBJECTIVE To determine if brincidofovir, an oral analog of cidofovir that achieves high tissue levels of the active metabolite with low systemic toxicity, has an observable effect on HPV-related disease of the larynx. METHODS Two patients with laryngeal recurrent respiratory papillomatosis (one each of genotypes 6 and 11) and 1 with recurring aryepiglottic fold carcinoma in situ (genotype 16) received oral brincidofovir according to protocol. Close-range videoendoscopic examinations were done during and after the study period to observe disease behavior in the absence of other interventions, and after subsequent surgical intervention. Disease character and magnitude of recurrence for each patient were compared to their patterns prior to brincidofovir. RESULTS Brincidofovir reduced papilloma burden in 1 patient and markedly attenuated the rate and magnitude of recurrence in both. After surgical intervention, Patient 1 remains disease-free at 10 years (7 years from last intervention) and Patient 2 has no symptoms at 8 years. Patient 3 with recurring carcinoma in situ has required less frequent resections and specimens show reduced degrees of dysplasia present only in islands amid normal mucosa at 8 years (currently no evidence of disease at 21 months from last intervention). CONCLUSION Brincidofovir appears to attenuate HPV disease of the larynx in this small pilot study, though further investigation is required because of the highly variable nature of the disease and potential confounding factors.
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34
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Sun X, Song L, Yang W, Zhang L, Liu M, Li X, Tian G, Wang W. Nanopore Sequencing and Its Clinical Applications. Methods Mol Biol 2021; 2204:13-32. [PMID: 32710311 DOI: 10.1007/978-1-0716-0904-0_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Nanopore sequencing is a method for determining the order and modifications of DNA/RNA nucleotides by detecting the electric current variations when DNA/RNA oligonucleotides pass through the nanometer-sized hole (nanopore). Nanopore-based DNA analysis techniques have been commercialized by Oxford Nanopore Technologies, NabSys, and Sequenom, and widely used in scientific researches recently including human genomics, cancer, metagenomics, plant sciences, etc., moreover, it also has potential applications in the field of healthcare due to its fast turn-around time, portable and real-time data analysis. Those features make it a promising technology for the point-of-care testing (POCT) and its potential clinical applications are briefly discussed in this chapter.
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Affiliation(s)
- Xue Sun
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Lei Song
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Wenjuan Yang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Lili Zhang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Meng Liu
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Xiaoshuang Li
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Geng Tian
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China
| | - Weiwei Wang
- Geneis (Beijing) Co., Ltd., Beijing, People's Republic of China.
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35
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The Role of NK Cells in EBV Infection and EBV-Associated NPC. Viruses 2021; 13:v13020300. [PMID: 33671917 PMCID: PMC7918975 DOI: 10.3390/v13020300] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/08/2021] [Accepted: 02/10/2021] [Indexed: 12/20/2022] Open
Abstract
A vast majority of the population worldwide are asymptomatic carriers of Epstein-Barr Virus (EBV). However, some infected individuals eventually develop EBV-related cancers, including Nasopharyngeal Carcinoma (NPC). NPC is one of the most common EBV-associated epithelial cancers, and is highly prevalent in Southern China and Southeast Asia. While NPC is highly sensitive to radiotherapy and chemotherapy, there is a lack of effective and durable treatment among the 15%–30% of patients who subsequently develop recurrent disease. Natural Killer (NK) cells are natural immune lymphocytes that are innately primed against virus-infected cells and nascent aberrant transformed cells. As EBV is found in both virally infected and cancer cells, it is of interest to examine the NK cells’ role in both EBV infection and EBV-associated NPC. Herein, we review the current understanding of how EBV-infected cells are cleared by NK cells, and how EBV can evade NK cell-mediated elimination in the context of type II latency in NPC. Next, we summarize the current literature about NPC and NK cell biology. Finally, we discuss the translational potential of NK cells in NPC. This information will deepen our understanding of host immune interactions with EBV-associated NPC and facilitate development of more effective NK-mediated therapies for NPC treatment.
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36
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Intra-host changes in Kaposi sarcoma-associated herpesvirus genomes in Ugandan adults with Kaposi sarcoma. PLoS Pathog 2021; 17:e1008594. [PMID: 33465147 PMCID: PMC7845968 DOI: 10.1371/journal.ppat.1008594] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 01/29/2021] [Accepted: 11/24/2020] [Indexed: 12/14/2022] Open
Abstract
Intra-host tumor virus variants may influence the pathogenesis and treatment responses of some virally-associated cancers. However, the intra-host variability of Kaposi sarcoma-associated herpesvirus (KSHV), the etiologic agent of Kaposi sarcoma (KS), has to date been explored with sequencing technologies that possibly introduce more errors than that which occurs in the viral population, and these studies have only studied variable regions. Here, full-length KSHV genomes in tumors and/or oral swabs from 9 Ugandan adults with HIV-associated KS were characterized. Furthermore, we used deep, short-read sequencing using duplex unique molecular identifiers (dUMI)–random double-stranded oligonucleotides that barcode individual DNA molecules before library amplification. This allowed suppression of PCR and sequencing errors to ~10−9/base as well as afforded accurate determination of KSHV genome numbers sequenced in each sample. KSHV genomes were assembled de novo, and rearrangements observed were confirmed by PCR and Sanger sequencing. 131-kb KSHV genome sequences, excluding major repeat regions, were successfully obtained from 23 clinical specimens, averaging 2.3x104 reads/base. Strikingly, KSHV genomes were virtually identical within individuals at the point mutational level. The intra-host heterogeneity that was observed was confined to tumor-associated KSHV mutations and genome rearrangements, all impacting protein-coding sequences. Although it is unclear whether these changes were important to tumorigenesis or occurred as a result of genomic instability in tumors, similar changes were observed across individuals. These included inactivation of the K8.1 gene in tumors of 3 individuals and retention of a region around the first major internal repeat (IR1) in all instances of genomic deletions and rearrangements. Notably, the same breakpoint junctions were found in distinct tumors within single individuals, suggesting metastatic spread of rearranged KSHV genomes. These findings define KSHV intra-host heterogeneity in vivo with greater precision than has been possible in the past and suggest the possibility that aberrant KSHV genomes may contribute to aspects of KS tumorigenesis. Furthermore, study of KSHV with use of dUMI provides a proof of concept for utilizing this technique for detailed study of other virus populations in vivo. Kaposi sarcoma (KS) is a leading cancer in sub-Saharan Africa and in persons with HIV co-infection. Kaposi sarcoma-associated herpesvirus (KSHV, also referred to as human herpesvirus-8, or HHV-8) is the etiologic agent of KS, but the factors that contribute to the development of KS, which occurs in only a small subset of infected individuals, remain largely unknown. While strain differences or mutations in other tumor viruses are known to affect the risk and progression of their associated cancers, whether genetic variation in KSHV is important to the natural history of KS is unclear. Most studies of KSHV diversity have only characterized ~4% of its 165-kb genome, and the observed variation in some studies is likely to have been impacted by PCR or cloning artifacts. To precisely define genomic diversity of KSHV in vivo, we evaluated full-length viral genomes (except the internal repeat regions) using a technique that greatly lowers sequencing error rates and thus measures genomic diversity much more accurately than previous studies. In addition, we extended our analyses to look for potential tumor-specific changes in the KSHV genomes by examining viruses in both tumor and non-tumor tissues. To these ends, we performed highly sensitive, single-molecule sequencing of whole KSHV genomes in paired KS tumors and oral swabs from 9 individuals with KS. We found that KSHV genomes were virtually identical within the 9 individuals, with no evidence of quasispecies formation or multi-strain infection. However, KSHV genome aberrations and gene-inactivating mutations were found to be common in KS tumors, often impacting the same genes and genomic regions across individuals. Whether theses mutations influence KS tumorigenesis or result from genomic instability commonly found in tumors warrants further study. Lastly, aberrant KSHV genomes were found to be shared by distinct tumors within individuals, suggesting the capacity of KS tumor cells to metastasize and seed new lesions.
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37
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Zeng X, Zhao L, Shen C, Zhou Y, Li G, Sung WK. HIVID2: an accurate tool to detect virus integrations in the host genome. Bioinformatics 2021; 37:1821-1827. [PMID: 33453108 DOI: 10.1093/bioinformatics/btab031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 12/27/2020] [Accepted: 01/12/2021] [Indexed: 12/11/2022] Open
Abstract
MOTIVATION Virus integration in the host genome is frequently reported to be closely associated with many human diseases, and the detection of virus integration is a critically challenging task. However, most existing tools show limited specificity and sensitivity. Therefore, the objective of this study is to develop a method for accurate detection of virus integration into host genomes. RESULTS Herein, we report a novel method termed HIVID2 that is a significant upgrade of HIVID. HIVID2 performs a paired-end combination (PE-combination) for potentially integrated reads. The resulting sequences are then remapped onto the reference genomes, and both split and discordant chimeric reads are used to identify accurate integration breakpoints with high confidence. HIVID2 represents a great improvement in specificity and sensitivity, and predicts breakpoints closer to the real integrations, compared with existing methods. The advantage of our method was demonstrated using both simulated and real data sets. HIVID2 uncovered novel integration breakpoints in well-known cervical cancer-related genes, including FHIT and LRP1B, which was verified using protein expression data. In addition, HIVID2 allows the user to decide whether to automatically perform advanced analysis using the identified virus integrations. By analyzing the simulated data and real data tests, we demonstrated that HIVID2 is not only more accurate than HIVID but also better than other existing programs with respect to both sensitivity and specificity. We believe that HIVID2 will help in enhancing future research associated with virus integration. AVAILABILITY HIVID2 can be accessed at https://github.com/zengxi-hada/HIVID2/. CONTACT Xi Zeng (zengxi@mail.hzau.edu.cn), Linghao Zhao (michael_yifan@126.com). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xi Zeng
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Linghao Zhao
- Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai 200438, China
| | - Chenhang Shen
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Yi Zhou
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Computer Science, National University of Singapore, Singapore, 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore, 138672, Singapore
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38
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Cao Y, Xie L, Shi F, Tang M, Li Y, Hu J, Zhao L, Zhao L, Yu X, Luo X, Liao W, Bode AM. Targeting the signaling in Epstein-Barr virus-associated diseases: mechanism, regulation, and clinical study. Signal Transduct Target Ther 2021; 6:15. [PMID: 33436584 PMCID: PMC7801793 DOI: 10.1038/s41392-020-00376-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Epstein–Barr virus-associated diseases are important global health concerns. As a group I carcinogen, EBV accounts for 1.5% of human malignances, including both epithelial- and lymphatic-originated tumors. Moreover, EBV plays an etiological and pathogenic role in a number of non-neoplastic diseases, and is even involved in multiple autoimmune diseases (SADs). In this review, we summarize and discuss some recent exciting discoveries in EBV research area, which including DNA methylation alterations, metabolic reprogramming, the changes of mitochondria and ubiquitin-proteasome system (UPS), oxidative stress and EBV lytic reactivation, variations in non-coding RNA (ncRNA), radiochemotherapy and immunotherapy. Understanding and learning from this advancement will further confirm the far-reaching and future value of therapeutic strategies in EBV-associated diseases.
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Affiliation(s)
- Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China. .,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China. .,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China. .,Research Center for Technologies of Nucleic Acid-Based Diagnostics and Therapeutics Hunan Province, 410078, Changsha, China. .,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China. .,National Joint Engineering Research Center for Genetic Diagnostics of Infectious Diseases and Cancer, 410078, Changsha, China. .,Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.
| | - Longlong Xie
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Feng Shi
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Min Tang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China.,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China
| | - Yueshuo Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Jianmin Hu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Lin Zhao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Luqing Zhao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China
| | - Xinfang Yu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China.,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China
| | - Weihua Liao
- Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
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Chen B, Zhang Y, Dai S, Zhou P, Luo W, Wang Z, Chen X, Cheng P, Zheng G, Ren J, Yang X, Li W. Molecular characteristics of primary pulmonary lymphoepithelioma-like carcinoma based on integrated genomic analyses. Signal Transduct Target Ther 2021; 6:6. [PMID: 33414372 PMCID: PMC7791019 DOI: 10.1038/s41392-020-00382-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/04/2020] [Accepted: 09/30/2020] [Indexed: 02/05/2023] Open
Abstract
Primary pulmonary lymphoepithelioma-like carcinoma (pLELC) is a rare non-small cell lung cancer (NSCLC) subtype. Clinical features have been described in our previous report, but molecular characteristics remain unclear. Herein, pLELC genomic features were explored. Among 41,574 lung cancers, 128 pLELCs and 162 non-pLELC NSCLCs were enrolled. Programmed cell death ligand 1 (PD-L1) and protein 53 (p53) expression was detected in 47 surgically resected pLELC samples by immunohistochemical assays. Multiomics genomic analyses, including whole-genome sequencing (WGS), RNA whole-transcriptome sequencing (RNA-seq), and Epstein-Barr virus (EBV) integration analyses, were performed on eight frozen pLELC tissues and compared with 50 lung adenocarcinomas (LUADs) and 50 lung squamous cell carcinomas (LUSCs) from The Cancer Genome Atlas (TCGA) and another 26 EBV-positive nasopharynx cancers (EBV+-NPCs). Progression-free survival (PFS) and overall survival (OS) of pLELC patients were better than those of non-pLELC patients. High PD-L1 or p53 expression was associated with extended disease-free survival (DFS). pLELC had 14 frequently mutated genes (FMGs). Somatically mutated genes and enrichment of genetic lesions were found, which differed from observations in LUAD, LUSC, and EBV+-nasopharyngeal carcinoma (NPC). Three tumor-associated genes, zinc finger and BTB domain-containing 16 (ZBTB16), peroxisome proliferator activated receptor gamma (PPARG), and transforming growth factor beta receptor 2 (TGFBR2), were downregulated with copy number variation (CNV) loss. EBV was prone to integrating into intergenic and intronic regions with two upregulated miR-BamH1-A rightward transcripts (BARTs), BART5-3P and BART20-3P. Our findings reveal that pLELC has a distinct genomic signature. Three tumor-associated genes with CNV loss and two miR-BARTs might be involved in pLELC tumorigenesis.
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Affiliation(s)
- Bojiang Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China
| | - Yu Zhang
- Novogene Co., Ltd, Beijing, China
| | - Sisi Dai
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China
| | - Ping Zhou
- Department of Pathology, West China Hospital of Sichuan University, Chengdu, Sichuan, China
| | - Wenxin Luo
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China
| | - Zhoufeng Wang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China
| | - Xuping Chen
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Department of Respiratory and Critical Care Medicine, Guangyuan Central Hospital, No. 16, Jing Jia Alley, Lizhou District, Guangyuan,, 628099, Sichuan, China
| | | | | | - Jing Ren
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China
| | - Xiaodong Yang
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China.
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital of Sichuan University, No. 37, Guo Xue Alley, 610041, Chengdu, Sichuan, China.
- Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu Sichuan, China.
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40
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Mundo L, Del Porro L, Granai M, Siciliano MC, Mancini V, Santi R, Marcar L, Vrzalikova K, Vergoni F, Di Stefano G, Schiavoni G, Segreto G, Onyango N, Nyagol JA, Amato T, Bellan C, Anagnostopoulos I, Falini B, Leoncini L, Tiacci E, Lazzi S. Frequent traces of EBV infection in Hodgkin and non-Hodgkin lymphomas classified as EBV-negative by routine methods: expanding the landscape of EBV-related lymphomas. Mod Pathol 2020; 33:2407-2421. [PMID: 32483241 PMCID: PMC7685982 DOI: 10.1038/s41379-020-0575-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 05/04/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022]
Abstract
The Epstein-Barr virus (EBV) is linked to various B-cell lymphomas, including Burkitt lymphoma (BL), classical Hodgkin lymphoma (cHL) and diffuse large B-cell lymphoma (DLBCL) at frequencies ranging, by routine techniques, from 5 to 10% of cases in DLBCL to >95% in endemic BL. Using higher-sensitivity methods, we recently detected EBV traces in a few EBV-negative BL cases, possibly suggesting a "hit-and-run" mechanism. Here, we used routine and higher-sensitivity methods (qPCR and ddPCR for conserved EBV genomic regions and miRNAs on microdissected tumor cells; EBNA1 mRNA In situ detection by RNAscope) to assess EBV infection in a larger lymphoma cohort [19 BL, 34 DLBCL, 44 cHL, 50 follicular lymphomas (FL), 10 T-lymphoblastic lymphomas (T-LL), 20 hairy cell leukemias (HCL), 10 mantle cell lymphomas (MCL)], as well as in several lymphoma cell lines (9 cHL and 6 BL). qPCR, ddPCR, and RNAscope consistently documented the presence of multiple EBV nucleic acids in rare tumor cells of several cases EBV-negative by conventional methods that all belonged to lymphoma entities clearly related to EBV (BL, 6/9 cases; cHL, 16/32 cases; DLBCL, 11/30 cases), in contrast to fewer cases (3/47 cases) of FL (where the role of EBV is more elusive) and no cases (0/40) of control lymphomas unrelated to EBV (HCL, T-LL, MCL). Similarly, we revealed traces of EBV infection in 4/5 BL and 6/7 HL cell lines otherwise conventionally classified as EBV negative. Interestingly, additional EBV-positive cases (1 DLBCL, 2 cHL) relapsed as EBV-negative by routine methods while showing EBNA1 expression in rare tumor cells by RNAscope. The relapse specimens were clonally identical to their onset biopsies, indicating that the lymphoma clone can largely loose the EBV genome over time but traces of EBV infection are still detectable by high-sensitivity methods. We suggest EBV may contribute to lymphoma pathogenesis more widely than currently acknowledged.
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Affiliation(s)
- Lucia Mundo
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Leonardo Del Porro
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Massimo Granai
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Maria Chiara Siciliano
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Virginia Mancini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Raffaella Santi
- Section of Pathology, University of Florence, Florence, Italy
| | - Lynnette Marcar
- BioMaterials Cluster, Bernal Institute, University of Limerick, Limerick, Ireland
- Ireland, Health Research Institute (HRI), University of Limerick, Limerick, Ireland
| | - Katerina Vrzalikova
- Institute of immunology and Immunotherapy, University of Birmingham, Birmingham, UK
| | | | | | - Gianluca Schiavoni
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy
| | - Giovanna Segreto
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Noel Onyango
- Department of Clinical Medicine and Therapeutics, Unit of Medical Oncology, University of Nairobi, Nairobi, Kenya
| | - Joshua Akelo Nyagol
- Department of Clinical Medicine and Therapeutics, Unit of Medical Oncology, University of Nairobi, Nairobi, Kenya
| | - Teresa Amato
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Cristiana Bellan
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | | | - Brunangelo Falini
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy
| | - Lorenzo Leoncini
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Enrico Tiacci
- Section of Haematology and Clinical Immunology, Department of Medicine, University and Hospital of Perugia, Perugia, Italy.
| | - Stefano Lazzi
- Section of Pathology, Department of Medical Biotechnology, University of Siena, Siena, Italy.
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Hu J, Li Y, Li H, Shi F, Xie L, Zhao L, Tang M, Luo X, Jia W, Fan J, Zhou J, Gao Q, Qiu S, Wu W, Zhang X, Liao W, Bode AM, Cao Y. Targeting Epstein-Barr virus oncoprotein LMP1-mediated high oxidative stress suppresses EBV lytic reactivation and sensitizes tumors to radiation therapy. Theranostics 2020; 10:11921-11937. [PMID: 33204320 PMCID: PMC7667690 DOI: 10.7150/thno.46006] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 09/28/2020] [Indexed: 12/24/2022] Open
Abstract
Generating oxidative stress is a critical mechanism by which host cells defend against infection by pathogenic microorganisms. Radiation resistance is a critical problem in radiotherapy against cancer. Epstein-Barr virus (EBV) is a cancer-causing virus and its reactivation plays an important role in the development of EBV-related tumors. This study aimed to explore the inner relationship and regulatory mechanism among oxidative stress, EBV reactivation, and radioresistance and to identify new molecular subtyping models and treatment strategies to improve the therapeutic effects of radiotherapy. Methods: ROS, NADP+/NADPH, and GSSG/GSH were detected to evaluate the oxidative stress of cells. 8-OHdG is a reliable oxidative stress marker to evaluate the oxidative stress in patients. Its concentration in serum was detected using an ELISA method and in biopsies was detected using IHC. qPCR array was performed to evaluate the expression of essential oxidative stress genes. qPCR, Western blot, and IHC were used to measure the level of EBV reactivation in vitro and in vivo. A Rta-IgG ELISA kit and EBV DNA detection kit were used to analyze the reactivation of EBV in serum from NPC patients. NPC tumor tissue microarrays was used to investigate the prognostic role of oxidative stress and EBV reactivation. Radiation resistance was evaluated by a colony formation assay. Xenografts were treated with NAC, radiation, or a combination of NAC and radiation. EBV DNA load of tumor tissue was evaluated using an EBV DNA detection kit. Oxidative stress, EBV reactivation, and the apoptosis rate in tumor tissues were detected by using 8-OHdG, EAD, and TUNEL assays, respectively. Results: We found that EBV can induce high oxidative stress, which promotes its reactivation and thus leads to radioresistance. Basically, EBV caused NPC cells to undergo a process of 'Redox Resetting' to acquire a new redox status with higher levels of ROS accumulation and stronger antioxidant systems by increasing the expression of the ROS-producing enzyme, NOX2, and the cellular master antioxidant regulator, Nrf2. Also, EBV encoded driving protein LMP1 promotes EBV reactivation through production of ROS. Furthermore, high oxidative stress and EBV reactivation were positively associated with poor overall survival of patients following radiation therapy and were significant related to NPC patients' recurrence and clinical stage. By decreasing oxidative stress using an FDA approved antioxidant drug, NAC, sensitivity of tumors to radiation was increased. Additionally, 8-OHdG and EBV DNA could be dual prognostic markers for NPC patients. Conclusions: Oxidative stress mediates EBV reactivation and leads to radioresistance. Targeting oxidative stress can provide therapeutic benefits to cancer patients with radiation resistance. Clinically, we, for the first time, generated a molecular subtyping model for NPC relying on 8-OHdG and EBV DNA level. These dual markers could identify patients who are at a high risk of poor outcomes but who might benefit from the sequential therapy of reactive oxygen blockade followed by radiation therapy, which provides novel perspectives for the precise treatment of NPC.
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Yakushina SA, Kisteneva LB. [Epstein-Barr virus ( Herpesviridae: Gammaherpesvirinae: Lymphocryptovirus: Human gammaherpesvirus 4): replication strategies]. Vopr Virusol 2020; 65:191-202. [PMID: 33533222 DOI: 10.36233/0507-4088-2020-65-4-191-202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 09/16/2020] [Indexed: 01/15/2023]
Abstract
The Epstein-Barr virus (EBV), one of the most common in the human population, is capable of lifelong persistence in resting memory B-cells, in T-cells in case of type 2 EBV, and in some undifferentiated epithelial cells. In most people, EBV persistence is not accompanied by significant symptoms, but frequent virus activations are associated with the increased risks of severe diseases, such as chronic active Epstein-Barr virus infection, hemophagocytic lymphohistiocytosis, multiple sclerosis, systemic lupus erythematosus, gastric and nasopharyngeal carcinomas, and a variety of T- and B-cell lymphomas. Therefore, the molecular viral and host cell processes during asymptomatic or low-symptom EBV persistence are of great interest. This review describes the behavior of the viral DNA in an infected cell and the forms of its existence (linear, circular episome, chromosomally integrated forms), as well as methods of EBV genome copying. Two closely related cycles of viral reproduction are considered. Lytic activation is unfavorable for the survival of a particular viral genome in the cell, and may be a result of differentiation of a latently infected cell, or the arrival of stress signals due to adverse extracellular conditions. The EBV has a large number of adaptive mechanisms for limiting lytic reactivation and reducing hostility of host immune cells. Understanding the molecular aspects of EBV persistence will help in the future develop more effective targeted drugs for the treatment of both viral infection and associated diseases.
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Affiliation(s)
- S A Yakushina
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Ministry of Health of Russian Federation
| | - L B Kisteneva
- National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya, Ministry of Health of Russian Federation
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Chiang C, Zhang M, Wang D, Xiao T, Zhu L, Chen K, Huang J, Huang J, Zhu J, Li L, Chen C, Chen Y, Hu H, Jiang W, Zou Y, Wang T, Zheng D. Therapeutic potential of targeting MKK3-p38 axis with Capsaicin for Nasopharyngeal Carcinoma. Am J Cancer Res 2020; 10:7906-7920. [PMID: 32685028 PMCID: PMC7359099 DOI: 10.7150/thno.45191] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 06/10/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Capsaicin is an active compound found in plants of the Capsicum genus; it has a range of therapeutic benefits, including anti-tumor effects. Here we aimed to delineate the inhibitory effects of capsaicin on nasopharyngeal carcinoma (NPC). Methods: The anti-cancer effects of capsaicin were confirmed in NPC cell lines and xenograft mouse models, using CCK-8, clonogenic, wound-healing, transwell migration and invasion assays. Co-immunoprecipitation, western blotting and pull-down assays were used to determine the effects of capsaicin on the MKK3-p38 axis. Cell proliferation and EMT marker expression were monitored in MKK3 knockdown (KD) or over-expression NPC cell lines treated with or without capsaicin. Finally, immunohistochemistry was performed on NPC specimens from NPC patients (n = 132) and the clinical relevance was analyzed. Results: Capsaicin inhibited cell proliferation, mobility and promoted apoptosis in NPC cells. Then we found that capsaicin directly targets p38 for dephosphorylation. As such, MKK3-induced p38 activation was inhibited by capsaicin. Furthermore, we found that capsaicin-induced inhibition of cell motility was mediated by fucokinase. Xenograft models demonstrated the inhibitory effects of capsaicin treatment on NPC tumor growth in vivo, and analysis of clinical NPC samples confirmed that MKK3 phosphorylation was associated with NPC tumor growth and lymphoid node metastasis. Conclusions: The MKK3-p38 axis represents a potential therapeutic target for capsaicin. MKK3 phosphorylation might serve as a biomarker to identify NPC patients most likely to benefit from adjunctive capsaicin treatment.
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Miliotis CN, Slack FJ. Multi-layered control of PD-L1 expression in Epstein-Barr virus-associated gastric cancer. ACTA ACUST UNITED AC 2020; 6. [PMID: 34212113 PMCID: PMC8244904 DOI: 10.20517/2394-4722.2020.12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gastric cancer (GC) is the fifth most common cancer worldwide. In approximately 10% of GC cases, cancer cells show ubiquitous and monoclonal Epstein-Barr virus (EBV) infection. A significant feature of EBV-associated GC (EBVaGC) is high lymphocytic infiltration and high expression of immune checkpoint proteins, including programmed death-ligand 1 (PD-L1). This highlights EBVaGC as a strong candidate for immune checkpoint blockade therapy. Indeed, several recent studies have shown that EBV positivity in GC correlates with positive response to programmed cell death protein 1 (PD-1)/PD-L1 blockade therapy. Understanding the mechanisms that control PD-L1 expression in EBVaGC can indicate new predictive biomarkers for immunotherapy, as well as therapeutic targets for combination therapy. Various mechanisms have been implicated in PD-L1 expression regulation, including structural variations, post-transcriptional control, oncogenic activation of intrinsic signaling pathways, and increased sensitivity to extrinsic signals. This review provides the most recent updates on the multilayered control of PD-L1 expression in EBVaGC.
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Affiliation(s)
- Christos N Miliotis
- HMS Initiative for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Frank J Slack
- HMS Initiative for RNA Medicine, Department of Pathology, Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
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Li S, Dai X, Gong K, Song K, Tai F, Shi J. PA28α/β Promote Breast Cancer Cell Invasion and Metastasis via Down-Regulation of CDK15. Front Oncol 2019; 9:1283. [PMID: 31824858 PMCID: PMC6883405 DOI: 10.3389/fonc.2019.01283] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 11/05/2019] [Indexed: 12/22/2022] Open
Abstract
PA28α/β activated immunoproteasome frequently participates in MHC class I antigen processing, however, whether it is involved in breast tumor progression remains largely unclear. Here, our evidences show that PA28α/β proteins are responsible for breast cancer cell migration, invasion, and metastasis. Knockdown of immunoproteasome core subunit β5i also robustly suppresses the tumor cell migration and invasion. Interestingly, silencing of PA28α/β and β5i up-regulates the protein expression of cyclin-dependent kinase 15 (CDK15). Our data further indicate that the loss of CDK15 is important for breast tumor cell invasion and metastasis. Taken together, this study implicates that targeting of PA28α/β represents a potential way for treatment of metastatic breast cancer.
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Affiliation(s)
- Shengnan Li
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Xiaoqin Dai
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China.,Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangdong, China
| | - Kunxiang Gong
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Kai Song
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Fang Tai
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
| | - Jian Shi
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Tumor Pathology, Southern Medical University, Guangdong, China
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Li ZX, Zheng ZQ, Wei ZH, Zhang LL, Li F, Lin L, Liu RQ, Huang XD, Lv JW, Chen FP, He XJ, Guan JL, Kou J, Ma J, Zhou GQ, Sun Y. Comprehensive characterization of the alternative splicing landscape in head and neck squamous cell carcinoma reveals novel events associated with tumorigenesis and the immune microenvironment. Am J Cancer Res 2019; 9:7648-7665. [PMID: 31695792 PMCID: PMC6831462 DOI: 10.7150/thno.36585] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative splicing (AS) has emerged as a key event in tumor development and microenvironment formation. However, comprehensive analysis of AS and its clinical significance in head and neck squamous cell carcinoma (HNSC) is urgently required. Methods: Genome-wide profiling of AS events using RNA-Seq data from The Cancer Genome Atlas (TCGA) program was performed in a cohort of 464 patients with HNSC. Cancer-associated AS events (CASEs) were identified between paired HNSC and adjacent normal tissues and evaluated in functional enrichment analysis. Splicing networks and prognostic models were constructed using bioinformatics tools. Unsupervised clustering of the CASEs identified was conducted and associations with clinical, molecular and immune features were analyzed. Results: We detected a total of 32,309 AS events and identified 473 CASEs in HNSC; among these, 91 were validated in an independent cohort (n = 15). Functional protein domains were frequently altered, especially by CASEs affecting cancer drivers, such as PCSK5. CASE parent genes were significantly enriched in pathways related to HNSC and the tumor immune microenvironment, such as the viral carcinogenesis (FDR < 0.001), Human Papillomavirus infection (FDR < 0.001), chemokine (FDR < 0.001) and T cell receptor (FDR < 0.001) signaling pathways. CASEs enriched in immune-related pathways were closely associated with immune cell infiltration and cytolytic activity. AS regulatory networks suggested a significant association between splicing factor (SF) expression and CASEs and might be regulated by SF methylation. Eighteen CASEs were identified as independent prognostic factors for overall and disease-free survival. Unsupervised clustering analysis revealed distinct correlations between AS-based clusters and prognosis, molecular characteristics and immune features. Immunogenic features and immune subgroups cooperatively depict the immune features of AS-based clusters. Conclusion: This comprehensive genome-wide analysis of the AS landscape in HNSC revealed novel AS events related to carcinogenesis and immune microenvironment, with implications for prognosis and therapeutic responses.
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De Leo A, Calderon A, Lieberman PM. Control of Viral Latency by Episome Maintenance Proteins. Trends Microbiol 2019; 28:150-162. [PMID: 31624007 DOI: 10.1016/j.tim.2019.09.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/30/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022]
Abstract
The human DNA tumor viruses Epstein-Barr virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and human papillomavirus (HPV) share the common property of persisting as multicopy episomes in the nuclei of rapidly dividing host cells. These episomes form the molecular basis for viral latency and are etiologically linked to virus-associated cancers. Episome maintenance requires epigenetic programming to ensure the proper control of viral gene expression, DNA replication, and genome copy number. For these viruses, episome maintenance requires a dedicated virus-encoded episome maintenance protein (EMP), namely LANA (KSHV), EBNA1 (EBV), and E2 (HPV). Here, we review common features of these viral EMPs and discuss recent advances in understanding how they contribute to the epigenetic control of viral episome maintenance during latency.
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