1
|
Eldem V, Kuralay SC, Özdoğan G, Özçelik GH, Aydın D, Çakmak G, Gürler MÖ, Çay SB, Çınar YU, Dikmen F, Yusuf I, Obut O, Kayalar Ö, Zararsız GE, Edizadeh M, Zararsız G, Akdeniz E, Özgür H, Tekin IM. Comprehensive analysis of circulating viral DNA in maternal plasma at population-scale using low-pass whole-genome sequencing. Genomics 2023; 115:110556. [PMID: 36599399 DOI: 10.1016/j.ygeno.2022.110556] [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: 06/29/2022] [Revised: 11/04/2022] [Accepted: 12/30/2022] [Indexed: 01/02/2023]
Abstract
As the most readily adopted molecular screening test, low-pass WGS of maternal plasma cell-free DNA for aneuploidy detection generates a vast amount of genomic data. This large-scale method also allows for high-throughput virome screening. NIPT sequencing data, yielding 6.57 terabases of data from 187.8 billion reads, from 12,951 pregnant Turkish women was used to investigate the prevalence and abundance of viral DNA in plasma. Among the 22 virus sequences identified in 12% of participants were human papillomavirus, herpesvirus, betaherpesvirus and anellovirus. We observed a unique pattern of circulating viral DNA with a high prevalence of papillomaviruses. The prevalence of herpesviruses/anellovirus was similar among Turkish, European and Dutch populations. Hepatitis B prevalence was remarkably low in Dutch, European and Turkish populations, but higher in China. WGS data revealed that herpesvirus/anelloviruses are naturally found in European populations. This represents the first comprehensive research on the plasma virome of pregnant Turkish women.
Collapse
Affiliation(s)
- Vahap Eldem
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey.
| | - Selim Can Kuralay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Gülperi Özdoğan
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Dilşah Aydın
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökçe Çakmak
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | | - Selahattin Barış Çay
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Yusuf Ulaş Çınar
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Fatih Dikmen
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Ishak Yusuf
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Onur Obut
- Department of Biology, Faculty of Science, Istanbul University, Istanbul 34134, Turkey
| | - Özgecan Kayalar
- Koc University Research Center for Translational Medicine (KUTTAM), Koc University School of Medicine, Istanbul 34010, Turkey
| | - Gözde Ertürk Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Masoud Edizadeh
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Gökmen Zararsız
- Department of Biostatistics, Erciyes University Medical Faculty, Kayseri 38280, Turkey; Erciyes University, Drug Application and Research Center (ERFARMA), Kayseri 38280, Turkey
| | - Eren Akdeniz
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | - Hilal Özgür
- GENOKS Genetic Disease Diagnostic Center, Ankara 06560, Turkey
| | | |
Collapse
|
2
|
PCR Detection of Epstein-Barr Virus (EBV) DNA in Patients with Head and Neck Squamous Cell Carcinoma, in Patients with Chronic Tonsillitis, and in Healthy Individuals. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8506242. [PMID: 35993047 PMCID: PMC9381848 DOI: 10.1155/2022/8506242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/24/2022] [Accepted: 07/27/2022] [Indexed: 11/26/2022]
Abstract
Epstein-Barr virus (EBV) is a common virus worldwide that is an etiologic agent in the development of many diseases, including cancer. Recent reports have shown the association of EBV with tumorigenesis in head and neck squamous cell carcinoma (HNSCC). Moreover, EBV has been reported to be present in tonsillar tissues, which suggests a close relationship between viral infections and tonsillar diseases, including chronic tonsillitis. The aim of the study was to analyze the prevalence of EBV DNA in 86 patients with HNSCC, in 70 patients with chronic tonsillitis, and in 144 healthy individuals (control group) and the associations between EBV infection and clinicopathological and demographic characteristics and the use of stimulants in all study groups. The objective of this study was also to analyze the prevalence of coinfection with human papillomavirus (HPV). After prior DNA isolation, EBV detection was performed using an EBV kit by real-time polymerase chain reaction. The prevalence of EBV infection in patients with HNSCC, patients with chronic tonsillitis, and the control group was 47.7%, 60%, and 24.3%, respectively. Compared to controls, a significantly higher prevalence of EBV in patients with chronic tonsillitis and HNSCC may suggest that EBV is a potential risk factor. No association was found between EBV infection and demographic or clinical data. Further studies are warranted due to inconclusive reports that were mainly related to geographic distribution, sample type, and detection technique. Considering the prevalence of the virus and the risk of serious diseases, attention should be paid to screening diagnosis and prevention of the infection.
Collapse
|
3
|
Gupta I, Nasrallah GK, Sharma A, Jabeen A, Smatti MK, Al-Thawadi HA, Sultan AA, Alkhalaf M, Vranic S, Al Moustafa AE. Correction to: Co-prevalence of human Papillomaviruses (HPV) and Epstein–Barr virus (EBV) in healthy blood donors from diverse nationalities in Qatar. Cancer Cell Int 2022; 22:45. [PMID: 35093069 PMCID: PMC8801089 DOI: 10.1186/s12935-022-02459-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2022] [Indexed: 11/10/2022] Open
|
4
|
Gupta I, Ulamec M, Peric-Balja M, Ramic S, Al Moustafa AE, Vranic S, Al-Farsi HF. Presence of high-risk HPVs, EBV, and MMTV in human triple-negative breast cancer. Hum Vaccin Immunother 2021; 17:4457-4466. [PMID: 34623225 PMCID: PMC8828071 DOI: 10.1080/21645515.2021.1975452] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Breast cancer, the most frequent disease amongst women worldwide, accounts for the highest cancer-related mortality rate. Triple-negative breast cancer (TNBC) subtype encompasses ~15% of all breast cancers and lack estrogen, progesterone, and HER2 receptors. Although risk factors for breast cancer are well-known, factors underpinning breast cancer onset and progression remain unknown. Recent studies suggest the plausible role of oncoviruses including human papillomaviruses (HPVs), Epstein-Barr virus (EBV), and mouse mammary tumor virus (MMTV) in breast cancer pathogenesis. However, the role of these oncoviruses in TNBC is still unclear. In the current study, we explored the status of high-risk HPVs, EBV, and MMTV in a well-defined TNBC cohort from Croatia in comparison to 16 normal/non TNBC samples (controls) using polymerase chain reaction assay. We found high-risk HPVs and EBV present in 37/70 (53%) and 25/70 (36%) of the cases, respectively. The most common HPV types are 52, 45, 31, 58 and 68. We found 16% of the samples positive for co-presence of high-risk HPVs and EBV. Moreover, our data revealed that 5/70 (7%) samples are positive for MMTV. In addition, only 2/70 (3%) samples had co-presence of HPVs, EBV, and MMTV without any significant association with the clinicopathological variables. While, 6/16 (37.5%) controls were positive for HPV (p = .4), EBV was absent in all controls (0/16, 0%) (p = .01). In addition, we did not find the co-presence of the oncoviruses in the controls (p > .05). Nevertheless, further investigations are essential to understand the underlying mechanisms of multiple-oncogenic viruses' interaction in breast carcinogenesis, especially TNBC.
Collapse
Affiliation(s)
- Ishita Gupta
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
| | - Monika Ulamec
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
- Department of Pathology and Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Melita Peric-Balja
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Oncological Pathology Department, Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Snjezana Ramic
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Oncological Pathology Department, Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre Milosrdnice University Hospital Center, Zagreb, Croatia
| | - Ala-Eddin Al Moustafa
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Biomedical Research Center, QU Health, Qatar University, Doha, Qatar
- CONTACT Ala-Eddin Al Moustafa College of Medicine, Qu Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Semir Vranic
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
| | - Halema F. Al-Farsi
- College of Medicine, Qu Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qu Health, Qatar University, Doha, Qatar
- Halema F. Al-Farsi College of Medicine, Qu Health, Qatar University, PO Box2713, Doha, Qatar
| |
Collapse
|
5
|
Nagi K, Gupta I, Jurdi N, Jabeen A, Yasmeen A, Batist G, Vranic S, Al-Moustafa AE. High-risk human papillomaviruses and Epstein-Barr virus in breast cancer in Lebanese women and their association with tumor grade: a molecular and tissue microarray study. Cancer Cell Int 2021; 21:308. [PMID: 34112166 PMCID: PMC8194154 DOI: 10.1186/s12935-021-02009-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 12/11/2022] Open
Abstract
Background High-risk human papillomaviruses (HPVs) are present and can cooperate with Epstein–Barr virus (EBV) to initiate and/or enhance the progression of several types of human carcinomas including cervical as well as head and neck; in parallel, it has been recently pointed out that these oncoviruses can be detected in human breast cancers. Thus, we herein explored the presence/co-presence of high-risk HPVs and EBV in breast cancer in Lebanese women. Methods A cohort of 102 breast cancer samples and 14 normal breast tissues were assessed for the presence of HPVs and EBV. Polymerase chain reaction (PCR) and immunohistochemistry (IHC) analysis in addition to tissue microarray (TMA) platform were used in this study. Results We found the presence of HPV in 66/102 (65%) of our samples, while EBV is present in 41/102 (40%) of the cohort. Additionally, our data showed that high-risk HPV types (52, 35, 58, 45, 16 and 51) are the most frequent in breast cancer in Lebanese women. Meanwhile, we report that high-risk HPVs and EBV are co-present in 30/102 (29%) of the samples; more significantly, our results indicate that their co-presence is associated with tumor grade (p = 0.03). Conclusion Our data revealed that HPVs and EBV are present/co-present in human breast cancer where they may play an important role in its development and/or progression; thus, we believe that further investigations are essential to confirm and elucidate the presence/co-presence of these oncoviruses and the underlying mechanisms of their interaction in breast carcinogenesis.
Collapse
Affiliation(s)
- Karim Nagi
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar. .,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar.
| | - Ishita Gupta
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical Research Centre, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Nawaf Jurdi
- Department of Pathology and Laboratory Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ayesha Jabeen
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical Research Centre, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Amber Yasmeen
- Segal Cancer Centre, Lady Davis Institute for Medical Research/JGH, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Gerald Batist
- Segal Cancer Centre, Lady Davis Institute for Medical Research/JGH, McGill University, Montreal, QC, H3A 0G4, Canada.,Oncology Department, McGill University, Montreal, QC, H3A 0G4, Canada
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar.,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar
| | - Ala-Eddin Al-Moustafa
- College of Medicine, QU Health, Qatar University, PO Box 2713, Doha, Qatar. .,Biomedical and Pharmaceutical Research Unit, QU Health, Qatar University, PO Box 2713, Doha, Qatar. .,Biomedical Research Centre, QU Health, Qatar University, PO Box 2713, Doha, Qatar.
| |
Collapse
|
6
|
Gupta I, Jabeen A, Vranic S, Al Moustafa AE, Al-Thawadi H. Oncoproteins of High-Risk HPV and EBV Cooperate to Enhance Cell Motility and Invasion of Human Breast Cancer Cells via Erk1/Erk2 and β-Catenin Signaling Pathways. Front Oncol 2021; 11:630408. [PMID: 33777781 PMCID: PMC7994530 DOI: 10.3389/fonc.2021.630408] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/08/2021] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is a leading cause of death in women around the world. Most breast cancer-related deaths are a result of complications from the metastatic spread. Several recent studies reported that high-risk human papillomaviruses (HPVs) and Epstein-Barr virus (EBV) are co-presented in different types of human carcinomas including breast; however, the cooperative effects between high-risk HPVs and EBV oncoproteins in human breast cancer have not been investigated yet. Thus, we herein explored the cooperation outcome between E6/E7 and latent membrane protein 1 (LMP1) oncoproteins of high-risk HPV type 16 and EBV, respectively, in two human breast cancer cell lines, MCF7 and MDA-MB-231. Our data revealed that the cooperation of E6/E7 and LMP1 oncoproteins stimulates cell proliferation and deregulates cell cycle progression of human breast cancer and normal mammary cells; in parallel, we noted that E6/E7/LMP1 incite colony formation of both breast cancer cell lines but not normal cells. More significantly, our results point out that the co-expression of E6/E7 and LMP1 oncoproteins enhances cell motility and invasion of MCF7 and MDA-MB-231 cell lines; this is accompanied by deregulation of epithelial-mesenchymal transition biomarkers including E-cadherin, β-catenin, fascin, and vimentin. The molecular pathway analysis of HPV and EBV oncoproteins cooperation shows that it can enhance the phosphorylation of extracellular signal-regulated kinases (Erk1/Erk2) in addition to β-catenin, which could be behind the effect of this cooperation in our cell models. The study clearly suggests that high-risk HPV and EBV coinfection can play an important role in breast cancer progression via Erk1/Erk2 and β-catenin signaling pathways.
Collapse
Affiliation(s)
- Ishita Gupta
- College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Ayesha Jabeen
- College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Semir Vranic
- College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qatar University Health, Qatar University, Doha, Qatar
| | - Ala-Eddin Al Moustafa
- College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical Research Centre, Qatar University, Doha, Qatar
| | - Hamda Al-Thawadi
- College of Medicine, Qatar University Health, Qatar University, Doha, Qatar
- Biomedical and Pharmaceutical Research Unit, Qatar University Health, Qatar University, Doha, Qatar
| |
Collapse
|
7
|
Gupta I, Jabeen A, Al-Sarraf R, Farghaly H, Vranic S, Sultan AA, Al Moustafa AE, Al-Thawadi H. The co-presence of high-risk human papillomaviruses and Epstein-Barr virus is linked with tumor grade and stage in Qatari women with breast cancer. Hum Vaccin Immunother 2020; 17:982-989. [PMID: 33006291 PMCID: PMC8018460 DOI: 10.1080/21645515.2020.1802977] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
High-risk human papillomaviruses (HPV) can be present and cooperate with Epstein–Barr virus (EBV) to promote the onset and/or progression of various cancers including cervical, breast, head and neck as well as colorectal. In this investigation, we explored the co-prevalence of high-risk HPV and EBV in 74 breast cancer tissues from Qatari women using polymerase chain reaction. We found that high-risk HPV and EBV are present in 48/74 (65%) and 36/74 (49%) of the cases, respectively. While we noted that the presence of HPV presence is associated with triple-negative breast cancer (TNBC) (p = .008), however, the presence of EBV did not correlate with any breast cancer subgroup. Moreover, our data revealed that high-risk HPV and EBV are co-present in 35/74 (47%) of the samples and their co-presence is significantly associated with tumor grade (p = .04) and tumor stage (p = .04). These data indicate that HPV and EBV are commonly co-present in breast cancer and their association could be linked with a more aggressive tumor phenotype. Thus, further investigations are essential to understand the underlying mechanisms of HPV and EBV cooperation in breast carcinogenesis.
Collapse
Affiliation(s)
- Ishita Gupta
- College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Centre, QU Health, Qatar University, Doha, Qatar
| | - Ayesha Jabeen
- College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Centre, QU Health, Qatar University, Doha, Qatar
| | - Reem Al-Sarraf
- Department of Pathology, Hamad General Hospital, Doha, Qatar
| | - Hanan Farghaly
- Department of Pathology, Hamad General Hospital, Doha, Qatar
| | - Semir Vranic
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Ali A Sultan
- Department of Microbiology and Immunology, Weill Cornell Medicine - Qatar, Doha, Qatar
| | - Ala-Eddin Al Moustafa
- College of Medicine, QU Health, Qatar University, Doha, Qatar.,Biomedical Research Centre, QU Health, Qatar University, Doha, Qatar
| | | |
Collapse
|
8
|
Lawson JS, Glenn WK. Evidence for a causal role by human papillomaviruses in prostate cancer - a systematic review. Infect Agent Cancer 2020; 15:41. [PMID: 32684946 PMCID: PMC7359253 DOI: 10.1186/s13027-020-00305-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/25/2020] [Indexed: 12/17/2022] Open
Abstract
It is hypothesised that high risk for cancer human papillomaviruses (HPVs) have a causal role in prostate cancer. In 26 case control studies, high risk HPVs have been identified in benign and prostate cancers. High risk HPVs were identified in 325 (22.6%) of 1284 prostate cancers and in 113 (8.6%) of 1313 normal or benign prostate controls (p = 0.001). High risk HPVs of the same type have been identified in both normal and benign prostate tissues prior to the development of HPV positive prostate cancer. High risk HPVs can be associated with inflammatory prostatitis leading to benign prostate hyperplasia and later prostate cancer. Normal human prostate epithelial cells can be immortalised by experimental exposure to HPVs. HPVs are probably sexually transmitted. The role of HPVs in prostate cancer is complex and differs from HPVs associated cervical cancer. HPV infections may initiate prostate oncogenesis directly and influence oncogenesis indirectly via APOBEC enzymes. HPVs may collaborate with other pathogens in prostate oncogenesis. Although HPVs are only one of many pathogens that have been identified in prostate cancer, they are the only infectious pathogen which can be prevented by vaccination. A causal role for HPVs in prostate cancer is highly likely.
Collapse
Affiliation(s)
- James S Lawson
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| | - Wendy K Glenn
- School of Biotechnology and Biomolecular Science, University of New South Wales, Sydney, Australia
| |
Collapse
|