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Schäffer AA, Dominguez DA, Chapman LM, Gertz EM, Budhu A, Forgues M, Chaisaingmongkol J, Rabibhadana S, Pupacdi B, Wu X, Bayarsaikhan E, Harris CC, Ruchirawat M, Ruppin E, Wang XW. Integration of adeno-associated virus (AAV) into the genomes of most Thai and Mongolian liver cancer patients does not induce oncogenesis. BMC Genomics 2021; 22:814. [PMID: 34763675 PMCID: PMC8588581 DOI: 10.1186/s12864-021-08098-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/19/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Engineered versions of adeno-associated virus (AAV) are commonly used in gene therapy but evidence revealing a potential oncogenic role of natural AAV in hepatocellular carcinoma (HCC) has raised concerns. The frequency of potentially oncogenic integrations has been reported in only a few populations. AAV infection and host genome integration in another type of liver cancer, cholangiocarcinoma (CCA), has been studied only in one cohort. All reported oncogenic AAV integrations in HCC come from strains resembling the fully sequenced AAV2 and partly sequenced AAV13. When AAV integration occurs, only a fragment of the AAV genome is detectable in later DNA or RNA sequencing. The integrated fragment is typically from the 3' end of the AAV genome, and this positional bias has been only partly explained. Three research groups searched for evidence of AAV integration in HCC RNAseq samples in the Cancer Genome Atlas (TCGA) but reported conflicting results. RESULTS We collected and analyzed whole transcriptome and viral capture DNA sequencing in paired tumor and non-tumor samples from two liver cancer Asian cohorts from Thailand (N = 147, 47 HCC and 100 intrahepatic cholangiocarcinoma (iCCA)) and Mongolia (N = 70, all HCC). We found only one HCC patient with a potentially oncogenic integration of AAV, in contrast to higher frequency reported in European patients. There were no oncogenic AAV integrations in iCCA patients. AAV genomic segments are present preferentially in the non-tumor samples of Thai patients. By analyzing the AAV genome positions of oncogenic and non-oncogenic integrated fragments, we found that almost all the putative oncogenic integrations overlap the X gene, which is present and functional only in the strain AAV2 among all fully sequenced strains. This gene content difference could explain why putative oncogenic integrations from other AAV strains have not been reported. We resolved the discrepancies in previous analyses of AAV presence in TCGA HCC samples and extended it to CCA. There are 12 TCGA samples with an AAV segment and none are in Asian patients. AAV segments are present in preferentially in TCGA non-tumor samples, like what we observed in the Thai patients. CONCLUSIONS Our findings suggest a minimal AAV risk of hepatocarcinogenesis in Asian liver cancer patients. The partial genome presence and positional bias of AAV integrations into the human genome has complicated analysis of possible roles of AAV in liver cancer.
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Affiliation(s)
- Alejandro A Schäffer
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Dana A Dominguez
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lesley M Chapman
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - E Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Anuradha Budhu
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Marshonna Forgues
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jittiporn Chaisaingmongkol
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Siritida Rabibhadana
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand
| | - Benjarath Pupacdi
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand
| | - Xiaolin Wu
- Frederick National Laboratory for Cancer Research, Leidos Biomedical Research Inc, Frederick, MD, USA
| | | | - Curtis C Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mathuros Ruchirawat
- Laboratory of Chemical Carcinogenesis, Chulabhorn Research Institute, Bangkok, Thailand.,Center of Excellence on Environmental Health and Toxicology, Office of Higher Education Commission, Ministry of Education, Bangkok, Thailand
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA. .,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
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4
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da Silva BEB, de Lemos LMD, de Aragão Batista MV, Lima CA, Martins-Filho PR, Santos VS. Prevalence of human papillomavirus infection in Brazilian women living with HIV: a systematic review and meta-analysis. Expert Rev Anti Infect Ther 2021; 20:611-620. [PMID: 34612128 DOI: 10.1080/14787210.2022.1990039] [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: 10/20/2022]
Abstract
OBJECTIVE We systematically investigated the prevalence of HPV, high-risk HPV and its genotypes in women living with human immunodeficiency virus (WLHIV) in Brazil. METHODS A systematic search was performed up to 15 December 2020. We included studies that used molecular methods for HPV detection in cervical samples and reported the prevalence of HPV in Brazilian WLHIV. The pooled prevalence of HPV, high-risk HPV (HR HPV) and HPV types and their 95% confidence interval (CI) were estimated. Subgroup analyses and meta-regression were conducted. RESULTS Thity-seven studies accounting for 8,436 WLHIV were included. The pooled HPV prevalence was 62% (95%CI 55-68%; I2 = 96.98%; P < 0.001). Prevalence of high-risk HPV was 40% (95%CI, 54-68%; I2 = 94.23%; P < 0.001). We found a wide variety of high-risk HPV genotypes. The high-risk HPV types most reported were HPV 16 (16%) and HPV 58 (6%). We found an increasing ratio of positivity from normal cervix to cancer. There were different factors associated with high-risk HPV, with low CD4+ count the most frequent. CONCLUSION The increase in the ratio of high-risk HPV positivity from normal cervix to carcinogenic lesions highlights the need to implement well-established testing for high-risk HPV in this population.
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Affiliation(s)
| | | | | | - Carlos Anselmo Lima
- Graduate Program in Health Sciences, Federal University of Sergipe, Aracaju, Brazil
| | - Paulo Ricardo Martins-Filho
- Graduate Program in Health Sciences, Federal University of Sergipe, Aracaju, Brazil.,Investigative Pathology Laboratory, Federal University of Sergipe, Aracaju, Brazil
| | - Victor Santana Santos
- Graduate Program in Health Sciences, Federal University of Sergipe, Aracaju, Brazil.,Centre for Epidemiology and Public Health, Federal University of Alagoas, Arapiraca, Brazil.,Graduate Program in Health Sciences, Federal University of Alagoas, Maceió, Brazil
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8
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Nault JC, Datta S, Imbeaud S, Franconi A, Mallet M, Couchy G, Letouzé E, Pilati C, Verret B, Blanc JF, Balabaud C, Calderaro J, Laurent A, Letexier M, Bioulac-Sage P, Calvo F, Zucman-Rossi J. AAV2 and Hepatocellular Carcinoma. Hum Gene Ther 2016; 27:211-3. [PMID: 26935016 DOI: 10.1089/hum.2016.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Affiliation(s)
- Jean-Charles Nault
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
- 5 APHP, Hôpitaux Universitaires Paris-Seine Saint-Denis , Site Jean Verdier, Pôle d'Activité Cancérologique Spécialisée, Service d'Hépatologie, Bondy, France
| | - Shalini Datta
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Sandrine Imbeaud
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Andrea Franconi
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Maxime Mallet
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Gabrielle Couchy
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Eric Letouzé
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Camilla Pilati
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Benjamin Verret
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 4 Université Paris Diderot , IUH, Paris, France
| | - Jean-Frédéric Blanc
- 6 CHU de Bordeaux, Department of Hepatology, Hôpital Saint-André , Bordeaux, France
- 7 INSERM, UMR-1053; Université de Bordeaux, Bordeaux , France
| | | | - Julien Calderaro
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
- 8 Assistance Publique-Hôpitaux de Paris , Department of Pathology, CHU Henri Mondor, Créteil, France
| | - Alexis Laurent
- 9 Assistance Publique-Hôpitaux de Paris , Department of Digestive and Hepatobiliary Surgery, CHU Henri Mondor, Créteil, France
- 10 INSERM , U955, Créteil, France
| | | | - Paulette Bioulac-Sage
- 7 INSERM, UMR-1053; Université de Bordeaux, Bordeaux , France
- 12 CHU de Bordeaux, Pellegrin Hospital , Department of Pathology, Bordeaux, France
| | - Fabien Calvo
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
- 13 Institut Gustave Roussy , Core Europe, Villejuif, France
| | - Jessica Zucman-Rossi
- 1 INSERM, UMR-1162, Génomique fonctionnelle des Tumeurs solides, Equipe Labellisée Ligue Contre le Cancer , Paris, France
- 2 Labex Immuno-Oncology, Université Paris Descartes , Sorbonne Paris Cité, Paris, France
- 3 Université Paris 13 , Sorbonne Paris Cité, UFR SMBH, Bobigny, France
- 4 Université Paris Diderot , IUH, Paris, France
- 14 Assistance Publique-Hôpitaux de Paris , Hopital Europeen Georges Pompidou, Paris, France
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