Abstract:Bats are associated with several important zoonotic viruses from different families. One example includes adeno-associated viruses (AAVs), that are extensively detected in several animals, especially primates. To understand AAVs distribution and genetic diversity in the coastal areas of Southeast China, a total of 415 intestine samples were mostly collected from two provinces of southeast China, i.e., Zhejiang and Fujian province. Intestine samples from five bat species were collected for AAVs detection. The a… Show more
“…Cao et al suggested that there may be shorter isoforms that are suffixes of the above sequence starting from one of the other two methionines among the first 50 amino acids [ 22 ]. A search of the protein non-redundant (nr) database with X protein as query found only one significant match (E-value 0.0002 to sequence QDX47270.1, which is the 760aa capsid protein of another AAV found in the Chinese bat species Rhinolophus pusillus [ 36 ]. Interestingly a BLASTP search [ 29 ] with QDX47270.1 as query finds many capsid proteins from AAV sequences aligning within the interval [1.435] of QDX47270.…”
Section: Resultsmentioning
confidence: 99%
“… Fig. 1 Visualization of the adeno-associated virus strain 2 (AAV2) genome including the X gene [ 20 ] and a promoter-enhancer region [ 36 ] that may be important to carcinogenesis but are not typically shown in schematic illustrations of AAV2 …”
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.
“…Cao et al suggested that there may be shorter isoforms that are suffixes of the above sequence starting from one of the other two methionines among the first 50 amino acids [ 22 ]. A search of the protein non-redundant (nr) database with X protein as query found only one significant match (E-value 0.0002 to sequence QDX47270.1, which is the 760aa capsid protein of another AAV found in the Chinese bat species Rhinolophus pusillus [ 36 ]. Interestingly a BLASTP search [ 29 ] with QDX47270.1 as query finds many capsid proteins from AAV sequences aligning within the interval [1.435] of QDX47270.…”
Section: Resultsmentioning
confidence: 99%
“… Fig. 1 Visualization of the adeno-associated virus strain 2 (AAV2) genome including the X gene [ 20 ] and a promoter-enhancer region [ 36 ] that may be important to carcinogenesis but are not typically shown in schematic illustrations of AAV2 …”
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.
“…Bat adeno-associated virus (BtAAV, Chiropteran dependoparvovirus 1 ) was identified in fecal swabs of 19 bat species in five Chinese provinces in 2007–2008 [ 219 ]. Intestinal samples from 5 species of bats in Southeast China showed that 18.6% were positive for AAVs, suggesting a wide distribution of these viruses [ 220 ]. Analysis of the BtAAV capsid structure using sequence analysis and cryo-EM revealed unique structural differences to human AAVs, including insertions and deletions in the capsid surface loops [ 221 ].…”
In line with the Latin expression “sed parva forti” meaning “small but mighty,” the family Parvoviridae contains many of the smallest known viruses, some of which result in fatal or debilitating infections. In recent years, advances in metagenomic viral discovery techniques have dramatically increased the identification of novel parvoviruses in both diseased and healthy individuals. While some of these discoveries have solved etiologic mysteries of well-described diseases in animals, many of the newly discovered parvoviruses appear to cause mild or no disease, or disease associations remain to be established. With the increased use of animal parvoviruses as vectors for gene therapy and oncolytic treatments in humans, it becomes all the more important to understand the diversity, pathogenic potential, and evolution of this diverse family of viruses. In this review, we discuss parvoviruses infecting vertebrate animals, with a special focus on pathogens of veterinary significance and viruses discovered within the last four years.
“…Bats are a rich source of AAV genetic diversity [ 68 , 69 ] and may provide capsids with improved tropism and immune evasion properties. For example, bat AAV sequences have low capsid sequence identity (<60%), reduced antibody neutralization profiles, and increased muscle to liver transduction ratios compared to primate AAVs [ 70 ].…”
Human gene therapy has advanced from twentieth-century conception to twenty-first-century reality. The recombinant Adeno-Associated Virus (rAAV) is a major gene therapy vector. Research continues to improve rAAV safety and efficacy using a variety of AAV capsid modification strategies. Significant factors influencing rAAV transduction efficiency include neutralizing antibodies, attachment factor interactions and receptor binding. Advances in understanding the molecular interactions during rAAV cell entry combined with improved capsid modulation strategies will help guide the design and engineering of safer and more efficient rAAV gene therapy vectors.
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