Self-complementary adeno-associated virus

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Self-complementary adeno-associated virus (scAAV) is a viral vector engineered from the naturally occurring adeno-associated virus (AAV) to be used as a tool for gene therapy. [1] Use of recombinant AAV (rAAV) has been successful in clinical trials addressing a variety of diseases. [2] This lab-made progeny of rAAV is termed "self-complementary" because the coding region has been designed to form an intra-molecular double-stranded DNA template. A rate-limiting step for the standard AAV genome involves the second-strand synthesis since the typical AAV genome is a single-stranded DNA template. [3] [4] However, this is not the case for scAAV genomes. Upon infection, rather than waiting for cell mediated synthesis of the second strand, the two complementary halves of scAAV will associate to form one double stranded DNA (dsDNA) unit that is ready for immediate replication and transcription. The caveat of this construct is that instead of the full coding capacity found in rAAV (4.7–6kb) [5] scAAV can only hold about half of that amount (≈2.4kb). [6]

Contents

In gene therapy application utilizing rAAV, the virus transduces the cell with a single stranded DNA (ssDNA) flanked by two inverted terminal repeats (ITRs). These ITRs form hairpins at the end of the sequence to serve as primers to initiate synthesis of the second strand before subsequent steps of infection can begin. The second strand synthesis is considered to be one of several blocks to efficient infection. [7] Additional advantages of scAAV include increased and prolonged transgene expression in vitro and in vivo , as well as "higher in vivo DNA stability and more effective circularization." [8]

In gene therapy

scAAV is an attractive vector for use in gene therapy for many reasons. Its parent vector, AAV, is already being used in clinical trials. [9] Due to a variety of scAAV serotypes available, scientists can choose a serotype which has properties desirable for their therapy. Selecting only a subset of cells improves specificity and lowers the risk of being inhibited by the immune system. Different scAAV and AAV serotypes can efficiently transfect a variety of cellular targets. [10] [11] Like all vector-based approaches to gene therapy, one obstacle in translating therapies from pre-clinical trials into a human clinical application will be the production of large quantities of highly concentrated virus. [12] One disadvantage that scAAV faces is that due to robust gene expression, transgene products delivered via scAAV elicit a stronger immune response than those same transgenes delivered via a single-stranded AAV vector. [13]

Virus classification

Like AAV, scAAV is a member of the family Parvoviridae, commonly known as parvoviruses. These viruses are nonenveloped, single-strand DNA (ssDNA) viruses. Within Parvoviridae, scAAV further belongs to the Dependovirus genus, characteristically defined by an inability to replicate on their own. In nature, these viruses depend on another virus to provide replication machinery; adeno-associated virus can only replicate during an active infection of adenovirus or some types of herpesvirus. In lab use, this obstacle is overcome by addition of the helper plasmids, which exogenously expresses replication genes which AAV itself lacks. [14]

Viral replication

As a dependovirus, scAAV remains in a latent state within the cell until the cell experiences certain permissive conditions. These can include presence of a helper virus infection (such as adenovirus) or other toxic events such as exposure to UV light or carcinogens. [14] Because the endogenous rep ORF has been replaced with transgene, exogenously provided rep genes encode the proteins required for genome replication and other viral life cycle components. The ITRs located 5' and 3' of the viral genome serve as the origin of replication. [15]

Viral packaging

Like the rep ORF, scAAV's cap ORF has been replaced by transgene and therefore is provided exogenously in a lab environment. The genes encoded in this ORF build capsid proteins and are responsible (along with intracellular processing) for conveying target specificity. Rep proteins participate in the integration of the genome into preformed capsids. [15] Despite the fact that scAAV is designed to form dsDNA upon infection, the two complementary strands are not packaged in a double stranded manner. Parvoviruses package their viral genome such that the ssDNA bases come in contact with the amino acids on the inside of the viral capsid. Thus the sequence of scAAV is likely unwound by a virally encoded DNA helicase before being packaged into viral protein capsid. [7]

Related Research Articles

An episome is a special type of plasmid, which remains as a part of the eukaryotic genome without integration. Episomes manage this by replicating together with the rest of the genome and subsequently associating with metaphase chromosomes during mitosis. Episomes do not degrade, unlike standard plasmids, and can be designed so that they are not epigenetically silenced inside the eukaryotic cell nucleus. Episomes can be observed in nature in certain types of long-term infection by adeno-associated virus or Epstein-Barr virus. In 2004, it was proposed that non-viral episomes might be used in genetic therapy for long-term change in gene expression.

<i>Parvoviridae</i> Family of viruses

Parvoviruses are a family of animal viruses that constitute the family Parvoviridae. They have linear, single-stranded DNA (ssDNA) genomes that typically contain two genes encoding for a replication initiator protein, called NS1, and the protein the viral capsid is made of. The coding portion of the genome is flanked by telomeres at each end that form into hairpin loops that are important during replication. Parvovirus virions are small compared to most viruses, at 23–28 nanometers in diameter, and contain the genome enclosed in an icosahedral capsid that has a rugged surface.

<span class="mw-page-title-main">Poliovirus</span> Enterovirus

Poliovirus, the causative agent of polio, is a serotype of the species Enterovirus C, in the family of Picornaviridae. There are three poliovirus serotypes: types 1, 2, and 3.

<i>Adenoviridae</i> Family of viruses

Adenoviruses are medium-sized, nonenveloped viruses with an icosahedral nucleocapsid containing a double-stranded DNA genome. Their name derives from their initial isolation from human adenoids in 1953.

Cauliflower mosaic virus (CaMV) is a member of the genus Caulimovirus, one of the six genera in the family Caulimoviridae, which are pararetroviruses that infect plants. Pararetroviruses replicate through reverse transcription just like retroviruses, but the viral particles contain DNA instead of RNA.

<i>Geminiviridae</i> Family of viruses

Geminiviridae is a family of plant viruses that encode their genetic information on a circular genome of single-stranded (ss) DNA. There are 520 species in this family, assigned to 14 genera. Diseases associated with this family include: bright yellow mosaic, yellow mosaic, yellow mottle, leaf curling, stunting, streaks, reduced yields. They have single-stranded circular DNA genomes encoding genes that diverge in both directions from a virion strand origin of replication. According to the Baltimore classification they are considered class II viruses. It is the largest known family of single stranded DNA viruses.

<span class="mw-page-title-main">Adeno-associated virus</span> Species of virus

Adeno-associated viruses (AAV) are small viruses that infect humans and some other primate species. They belong to the genus Dependoparvovirus, which in turn belongs to the family Parvoviridae. They are small replication-defective, nonenveloped viruses and have linear single-stranded DNA (ssDNA) genome of approximately 4.8 kilobases (kb).

Lentivirus is a genus of retroviruses that cause chronic and deadly diseases characterized by long incubation periods, in humans and other mammalian species. The genus includes the human immunodeficiency virus (HIV), which causes AIDS. Lentiviruses are distributed worldwide, and are known to be hosted in apes, cows, goats, horses, cats, and sheep as well as several other mammals.

<i>Gammaretrovirus</i> Genus of viruses

Gammaretrovirus is a genus in the Retroviridae family. Example species are the murine leukemia virus and the feline leukemia virus. They cause various sarcomas, leukemias and immune deficiencies in mammals, reptiles and birds.

Baltimore classification is a system used to classify viruses based on their manner of messenger RNA (mRNA) synthesis. By organizing viruses based on their manner of mRNA production, it is possible to study viruses that behave similarly as a distinct group. Seven Baltimore groups are described that take into consideration whether the viral genome is made of deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), whether the genome is single- or double-stranded, and whether the sense of a single-stranded RNA genome is positive or negative.

Viral vectors are tools commonly used by molecular biologists to deliver genetic material into cells. This process can be performed inside a living organism or in cell culture. Viruses have evolved specialized molecular mechanisms to efficiently transport their genomes inside the cells they infect. Delivery of genes or other genetic material by a vector is termed transduction and the infected cells are described as transduced. Molecular biologists first harnessed this machinery in the 1970s. Paul Berg used a modified SV40 virus containing DNA from the bacteriophage λ to infect monkey kidney cells maintained in culture.

A helper dependent virus, also termed a gutless virus, is a synthetic viral vector dependent on the assistance of a helper virus in order to replicate, and can be used for purposes such as gene therapy. Naturally-occurring satellite viruses are also helper virus dependent, and can sometimes be modified to become viral vectors.

<span class="mw-page-title-main">Gene delivery</span> Introduction of foreign genetic material into host cells

Gene delivery is the process of introducing foreign genetic material, such as DNA or RNA, into host cells. Gene delivery must reach the genome of the host cell to induce gene expression. Successful gene delivery requires the foreign gene delivery to remain stable within the host cell and can either integrate into the genome or replicate independently of it. This requires foreign DNA to be synthesized as part of a vector, which is designed to enter the desired host cell and deliver the transgene to that cell's genome. Vectors utilized as the method for gene delivery can be divided into two categories, recombinant viruses and synthetic vectors.

<i>Dependoparvovirus</i> Genus of viruses

Dependoparvovirus is a genus in the subfamily Parvovirinae of the virus family Parvoviridae; they are Group II viruses according to the Baltimore classification. Some dependoparvoviruses are also known as adeno-associated viruses because they cannot replicate productively in their host cell without the cell being coinfected by a helper virus such as an adenovirus, a herpesvirus, or a vaccinia virus.

Gene therapy using lentiviral vectors was being explored in early stage trials as of 2009.

Retinal gene therapy holds a promise in treating different forms of non-inherited and inherited blindness.

Saswati Chatterjee is a virologist working as a professor at the Los Angeles City of Hope National Medical Center in the research department. Some of the viral areas she researches are: stem cells, gene therapy, genome editing, and parvovirus. Her main and current area of research is using Adeno-Associated Virus Vectors (AAV-Vectors). Additionally, she has had a role in many publications.

Adeno-associated virus (AAV) has been researched as a viral vector in gene therapy for cancer treatment as an Oncolytic Virus. Currently there are not any FDA approved AAV cancer treatments, as the first FDA approved AAV treatment was approved December 2017. However, there are many Oncolytic AAV applications that are in development and have been researched.

Mavis Agbandje-McKenna was a Nigerian-born British medical biophysicist, structural virologist, and a professor of structural biology, as well as the director of the Center for Structural Biology at the University of Florida in Gainesville, Florida. Agbandje-McKenna studied parvovirus structures using X-ray crystallography and cryogenic electron microscopy and did much of the initial work to elucidate the basic structure and function of adeno-associated viruses (AAVs). Her viral characterization and elucidation of antibody binding sites on AAV capsids has led to the development of viral capsid development and gene therapy approaches that evade immune detection and can be used to treat human diseases such as muscular dystrophies. Agbandje-McKenna was recognized with the 2020 American Society of Gene and Cell Therapy Outstanding Achievement Award for her contributions to the field. She died in 2021 from amyotrophic lateral sclerosis.

Rolling hairpin replication (RHR) is a unidirectional, strand displacement form of DNA replication used by parvoviruses, a group of viruses that constitute the family Parvoviridae. Parvoviruses have linear, single-stranded DNA (ssDNA) genomes in which the coding portion of the genome is flanked by telomeres at each end that form hairpin loops. During RHR, these hairpin loops repeatedly unfold and refold to change the direction of DNA replication so that replication progresses in a continuous manner back and forth across the genome. RHR is initiated and terminated by an endonuclease encoded by parvoviruses that is variously called NS1 or Rep, and RHR is similar to rolling circle replication, which is used by ssDNA viruses that have circular genomes.

References

  1. ↑ McCarty, D M; Monahan, P E; Samulski, R J (2001). "Self-complementary recombinant adeno-associated virus (scAAV) vectors promote efficient transduction independently of DNA synthesis". Gene Therapy. 8 (16): 1248–54. doi: 10.1038/sj.gt.3301514 . PMID   11509958.
  2. ↑ "Gene Therapy Clinical Trials Worldwide".
  3. ↑ Ferrari, FK; Samulski, T; Shenk, T; Samulski, RJ (1996). "Second-strand synthesis is a rate-limiting step for efficient transduction by recombinant adeno-associated virus vectors". Journal of Virology. 70 (5): 3227–34. doi:10.1128/JVI.70.5.3227-3234.1996. PMC   190186 . PMID   8627803.
  4. ↑ Fisher, KJ; Gao, GP; Weitzman, MD; Dematteo, R; Burda, JF; Wilson, JM (1996). "Transduction with recombinant adeno-associated virus for gene therapy is limited by leading-strand synthesis". Journal of Virology. 70 (1): 520–32. doi:10.1128/JVI.70.1.520-532.1996. PMC   189840 . PMID   8523565.
  5. ↑ Grieger, J. C.; Samulski, R. J. (2005). "Packaging Capacity of Adeno-Associated Virus Serotypes: Impact of Larger Genomes on Infectivity and Postentry Steps". Journal of Virology. 79 (15): 9933–44. doi:10.1128/JVI.79.15.9933-9944.2005. PMC   1181570 . PMID   16014954.
  6. ↑ Wu, J; Zhao, W; Zhong, L; Han, Z; Li, B; Ms, W; Weigel-Kelley, KA; Warrington, KH; Srivastava, A (Feb 2007). "Self-complementary recombinant adeno-associated viral vectors: packaging capacity and the role of rep proteins in vector purity". Human Gene Therapy. 18 (2): 171–82. doi:10.1089/hum.2006.088. PMID   17328683.
  7. 1 2 McCarty, Douglas M (2008). "Self-complementary AAV Vectors; Advances and Applications". Molecular Therapy. 16 (10): 1648–56. doi: 10.1038/mt.2008.171 . PMID   18682697.
  8. ↑ Wang, Z; Ma, H-I; Li, J; Sun, L; Zhang, J; Xiao, X (2003). "Rapid and highly efficient transduction by double-stranded adeno-associated virus vectors in vitro and in vivo". Gene Therapy. 10 (26): 2105–11. doi: 10.1038/sj.gt.3302133 . PMID   14625564.
  9. ↑ Aalbers, Caroline J.; Tak, Paul P.; Vervoordeldonk, Margriet J. (2011). "Advancements in adeno-associated viral gene therapy approaches: Exploring a new horizon". F1000 Medicine Reports. 3: 17. doi: 10.3410/M3-17 . PMC   3169911 . PMID   21941595.
  10. ↑ Hillestad, ML; Guenzel, AJ; Nath, KA; Barry, MA (Oct 2012). "A vector-host system to fingerprint virus tropism". Hum Gene Ther. 23 (10): 1116–26. doi:10.1089/hum.2011.116. PMC   3472556 . PMID   22834781.
  11. ↑ Zincarelli, C; Soltys, S; Rengo, G; Rabinowitz, JE (Jun 2008). "Analysis of AAV serotypes 1–9 mediated gene expression and tropism in mice after systemic injection". Mol. Ther. 16 (6): 1073–80. doi: 10.1038/mt.2008.76 . PMID   18414476.
  12. ↑ Clément, N; Knop, DR; Byrne, BJ (Aug 2009). "Large-scale adeno-associated viral vector production using a herpesvirus-based system enables manufacturing for clinical studies". Hum Gene Ther. 20 (8): 796–806. doi:10.1089/hum.2009.094. PMC   2861951 . PMID   19569968.
  13. ↑ Wu, T; Töpfer, K; Lin, SW; Li, H; Bian, A; Zhou, XY; High, KA; Ertl, HC (Mar 2012). "Self-complementary AAVs induce more potent transgene product-specific immune responses compared to a single-stranded genome". Mol. Ther. 20 (3): 572–9. doi:10.1038/mt.2011.280. PMC   3293612 . PMID   22186792.
  14. 1 2 Berns, KI (Sep 1990). "Parvovirus replication". Microbiol. Rev. 54 (3): 316–29. doi:10.1128/mmbr.54.3.316-329.1990. PMC   372780 . PMID   2215424.
  15. 1 2 Büning, H; Perabo, L; Coutelle, O; Quadt-Humme, S; Hallek, M (Jul 2008). "Recent developments in adeno-associated virus vector technology". J. Gene Med. 10 (7): 717–33. doi:10.1002/jgm.1205. PMID   18452237. S2CID   41510186.
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