Deep-Inspiration Breath-Hold Stereotactic Body Radiation Therapy by Combining Spirometer-Guided Breath-Hold and a Real-Time Tumor Tracking System: A Novel Approach

PURPOSE/OBJECTIVE(S)

There are several methods used against respiratory motion (RM). Expiratory breath-hold (BH) is considered more stable and reproducible than inspiratory BH; therefore, BH with spirometry is often used for expiration. The real-time tumor tracking radiotherapy (RTRT) system is a highly effective method for reducing the margin of RM. This system ambushes and irradiates tumors during the expiratory phase when tumors move slowly. Although these methods usually involve expiration, it is advantageous to expand the lungs with inspiration to reduce the risk of adverse events. Here, we developed a new approach of performing stereotactic body radiation therapy (SBRT) under deep-inspiration BH (DIBH) by combining these two methods.

MATERIALS/METHODS

Lung tumors with respiratory motion ≥ 1 cm were included. Three or four fiducial markers were placed near the tumor via bronchoscopy. DIBH CT (CT-IN) was performed under the guidance of spirometer. The PTV was obtained by adding a 5-mm margin to the GTV delineated on CT-IN. The prescribed dose was 42 Gy in four fractions for the D95 of the PTV. An error of 2.0 mm around the planned position of the fiducial marker on CT-IN was permitted along each orthogonal axis as a gating box. In preparation for cases in which the reproducibility of DIBH is low and treatment cannot be performed, light expiration BH CT (CT-EX) was also performed, and a radiotherapy plan was prepared for the conventional RTRT system so that it could be switched at any time. Lung volumes and doses (mean dose, V20 Gy, V10 Gy, and V5 Gy) on CT-EX and CT-IN were compared.

RESULTS

Five patients underwent SBRT with DIBH, and all completed the planned irradiation course. The median treatment time per fraction was 27.86 min (range, 25.5-40.6). Four tumors were located in the left lower lobe and one in the right lower lobe. The median volume of PTV was 12.4 (range, 5.2-26.2) mL. The lung volumes and doses on CT-EX and CT-IN are shown in the Table. The lung volume on CT-IN was 1.6 times larger than that on CT-EX. The PTV-to-lung ratio on CT-IN was significantly lower than that on CT-EX. V20 Gy and V10 Gy on CT-IN were significantly lower than those on CT-EX.

CONCLUSION

SBRT with DIBH was achieved by combining the spirometer and RTRT system. This can help to eliminate concerns about reproducibility and high-speed tumor movement during inspiration, which are weaknesses of spirometer-guided breath-hold and the RTRT system, respectively, while ensuring the accuracy of the RTRT system. DIBH SBRT is a promising method that can reduce lung dose.

Necessity of Flanking Repeats R1' and R8' of Human Pumilio1 Protein for RNA Binding

Human Pumilio (hPUM) is a structurally well-analyzed RNA-binding protein that has been used recently for artificial RNA binding. Structural analysis revealed that amino acids at positions 12, 13, and 16 in the repeats from R1 to R8 each contact one specific RNA base in the eight-nucleotide RNA target. The functions of the N- and C-terminal flanking repeats R1' and R8', however, remain unclear. Here, we report how the repeats contribute to overall RNA binding. We first prepared three mutants in which R1' and/or R8' were deleted and then analyzed RNA binding using gel shift assays. The assays showed that all deletion mutants bound to their target less than the original hPUM, but that R1' contributed more than R8', unlike Drosophila PUM. We next investigated which amino acid residues of R1' or R8' were responsible for RNA binding. With detailed analysis of the protein tertiary structure, we found a hydrophobic core in each of the repeats. We therefore mutated all hydrophobic amino residues in each core to alanine. The gel shift assays with the resulting mutants revealed that both hydrophobic cores contributed to the RNA binding: especially the hydrophobic core of R1' had a significant influence. In the present study, we demonstrated that the flanking R1' and R8' repeats are indispensable for RNA binding of hPUM and suggest that hydrophobic R1'-R1 interactions may stabilize the whole hPUM structure.

Genome sequence analysis of new plum pox virus isolates from Japan

Objective

To find mutations that may have recently occurred in Plum pox virus (PPV), we collected six PPV-infected plum/peach trees from the western part of Japan and one from the eastern part. After sequencing the full-length PPV genomic RNAs, we compared the amino acid sequences with representative isolates of each PPV strain.

Results

All new isolates were found to belong to the PPV-D strain: the six isolates collected from western Japan were identified as the West-Japan strain while the one collected from eastern Japan as the East-Japan strain. Amino acid sequence analysis of these seven isolates suggested that the 1407th and 1529th amino acid residues are characteristic of the West-Japan and the East-Japan strains, respectively. Comparing them with the corresponding amino acid residues of the 47 non-Japanese PPV-D isolates revealed that these amino acid residues are undoubtedly unique. A further examination of the relevant amino acid residues of the other 210 PPV-D isolates collected in Japan generated a new hypothesis regarding the invasion route from overseas and the subsequent diffusion route within Japan: a PPV-D strain might have invaded the western part of Japan from overseas and spread throughout Japan.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05683-9.

Development of a method to rapidly assess resistance/susceptibility of Micro-Tom tomatoes to Tomato yellow leaf curl virus via agroinoculation of cotyledons

Objective

Tomato yellow leaf curl virus (TYLCV) is one of the pathogens severely damaging tomato crops. Therefore, methods to treat or prevent TYLCV infection need to be developed. For this purpose, a method to conveniently and quickly assess infection of tomatoes by TYLCV is desired. In the present study, we established a quick method to evaluate TYLCV infection using cotyledons of Micro-Tom, a miniature tomato cultivar.

Results

First, we constructed a binary plasmid harboring 1.5 copies of the TYLCV genome and transformed Agrobacterium with the plasmid. By injecting agroinoculum from the resulting transformant into the branches of Micro-Tom, we confirmed the susceptibility of Micro-Tom to TYLCV. To shorten the evaluation process of TYLCV infection further, we agroinoculated cotyledons of Micro-Tom 10 days after sowing seeds. We consistently observed typical symptoms of TYLCV infection on true leaves 10 days after agroinoculation. Molecular analysis detected TYLCV progeny DNA in all leaves demonstrating symptoms 6 days after agroinoculation. Therefore, our new protocol enabled assessment of TYLCV infection within 20 days after sowing seeds. Thus, agroinoculation of Micro-Tom cotyledons will accelerate the process of screening TYLCV-resistant Micro-Toms and enable screening of larger numbers of plants more quickly, contributing to the development of TYLCV-resistant tomatoes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s13104-021-05651-3.

Harmonisation of PET/CT contrast recovery performance for brain studies

PURPOSE

In order to achieve comparability of image quality, harmonisation of PET system performance is imperative. In this study, prototype harmonisation criteria for PET brain studies were developed.

METHODS

Twelve clinical PET/CT systems (4 GE, 4 Philips, 4 Siemens, including SiPM-based "digital" systems) were used to acquire 30-min PET scans of a Hoffman 3D Brain phantom filled with ~ 33 kBq·mL^-1 [¹⁸F]FDG. Scan data were reconstructed using various reconstruction settings. The images were rigidly coregistered to a template (voxel size 1.17 × 1.17 × 2.00 mm³) onto which several volumes of interest (VOIs) were defined. Recovery coefficients (RC) and grey matter to white matter ratios (GMWMr) were derived for eroded (denoted in the text by subscript e) and non-eroded grey (GM) and white (WM) matter VOIs as well as a mid-phantom cold spot (VOI_cold) and VOIs from the Hammers atlas. In addition, left-right hemisphere differences and voxel-by-voxel differences compared to a reference image were assessed.

RESULTS

Systematic differences were observed for reconstructions with and without point-spread-function modelling (PSF_ON and PSF_OFF, respectively). Normalising to image-derived activity, upper and lower limits ensuring image comparability were as follows: for PSF_ON, RC_GMe = [0.97-1.01] and GMWMr_e = [3.51-3.91] for eroded VOI and RC_GM = [0.78-0.83] and GMWMr = [1.77-2.06] for non-eroded VOI, and for PSF_OFF, RC_GMe = [0.92-0.99] and GMWMr_e = [3.14-3.68] for eroded VOI and RC_GM = [0.75-0.81] and GMWMr = [1.72-1.95] for non-eroded VOI.

CONCLUSIONS

To achieve inter-scanner comparability, we propose selecting reconstruction settings based on RC_GMe and GMWMr_e as specified in "Results". These proposed standards should be tested prospectively to validate and/or refine the harmonisation criteria.

Site-Specific Integration by Recruitment of a Complex of ΦC31 Integrase and Donor DNA to a Target Site by Using a Tandem, Artificial Zinc-Finger Protein

To solve the problem of uncontrolled therapeutic gene integration, which is a critical drawback of retroviral vectors for gene therapy, the integration sites of exogenous genes should be precisely controlled not to perturb endogenous gene expression. To accomplish this, we explored the possibility of site-specific integration using two six-finger artificial zinc-finger proteins (AZPs) tandemly conjugated via a flexible peptide linker (designated "Tandem AZP"). A Tandem AZP in which two AZPs recognize specific 19 bp targets in a donor and acceptor DNA was expected to site-specifically recruit the donor DNA to the acceptor DNA. Thereafter, an exogenously added integrase was expected to integrate the donor DNA into a specific site in the acceptor DNA (as it might be in the human genome). We demonstrated in vitro that in the presence of Tandem AZP, ΦC31 integrase selectively integrated a donor plasmid into a target acceptor plasmid not only at 30 °C (the optimum temperature of the integrase) but also at 37 °C (for future application in humans). We expect that with further improvement of our current system, a combination of Tandem AZP with integrase/recombinase will enable site-specific integration in mammalian cells and provide safer gene therapy technology.

Abstract 1922: Targeted silencing of SOX2 by an artificial transcription factor showed antitumor effect in lung and esophageal squamous cell carcinoma

S0X2 is a transcription factor essential for early mammalian development and for the maintenance of stem cells. Recently, SOX2 was identified as a lineage specific oncogene, recurrently amplified and activated in lung and esophageal squamous cell carcinoma (SCC). In this study, we have developed a zinc finger-based artificial transcription factor (ATF) to selectively suppress SOX2 expression in cancer cells and termed the system ATF/SOX2. We engineered the ATF using six zinc finger arrays designed to target a 19 bp site in the SOX2 distal promoter and a KOX transcriptional repressor domain. A recombinant adenoviral vector Ad- ATF/SOX2 that expresses ATF/SOX2 suppressed SOX2 at the mRNA and protein levels in lung and esophageal SCC cells expressing SOX2. In these kinds of cells, Ad-ATF/SOX2 decreased cell proliferation and colony formation more effectively than the recombinant adenoviral vector Ad-shSOX2, which expresses SOX2 short hairpin RNA (shSOX2). Ad-ATF/SOX2 induced the cell cycle inhibitor CDKN1A more strongly than Ad-shSOX2. Importantly, the ATF did not suppress the cell viability of normal human cells. Moreover, Ad-ATF/SOX2 effectively inhibited tumor growth in a lung SCC xenograft mouse model. These results indicate that ATF/SOX2 would lead to the development of an effective molecular-targeted therapy for lung and esophageal SCC.

Citation Format: Etsuko Yokota, Tomoki Yamatsuji, Munenori Takaoka, Minoru Haisa, Nagio Takigawa, Noriko Miyake, Tomoko Ikeda, Tomoaki Mori, Ohno Serika, Takashi Sera, Takuya Fukazawa, Yoshio Naomoto. Targeted silencing of SOX2 by an artificial transcription factor showed antitumor effect in lung and esophageal squamous cell carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1922.

Targeted silencing of SOX2 by an artificial transcription factor showed antitumor effect in lung and esophageal squamous cell carcinoma

SOX2 is a transcription factor essential for early mammalian development and for the maintenance of stem cells. Recently, SOX2 was identified as a lineage specific oncogene, recurrently amplified and activated in lung and esophageal squamous cell carcinoma (SCC). In this study, we have developed a zinc finger-based artificial transcription factor (ATF) to selectively suppress SOX2 expression in cancer cells and termed the system ATF/SOX2. We engineered the ATF using six zinc finger arrays designed to target a 19 bp site in the SOX2 distal promoter and a KOX transcriptional repressor domain. A recombinant adenoviral vector Ad-ATF/SOX2 that expresses ATF/SOX2 suppressed SOX2 at the mRNA and protein levels in lung and esophageal SCC cells expressing SOX2. In these kinds of cells, Ad-ATF/SOX2 decreased cell proliferation and colony formation more effectively than the recombinant adenoviral vector Ad-shSOX2, which expresses SOX2 short hairpin RNA (shSOX2). Ad-ATF/SOX2 induced the cell cycle inhibitor CDKN1A more strongly than Ad-shSOX2. Importantly, the ATF did not suppress the cell viability of normal human cells. Moreover, Ad-ATF/SOX2 effectively inhibited tumor growth in a lung SCC xenograft mouse model. These results indicate that ATF/SOX2 would lead to the development of an effective molecular-targeted therapy for lung and esophageal SCC.

Cleavage of influenza RNA by using a human PUF-based artificial RNA-binding protein-staphylococcal nuclease hybrid

Various viruses infect animals and humans and cause a variety of diseases, including cancer. However, effective methodologies to prevent virus infection have not yet been established. Therefore, development of technologies to inactivate viruses is highly desired. We have already demonstrated that cleavage of a DNA virus genome was effective to prevent its replication. Here, we expanded this methodology to RNA viruses. In the present study, we used staphylococcal nuclease (SNase) instead of the PIN domain (PilT N-terminus) of human SMG6 as an RNA-cleavage domain and fused the SNase to a human Pumilio/fem-3 binding factor (PUF)-based artificial RNA-binding protein to construct an artificial RNA restriction enzyme with enhanced RNA-cleavage rates for influenzavirus. The resulting SNase-fusion nuclease cleaved influenza RNA at rates 120-fold greater than the corresponding PIN-fusion nuclease. The cleaving ability of the PIN-fusion nuclease was not improved even though the linker moiety between the PUF and RNA-cleavage domain was changed. Gel shift assays revealed that the RNA-binding properties of the PUF derivative used was not as good as wild type PUF. Improvement of the binding properties or the design method will allow the SNase-fusion nuclease to cleave an RNA target in mammalian animal cells and/or organisms.

Sandwiched zinc-finger nucleases demonstrating higher homologous recombination rates than conventional zinc-finger nucleases in mammalian cells

We previously reported that our sandwiched zinc-finger nucleases (ZFNs), in which a DNA cleavage domain is inserted between two artificial zinc-finger proteins, cleave their target DNA much more efficiently than conventional ZFNs in vitro. In the present study, we compared DNA cleaving efficiencies of a sandwiched ZFN with those of its corresponding conventional ZFN in mammalian cells. Using a plasmid-based single-strand annealing reporter assay in HEK293 cells, we confirmed that the sandwiched ZFN induced homologous recombination more efficiently than the conventional ZFN; reporter activation by the sandwiched ZFN was more than eight times that of the conventional one. Western blot analysis showed that the sandwiched ZFN was expressed less frequently than the conventional ZFN, indicating that the greater DNA-cleaving activity of the sandwiched ZFN was not due to higher expression of the sandwiched ZFN. Furthermore, an MTT assay demonstrated that the sandwiched ZFN did not have any significant cytotoxicity under the DNA-cleavage conditions. Thus, because our sandwiched ZFN cleaved more efficiently than its corresponding conventional ZFN in HEK293 cells as well as in vitro, sandwiched ZFNs are expected to serve as an effective molecular tool for genome editing in living cells.

Gene- and protein-delivered zinc finger-staphylococcal nuclease hybrid for inhibition of DNA replication of human papillomavirus

Previously, we reported that artificial zinc-finger proteins (AZPs) inhibited virus DNA replication in planta and in mammalian cells by blocking binding of a viral replication protein to its replication origin. However, the replication mechanisms of viruses of interest need to be disentangled for the application. To develop more widely applicable methods for antiviral therapy, we explored the feasibility of inhibition of HPV-18 replication as a model system by cleaving its viral genome. To this end, we fused the staphylococcal nuclease cleaving DNA as a monomer to an AZP that binds to the viral genome. The resulting hybrid nuclease (designated AZP–SNase) cleaved its target DNA plasmid efficiently and sequence-specifically in vitro. Then, we confirmed that transfection with a plasmid expressing AZP–SNase inhibited HPV-18 DNA replication in transient replication assays using mammalian cells. Linker-mediated PCR analysis revealed that the AZP–SNase cleaved an HPV-18 ori plasmid around its binding site. Finally, we demonstrated that the protein-delivered AZP–SNase inhibited HPV-18 DNA replication as well and did not show any significant cytotoxicity. Thus, both gene- and protein-delivered hybrid nucleases efficiently inhibited HPV-18 DNA replication, leading to development of a more universal antiviral therapy for human DNA viruses.

Unidirectional cloning by cleaving heterogeneous sites with a single sandwiched zinc finger nuclease

We previously developed a novel type of zinc finger nucleases (ZFNs), sandwiched ZFNs that can discriminate DNA substrates from cleavage products and thus cleave DNA much more efficiently than conventional ZFNs as well as perform with multiple turnovers like restriction endonucleases. In the present study, we used the sandwiched ZFN to unidirectionally clone exogenous genes into target vectors by cleaving heterogeneous sites that contained heterogeneous spacer DNAs between two zinc-finger protein binding sites with a single sandwiched ZFN. We demonstrated that the sandwiched ZFN cleaved a 40-fold excess of both insert and vector plasmids within 1h and confirmed by sequencing that the resulting recombinants harbored the inserted DNA fragment in the desired orientation. Because sandwiched ZFNs can recognize and cleave a variety of long (≥ 26-bp) target DNAs, they may not only expand the utility of ZFNs for construction of recombinant plasmids, but also serve as useful meganucleases for synthesis of artificial genomes.

Expression patterns of three α-expansin isoforms in Coffea arabica during fruit development

As a first step towards understanding the physiological role and regulation of the expansin gene (EXP) family in Coffea arabica fruits during growth and maturation, we identified 11 expansin genes, nine belonging to the α-expansin family (EXPA), one EXLA and one EXLB, through in silico analysis of expressed sequence tags (ESTs). Within the α-expansin family, three isoforms were selected for detailed examination based on their high expression in coffee fruits or because they were specifically induced during different fruit developmental stages, according to the EST information. The expression patterns were analysed in different fruit tissues (perisperm, endosperm and pericarp) of C. arabica cv. IAPAR-59 and C. arabica cv. IAPAR-59 Graúdo, the latter being a closely related cultivar with a larger fruit size. Accumulation of CaEXPA1 and CaEXPA3 transcripts was high in the perisperm (tissue responsible for coffee bean size) and in the early stages of pericarp development. Transcripts of CaEXPA2 were detected only in the pericarp during the later stages of fruit maturation and ripening. There was no detectable transcription of the three EXPs analysed in the endosperm. The observed differences in mRNA expression levels of CaEXPA1 and CaEXP3 in the perisperm of IAPAR-59 and IAPAR-59 Graúdo suggest the participation of these two isoforms in the regulation of grain size.

Modulation of endogenous VEGF-A expression under hypoxia by using artificial transcription factors

The vascular endothelial growth factor A (VEGF-A) gene is an attractive therapeutic target because both activation and repression of the gene are useful for treatment or cure of many diseases related to abnormal angiogenesis. To modulate the endogenous gene expression artificially, we previously designed a six-finger AZP to recognize a 19-bp DNA in the VEGF-A gene, and fused the AZP with a nuclear localization signal and a repressor domain to generate an artificial transcription factor (ATF). Using the ATF, we demonstrated efficient modulation of the VEGF-A expression. In the present study, we evaluate the ability of the ATF to modulate the gene expression under hypoxic conditions. Enzyme-linked immunosorbent assays (ELISA) for VEGF-A protein in the culture medium revealed that the gene-delivered ATF also repressed the expression of the endogenous VEGF-A gene under hypoxia.

Inhibition of human papillomavirus replication by using artificial zinc-finger nucleases

Recently, we have designed artificial zinc-finger proteins (AZPs) that prevent a viral replication protein, E2, of human papillomavirus type 18 (HPV-18) from binding to its replication origin and demonstrated that the gene-delivered AZPs inhibited HPV-18 DNA replication in mammalian cells. In the present study, we examined a new approach to inhibition of DNA virus replication by using an AZP-nuclease fusion. In transient replication assays for HPV-18, the gene-delivered AZP-nuclease fusion reduced the viral DNA replication rate significantly. Moreover, it was demonstrated by ligation-mediated PCR that viral DNA regions close to the AZP-binding site were cleaved in the cells by the AZP-nuclease. Thus, our results demonstrate that AZP-nucleases have potentials to inhibit replication of any DNA viruses whose replication mechanisms remain unsolved.

Generation of plants resistant to tomato yellow leaf curl virus by using artificial zinc-finger proteins

Previously, we designed an artificial zinc-finger protein (AZP) for blocking a replication protein (Rep) of beet severe curly top virus (BSCTV) from binding to its replication origin and demonstrated that transgenic Arabidopsis plants expressing the AZP are completely resistant to the virus infection. Here we applied the AZP technology to tomato yellow leaf curl virus (TYLCV) infective to an important agricultural crop, tomato. We designed and constructed an AZP binding to the direct repeat to block the TYLCV Rep binding. In gel shift assays, we confirmed that the designed AZP has a higher affinity to the replication origin than that of Rep and that the AZP effectively inhibited the Rep binding to its replication origin in vitro. The AZP gene was then introduced into a plant genome with the help of Agrobacterium tumefaciens to generate the transgenic plants. We will discuss properties of the AZP-transgenic plants against TYLCV infection.

Construction of plants resistant to TYLCV by using artificial zinc-finger proteins

Previously, we have demonstrated that plant DNA virus replication could be inhibited in Arabidopsis thaliana by using an artificial zinc-finger protein (AZP) and created AZP-based transgenic A. thaliana resistant to DNA virus infection. Here we apply the AZP technology to tomato yellow leaf curl virus (TYLCV) causing serious damage to an important agricultural crop, tomato. An AZP was designed to block binding of the TYLCV replication protein (Rep) to the replication origin. The designed AZP had much higher affinities towards the replication origin than did the Rep, and efficiently blocked Rep binding in vitro. The AZP gene was then introduced into a plant genome with the help of Agrobacterium tumefaciens to generate the transgenic plants. The current status of the construction of the AZP-expressing transgenic plants will be reported.

Generation of cell-permeable artificial zinc finger protein variants

Designed or artificial zinc finger proteins (ZFPs) are one of the most promising DNA-binding proteins that target genomic sequences of interest in vitro and in vivo. Conjugation of other functional domains such as transcriptional regulatory domains and endonucleases to ZFPs provided powerful molecular tools to modulate endogenous gene expression and genetic information. These ZFP variants have been introduced into cells as DNA-encoding ZFP variants by using plasmids or viral vectors. As an alternative delivery method of ZFP variants, we developed cell-permeable ZFP variants by fusing cell-penetrating peptides to ZFP variants. We will describe how to generate cell-permeable artificial ZFP variants and how to examine the cell permeabilities by immunofluorescent staining.

Regulation of vascular endothelial growth factor gene under hypoxia by using artificial transcription factors

The vascular endothelial growth factor A (VEGF-A) gene is an attractive therapeutic target because both activation and repression of the gene are useful for treatment or cure of many diseases related to abnormal angiogenesis. To up- or downregulate the endogenous gene expression at will, we previously designed a 6-finger AZP to recognize a 19-bp target DNA in the VEGF-A gene, and fused the AZP with a nuclear localization signal and a transcriptional regulatory domain to generate artificial transcription factors (ATFs) for VEGF-A. Using the ATFs, we previously demonstrated efficient modulation of the endogenous VEGF-A expression under normoxia. In the present study, we examined whether these ATFs modulate the endogenous VEGF-A gene expression under hypoxic conditions as well. Enzyme-linked immunosorbent assays revealed that the gene-delivered ATFs up- or downregulated the VEGF-A expression efficiently under hypoxia.

Zinc-finger-based artificial transcription factors and their applications

Artificial transcription factors (ATFs) are potentially a powerful molecular tool to modulate endogenous target gene expression in living cells and organisms. To date, many DNA-binding molecules have been developed as the DNA-binding domains for ATFs. Among them, ATFs comprising Cys(2)His(2)-type zinc-finger proteins (ZFPs) as the DNA-binding domain have been extensively explored. The zinc-finger-based ATFs specifically recognize targeting sites in chromosomes and effectively up- and downregulate expression of their target genes not only in vitro, but also in vivo. In this review, after briefly introducing Cys(2)His(2)-type ZFPs, I will review the studies of endogenous human gene regulation by zinc-finger-based ATFs and other applications as well.

Multiple-turnover cleavage of double-stranded DNA by sandwiched zinc-finger nuclease

To refine zinc-finger nuclease (ZFN) technology, we constructed a sandwiched ZFN, in which a DNA cleavage enzyme was sandwiched with two artificial zinc-finger proteins (AZPs). Because the sandwiched ZFN is designed to cleave the DNA between the two AZP-binding sites, the sandwiched ZFN is expected to bind preferentially to a DNA substrate rather than to cleavage products and thereby cleave it with multiple turnovers. To prove the concept, we sandwiched a staphylococcal nuclease (SNase), which cleaves DNA as a monomer, between two 3-finger AZPs. The AZP-sandwiched SNase cleaved large amounts of dsDNA site-specifically. Such multiple-turnover cleavage was not observed with control nucleases that possess a single AZP.

Development of protein-based antiviral drugs for human papillomaviruses

Recently, we designed artificial zinc-finger proteins (AZPs) that prevent a viral replication protein, E2, of human papillomavirus type 18 (HPV-18) from binding to its replication origin and demonstrated that the gene-delivered AZPs inhibited HPV-18 DNA replication in mammalian cells. In the present study, we examined another approach to delivery of AZPs. We constructed cell-permeable AZPs by fusing an AZP previously generated for inhibition of HPV-18 DNA replication with a cell-penetrating peptide (CPP), and confirmed that these CPP-AZP fusions reduced the replication rate in transient replication assays when added to the culture medium. In particular, 250 nM CPP-AZP reduced HPV-18 DNA replication to 3% of that of a control experiment. Western blot analysis detected 7% of the CPP-AZP added to the culture medium in the cell lysates, and demonstrated that greater internalization of CPP-AZP into mammalian cells causes greater inhibition of viral DNA replication. Furthermore, CPP-AZP did not show any significant cytotoxixity in MTT assays. Thus, our results demonstrate that cell-permeable AZPs could serve as potent protein-based antiviral drugs.

Inhibition of DNA replication of human papillomavirus by artificial zinc finger proteins

Recently, we demonstrated that plant DNA virus replication was inhibited in planta by using an artificial zinc finger protein (AZP) and created AZP-based transgenic plants resistant to DNA virus infection. Here we apply the AZP technology to the inhibition of replication of a mammalian DNA virus, human papillomavirus type 18 (HPV-18). Two AZPs, designated AZP(HPV)-1 and AZP(HPV)-2, were designed by using our nondegenerate recognition code table and were constructed to block binding of the HPV-18 E2 replication protein to the replication origin. Both of the newly designed AZPs had much higher affinities towards the replication origin than did the E2 protein, and they efficiently blocked E2 binding in vitro. In transient replication assays, both AZPs inhibited viral DNA replication, especially AZP(HPV)-2, which reduced the replication level to approximately 10%. We also demonstrated in transient replication assays, using plasmids with mutant replication origins, that AZP(HPV)-2 could precisely recognize the replication origin in mammalian cells. Thus, it was demonstrated that the AZP technology could be applied not only to plant DNA viruses but also to mammalian DNA viruses.

Modulation of endogenous VEGF-A expression by artificial transcription factors

The vascular endothelial growth factor A (VEGF-A) gene is an attractive therapeutic target because both activation and repression of the gene are useful for treatment or cure of many diseases related to abnormal angiogenesis. To modulate the endogenous gene expression artificially, we previously designed a six-finger AZP to recognize a 19-bp DNA in the VEGF-A gene, and fused the AZP with a nuclear localization signal and a repressor domain to generate an artificial transcription factor (ATF). Using the ATF, we demonstrated efficient modulation of the VEGF-A expression. In the present study, we evaluate the ability of the ATF to modulate the gene expression in more detail. First we examined the ability of the ATF under hypoxia condition. ELISA of the VEGF-A protein in the culture medium revealed that the gene-delivered ATF repressed the expression rate of the VEGF-A gene under hypoxia condition.

Regulation of cancer-related growth factor expression by artificial zinc-finger proteins

One attractive approach to anticancer therapy is repression of expression of vascular endothelial growth factor (VEGF) gene, which is a potent target for prevention of tumor growth. To achieve this, artificial transcription factors (ATF) designed for VEGF gene regulation were fused to cell-penetrating peptides (CPPs). We demonstrated ATFs fused to CPPs, designated CPP-ATFs or designed regulatory proteins (DRPs), could penetrate into mammalian cells and transiently repress expression of a reporter gene, which was under control of the VEGF promoter/5'-UTR. We discuss gene-regulatory properties of CPP-ATFs in detail.

Cerasome as an Infusible, Cell-Friendly, and Serum-Compatible Transfection Agent in a Viral Size

Alanine-based cationic lipid 1 having a (EtO)3SiCH2CH2CH2 group on the quaternized ammonium nitrogen forms a liposome which self-rigidifies via in situ sol-gel processes (Si-OEt + H2O --> Si-OH + EtOH followed by 2Si-OH --> Si-O-Si + H2O) on the surface. The resulting cerasome (partially ceramic- or silica-coated liposome) (60-70 nm) retains the integrity of such in the complexation with lucifarase-encoding plasmid DNA pGL3. The resultant pGL3 complex of infusible or monomeric cerasome in a viral size ( approximately 70 nm) exhibits a remarkable transfection performance toward HeLa and HepG2 cells with a 102-3-fold higher efficiency (relative to that of the nonsilylated reference lipid 2), minimized cytotoxicity, and serum compatibility. Reference lipid 2, i.e., alanine-based lipid having a simple quaternized ammonium headgroup, forms liposome (60-70 nm) which is less self-confined and more mobile undergoes DNA-induced fusion to give endocytosis-irrelevant and more toxic bigger (100-300 nm) particles. The silicon strategy thus provides a simple and widely applicable tool to overcome general problems associated with current technology of artificial gene delivery.

Refraction-enhanced tomography of mouse and rabbit lungs

In order to evaluate the effectiveness of edge enhancement by refraction in computed tomography, images of a cross section of a euthanized mouse thorax were recorded at low (20 keV) and high (72 keV) x-ray energies at a spatial resolution of about 40 microm. Compared with the images obtained with the detector at 30 cm from an object, when the object was located at 113 cm from the detector, the contrast between tissues and air was improved at both energies. The improvement was more pronounced at 72 keV where the absorption contrast was weaker. This effect was due to refraction at the surfaces of alveolar membranes and small airways which creates areas with apparently high and low linear attenuation coefficients within tissues. The edge enhancement by refraction was also effective in images of a euthanized rabbit thorax at x-ray energies of 40 and 70 keV at a spatial resolution of about 0.15 mm. These results raise the possibility that the refraction contrast may be utilized to obtain a high-resolution tomographic image of human lung and bone with low dose.

Application of artificial zinc-finger proteins to inhibition of DNA replication of human papillomavirus

Recently, we have demonstrated that plant DNA virus replication could be inhibited in Arabidopsis thaliana by using an artificial zinc-finger protein (AZP) and created AZP-based transgenic A. thaliana resistant to DNA virus infection. Here we apply the AZP technology to inhibition of replication of a mammalian DNA virus, human papillomavirus (HPV) type 18. Two AZPs, designated AZP(HPV)-1 and AZP(HPV)-2, were designed to block binding of the HPV-18 E2 replication protein to the replication origin. Both the designed AZPs had much higher affinities towards the replication origin than did the E2 protein, and efficiently blocked E2 binding in vitro. In transient replication assays, both AZPs inhibited the viral DNA replication: AZP(HPV)-2, especially, reduced the replication level to approximately 10%. Thus, it was demonstrated that the AZP technology could be applied not only to plant DNA viruses, but also to mammalian DNA viruses.

RNAi Silencing of Exogenous and Endogenous Reporter Genes Using a Macrocyclic Octaamine as a “Compact” siRNA Carrier. Studies on the Nonsilenced Residual Activity

A macrocyclic octaamine 1 having a covalently linked lipid-bundle structure was introduced as a new type of siRNA carrier. Gel electrophoresis, DLS, and SPR results indicate that it strongly binds to a luciferase-targeting 21-mer (42P) siRNA with a ratio of 1/P congruent with 0.3 (1/N congruent with 2.4) to give remarkably compact 1-siRNA complexes with an average size of approximately 10 nm. The 1-mediated siRNA silencing of the exogenous luciferase gene occurs with a 90-95% efficiency. The overall suppression-[siRNA] profile with a 5-10% residual activity in the saturation region is commonly observed irrespective of the cell type (HeLa, HepG2, or HEK293), the order, or timing (stepwise or simultaneous) of supply of the siRNA and that of the luciferase-encoding plasmid, the level of mRNA transcribed, or the type of carriers (1 vs lipofectamine 2000). The silencing of the endogenous DsRed2 gene stably incorporated in the genome of HeLa cells also has a similar overall profile. These results suggest that (1) the cellular uptake of the plasmid and that of the siRNA are basically independent of each other and (2) the incomplete silencing is not due to insufficient siRNA delivery. Implication of item 2 is briefly discussed.

Inhibition of virus DNA replication by artificial zinc finger proteins

Prevention of virus infections is a major objective in agriculture and human health. One attractive approach to the prevention is inhibition of virus replication. To demonstrate this concept in vivo, an artificial zinc finger protein (AZP) targeting the replication origin of the Beet severe curly top virus (BSCTV), a model DNA virus, was created. In vitro DNA binding assays indicated that the AZP efficiently blocked binding of the viral replication protein (Rep), which initiates virus replication, to the replication origin. All of the transgenic Arabidopsis plants expressing the AZP showed phenotypes strongly resistant to virus infection, and 84% of the transgenic plants showed no symptom. Southern blot analysis demonstrated that BSCTV replication was completely suppressed in the transgenic plants. Since the mechanism of viral DNA replication is well conserved among plants and mammals, this approach could be applied not only to agricultural crop protection but also to the prevention of virus infections in humans.

Regulation of the endogenous VEGF-A gene by exogenous designed regulatory proteins

We describe a facile method to activate or repress transcription of endogenous genes in a quantitative and specific manner by treatment with designed regulatory proteins (DRPs), in which artificial transcription factors (ATFs) are fused to cell-penetrating peptides (CPPs). Penetration of DRPs into cells is mediated by an N-terminal CPP fused to a nuclear localization signal; a DNA-binding domain and a transactivation domain follow. The DNA-binding domain was targeted to the vascular endothelial growth factor (VEGF)-A gene. An agonist DRP was rapidly taken up by cells and transported to the nucleus; soon after, the cells began transcribing the gene and secreting VEGF-A protein in a dose-dependent manner. Multiple copies of a short oligopeptide derived from a minimal transactivation domain of human beta-catenin was stronger than VP-16. The SRDX domain from the plant transcription factor, SUPERMAN, changed the DRP to a hypoxia-induced antagonist of VEGF-A. DRPs combine many of the potential benefits of transgenes with those of recombinant proteins.

A Quantum Dot Conjugated Sugar Ball and Its Cellular Uptake. On the Size Effects of Endocytosis in the Subviral Region

The lipophilic CdSe quantum dot (QD) coated with trioctylphosphine oxide (TOPOQD) can be extracted from chloroform into water upon interaction with macrocyclic glycocluster amphiphile 1. The QD-conjugated and highly fluorescent sugar ball of a size of 15 nm (TOPOQD1) thus solubilized in water readily invades Hela cells via endocytosis. The endocytic activity of TOPOQD1 (15 nm), in light of those of the micellar homoaggregate of 1 (5 nm) and the virus-like 1-DNA conjugate (50 nm) as references, reveals a dramatic size effect (50 > 15 > 5) in the subviral size region. The optimal size at approximately 50 nm indicates that size complementarity which governs molecular recognition in small host-guest systems also plays key roles in the encapsulation of nanometric guest particles by the endocytic vesicles (</=100 nm) as a macrobiomolecular host. The work thus suggests an utmost importance of size control at the viral size when designing molecular (gene, drug, probe, etc.) delivery machines.

Macrocyclic proteoglycan mimics. Potent inhibition of cell adhesion by a bundle of chondroitin sulfate chains assembled on the calix[4]resorcarene platform

Tailed calix[4]resorcarene macrocycle (tail=undecyl) can be used as a platform to assemble four glycosaminoglycan polysaccharide chains to give a new type of proteoglycan mimics. A tetra(chondroitin sulfate) derivative thus obtained from the reaction of macrocyclic octaamine and chondroitin sulfate lactone is readily immobilized on a tissue culture plastic (polystyrene) plate and inhibits fibronectin-mediated adhesion of BHK (baby hamster kidney) cells thereon remarkably strongly with 50% inhibition occurring at a 10 ng/mL or 40 pM concentration range.

Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table

We have developed a novel and simple method to rationally design artificial zinc-finger proteins (AZPs) targeting diverse DNA sequences using a nondegenerate recognition code table. The table was constructed based on known and potential DNA base-amino acid interactions. The table permits identification of an amino acid for each position (-1, 2, 3, and 6) of the alpha-helical region of the zinc-finger domain (position 1 is the starting amino acid in the alpha-helix) from overlapping 4-bp sequences in a given DNA target. Based on the table, we designed ten 3-finger AZPs, each of which targeted an arbitrarily chosen 10-bp DNA sequence, and characterized the binding properties. In vitro DNA-binding assays showed five of the AZPs tightly and specifically bound to their targets containing more than three guanine bases in the first 9-bp region. In addition, 6-finger AZPs, each of which was produced by combining two functional 3-finger AZPs, bound to their 19-bp targets with the dissociation constant of less than 3 pM. The in vivo functionality of the AZP was tested using Arabidopsis protoplasts. The AZP fused to a transcriptional activation domain efficiently activated expression of a reporter gene linked to a native promoter containing the AZP target site. Our simple AZP design method will provide a powerful approach to manipulation of endogenous gene expression by enabling rapid creation of numerous artificial DNA-binding proteins.

Directed evolution of novel polymerase activities: mutation of a DNA polymerase into an efficient RNA polymerase

The creation of novel enzymatic function is of great interest, but remains a challenge because of the large sequence space of proteins. We have developed an activity-based selection method to evolve DNA polymerases with RNA polymerase activity. The Stoffel fragment (SF) of Thermus aquaticus DNA polymerase I is displayed on a filamentous phage by fusing it to a pIII coat protein, and the substrate DNA template/primer duplexes are attached to other adjacent pIII coat proteins. Phage particles displaying SF polymerases, which are able to extend the attached oligonucleotide primer by incorporating ribonucleoside triphosphates and biotinylated UTP, are immobilized to streptavidin-coated magnetic beads and subsequently recovered. After four rounds of screening an SF library, three SF mutants were isolated and shown to incorporate ribonucleoside triphosphates virtually as efficiently as the wild-type enzyme incorporates dNTP substrates.

Antitumour activity and side effects of combined treatment with chitosan and cisplatin in sarcoma 180-bearing mice

We examined the possible modulation by chitosan of the antitumour effects and side effects of cisplatin (cis-diaminedichloroplatinum, CDDP). The study showed that CDDP had potent antitumour activity when administered orally as well as intraperitoneally. We also compared the antitumour activity and side effects of orally administered CDDP plus orally administered chitosan versus intraperitoneally administered CDDP plus orally administered chitosan in sarcoma 180-bearing mice. When CDDP (1.25 mgkg(-1) x 2 day(-1)) was intraperitoneally administered to sarcoma 180-bearing mice, myelotoxicity (the reduction of leucocyte and platelet numbers), nephrotoxicity (the increase of blood nitrogen urea level), immunotoxicity (the reduction of spleen and thymus weight) and a reduction in body weight resulted. These intraperitoneally administered CDDP-induced side effects were not prevented by oral administration of chitosan (150 mgkg(-1) x 2 day(-1) and 750 mgkg(-1) x 2 day(-1)) for 14 consecutive days. On the other hand, the side effects such as the reductions of body and spleen weights induced by orally administered CDDP (1.25 mgkg(-1) x 2 day(-1)) were prevented by the oral administration of chitosan (150 mgkg(-1) x 2 day(-1) and 750 mg kg(-1) x 2 day(-1)). From these results, we conclude that the orally administered chitosan plus CDDP might be useful for the prevention of body weight reduction and immunotoxicity (the reduction of spleen weight) induced by the orally administered CDDP without diminishing antitumour activity.