Arrangement of a highly repeated DNA sequence in the genome and chromatin of the African green monkey

Evaluation of the Efficacy of the Vaccine Production Process in Removing Residual Host Cell DNA from the Vero Cell Rabies Vaccine

BACKGROUND

The Vero cell rabies vaccine is currently the most widely used human rabies vaccine. However, owing to the presence of residual host cell DNA (HCD) in the final product and the potential tumorigenicity of the DNA of high-passage Vero cells, the WHO not only sets a limit on the number of times cells used in production can be passaged, but also imposes strict requirements on the amount of residual HCD in the final vaccine product.

OBJECTIVES

To systematically reduce the HCD level in the final vaccine product, multiple purification steps are included in the vaccine production process. This study investigated the effectiveness of key production steps in antigen recovery and DNA removal.

METHODS

The residual HCD fragment content and size distribution were detected using fluorescence quantitative PCR (qPCR) and capillary gel electrophoresis (CGE), and the rabies virus glycoprotein antigen content was detected using enzyme-linked immunosorbent assay (ELISA). The antigen recovery rate and HCD removal rate in each key process were calculated to evaluate the scientific basis and effectiveness of each production step. Additionally, the stability of the process was studied using multiple commercial batches of the product.

RESULTS

The results revealed that the total antigen recovery rate in the production process described in this report was no less than 8.5%, and the effective removal rate of residual HCD was not lower than 99.99%. Moreover, the amount of residual HCD in the final product was far below the quality standard of 2 ng/dose, and most of the residual HCD fragments were smaller than 200 bp. The results of the process stability studies on multiple commercial batches showed that the bulk human rabies vaccine produced by this process had excellent safety and efficacy and that the production process was stable and thus suitable for large-scale batch production.

CONCLUSIONS

The production process described in this study achieved effective recovery of viral antigens and efficient removal of residual HCD, and the process was stable and controllable, enabling the continuous and stable production of vaccine products that meet WHO recommendations and the relevant requirements of the current edition of the Chinese Pharmacopeia. In addition, this study provides theoretical guidance for optimizing the vaccine production process.

A flow-through chromatography purification process for Vero cell-derived influenza virus (H7N9)

Immunization is the most effective way to respond to an influenza epidemic. To produce Vero cell-derived influenza vaccines, a more efficient, stable and economical purification process is required. In this study, we purified the H7N9 influenza virus grown in Vero cells that were cultured in a serum-free medium by using a combination of anion exchange chromatography (AEC) and ligand-activated core chromatography (LCC), which avoids the virus capture step. After purification, 99.95 % host cell DNA (hcDNA) (final concentration: 28.69 pg/dose) and 98.87 % host cell protein (HCP) (final concentration: 28.28 ng/dose) were removed. The albumin content was 11.36 ng/dose. All these remnants met the current Chinese Pharmacopoeia and WHO requirements. The final virus recovery rate was 58.74 %, with the concentration of hemagglutinin recorded at 132.12 μg/mL. The flow-through chromatography purification process represents an alternative to the existing processes for cell-derived influenza viruses and might be suitable for the purification of other viruses as well.

Development of a Vero cell DNA reference standard for residual DNA measurement in China

This collaborative study developed a Vero cell DNA reference for standardizing dot blot hybridization, an assay widely employed to measure residual DNA contents of viral vaccines prepared with Vero cells. High purity of Vero cell DNA was extracted and characterized by Hind III enzyme digestion and DNA sequencing. Then, with a cooperative calibration, the concentration of Vero cell DNA reference bulk solution was determined (64.0 ± 1.9 μg/mL, OD 260/OD 280 = 1.87) and diluted (40 ng/mL) with Tris-EDTA buffer containing bovine serum albumin as freeze-dried excipients. With industrial filling apparatus, the diluted bulk was loaded into ampoules (0.5 mL each) which were heat sealed after nitrogen filling. Finally, a collaborative study showed that the Vero cell DNA reference could reach a sensitivity of 1 to 5 pg/dot and maintained good stability after accelerated destruction test. The successful establishment of the Vero cell DNA quantitative reference will facilitate the standardization of dot blot hybridization for testing residual host cell DNA.

DNA engineering shows that nucleosome phasing on the African green monkey alpha-satellite is the result of multiple additive histone-DNA interactions

The mechanism underlying sequence-specific positioning of nucleosomes on DNA was investigated. African green monkey alpha-satellite DNA was reconstituted in vitro with histones. Histone octamers were found to adopt one major and several minor positions on the satellite repeat unit, very similar to those positions found previously in vitro, demonstrating that sequence-specific histone-DNA interactions are responsible for nucleosome positioning on this DNA. In order to understand the nature of these interactions in more detail, we have constructed a variant satellite fragment containing an insertion of half a helical DNA turn. The parent fragment directs histones to one major and two overlapping minor positions that are all affected by the insertion. All three frames respond in a unique fashion to the additional five base-pairs. From a quantitative analysis of the nucleosome positions on the engineered fragment, consensus "phasing boxes" as the basis for nucleosome positioning can be ruled out. Instead, our results argue very strongly that nucleosome positioning is due to the independent contribution of many different DNA-histone contacts along the entire core particle, in an apparently additive fashion.

Isolation of low-copy-number sequences that neighbor satellite DNA in mammals

To investigate the role of satellite DNA in eukaryotic genomes, we isolated from an African green monkey (Cercopithecus aethiops) genomic library cloned segments containing the previously described deca-satellite linked to low-copy-number genomic sequences. Three such clones were obtained. The low-copy-number sequences in the three clones do not cross-hybridize suggesting that they derive from different genomic loci. The structure of one of the clones, lambda MkA, is described in detail. Subcloned segments containing the low-copy-number sequences from lambda MkA anneal to monkey, human and mouse genomic DNA. The subcloned probes were used to select clones containing homologous sequences from a second, independent monkey library as well as from human and mouse genomic libraries. Several of the newly isolated monkey clones hybridized to probes containing the species-specific deca- and alpha-satellites, confirming the genomic association of the low-copy-number sequence in lambda MkA with satellite DNA. Moreover, several of the human and mouse clones hybridized to species-specific human and mouse satellite DNAs, respectively. These experiments indicate that the low-copy-number sequence in lambda MkA and its association with satellite DNA is conserved in primates and rodents.

Continuous reorganization leads to extensive polymorphism in a monkey centromeric satellite

Previously we reported the existence of a highly polymorphic satellite, deca-satellite, in the African green monkey genome; deca-satellite probe anneals to complex sets of repeated restriction endonuclease fragments that differ from individual to individual in the monkey population. Here we present experiments aimed at clarifying the structure and organization of deca-satellite sequences and investigating the mechanisms that generate the polymorphisms. Deca-satellite represents less than 1% of the monkey genome but the percentage varies from one monkey to another. The core sequence 5'-C-C-G-G within the ten base-pair deca-satellite repeat unit is well conserved and the central 5'-C-G is sometimes but not always methylated. Restriction endonuclease analysis with BamHI and EcoRI defines separate satellite domains that have evolved in an independent manner. In situ hybridization shows deca-satellite to be located at the centromeric regions of some but not all monkey chromosomes. This location is independently confirmed by a high frequency, in monkey libraries, of segments containing junctions between deca-satellite and alpha-satellite, the main monkey centromeric satellite. The total number of metaphase chromosomes that show centromeric grains after in situ hybridization with a deca-satellite probe varies from one monkey to another. Moreover, in situ hybridization to endoreduplicated diplochromosomes showed that deca-satellite is occasionally distributed asymmetrically on one or the other of the two pairs of sister chromatids in one diplochromosome. This indicates that major reorganization of the satellite can occur frequently in somatic cells. We discuss several possible mechanisms by which deca-satellite sequences could be either amplified or deleted during a single replicative cycle. Also, on the basis of the marked fluidity of deca-satellite abundance and organization and other well-known attributes of centromeric satellites, we suggest that the existence and maintenance of centromeric satellite rests on the role of the tandem repeats themselves and not on any particular nucleotide sequence, repeat length or organization.

Transcriptionally active chromatin

Eukaryotic chromatin has a dynamic, complex hierarchical structure. Active gene transcription takes place on only a small proportion of it at a time. While many workers have tried to characterize active chromatin, we are still far from understanding all the biochemical, morphological and compositional features that distinguish it from inactive nuclear material. Active genes are apparently packaged in an altered nucleosome structure and are associated with domains of chromatin that are less condensed or more open than inactive domains. Active genes are more sensitive to nuclease digestions and probably contain specific nonhistone proteins which may establish and/or maintain the active state. Variant or modified histones as well as altered configurations or modifications of the DNA itself may likewise be involved. Practically nothing is known about the mechanisms that control these nuclear characteristics. However, controlled accessibility to regions of chromatin and specific sequences of DNA may be one of the primary regulatory mechanisms by which higher cells establish potentially active chromatin domains. Another control mechanism may be compartmentalization of active chromatin to certain regions within the nucleus, perhaps to the nuclear matrix. Topological constraints and DNA supercoiling may influence the active regions of chromatin and be involved in eukaryotic genomic functions. Further, the chromatin structure of various DNA regulatory sequences, such as promoters, terminators and enhancers, appears to partially regulate transcriptional activity.

Formation and repair of furocoumarin adducts in alpha deoxyribonucleic acid and bulk deoxyribonucleic acid of monkey cells

We have extended our previous finding that excision repair of furocoumarin photoadducts is deficient in the highly repetitive alpha DNA sequences in cultured African green monkey cells. The formation and removal from DNA of the individual photoadducts of 4'-(hydroxymethyl)-4,5',8-trimethylpsoralen (HMT) were monitored by analysis of DNA hydrolysates using a high-pressure liquid chromatography procedure that separated the major adducts from each other and also resolved the two diastereomers of the most frequent monoadduct. The overall deficiency in removal of HMT adducts from alpha DNA was similar to that previously observed by us with 4'-(aminomethyl)-4,5',8-trimethylpsoralen and angelicin. The two diastereomers of the furan-T monoadducts were formed in the same relative amounts in alpha DNA and bulk DNA whether photoaddition was in vivo or in vitro, and they were removed from cellular DNA at the same relative rates. Therefore, the deficient removal of furocoumarin adducts from alpha cannot be due to preferential formation of some adduct inherently refractory to repair. However, in vivo, the photochemical conversion of the furan-T monoadducts to diadducts was markedly reduced in alpha DNA, relative to that in bulk DNA. This indicates a possible conformational constraint in the internucleosomal DNA in alpha-chromatin which may account for the deficiency in repair.

Nucleosome arrangement in green monkey alpha-satellite chromatin. Superimposition of non-random and apparently random patterns

We have studied the structure of tandemly repetitive alpha-satellite chromatin (alpha-chromatin) in African green monkey cells (CV-1 line), using restriction endonucleases and staphylococcal nuclease as probes. While more than 80% of the 172-base-pair (bp) alpha-DNA repeats have a HindIII site, less than 15% of the alpha-DNA repeats have an EcoRI site, and most of the latter alpha-repeats are highly clustered within the CV-1 genome. EcoRI and HindIII solubilize approximately 8% and 2% of the alpha-chromatin, respectively, under the conditions used. EcoRI is thus approximately 30 times more effective than HindIII in solubilizing alpha-chromatin, with relation to the respective cutting frequencies of HindIII and EcoRI on alpha-DNA. EcoRI and HindIII solubilize largely non-overlapping subsets of alpha-chromatin. The DNA size distributions of both EcoRI- and HindIII-solubilized alpha-chromatin particles peak at alpha-monomers. These DNA size distributions are established early in digestion and remain strikingly constant throughout the digestion with either EcoRI or HindIII. Approximately one in every four of both EcoRI- and HindIII-solubilized alpha-chromatin particles is an alpha-monomer. Two-dimensional (deoxyribonucleoprotein leads to DNA) electrophoretic analysis of the EcoRI-solubilized, sucrose gradient-fractionated alpha-oligonucleosomes shows that they do not contain "hidden" EcoRI cuts. Moreover, although the EcoRI-solubilized alpha-oligonucleosomes contain one EcoRI site in every 172-bp alpha-DNA repeat, they are completely resistant to redigestion with EcoRI. This striking difference between the EcoRI-accessible EcoRI sites flanking an EcoRI-solubilized alpha-oligonucleosome and completely EcoRI-resistant internal EcoRI sites in the same alpha-oligonucleosome indicates either that the flanking EcoRI sites occur within a modified chromatin structure or that an altered nucleosome arrangement in the vicinity of a flanking EcoRI site is responsible for its location in the nuclease-sensitive internucleosomal (linker) region. Analogous redigestions of the EcoRI-solubilized alpha-oligonucleosomes with either HindIII, MboII or HaeIII (both before and after selective removal of histone H1 by an exchange onto tRNA) produce a self-consistent pattern of restriction site accessibilities. Taken together, these data strongly suggest a preferred nucleosome arrangement within the EcoRI-solubilized subset of alpha-oligonucleosomes, with the centers of most of the nucleosomal cores being approximately 20 bp and approximately 50 bp away from the nearest EcoRI and HindIII sites, respectively, within the 172-bp alpha-DNA repeat. However, as noted above, the clearly preferred pattern of nucleosome arrangement within the EcoRI-solubilized alpha-oligonucleosomes is invariably violated at the ends of every such alpha-oligonucleosomal particle, suggesting at least a partially statistical origin of this apparently non-random nucleosome arrangement.(ABSTRACT TRUNCATED AT 400 WORDS)

Hinf family: a novel repeated DNA family of the human genome

The isolation of a mutant adenovirus carrying an insertion of cellular DNA has led to the identification of a new family of human repetitive sequences, which are found tandemly arranged in the genome. The sequence of the viral insert resembles that of eukaryotic transposable elements.

Another potential artifact in the study of nucleosome phasing by chromatin digestion with micrococcal nuclease

We show that, contrary to expectations, restriction enzyme cleavage of chicken erythrocyte nucleosome core particle DNA generates a series of distinct subnucleosome fragments. These fragments do not result from bulk nucleosome phasing in vivo, but arise from micrococcal nuclease cleavages internal to the core particle, at roughly 10-base pair intervals and at AT-rich sequences. Those 145-base pair DNA fragments remaining intact are a biased population in which the guanine content can fluctuate by as much as 10%, with a 10-base pair period. We suggest that these same considerations, when applied to a unique DNA sequence, are the true explanation for several previous claims for nucleosome phasing.

Comparative DNA/DNA reassociation kinetics in three hamster species

1. Three major DNA repetition classes can be distinguished in the genomes of three hamster species Mesocricetus auratus, Cricetulus griseus, and Phodopus sungorus sungorus: A very fast reassociating fraction of about 13% of the DNA, a fast reassociating fraction comprising 10-23% of the DNA, and a slowly reassociating fraction containing single-copy sequences of 63-78% of hamster DNA. 2. In the DNA of the Syrian and Djungarian hamster 43%-53%, and in the DNA of the Chinese hamster 80% of the single-copy sequences are interspersed with repetitive sequences. 3. The lengths of repetitive DNA sequences, vary between more than 3 kb and 0.3 kb, with the majority of sequences having a length of 0.3 kb to 0.5 kb. 4. The findings suggest that the genomes of the hamster species studied are organized in a short period interspersion pattern. 5. Unlike other vertebrate and invertebrate genomes, moderately repetitive sequences exhibit a high degree of intraspecific homology in the hamster genome.

Cloning and organization of genes for 5S ribosomal RNA in the sea urchin. Lytechinus variegatus

A 1.35-kb EcoRI fragment of Lytechinus variegatus DNA containing a single 5S rRNA gene has been cloned into the plasmid vector pACYC184. Four clones from different transformation experiments contain 5S rDNA inserts of about the same size and have the same restriction enzyme digestion patterns for the enzymes HaeIII, HinfI, HhaI, and AluI. One EcoRI site near the HindIII site of the plasmid vector pACYC184 is missing in all the four clones. By DNA sequencing, the missing EcoRI ws found to be EcoRI site, d(AAATTN)d(TTTAAN) in pLu103, one of the four 5S rDNA clones. The structure of pLu103 was determined by restriction mapping and blot hybridization. Three restriction fragments, 1.0-kb HaeIII/HaeIII, 0.375-kb AluI/AluI and 0.249-kb MboII/MboII, which contain the 5S rRNA coding region, have been subcloned into the EcoRI site of the plasmid pACYC184. The organization of 5S rRNA genes in the sea urchin genome was also investigated. It was found that restriction endonuclease HaeIII has a single recognition site within each 5S rDNA repeat, and yields two fragment lengths, 1.2 and 1.3 kb. The behavior of these 5S rRNA genes when total L. variegatus DNA is partially digested with HaeIII is consistent with an arrangement of 5S rRNA genes in at least two tandemly repeated, non-interspersed families. Both the coding region and spacer region of the 5S rRNA gene in pLu103 hybridize to 1.2 and 1.3-kb rDNA families. This indicates that the cloned EcoRI fragment of 5S rDNA in pLu103 represents one single repeat of 5S rDNA in the genome.

Integration of the simian virus 40 genome into cellular DNA in temperature-sensitive (N) and temperature-insensitive (A) transformants of 3T3 rat and Chinese hamster lung cells

We studied the pattern of integration of the simian virus 40 (SV40) genome into the cellular DNA of N-transformants (temperature sensitive) and A-transformants (temperature insensitive) derived from 3T3-Fisher rat and Chinese hamster lung cells. The SV40 DNA was covalently linked to the cellular DNA in both types of transformants. In the rat cells, most N-transformants contained SV40 sequences integrated at a single site; most A-transformants contained SV40 sequences integrated at two to five sites. In the Chinese hamster cells, no significant correlation between the number of integration sites and the phenotype of the transformant was found; one of three integration sites were observed for both the N- and A-transformants. Single copies and tandem repeats of SV40 sequences were observed in A- and N-transformants derived from rat cells. A-transformants arise neither by amplification of the SV40 genome nor by integration at a unique site.