Genome Databank Research Articles

Genomic databanks provide robust assessment of invasive mosquito movement pathways and cryptic establishment

Biosecurity strategies that aim to restrict the spread of invasive pests can benefit from knowing where incursions have come from and whether cryptic establishment has taken place. This knowledge can be acquired with genomic databanks, by comparing genetic variation in incursion samples against reference samples. Here we use genomic databanks to characterise incursions of two mosquito species within Australia, and to observe how genomic tracing methods perform when databank samples have limited genetic differentiation and were collected tens of generations ago. We used a deep learning method to trace a 2021 invasion of Aedes aegypti in Tennant Creek, Northern Territory, to Townsville, Queensland, and to trace two years of Ae. albopictus incursions to two specific islands in the Torres Strait. Tracing had high precision despite 30–70 generations separating incursion and reference samples, and cross-validation of reference samples assigned them to the correct origin in 87% of cases. Similar precision was not achieved with PCAs, which performed particularly poorly for tracing when the invasion had been subject to strong drift effects. Targeted assays also provided additional information on the origin of the Tennant Creek Ae. aegypti, in this case by comparing Wolbachia infection data and mitochondrial DNA variation. Patterns of relatedness and inbreeding indicated that Tennant Creek was likely invaded by one family of Ae. aegypti, while Torres Strait incursions were independent and indicated no cryptic establishment. Our results highlight the value of genomic databanks that remain informative over years and for a range of biological conditions.

Dynamics of the personalities of PCSK9 on missense variants (rs505151 and rs562556) from elderly cohort studies in Brazil

The Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) promotes the degradation of the low-density lipoprotein receptors (LDLR). Gain-of-function (GOF) variants of PCSK9 significantly affects lipid metabolism leading to coronary artery disease (CAD), owing to the raising the plasma low-density lipoprotein (LDL). Considering the public health matter, large-scale genomic studies have been conducted worldwide to provide the genetic architecture of populations for the implementation of precision medicine actions. Nevertheless, despite the advances in genomic studies, non-European populations are still underrepresented in public genomic data banks. Despite this, we found two high-frequency variants (rs505151 and rs562556) in the ABraOM databank (Brazilian genomic variants) from a cohort SABE study conducted in the largest city of Brazil, São Paulo. Here, we assessed the structural and dynamical features of these variants against WT through a molecular dynamics study. We sought fundamental dynamical interdomain relations through Perturb Response Scanning (PRS) and we found an interesting change of dynamical relation between prodomain and Cysteine-Histidine-Rich-Domain (CHRD) in the variants. The results highlight the pivotal role of prodomain in the PCSK9 dynamic and the implications for the development of new drugs depending on patient group genotype.

In silico Analysis and Characterization of a Putative Aspartic Proteinase Inhibitor, IA3 from Lachancea kluyveri

Aspartic proteinases play important role in various physiological and biological processes. Understanding catalytic mechanisms of these enzymes could lead to crucial medical and biological applications. Two types of aspartic proteinase inhibitors have been identified i.e. small molecule inhibitor and naturally occurring peptides. Most of aspartic proteinases are highly susceptible to inhibition by a series of small, non-proteinaceous natural products; pepstatin. However, only limited number of naturally-occurring polypeptide inhibitors of aspartic proteinases has so far been discovered. One among these inhibitors is Saccharomyces cerevisiae IA3. The S. cerevisiae Proteinase A (ScPrA) is solely and potently inhibited by this small polypeptide at sub-nanomolar level. It was proven that, not only IA3 has no detectable effect against a wide range of aspartic proteinases, but it was also shown to be cleaved as a substrate of these non-target enzymes. Bioinformatics analysis of the IA3 structure has been undertaken in this study. Database searching for sequence homology from available fungal genome data bank using the Basic Local Alignment Search Tool (BLAST) revealed that 4 structurally related, IA3-like proteins have successfully been identified. The amino acid sequence of IA3-like proteins from Lachancea kluyveri share highest degree of similarity toward wild-type IA3. The Lk-IA3-like gene was synthesized using a PCR-based gene synthesis method. Protein expression in E. coli, protein purification and characterization of Lk-IA3-like by enzyme kinetic assays were performed. The results indicated that Lk-IA3-like protein inhibits ScPrA at the Ki value of 190 ± 0.11 nM and possesses no inhibitory effect toward AfPrA (Aspergillus fumigatus proteinase A) or HuCatD (Human cathepsin D). HIGHLIGHTS Aspartic proteinases enzyme family is crucially involved in various physiological and biological processes including in the pathogenesis of numerous diseases which make them a possible target for drug design Inhibitors of aspartic proteinases are not only applied for human disease treatment but also extended to plant and other economically important animals Aspartic proteinase from cerevisiae (Proteinase A) is solely and potently inhibited by a small peptideinhibitor, IA3 Bioinformatics analysis of the naturally occurring aspartic proteinases inhibitor, IA3 structure has been undertaken in this research and putative IA3-like proteins have successfully been identified IA3-like proteins from Lachancea kluyveri were produced in coli and enzyme inhibition assays revealed that Lk-IA3-like protein inhibits ScPrA at the Ki value of 190 ± 0.11 nM GRAPHICAL ABSTRACT

Effect of condylar chondrocyte exosomes on condylar cartilage osteogenesis in rats under tensile stress.

Background: Functional orthoses are commonly used to treat skeletal Class II malocclusion, but the specific mechanism through which they do this has been a challenging topic in orthodontics. In the present study, we aimed to explore the effect of tensile stress on the osteogenic differentiation of condylar chondrocytes from an exosomal perspective. Methods: We cultured rat condylar chondrocytes under resting and tensile stress conditions and subsequently extracted cellular exosomes from them. We then screened miRNAs that were differentially expressed between the two exosome extracts by high-throughput sequencing and performed bioinformatics analysis and osteogenesis-related target gene prediction using the TargetScan and miRanda softwares. Exosomes cultured under resting and tensile stress conditions were co-cultured with condylar chondrocytes for 24h to form the Control-Exo and Force-Exo exosome groups, respectively. Quantitative real time PCR(RT-qPCR) and western blotting were then used to determine the mRNA and protein expression levels of Runx2 and Sox9 in condylar chondrocytes. Results: The mRNA and protein expression levels of Runx2 and Sox9 in the Force-Exo group were significantly higher than those in the Control-Exo group (p < 0.05). The differential miRNA expression results were consistent with our sequencing results. Bioinformatics analysis and target gene prediction results showed that the main biological processes and molecular functions involved in differential miRNA expression in exosomes under tensile stress were biological processes and protein binding, respectively. Kyoto Gene and Genome Data Bank (KEGG) pathway enrichment analysis showed significant enrichment of differentially expressed miRNAs in the mTOR signaling pathway. The differentially expressed miRNAs were found to target osteogenesis-related genes. Conclusion: These results suggest that stimulation of rat condylar chondrocytes with tensile stress can alter the expression levels of certain miRNAs in their exosomes and promote their osteogenic differentiation. Exosomes under tensile stress culture conditions thus have potential applications in the treatment of Osteoarthritis (OA).

Estimation of the Minimum Number of Replication Origins Per Chromosome in any Organism.

Eukaryote nuclear genomes predominantly replicate through multiple replication origins. The number of replication origins activated per chromosome during the S-phase duration may vary according to many factors, but the predominant one is replication stress. Several studies have applied different approaches to estimate the number and map the positions of the replication origins in various organisms. However, without a parameter to restrict the minimum of necessary origins, less sensitive techniques may suggest conflicting results. The estimation of the minimum number of replication origins (MO) per chromosome is an innovative method that allows the establishment of a threshold, which serves as a parameter for genomic approaches that map origins. For this, the MO can be easily obtained through a formula that requires as parameters: chromosome size, S-phase duration, and replication rate. The chromosome size for any organism can be acquired in genomic databanks (such as NCBI), the S-phase duration can be estimated by monitoring DNA replication, and the replication rate is obtained through the DNA combing approach. The estimation of MO is a simple, quick, and easy method that provides a new methodological framework to assist studies of mapping replication origins in any organism.

High-Throughput Sequencing Reveals Differential Begomovirus Species Diversity in Non-Cultivated Plants in Northern-Pacific Mexico.

Plant DNA viruses of the genus Begomovirus have been documented as the most genetically diverse in the family Geminiviridae and present a serious threat for global horticultural production, especially considering climate change. It is important to characterize naturally existing begomoviruses, since viral genetic diversity in non-cultivated plants could lead to future disease epidemics in crops. In this study, high-throughput sequencing (HTS) was employed to determine viral diversity of samples collected in a survey performed during 2012–2016 in seven states of Northern-Pacific Mexico, areas of diverse climatic conditions where different vegetable crops are subject to intensive farming. In total, 132 plant species, belonging to 34 families, were identified and sampled in the natural ecosystems surrounding cultivated areas (agro-ecological interface). HTS analysis and subsequent de novo assembly revealed a number of geminivirus-related DNA signatures with 80 to 100% DNA similarity with begomoviral sequences present in the genome databank. The analysis revealed DNA signatures corresponding to 52 crop-infecting and 35 non-cultivated-infecting geminiviruses that, interestingly, were present in different plant species. Such an analysis deepens our knowledge of geminiviral diversity and could help detecting emerging viruses affecting crops in different agro-climatic regions.

Development of a Standardized Sanger-Based Method for Partial Sequencing and Genotyping of Dengue Viruses.

The global expansion of dengue viruses (DENV-1 to DENV-4) has contributed to the divergence, transmission, and establishment of genetic lineages of epidemiological concern; however, tracking the phylogenetic relationships of these virus is not always possible due to the inability of standardized sequencing procedures in resource-limited public health laboratories. Consequently, public genomic data banks contain inadequate representation of geographical regions and historical periods. In order to improve detection of the DENV-1 to DENV-4 lineages, we report the development of a serotype-specific Sanger-based method standardized to sequence DENV-1 to DENV-4 directly from clinical samples using universal primers that detect most DENV genotypes. The resulting envelope protein coding sequences are analyzed for genotyping with phylogenetic methods. We evaluated the performance of this method by detecting, amplifying, and sequencing 54 contemporary DENV isolates, including 29 clinical samples, representing a variety of genotypes of epidemiological importance and global presence. All specimens were sequenced successfully and phylogenetic reconstructions resulted in the expected genotype classification. To further improve genomic surveillance in regions where dengue is endemic, this method was transferred to 16 public health laboratories in 13 Latin American countries, to date. Our objective is to provide an accessible method that facilitates the integration of genomics with dengue surveillance.

Hope, hype and harms of Big Data.

Big Data are characterised by greater volumes of data from a greater variety of sources which are produced and processed at greater velocity. Huge digitised datasets from electronic medical records, registries, administrative datasets and genomic databanks can now be analysed by advanced computer programs to reveal patterns, trends and associations previously indiscernible using conventional analytic methods. These new insights may have important implications for clinical care. But Big Data can be limited by inaccuracies and bias inherent to observational datasets and which cannot be eliminated simply by using ever enlarging data sets or more sophisticated software. The hope and hype of Big Data cannot be allowed to override potential for harm, and the need for concurrent development of new research designs, better analytic methods and rigorous evaluation of predictive accuracy and effects on care and outcomes.

Mitochondrial tyrosyl-DNA phosphodiesterase 2 and its TDP2S short isoform.

Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs abortive topoisomerase II cleavage complexes. Here, we identify a novel short isoform of TDP2 (TDP2S) expressed from an alternative transcription start site. TDP2S contains a mitochondrial targeting sequence, contributing to its enrichment in the mitochondria and cytosol, while full-length TDP2 contains a nuclear localization signal and the ubiquitin-associated domain in the N-terminus. Our study reveals that both TDP2 isoforms are present and active in the mitochondria. Comparison of isogenic wild-type (WT) and TDP2 knockout (TDP2-/-/-) DT40 cells shows that TDP2-/-/- cells are hypersensitive to mitochondrial-targeted doxorubicin (mtDox), and that complementing TDP2-/-/- cells with human TDP2 restores resistance to mtDox. Furthermore, mtDox selectively depletes mitochondrial DNA in TDP2-/-/- cells. Using CRISPR-engineered human cells expressing only the TDP2S isoform, we show that TDP2S also protects human cells against mtDox. Finally, lack of TDP2 in the mitochondria reduces the mitochondria transcription levels in two different human cell lines. In addition to identifying a novel TDP2S isoform, our report demonstrates the presence and importance of both TDP2 isoforms in the mitochondria.

Exomic variants of an elderly cohort of Brazilians in the ABraOM database.

Brazilians are highly admixed with ancestry from Europe, Africa, America, and Asia and yet still underrepresented in genomic databanks. We hereby present a collection of exomic variants from 609 elderly Brazilians in a census-based cohort (SABE609) with comprehensive phenotyping. Variants were deposited in ABraOM (Online Archive of Brazilian Mutations), a Web-based public database. Population representative phenotype and genotype repositories are essential for variant interpretation through allele frequency filtering; since elderly individuals are less likely to harbor pathogenic mutations for early- and adult-onset diseases, such variant databases are of great interest. Among the over 2.3 million variants from the present cohort, 1,282,008 were high-confidence calls. Importantly, 207,621 variants were absent from major public databases. We found 9,791 potential loss-of-function variants with about 300 mutations per individual. Pathogenic variants on clinically relevant genes (ACMG) were observed in 1.15% of the individuals and were correlated with clinical phenotype. We conducted incidence estimation for prevalent recessive disorders based upon heterozygous frequency and concluded that it relies on appropriate pathogenicity assertion. These observations illustrate the relevance of collecting demographic data from diverse, poorly characterized populations. Census-based datasets of aged individuals with comprehensive phenotyping are an invaluable resource toward the improved understanding of variant pathogenicity.

Abstract 4860: Detection of genetically distinct subclones in cancer: a novel NGS algorithm with high spatial and genetic resolution

Abstract Despite the large number of genome data banks, reference sequences are not always the best match for high-throughput analysis. This is especially true in studies of intratumor heterogeneity where increased mutation rates are observed; the use of a reference genome can complicate the interpretation of the results. Current techniques attempt to circumvent this obstacle by applying de novo assembly algorithms, but the process is slow and often without viable results. Here, we introduce a new technique to decrease the dependency of these pipelines on reference sequences. Our clone discovery algorithm takes advantage of existing alignment data and correlates distant mutations, reported by an alignment algorithm. The algorithm makes no statistical assumption; it extracts information from the overlapping alignments in a step-wise fashion, using reference coordinates of aligned reads. Due to the randomness of noise, the algorithm can be very sensitive and identify clones of low frequency. Citation Format: Konstantinos Karagiannis, Konstantin Chumakov, Vahan Simonyan, Raja Mazumder. Detection of genetically distinct subclones in cancer: a novel NGS algorithm with high spatial and genetic resolution. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4860. doi:10.1158/1538-7445.AM2015-4860

Kynurenine Aminotransferase III and Glutamine Transaminase L Are Identical Enzymes that have Cysteine S-Conjugate β-Lyase Activity and Can Transaminate l-Selenomethionine

Three of the four kynurenine aminotransferases (KAT I, II, and IV) that synthesize kynurenic acid, a neuromodulator, are identical to glutamine transaminase K (GTK), α-aminoadipate aminotransferase, and mitochondrial aspartate aminotransferase, respectively. GTK/KAT I and aspartate aminotransferase/KAT IV possess cysteine S-conjugate β-lyase activity. The gene for the former enzyme, GTK/KAT I, is listed in mammalian genome data banks as CCBL1 (cysteine conjugate beta-lyase 1). Also listed, despite the fact that no β-lyase activity has been assigned to the encoded protein in the genome data bank, is a CCBL2 (synonym KAT III). We show that human KAT III/CCBL2 possesses cysteine S-conjugate β-lyase activity, as does mouse KAT II. Thus, depending on the nature of the substrate, all four KATs possess cysteine S-conjugate β-lyase activity. These present studies show that KAT III and glutamine transaminase L are identical enzymes. This report also shows that KAT I, II, and III differ in their ability to transaminate methyl-L-selenocysteine (MSC) and L-selenomethionine (SM) to β-methylselenopyruvate (MSP) and α-ketomethylselenobutyrate, respectively. Previous studies have identified these seleno-α-keto acids as potent histone deacetylase inhibitors. Methylselenol (CH3SeH), also purported to have chemopreventive properties, is the γ-elimination product of SM and the β-elimination product of MSC catalyzed by cystathionine γ-lyase (γ-cystathionase). KAT I, II, and III, in part, can catalyze β-elimination reactions with MSC generating CH3SeH. Thus, the anticancer efficacy of MSC and SM will depend, in part, on the endogenous expression of various KAT enzymes and cystathionine γ-lyase present in target tissue coupled with the ability of cells to synthesize in situ either CH3SeH and/or seleno-keto acid metabolites.

3D-ultrastructure, functions and stress responses of gastropod (Biomphalaria glabrata) rhogocytes.

Rhogocytes are pore cells scattered among the connective tissue of different body parts of gastropods and other molluscs, with great variation in their number, shape and size. They are enveloped by a lamina of extracellular matrix. Their most characteristic feature is the “slit apparatus”, local invaginations of the plasma membrane bridged by cytoplasmic bars, forming slits of ca. 20 nm width. A slit diaphragm creates a molecular sieve with permeation holes of 20×20 nm. In blue-blooded gastropods, rhogocytes synthesize and secrete the respiratory protein hemocyanin, and it has been proposed–though not proven–that in the rare red-blooded snail species they might synthesize and secrete the hemoglobin. However, the cellular secretion pathway for respiratory proteins, and the functional role(s) of the enigmatic rhogocyte slit apparatus are still unclear. Additional functions for rhogocytes have been proposed, notably a role in protein uptake and degradation, and in heavy metal detoxification. Here we provide new structural and functional information on the rhogocytes of the red-blooded freshwater snail Biomphalaria glabrata. By in situ hybridization of mantle tissues, we prove that rhogocytes indeed synthesize hemoglobin. By electron tomography, the first three dimensional (3D) reconstructions of the slit apparatus are provided, showing detail of highly dense material in the cytoplasmic bars close to the slits. By immunogold labelling, we collected evidence that a major component of this material is actin. By genome databank mining, the complete sequence of a B. glabrata nephrin was obtained, and localized to the rhogocytes by immunofluorescence microscopy. The presence of both proteins fit the ultrastructure-based hypothesis that rhogocytes are related to mammalian podocytes and insect nephrocytes. Reactions of the rhogocytes to deprivation of food and cadmium toxification are also documented, and a possible secretion pathway of newly synthesized respiratory proteins through the slit apparatus is discussed.

MSLoc-DT: A new method for predicting the protein subcellular location of multispecies based on decision templates

Revealing the subcellular location of newly discovered protein sequences can bring insight to their function and guide research at the cellular level. The rapidly increasing number of sequences entering the genome databanks has called for the development of automated analysis methods. Currently, most existing methods used to predict protein subcellular locations cover only one, or a very limited number of species. Therefore, it is necessary to develop reliable and effective computational approaches to further improve the performance of protein subcellular prediction and, at the same time, cover more species. The current study reports the development of a novel predictor called MSLoc-DT to predict the protein subcellular locations of human, animal, plant, bacteria, virus, fungi, and archaea by introducing a novel feature extraction approach termed Amino Acid Index Distribution (AAID) and then fusing gene ontology information, sequential evolutionary information, and sequence statistical information through four different modes of pseudo amino acid composition (PseAAC) with a decision template rule. Using the jackknife test, MSLoc-DT can achieve 86.5, 98.3, 90.3, 98.5, 95.9, 98.1, and 99.3% overall accuracy for human, animal, plant, bacteria, virus, fungi, and archaea, respectively, on seven stringent benchmark datasets. Compared with other predictors (e.g., Gpos-PLoc, Gneg-PLoc, Virus-PLoc, Plant-PLoc, Plant-mPLoc, ProLoc-Go, Hum-PLoc, GOASVM) on the gram-positive, gram-negative, virus, plant, eukaryotic, and human datasets, the new MSLoc-DT predictor is much more effective and robust. Although the MSLoc-DT predictor is designed to predict the single location of proteins, our method can be extended to multiple locations of proteins by introducing multilabel machine learning approaches, such as the support vector machine and deep learning, as substitutes for the K-nearest neighbor (KNN) method. As a user-friendly web server, MSLoc-DT is freely accessible at http://bioinfo.ibp.ac.cn/MSLOC_DT/index.html.

Identification of a metallopeptidase with TOP-like activity inParacoccidioides brasiliensis, with increased expression in a virulent strain

Paracoccidioidomycosis (PCM), caused by the pathogenic fungus Paracoccidioides brasiliensis, is a systemic mycosis with severe acute and chronic forms. The pathology of PCM is not completely understood, and the role of proteases in the infection is not clearly defined. In this report, we describe a metallopeptidase activity in P. brasiliensis total and cytosolic protein extracts similar to that of mammalian thimet oligopeptidase (TOP). The analogous enzyme was suggested by analysis of P. brasiliensis genome databank and by hydrolytic activity of the FRET peptide Abz-GFSPFRQ-EDDnp which was completely inhibited by o-phenanthrolin and significantly inhibited by the TOP inhibitor, JA-2. This activity was also partially inhibited by IgG purified from patients with PCM, but not from normal individuals. As shown by high-performance liquid chromatography (HPLC), the hydrolysis of bradykinin had the same pattern as that of mammalian TOP, and anti-mammalian TOP antibodies significantly inhibited fungal cytosolic peptidase activity. Moreover, anti-mammalian TOP antibodies recognized a component of 80 kDa on fungal cytosol. A P. brasiliensis virulent isolate showed higher gene expression and TOP-like peptidase activity than a non-virulent strain. The release of enzyme following fungal lysis would be consistent with host antibody production and may have a role in the pathogenesis, inflammation and further development of the mycosis.

SV40 host-substituted variants: a new look at the monkey DNA inserts and recombinant junctions

The available monkey genomic data banks were examined in order to determine the chromosomal locations of the host DNA inserts in 8 host-substituted SV40 variant DNAs. Five of the 8 variants contained more than one linked monkey DNA insert per tandem repeat unit and in all cases but one, the 19 monkey DNA inserts in the 8 variants mapped to different locations in the monkey genome. The 50 parental DNAs (32 monkey and 18 SV40 DNA segments) which spanned the crossover and flanking regions that participated in monkey/monkey and monkey/SV40 recombinations were characterized by substantial levels of microhomology of up to 8 nucleotides in length; the parental DNAs also exhibited direct and inverted repeats at or adjacent to the crossover sequences. We discuss how the host-substituted SV40 variants arose and the nature of the recombination mechanisms involved.

Novel opioid peptides from genomic data banks: phylogenetic and bioactivity studies

Novel opioid peptides from genomic data banks: phylogenetic and bioactivity studies

Abstract 2123: Novel integration sites for Friend murine leukemia virus

Abstract Background: Friend murine leukemia virus (F-MuLV), a type C retrovirus, induces erythroleukemia when injected into certain strains of mice. The Induction of erythroleukemia is associated with viral integration into Friend leukemia integration site-1 (Fli-1). In some F-MuLV-infected mice we did not observe viral integration into Fli-1 region by Southern blot analysis. We hypothesize that induction of leukemia in these mice is due to insertion of F-MuLV into a novel integration site distinct from Fli-1. Methods: The genomic DNA of F-MuLV-induced leukemic cells is digested by StuI restriction enzyme. DNA sequences of about 50 base pairs in length, termed adaptors, are then ligated to both ends of the digested fragments. Using primers for the adaptors and F-MuLV sequences, we performed PCR, followed by nested PCR to amplify those fragments that contain F-MuLV sequence. The PCR product is gel purified, cloned into a TA vector and sequenced. The sequences are compared to mouse genome databank to determine the F-MuLV flanking sequences. Results: We identified seven novel integration sites for F-MuLV. Three of these sites are located inside genes and the remaining four do not interrupt any genes. We performed PCR to check if any of these integration sites were also targets of F-MuLV in twenty other tumors of the same type. We found that one of these integration sites which is close to Myb gene occurred in twenty five percent of the tested tumors in an area 1 kb in length. Conclusion: We identified seven novel F-MuLV integration sites for F-MuLV. We showed that the integration site on chromosome 10 close to the Myb gene occurs in 25% of F-MuLV- induced tumors and is therefore a common integration site. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2123.

Reduced Genotoxicity of Avian Sarcoma Leukosis Virus Vectors in Rhesus Long-term Repopulating Cells Compared to Standard Murine Retrovirus Vectors

Insertional mutagenesis continues to be a major concern in hematopoietic stem-cell gene therapy. Nonconventional gene transfer vectors with more favorable integration features in comparison with conventional retrovirus and lentivirus vectors are being developed and optimized. In this study, we report for the first time a systematic analysis of 198 avian sarcoma leukosis virus (ASLV) insertion sites identified in rhesus long-term repopulating cells, and a comparison of ASLV insertion patterns to Moloney murine leukemia virus (MLV) (n = 396) and simian immunodeficiency virus (SIV) (n = 289) using the newly released rhesus genome databank. Despite a weak preference toward gene-coding regions, ASLV integration is nonclustered, does not favor gene-rich regions, transcription start sites, or CpG islands. There was no propensity for ASLV insertions within or near proto-oncogenes, and most importantly, no insertions close to or within the Mds1-Evi1 locus, which is in contrast to the significant over-representation of this insertion site for MLV vectors in the same transplantation model. Furthermore, ASLV long terminal repeats (LTRs) do not have detectable promoter and enhancer activity in a quantitative luciferase assay to measure neighboring gene activation. The combination of these features is unique for ASLV and suggests that optimized vectors based on this virus could be useful and safe for gene transfer to hematopoietic stem cells and progenitor cells.

The evolution of 5S ribosomal RNA genes linked to the rDNA units of fungal species

5S ribosomal RNA (rRNA) genes are known to move in and out of various tandemly repeated eukaryotic gene families during evolution. Here, we investigated the organization of 5S rRNA genes linked to the ribosomal DNA (rDNA) units in 147 fungal species using available sequence and genome databanks. Whereas some fungal species have no 5S rRNA genes in their rDNA units, others have one or two 5S rRNA copies linked on the same or the opposite strand. There were at least 13 independent changes during the evolution of fungal species. These include two 5S rRNA genes loss, five 5S rRNA genes inversions and six 5S rRNA genes insertions (including duplications). The lower frequency of 5S rRNA genes loss might be due to the fact that these events are more likely to affect fitness. The maximum time required for 5S rRNA gene organization to change between related species was estimated to be 7.5 millions years based on the sequences of the elongation factor alpha genes of Candida glabrata and Saccharomyces mikatae. This time is much longer than the homogenization time predicted from theoretical and experimental studies and likely reflects the lack of closely related species or strains in our data set.