scholarly journals Proteogenomic annotation of the Chinese hamster reveals extensive novel translation events and endogenous retroviral elements

2018 ◽  
Author(s):  
Shangzhong Li ◽  
Seong Won Cha ◽  
Kelly Hefner ◽  
Deniz Baycin Hizal ◽  
Michael Bowen ◽  
...  

AbstractA high quality genome annotation greatly facilitates successful cell line engineering. Standard draft genome annotation pipelines are based largely onde novogene prediction, homology, and RNA-Seq data. However, draft annotations can suffer from incorrectly predictions of translated sequence, incorrect splice isoforms and missing genes. Here we generated a draft annotation for the newly assembled Chinese hamster genome and used RNA-Seq, proteomics, and Ribo-Seq to experimentally annotate the genome. We identified 4,333 new proteins compared to the hamster RefSeq protein annotation and 2,503 novel translational events (e.g., alternative splices, mutations, novel splices). Finally, we used this pipeline to identify the source of translated retroviruses contaminating recombinant products from Chinese hamster ovary (CHO) cell lines, including 131 type-C retroviruses, thus enabling future efforts to eliminate retroviruses by reducing the costs incurred with retroviral particle clearance. In summary, the improved annotation provides a more accurate platform for guiding CHO cell line engineering, including facilitating the interpretation of omics data, defining of cellular pathways, and engineering of complex phenotypes.

2020 ◽  
Author(s):  
Romain Daveu ◽  
Caroline Hervet ◽  
Louane Sigrist ◽  
Davide Sassera ◽  
Aaron Jex ◽  
...  

AbstractWe studied a family of iflaviruses, a group of RNA viruses frequently found in arthropods, focusing on viruses associated with ticks. Our aim was to bring insight on the evolutionary dynamics of this group of viruses, which may interact with the biology of ticks. We explored systematically de novo RNA-Seq assemblies available for species of ticks which allowed to identify nine new genomes of iflaviruses. The phylogeny of virus sequences was not congruent with that of the tick hosts, suggesting recurrent host changes across tick genera along evolution. We identified five different variants with a complete or near-complete genome in Ixodes ricinus. These sequences were closely related, which allowed a fine-scale estimation of patterns of substitutions: we detected a strong excess of synonymous mutations suggesting evolution under strong positive selection. ISIV, a sequence found in the ISE6 cell line of Ixodes scapularis, was unexpectedly nearidentical with I. ricinus variants, suggesting a contamination of this cell line by I. ricinus material. Overall, our work constitutes a step in the understanding of the interactions between this family of viruses and ticks.


2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
M Fernandez Sanchez ◽  
H Višnová ◽  
C Blockeel ◽  
A Pinborg ◽  
Y Khalaf ◽  
...  

Abstract Study question Does addition of choriogonadotropin beta (CG beta) to follitropin delta increase the number of good-quality blastocysts following ovarian stimulation in a long GnRH agonist protocol? Summary answer At the doses investigated, the addition of CG beta reduced the number of intermediate follicles and decreased the number of oocytes and blastocysts. What is known already CG beta is a new recombinant hCG (rhCG) molecule expressed by a human cell line (PER.C6â) with a different glycosylation profile compared to urinary hCG or rhCG derived from a Chinese Hamster Ovary (CHO) cell-line. In the first-in-human trial, the CG beta pharmacokinetics were similar between men and women. In women, the area under the curve (AUC) and the peak serum concentration (Cmax) increased dose proportionally following single and multiple daily doses. In men, a single dose of CG beta provided higher exposure with a longer half-life and proportionately higher testosterone production than rhCG derived from a CHO cell line. Study design, size, duration Placebo-controlled, double-blind, randomised trial (RAINBOW) to explore the efficacy and safety of CG beta as add-on treatment to follitropin delta in women undergoing COS in a long GnRH agonist protocol. The primary endpoint was the number of good-quality blastocysts (grade 3 BB or higher, Gardner and Schoolcraft, 1999). Subjects were randomised to receive either placebo or 1, 2, 4, 8, or 12 µg CG beta added to the daily individualised follitropin delta dose during COS. Participants/materials, setting, methods In total 619 women (30-42 years) with AMH levels between 5 and 35 pmol/L were randomized in equal proportions to the six treatment groups. All subjects were treated with an individualised dose of follitropin delta determined based on AMH (Elecsys AMH Plus Immunoassay) and body weight. Triggering was performed when 3 follicles were ≥17 mm but no more than 25 follicles ≥12 mm were reached Main results and the role of chance The incidence of cycle cancellation (range 0%-2.9%), total follitropin delta dose (mean 112 µg) and duration of stimulation (mean 10 days) were similar across the groups. A reduced number of intermediate follicles (12 to 17 mm) and fewer oocytes (mean range 9.7 to 11.2) were observed for all doses of CG beta compared to the follitropin delta only group (mean 12.5). The mean number of goodquality blastocysts was 3.3 in the follitropin delta group and ranged between 2.1 and 3.0 across the CG beta groups. The incidence of transfer cancellation was higher in the 4, 8 and 12 µg group, mostly as no blastocyst was available for transfer. In the group receiving only follitropin delta, the ongoing pregnancy rate (10-11 weeks after transfer) was high i.e. 43% per started cycle vs 28-39% in CG beta groups and 49% per transfer vs 38-50% in the CG beta groups. In line with the number of collected oocytes, the OHSS incidence was overall lower following follitropin delta with CG beta than following follitropin delta only treatment. Regardless of the dose, CG beta was safe and well-tolerated with low risk of immunogenicity. Limitations, reasons for caution The effect of the unique glycosylation of CG beta and the associated potency implications in women were not known prior to this trial. Further studies will be needed to evaluate potentially lower doses of CG beta for this and/or different indications. Wider implications of the findings The high ongoing pregnancy rate in the follitropin delta group supports the use of individualised follitropin delta dosing in a long GnRH agonist protocol. The differential potency of CG beta may have impaired the growth of intermediate follicles with the investigated doses without affecting the ongoing pregnancy rates per transfer. Trial registration number NCT03564509


2021 ◽  
Vol 28 ◽  
Author(s):  
Shikha Joon ◽  
Rajeev K. Singla ◽  
Bairong Shen ◽  
Mohammad Amjad Kamal

Background: 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-ones are promising antitumor agents with enormous data on their profound cytotoxic effects on the human cancer cell lines. Objectives: We sought to perform a Quantitative structure cytotoxicity relationship (QSCR) analysis of a series of previously reported fluoroquinolone analogues using computer-assisted multiple regression analysis and investigate the cytotoxicity-inducing structural parameters among these congeners. Methods: The dataset was segregated into training and test sets of 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-ones by using a random selection method embedded in Vlife MDS 4.6 software and subjected to QSCR analysis. Next, cross-validation of the generated QSCR models was performed along with the external test set prediction. Finally, the data was analyzed, and contour plots were developed to deduce the cytotoxicity-inducing structural parameters among these congeners using Minitab® software. Results: The validated QSCR model exhibited a statistically significant predictive value of 92.27 percent. Our QSCR model revealed a direct proportionality between hydrogen counts and cytotoxicity and exclusion of sulphur and nitrogen with lesser crowding of cyclopropyl rings in future potential 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-one analogues. Based on the QSCR model predictions and contour plot analysis, the de novo REPUBLIC1986 molecule provided the best hit with predicted IC50 (µM) of 0.45 against CHO cell line and is amenable to salt formation crucial for anti-ovarian cancer activity. Conclusion: These findings suggest the relevancy of the developed QSCR model in designing novel, potent, and safer anti-cancer drugs with 6-Fluoro-3-(4H-1,2,4-triazol-3-yl)quinolin-4(1H)-ones as seed compounds.


1994 ◽  
Vol 180 (3) ◽  
pp. 1087-1096 ◽  
Author(s):  
A Wright ◽  
S L Morrison

Immunoglobulin G (IgG) molecules are glycosylated in CH2 at Asn297; the N-linked carbohydrates attached there have been shown to contribute to antibody (Ab) stability and various effector functions. The carbohydrate attached to the IgG constant region is a complex biantennary structure. Alterations in the structure of oligosaccharide have been associated with human diseases such as rheumatoid arthritis and osteoarthritis. To study the effects of altered carbohydrate structure on Ab effector function, we have used gene transfection techniques to produce mouse-human chimeric IgG1 Abs in the Chinese hamster ovary (CHO) cell line Lec 1, which is incapable of processing the high-mannose intermediate through the terminal glycosylation steps. We also produced IgG1 Abs in Pro-5, the wild-type CHO cell line that is the parent of Lec 1. The Pro-5-produced Ab (IgG1-Pro-5) was similar to IgG1-My 1, a myeloma-produced IgG1 Ab of the same specificity, in its biologic properties such as serum half-life, ability to effect complement-mediated cytolysis, and affinity for Fc gamma RI. Although the Lec 1-produced Ab, IgG1-Lec 1, was properly assembled and retained antigen specificity, it was incapable of complement-mediated hemolysis and was substantially deficient in complement consumption, C1q binding, and C1 activation. IgG1-Lec 1 also showed reduced but significant affinity for Fc gamma R1 receptors. The in vivo half-life of IgG1-Lec 1 was shorter than that of either the myeloma- or Pro-5-produced counterpart, with more being cleared during the alpha-phase and with more rapid clearance during the beta-phase. Clearance of IgG1-Lec 1 could be inhibited by the administration of yeast-derived mannan. Thus the uptake of IgG1-Lec 1 appears to be accelerated by the presence of terminally mannosylated oligosaccharide. Therefore, certain Ab functions as well as the in vivo fate of the protein are dramatically affected by altered carbohydrate structure. Expression of Igs in cell lines with defined glycosylation mutations is shown to be a useful technique for investigating the contribution of carbohydrate structure to Ab function.


2017 ◽  
Vol 313 (3) ◽  
pp. F585-F595 ◽  
Author(s):  
Megan L. Eshbach ◽  
Rahil Sethi ◽  
Raghunandan Avula ◽  
Janette Lamb ◽  
Deborah J. Hollingshead ◽  
...  

The OK cell line derived from the kidney of a female opossum Didelphis virginiana has proven to be a useful model in which to investigate the unique regulation of ion transport and membrane trafficking mechanisms in the proximal tubule (PT). Sequence data and comparison of the transcriptome of this cell line to eutherian mammal PTs would further broaden the utility of this culture model. However, the genomic sequence for D. virginiana is not available and although a draft genome sequence for the opossum Monodelphis domestica (sequenced in 2012 by the Broad Institute) exists, transcripts sequenced from both species show significant divergence. The M. domestica sequence is not highly annotated, and the majority of transcripts are predicted rather than experimentally validated. Using deep RNA sequencing of the D. virginiana OK cell line, we characterized its transcriptome via de novo transcriptome assembly and alignment to the M. domestica genome. The quality of the de novo assembled transcriptome was assessed by the extent of homology to sequences in nucleotide and protein databases. Gene expression levels in the OK cell line, from both the de novo transcriptome and genes aligned to the M. domestica genome, were compared with publicly available rat kidney nephron segment expression data. Our studies demonstrate the expression in OK cells of numerous PT-specific ion transporters and other key proteins relevant for rodent and human PT function. Additionally, the sequence and expression data reported here provide an important resource for genetic manipulation and other studies on PT cell function using these cells.


2021 ◽  
Author(s):  
Richard Finkers ◽  
Martijn P.W. van Kaauwen ◽  
Kai Ament ◽  
Karin Burger-Meijer ◽  
Raymond J. Egging ◽  
...  

Onion is an important vegetable crop with an estimated genome size of 16GB. We describe the de novo assembly and ab initio annotation of the genome of a doubled haploid onion line DHCU066619, which resulted in a final assembly of 14.9 Gb with a N50 of 461 Kb. Of which 2.2 Gb was ordered into 8 pseudomolecules using five genetic linkage maps. The remainder of the genome is available in 89.8 K scaffolds. Analysis of this genome shows that at least 72.4% of the genome is repetitive and consists, to a large extent, of (retro) transposons. Many (retro) transposons were already quite old as they had accumulated many mutations, facilitating their assembly, however, hampering their identification. The draft ab initio gene prediction indicated 540 925 putative gene models, which is far more than expected, possibly due to the presence of pseudogenes. 86,073 models showed similarity to published proteins (UNIPROT). No gene rich regions were found, genes are uniformly distributed over the genome. Analysis of synteny with A. sativum (garlic) showed collinearity but also major rearrangements between both species. Not-withstanding, this assembly is the first high-quality draft genome sequence available for the study of onion and will be a valuable resource for further research.


2017 ◽  
Author(s):  
Michael P. Dunne ◽  
Steven Kelly

AbstractBackgroundThe accurate determination of the genomic coordinates for a given gene – its gene model – is of vital importance to the utility of its annotation, and the accuracy of bioinformatic analyses derived from it. Currently-available methods of computational gene prediction, while on the whole successful, often disagree on the model for a given predicted gene, with some or all of the variant gene models failing to match the biologically observed structure. Many prediction methods can be bolstered by using experimental data such as RNA-seq and mass spectrometry. However, these resources are not always available, and rarely give a comprehensive portrait of an organism’s transcriptome due to temporal and tissue-specific expression profiles.ResultsOrthology between genes provides evolutionary evidence to guide the construction of gene models. OMGene (Optimise My Gene) aims to optimise gene models in the absence of experimental data by optimising the derived amino acid alignments for gene models within orthogroups. Using RNA-seq data sets from plants and fungi, considering intron/exon junction representation and exon coverage, and assessing the intra-orthogroup consistency of subcellular localisation predictions, we demonstrate the utility of OMGene for improving gene models in annotated genomes.ConclusionsWe show that significant improvements in the accuracy of gene model annotations can be made in both established and de novo annotated genomes by leveraging information from multiple species.


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