A scaffold for the Chinese hamster genome

Wlaschin, Katie F.; Hu, Wei Shou

doi:10.1002/bit.21430

Cited by 32 publications

(18 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Unassigned scaffolds and scaffolds assigned to the unseparated hamster chromosome 9 and 10 library were instead mapped to the mouse genome. Scaffolds that could be aligned uniquely were assigned to a hamster chromosome based on published hamster chromosome localization [Yang et al, 2000], [Wlaschin and Hu, 2007]. Fifteen scaffolds (18.79 Mb) could be assigned to chromosome 9 and 2 scaffolds (32.58 Mb) to chromosome 10.…”

Section: Resultsmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

102

119

View full text Add to dashboard Cite

Accurate and complete genome sequences are essential in biotechnology to facilitate genome-based cell engineering efforts. The current genome assemblies for Cricetulus griseus, the Chinese hamster, are fragmented and replete with gap sequences and misassemblies, consistent with most short-read based assemblies. Here, we completely resequenced C. griseus using Single Molecule Real Time (SMRT) sequencing and merged this with Illumina-based assemblies. This generated a more contiguous and complete genome assembly than either technology alone, reducing the number of scaffolds by >28-fold, with 90% of the sequence in the 122 longest scaffolds. Most genes are now found in single scaffolds, including up- and downstream regulatory elements, enabling improved study of noncoding regions. With >95% of the gap sequence filled, important CHO cell mutations have been detected in draft assembly gaps. This new assembly will be an invaluable resource for continued basic and pharmaceutical research.

show abstract

Section: Resultsmentioning

confidence: 99%

A reference genome of the Chinese hamster based on a hybrid assembly strategy

Rupp

MacDonald

et al. 2018

Biotech & Bioengineering

102

119

View full text Add to dashboard Cite

show abstract

“…Thus, we could have two distinct situations: either a functional coupling between the CFTR protein and an endogenous aquaporin, or a cAMP-stimulated aqueous pore within the CFTR protein. Quantitative information concerning the expression of endogenous proteins by CHO cells is scarce (Wlaschin and Hu, 2007). However, we have focussed our study on two aquaporins, AQP3 and AQP9, because it has been shown they are both cAMP-dependent 'aquaglycoporins', indirectly and positively activated by the CFTR protein (Schreiber et al, 1999;Pietrement et al, 2008).…”

Section: Resultsmentioning

confidence: 99%

The human CFTR protein expressed in CHO cells activates an aquaporin 3 in a cAMP dependent pathway: study by Digital Holographic Microscopy

Jourdain

Becq

Lengacher

et al. 2013

Journal of Cell Science

View full text Add to dashboard Cite

The transmembrane water movements during cellular processes and their relationship to ionic channel activity remain largely unknown. As an example, in epithelial cells it was proposed that the movement of water could be directly linked to cystic fibrosis transmembrane conductance regulator (CFTR) protein activity through a cAMP-stimulated aqueous pore, or be dependent on aquaporin. Here, we used digital holographic microscopy (DHM) an interferometric technique to quantify in situ the transmembrane water fluxes during the activity of the epithelial chloride channel, CFTR, measured by patch-clamp and iodide efflux techniques. We showed that the water transport measured by DHM is fully inhibited by the selective CFTR blocker CFTR inh172 and is absent in cells lacking CFTR. Of note, in cells expressing the mutated version of CFTR (F508del-CFTR), which mimics the most common genetic alteration encountered in cystic fibrosis, we also show that the water movement is profoundly altered but restored by pharmacological manipulation of F508del-CFTRdefective trafficking. Importantly, whereas activation of this endogenous water channel required a cAMP-dependent stimulation of CFTR, activation of CFTR or F508del-CFTR by two cAMP-independent CFTR activators, genistein and MPB91, failed to trigger water movements. Finally, using a specific smallinterfering RNA against the endogenous aquaporin AQP3, the water transport accompanying CFTR activity decreased. We conclude that water fluxes accompanying CFTR activity are linked to AQP3 but not to a cAMP-stimulated aqueous pore in the CFTR protein.

show abstract

“…Harvested cells (2 Â 10 6 cells) were centrifuged and the total RNA was extracted from the cell pellets using the RNeasy Kit (Qiagen GmbH, Hilden, Germany) according to manufacturer's protocol. Ten micrograms of the extracted biotin labeled cRNA was hybridized on a custom-made CHO-specific Affymetrix microarray (Yee et al, 2008b) containing 10,118 probe sets with 7,525 unique sequences that represent a subset from a collection of 16,136 unique CHO cell and Chinese hamster transcripts obtained by comprehensive EST sequencing as described by Wlaschin et al (2005) and Wlaschin and Hu (2007). Samples were scanned in highresolution mode and data were processed with an Affymetrix GeneChip Scanner 3000 system (Affymetrix, Inc., Santa Clara, CA).…”

Section: Methodsmentioning

confidence: 99%

CHO gene expression profiling in biopharmaceutical process analysis and design

Schaub¹,

Clemens²,

Schorn³

et al. 2009

Biotech & Bioengineering

View full text Add to dashboard Cite

Increase in both productivity and product yields in biopharmaceutical process development with recombinant protein producing mammalian cells can be mainly attributed to the advancements in cell line development, media, and process optimization. Only recently, genome-scale technologies enable a system-level analysis to elucidate the complex biomolecular basis of protein production in mammalian cells promising an increased process understanding and the deduction of knowledge-based approaches for further process optimization. Here, the use of gene expression profiling for the analysis of a low titer (LT) and high titer (HT) fed batch process using the same IgG producing CHO cell line was investigated. We found that gene expression (i) significantly differed in HT versus LT process conditions due to differences in applied chemically defined, serum-free media, (ii) changed over the time course of the fed batch processes, and that (iii) both metabolic pathways and 14 biological functions such as cellular growth or cell death were affected. Furthermore, detailed analysis of metabolism in a standard process format revealed the potential use of transcriptomics for rational media design as is shown for the case of lipid metabolism where the product titer could be increased by about 20% based on a lipid modified basal medium. The results demonstrate that gene expression profiling can be an important tool for mammalian biopharmaceutical process analysis and optimization.

show abstract

A scaffold for the Chinese hamster genome

Cited by 32 publications

References 48 publications

A reference genome of the Chinese hamster based on a hybrid assembly strategy

A reference genome of the Chinese hamster based on a hybrid assembly strategy

The human CFTR protein expressed in CHO cells activates an aquaporin 3 in a cAMP dependent pathway: study by Digital Holographic Microscopy

CHO gene expression profiling in biopharmaceutical process analysis and design

Contact Info

Product

Resources

About