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Scott RA, Rogers R, Balland A, Brady LJ. Rapid identification of an antibody DNA construct rearrangement sequence variant by mass spectrometry. MAbs 2015; 6:1453-63. [PMID: 25484040 DOI: 10.4161/mabs.36222] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
During cell line development for an IgG1 antibody candidate (mAb1), a C-terminal extension was identified in 2 product candidate clones expressed in CHO-K1 cell line. The extension was initially observed as the presence of anomalous new peaks in these clones after analysis by cation exchange chromatography (CEX-HPLC) and reduced capillary electrophoresis (rCE-SDS). Reduced mass analysis of these CHO-K1 clones revealed that a larger than expected mass was present on a sub-population of the heavy chain species, which could not be explained by any known chemical or post-translational modifications. It was suspected that this additional mass on the heavy chain was due to the presence of an additional amino acid sequence. To identify the suspected additional sequence, de novo sequencing in combination with proteomic searching was performed against translated DNA vectors for the heavy chain and light chain. Peptides unique to the clones containing the extension were identified matching short sequences (corresponding to 9 and 35 amino acids, respectively) from 2 non-coding sections of the light chain vector construct. After investigation, this extension was observed to be due to the re-arrangement of the DNA construct, with the addition of amino acids derived from the light chain vector non-translated sequence to the C-terminus of the heavy chain. This observation showed the power of proteomic mass spectrometric techniques to identify an unexpected antibody sequence variant using de novo sequencing combined with database searching, and allowed for rapid identification of the root cause for new peaks in the cation exchange and rCE-SDS assays.
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Key Words
- C-terminal extension
- CAN, acetonitrile
- CEX, cation exchange
- CHO, Chinese hamster ovary
- DNA, deoxyribonucleic acid
- DTT, dithiothreitol
- Da, Dalton
- FDR, false discovery rate
- HC, heavy chain
- HPLC, high performance liquid chromatography
- LC, light chain
- MS, mass spectrometer
- MS/MS, tandem mass spectrometry
- MW, molecular weight
- NCBI, National Center for Biotechnology Information
- NCG, non-concensus glycosylation
- PSM, peptide-spectrum matches
- RP-UPLC, reversed phase ultra-high pressure liquid chromatography
- SEC, size exclusion chromatography
- TFA, trifluoracetic acid
- TOF, time of flight mass spectrometer
- UV, ultraviolet
- aa, amino acids
- mass spectrometry
- ppm, parts per million
- rCE-SDS, reduced capillary electrophoresis-sodium dodecyl sulfate
- sequence variant
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Warda M, Prince A, Kim HK, Khafaga N, Scholkamy T, Linhardt RJ, Jin H. Proteomics of old world camelid (Camelus dromedarius): Better understanding the interplay between homeostasis and desert environment. J Adv Res 2013; 5:219-42. [PMID: 25685490 PMCID: PMC4294715 DOI: 10.1016/j.jare.2013.03.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 03/04/2013] [Accepted: 03/13/2013] [Indexed: 01/26/2023] Open
Abstract
Life is the interplay between structural–functional integrity of biological systems and the influence of the external environment. To understand this interplay, it is useful to examine an animal model that competes with harsh environment. The dromedary camel is the best model that thrives under severe environment with considerable durability. The current proteomic study on dromedary organs explains a number of cellular mysteries providing functional correlates to arid living. Proteome profiling of camel organs suggests a marked increased expression of various cytoskeleton proteins that promote intracellular trafficking and communication. The comparative overexpression of α-actinin of dromedary heart when compared with rat heart suggests an adaptive peculiarity to sustain hemoconcentration–hemodilution episodes associated with alternative drought-rehydration periods. Moreover, increased expression of the small heat shock protein, α B-crystallin facilitates protein folding and cellular regenerative capacity in dromedary heart. The observed unbalanced expression of different energy related dependent mitochondrial enzymes suggests the possibility of mitochondrial uncoupling in the heart in this species. The evidence of increased expression of H+-ATPase subunit in camel brain guarantees a rapidly usable energy supply. Interestingly, the guanidinoacetate methyltransferase in camel liver has a renovation effect on high energy phosphate with possible concomitant intercession of ion homeostasis. Surprisingly, both hump fat tissue and kidney proteomes share the altered physical distribution of proteins that favor cellular acidosis. Furthermore, the study suggests a vibrant nature for adipose tissue of camel hump by the up-regulation of vimentin in adipocytes, augmenting lipoprotein translocation, blood glucose trapping, and challenging external physical extra-stress. The results obtained provide new evidence of homeostasis in the arid habitat suitable for this mammal.
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Key Words
- 2D, two-dimensional
- ACTH, adrenocorticotropic hormone
- Actin
- CHAPS, 3-(3-cholamidopropyl)-dimethylammoniopropane sulfonate
- CHCA, α-cyano-4-signal-to-noise
- Camel
- Crystallin
- DAPLE, Dvl-associating protein with a high frequency of leucine residues
- DTT, dithiothreitol
- Dvl, dishevelled: scaffold protein involved in the regulation of the Wnt signaling pathway
- IPG, immobilized pH gradient
- MALDI, matrix assisted laser desorption ionization
- MAPK, map kinase
- MS, mass spectrometry
- Metabolism
- PAGE, polyacrylamide gel electrophoresis
- PDB, protein database
- PMF, peptide mass finger printing
- Proteome
- SDS, sodium dodecylsulfate
- TFA, trifluoracetic acid
- TOF, time of flight
- Vimentin
- hsp, heat shock protein
- pI, isoelectric point
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Affiliation(s)
- Mohamad Warda
- Department of Biochemistry, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt ; Biotechnology Center for Services and Researches, Cairo University, Giza, Egypt
| | - Abdelbary Prince
- Department of Biochemistry, Faculty of Veterinary Medicine, Cairo University, Giza, Egypt
| | - Hyoung Kyu Kim
- National Research Laboratory for Mitochondrial Signaling, Department of Physiology, Cardiovascular and Metabolic Disease Center, Inje University, Busan 614-735, Republic of Korea
| | - Nagwa Khafaga
- Animal Health Research Institute, Dokki, Giza, Egypt
| | - Tarek Scholkamy
- Field Investigation Department, Animal Reproduction Research Institute, Giza, Egypt
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Han Jin
- National Research Laboratory for Mitochondrial Signaling, Department of Physiology, Cardiovascular and Metabolic Disease Center, Inje University, Busan 614-735, Republic of Korea
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