Regulation of oxidative degradation of L-lysine in rat liver mitochondria

A blueprint from nature: miRNome comparison of plasma cells and CHO cells to optimize therapeutic antibody production

Chinese Hamster Ovary (CHO) cells are the most frequently used biopharmaceutical production hosts, although industry is presently suffering from their variable recombinant product quality, insufficient long-term stability and low productivity. Here, we present an effort to address overall cell line engineering by a novel bottom-up microRNA (miRNA) screening approach. miRNAs are small non-coding RNAs known to regulate global gene expression at the post-transcriptional level and have proved to serve as promising tools for cell line engineering for over a decade. Here the miRNome of plasma cells (PCs) has been analyzed as the natural blueprint for optimized production and secretion of antibodies. Performing comparative miRNome cross-species expression analysis of four murine/human PC-derived (PCD) and two CHO cell lines showed 147 conserved miRNAs to be differentially expressed between PCDs and CHOs. Conducting a targeted miRNA screen of this PC-specific miRNA subset revealed 14 miRNAs to improve bioprocess relevant parameters in CHO cells, among them the PC-characteristic miR-183 cluster. Finally, miRNA target prediction tools and transcriptome analysis were combined to elucidate differentially regulated lysine degradation and fatty acid metabolism pathways in monoclonal antibody (mAb) expressing CHO-DG44 and CHO-K1 cells, respectively. Thus, substantial new insights into molecular and cellular mechanisms of biopharmaceutical production cell lines can be gained by targeted bottom-up miRNA screenings.

Biochemical profiles of rat primary cultured hepatocytes following treatment with rotenone, FCCP, or (+)-usnic acid

The metabolomic profiles of rat primary hepatocytes following treatment with rotenone, FCCP, or (+)-usnic acid were determined using liquid chromatography-mass spectrometry/mass spectrometry and gas chromatography-mass spectrometry. Significant and similar changes in the levels of 283 biochemical metabolites were associated with the three treatments compared with solvent control samples. Overall, the three treatments generated similar global biochemical profiles, with some minor differences associated with rotenone treatment. All three treatments resulted in a shift in energy metabolism as demonstrated by decreased glycogen stores and glycolysis. A reduced antioxidant response was detected in cells following all treatments. In addition, bile acid biosynthesis decreased as a potential consequence of increased oxidative stress by all three treatments. Conversely, rotenone treatment induced a number of changes after 1 hr, which were not detected in FCCP- or (+)-usnic acid-treated samples; these changes were not sustained over time and included increased NAD+ salvage and lysine degradation. In conclusion, these biochemical profiles could provide new insights into the mechanism(s) of mitochondrial toxicity.

High-throughput oxidation screen of antibody-drug conjugates by analytical protein A chromatography following IdeS digest

OBJECTIVES

Oxidation of protein therapeutics is a major chemical degradation pathway which may impact bioactivity, serum half-life and stability. Therefore, oxidation is a relevant parameter which has to be monitored throughout formulation development. Methods such as HIC, RPLC and LC/MS achieve a separation of oxidized and non-oxidized species by differences in hydrophobicity. Antibody-drug conjugates (ADC) although are highly more complex due to the heterogeneity in linker, drug, drug-to-antibody ratio (DAR) and conjugation site. The analytical protein A chromatography can provide a simple and fast alternative to these common methods.

METHODS

A miniature analytical protein A chromatography method in combination with an IdeS digest was developed to analyse ADCs. The IdeS digest efficiency of an IgG1 was monitored using SEC-HPLC and non-reducing SDS-PAGE. An antibody-fluorescent dye conjugate was conjugated at different dye-to-antibody ratios as model construct to mimic an ADC.

KEY FINDINGS

With IdeS, an almost complete digest of a model IgG1 can be achieved (digested protein amount >98%). This enables subsequent analytical protein A chromatography, which consequently eliminates any interference of payload with the stationary phase.

CONCLUSION

A novel high-throughput method for an interchain cysteine-linked ADC oxidation screens during formulation development was developed.

Advanced Glycation End Products, Oxidation Products, and the Extent of Atherosclerosis During the VA Diabetes Trial and Follow-up Study

OBJECTIVE

To determine whether plasma levels of advanced glycation end products and oxidation products play a role in the development of atherosclerosis in patients with type 2 diabetes (T2D) over nearly 10 years of the VA Diabetes Trial and Follow-up Study.

RESEARCH DESIGN AND METHODS

Baseline plasma levels of methylglyoxal hydroimidazolone, Nε-carboxymethyl lysine, Nε-carboxyethyl lysine (CEL), 3-deoxyglucosone hydroimidazolone and glyoxal hydroimidazolone (G-H1), 2-aminoadipic acid (2-AAA), and methionine sulfoxide were measured in a total of 411 participants, who underwent ultrasound assessment of carotid intima-media thickness (CIMT), and computed tomography scanning of coronary artery calcification (CAC) and abdominal aortic artery calcification (AAC) after an average of 10 years of follow-up.

RESULTS

In risk factor-adjusted multivariable regression models, G-H1 was associated with the extent of CIMT and CAC. In addition, 2-AAA was strongly associated with the extent of CAC, and CEL was strongly associated with the extent of AAC. The combination of specific advanced glycation end products and oxidation products (G-H1 and 2-AAA) was strongly associated with all measures of subclinical atherosclerosis.

CONCLUSIONS

Specific advanced glycation end products and metabolic oxidation products are associated with the severity of subclinical atherosclerosis over the long term and may play an important role in the "negative metabolic memory" of macrovascular complications in people with long-standing T2D.

High-resolution MS for structural characterization of protein therapeutics: advances and future directions

High-resolution MS (HRMS) is a central analytical technique for the study of biomolecules and is widely used in the biopharmaceutical industry. This paper reviews recent advances in commonly used HRMS instrumentation and experimental strategies for HRMS-based structural characterization of protein therapeutics. An overview of protein higher order structural characterization using HRMS-based technologies is presented, including the use of hydrogen/deuterium exchange and hydroxyl radical footprinting methods for probing protein conformational dynamics and interactions in solution. Future directions in application of HRMS for characterizing protein therapeutics are also described.

Methionine oxidation in human IgG2 Fc decreases binding affinities to protein A and FcRn

Susceptibility of methionine residues to oxidation is a significant issue of protein therapeutics. Methionine oxidation may limit the product's clinical efficacy or stability. We have studied kinetics of methionine oxidation in the Fc portion of the human IgG2 and its impact on the interaction with FcRn and Protein A. Our results confirm previously published observations for IgG1 that two analogous solvent-exposed methionine residues in IgG2, Met 252 and Met 428, oxidize more readily than the other methionine residue, Met 358, which is buried inside the Fc. Met 397, which is not present in IgG1 but in IgG2, oxidizes at similar rate as Met 358. Oxidation of two labile methionines, Met 252 and Met 428, weakens the binding of the intact antibody with Protein A and FcRn, two natural protein binding partners. Both of these binding partners share the same binding site on the Fc. Additionally, our results shows that Protein A may serve as a convenient and inexpensive surrogate for FcRn binding measurements.

Determination of protein oxidation by mass spectrometry and method transfer to quality control

Characterization and quantitative analysis of oxidation plays an important role in biopharmaceutical development. This study demonstrates an approach to the assessment of susceptible to oxidation methionine residues in monoclonal antibodies and recombinant proteins. A method for the determination of oxidation levels by peptide mapping with mass spectrometric (MS) detection is described and its advantages compared to the UV detection are presented. Good linearity and reproducibility for determination of oxidation with MS detection are demonstrated (R2 > 0.99; RSDs of 4-9%). Aspects of method transfer to quality control group (QC) are discussed. As well, a quick and easy flow injection/MS method is proposed to substitute for peptide map analysis. Peptide coverage, linearity, reproducibility, robustness, sensitivity and quantitative oxidation results are compared for the flow injection/MS and LC/MS approaches.

Lysine alpha-ketoglutarate reductase and lysine oxidation are distributed in the extrahepatic tissues of chickens

In animals, lysine oxidation is thought to occur primarily via the activity of lysine alpha-ketoglutarate reductase (LKR). This activity was reported previously in chicken liver, but no work on the tissue distribution of the enzyme in chickens has been reported. Therefore, LKR activity was assayed in liver, kidney, pancreas, heart, brain, lung, spleen, muscle, and intestinal tissues in chickens as was the in vitro ability of tissue homogenates to oxidize lysine. Additionally, the expression of LKR mRNA was assessed by RT-PCR. We found LKR to be present in all tissues studied by both enzymatic analysis and mRNA abundance. Additionally, all tissues assayed oxidized lysine. The extent of lysine oxidation differed among the tissues, consistent with the different pathways of lysine oxidation in the different tissues. These studies demonstrate that LKR is widely distributed in chicken tissues and that tissues other than liver can contribute to whole-body lysine oxidation.

Starvation response in mouse liver shows strong correlation with life-span-prolonging processes

We have monitored global changes in gene expression in mouse liver in response to fasting and sugar-fed conditions using high-density microarrays. From ∼20,000 different genes, the significantly regulated ones were grouped into specific signaling and metabolic pathways. Striking changes in lipid signaling cascade, insulin and dehydroepiandrosterone (DHEA) hormonal pathways, urea cycle and S-adenosylmethionine-based methyl transfer systems, and cell apoptosis regulators were observed. Since these pathways have been implicated to play a role in the aging process, and since we observe significant overlap of genes regulated upon starvation with those regulated upon caloric restriction, our analysis suggests that starvation may elicit a stress response that is also elicited during caloric restriction. Therefore, many of the signaling and metabolic components regulated during fasting may be the same as those which mediate caloric restriction-dependent life-span extension.

Twenty-four-hour oral tracer studies with L-[1-13C]lysine at a low (15 mg.kg (-1).d (-1) and intermediate (29 mg.kg (-1).d(-1)) lysine intake in healthy adults

BACKGROUND

We proposed previously that the mean lysine requirement value is approximately 30 mg * kg(-)(1) * d(-)(1) rather than the proposed 1985 FAO/WHO/UNU estimate of the upper range of the requirement, which is 12 mg * kg(-)(1) * d(-)(1).

OBJECTIVE

Our objective was to explore the 24-h pattern and rate of whole-body lysine [l-(13)C]oxidation and status of whole-body lysine balance in healthy, young adults given an L-amino acid diet supplying either a low lysine intake (14-15 mg * kg(-)(1) * d(-)(1)) or an intermediate lysine intake (29 mg * kg(-)(1) * d(-)(1)) for 6 d before a continuous tracer study with L-[1-(13)C]lysine.

DESIGN

Five subjects received the low lysine intake, 6 subjects received the intermediate intake, and all were studied by using a standard 24-h oral tracer protocol that was described earlier for studies at a generous lysine intake.

RESULTS

The rate of lysine oxidation was not significantly different between the 12-h fasted and 12-h fed states. The daily oxidation rate (f1.gif" BORDER="0"> +/- SD) was 27. 9 +/- 8.8 and 27.3 +/- 17.6 mg lysine * kg(-)(1) * d(-)(1) for the low- and intermediate-intake groups, respectively (NS). Daily lysine balance was -12.4 +/- 92 and 1.8 +/- 17.7 mg * kg(-)(1) * d(-)(1), respectively (P < 0.025), for the low and intermediate intakes. The balance was significantly less than zero (P < 0.001) for the low intake.

CONCLUSION

The FAO/WHO/UNU lysine requirement value is not sufficient to maintain lysine homeostasis in healthy adults. From the results of this and tracer studies done by others, the mean lysine requirement of healthy adults was determined to be 30 mg * kg(-)(1) * d(-)(1).

Lysine degradation through the saccharopine pathway in mammals: involvement of both bifunctional and monofunctional lysine-degrading enzymes in mouse

Lysine-oxoglutarate reductase and saccharopine dehydrogenase are enzymic activities that catalyse the first two steps of lysine degradation through the saccharopine pathway in upper eukaryotes. This paper describes the isolation and characterization of a cDNA clone encoding a bifunctional enzyme bearing domains corresponding to these two enzymic activities. We partly purified those activities from mouse liver and showed for the first time that both a bifunctional lysine-oxoglutarate reductase/saccharopine dehydrogenase and a monofunctional saccharopine dehydrogenase are likely to be present in this organ. Northern analyses indicate the existence of two mRNA species in liver and kidney. The longest molecule, 3.4 kb in size, corresponds to the isolated cDNA and encodes the bifunctional enzyme. The 2.4 kb short transcript probably codes for the monofunctional dehydrogenase. Sequence analyses show that the bifunctional enzyme is likely to be a mitochondrial protein. Furthermore, enzymic and expression analyses suggest that lysine-oxoglutarate reductase/saccharopine dehydrogenase levels increase in livers of mice under starvation. Lysine-injected mice also show an increase in lysine-oxoglutarate reductase and saccharopine dehydrogenase levels.

Mitochondrial lysine uptake limits hepatic lysine oxidation in rats fed diets containing 5, 20 or 60% casein

Sixty male Sprague-Dawley rats were randomly allotted to receive diets containing 5, 20 or 60% casein. Rats had access to the diet only during the initial 8 h of the daily 12-h dark period. Hepatic mitochondrial lysine uptake, lysine alpha-ketoglutarate reductase (LKR) and saccharopine dehydrogenase (SacD) activities, and in vitro lysine oxidation (LOX) were measured 0, 6, 12, 18 and 24 h after the start of the dark period. Diurnal variation of mitochondrial lysine uptake was not detected (P > 0.10) although uptake varied 3-fold over 24 h. Mitochondrial lysine uptake was greater (P < 0.05) for rats fed diets containing 60% casein than for rats fed diets containing 5% casein. Diurnal variation of LKR was detected (P < 0. 05) in rats fed diets containing 20 and 60% casein. Diurnal variation of SacD was detected (P < 0.05) in rats fed diets containing 60% casein. Increased casein consumption resulted in increased LKR and SacD activities (4- to 5-fold; P < 0.05). Diurnal variation of LOX was detected in rats fed diets containing 20 and 60% casein (P < 0.05). Increasing the casein concentration in the diet from 5 to 60% resulted in a 7-fold increase in LOX (P < 0.05). To make rate comparisons, LKR and SacD activities and LOX were predicted from a range of substrate concentrations (0.1 to 5.0 mmol/L). Overall, LKR and SacD were 6-107 times that of LOX, suggesting that, in liver, mitochondrial lysine uptake limits LOX.

The biosynthesis and metabolism of the aspartate derived amino acids in higher plants

The essential amino acids lysine, threonine, methionine and isoleucine are synthesised in higher plants via a common pathway starting with aspartate. The regulation of the pathway is discussed in detail, and the properties of the key enzymes described. Recent data obtained from studies of regulation at the gene level and information derived from mutant and transgenic plants are also discussed. The herbicide target enzyme acetohydroxyacid synthase involved in the synthesis of the branched chain amino acids is reviewed.

Purification and Characterization of the Bifunctional Enzyme Lysine-Ketoglutarate Reductase-Saccharopine Dehydrogenase from Maize

The first enzyme of the lysine degradation pathway in maize (Zea mays L.), lysine-ketoglutarate reductase, condenses lysine and [alpha]-ketoglutarate into saccharopine using NADPH as a cofactor, whereas the second, saccharopine dehydrogenase, converts saccharopine to [alpha]-aminoadipic-[delta]-semialdehyde and glutamic acid using NAD+ or NADP+ as a cofactor. The reductase and dehydrogenase activities are optimal at pH 7.0 and 9.0, respectively. Both enzyme activities, co-purified on diethylaminoethyl-cellulose and gel filtration columns, were detected on nondenaturing polyacrylamide gels as single bands with identical electrophoretic mobilities and share tissue specificity for the endosperm. The highly purified preparation containing the reductase and dehydrogenase activities showed a single polypeptide band of 125 kD on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The native form of the enzyme is a dimer of 260 kD. Limited proteolysis with elastase indicated that lysine-ketoglutarate reductase and saccharopine dehydrogenase from maize endosperm are located in two functionally independent domains of a bifunctional polypeptide.