Discovery,characterization, and remediation of a C-terminal Fc-extension in proteins expressed in CHO cells

ABSTRACT

Protein-based biotherapeutics are produced in engineered cells through complex processes and may contain a wide variety of variants and post-translational modifications that must be monitored or controlled to ensure product quality. Recently, a low level (~1–5%) impurity was observed in a number of proteins derived from stably transfected Chinese hamster ovary (CHO) cells using mass spectrometry. These molecules include antibodies and Fc fusion proteins where Fc is on the C-terminus of the construct. By liquid chromatography-mass spectrometry (LC-MS), the impurity was found to be ~1177 Da larger than the expected mass. After tryptic digestion and analysis by LC-MS/MS, the impurity was localized to the C-terminus of Fc in the form of an Fc sequence extension. Targeted higher-energy collision dissociation was performed using various normalized collision energies (NCE) on two charge states of the extended peptide, resulting in nearly complete fragment ion coverage. The amino acid sequence, SLSLSPEAEAASASELFQ, obtained by the de novo sequencing effort matches a portion of the vector sequence used in the transfection of the CHO cells, specifically in the promoter region of the selection cassette downstream of the protein coding sequence. The modification was the result of an unexpected splicing event, caused by the resemblance of the commonly used GGU codon of the C-terminal glycine to a consensus splicing donor. Three alternative codons for glycine were tested to alleviate the modification, and all were found to completely eliminate the undesirable C-terminal extension, thus improving product quality.     

De novo discovery of antibody drugs – great promise demands scrutiny

ABSTRACT

We live in an era of rapidly advancing computing capacity and algorithmic sophistication. “Big data” and “artificial intelligence”find progressively wider use in all spheres of human activity, including healthcare. A diverse array of computational technologies is being applied with increasing frequency to antibody drug research and development (R&D). Their successful applications are met with great interest due to the potential for accelerating and streamlining the antibody R&D process. While this excitement is very likely justified in the long term, it is less likely that the transition from the first use to routine practice will escape challenges that other new technologies had experienced before they began to blossom. This transition typically requires many cycles of iterative learning that rely on the deconstruction of the technology to understand its pitfalls and define vectors for optimization. The study by Vasquez et al. identifies a key obstacle to such learning: the lack of transparency regarding methodology in computational antibody design reports, which has the potential to mislead the community efforts     

Non-referenced genome assembly from epigenomic short-read data

Current computational methods used to analyze changes in DNA methylation and chromatin modification rely on sequenced genomes. Here we describe a pipeline for the detection of these changes from short-read sequence data that does not require a reference genome. Open source software packages were used for sequence assembly, alignment, and measurement of differential enrichment. The method was evaluated by comparing results with reference-based results showing a strong correlation between chromatin modification and gene expression. We then used our de novo sequence assembly to build the DNA methylation profile for the non-referenced Psammomys obesus genome. The pipeline described uses open source software for fast annotation and visualization of unreferenced genomic regions from short-read data.     

A new Hemigrammus from the upper Río Vaupés,Colombia (Characiformes: Characidae), with a discussion on the presence of an enlarged urogenital papilla in the family

Hemigrammus xaveriellus sp. nov. is described from the upper Río Vaupés basin (Amazon basin), Departamento Guaviare, Colombia. It is distinguished from all congeners by the combination of the following characters: presence of a conspicuous, dark, longitudinal midlateral stripe extending along the body; presence of a conspicuous rounded, horizontally elongated humeral blotch anterior to the beginning of the dark midlateral stripe; seven scale rows between the dorsal fin and lateral line (vs. five to six); and five scale rows between the lateral line and pelvic-fin insertion (vs. three to four). The single mature male of He. xaveriellus possessed a well-developed urogenital papilla, an unusual feature among characids. The presence of an enlarged urogenital papilla in the family is discussed, and comments regarding the putative relationships of the new species are presented.     

Resource-related variables drive individual variation in flowering phenology and mediate population-level flowering responses to climate in an asynchronously reproducing palm

Many tropical plant species show wide intra-population variation in reproductive timing, resulting in the protracted presence of flowering and fruiting individuals. Various eco-evolutionary drivers have been proposed as ultimate causes for asynchronous phenology, yet little is known about the proximate factors that control reproductive onset among individuals or that influence the proportion of trees producing new inflorescences within a population. We employed a nine-year phenological record from 178 individuals of the hyperdominant, asynchronously flowering canopy palm, Oenocarpus bataua (Arecaceae)¸ to assess whether resource-related variables influence individual- and population-level flowering phenology. Among individuals, access to sunlight increased rates of inflorescence production, while the presence of resource sinks related to current investment in reproduction—developing infructescences—reduced the probability of producing new inflorescences. At the population level, climate anomalies induced by El Niño Southern Oscillation (ENSO) affected the proportion of the population producing inflorescences through time. Moreover, the effects of ENSO anomalies on flowering patterns depended on the prevalence of developing infructescences in the population, with stronger effects in periods of low developing-infructescence frequency. Taken together, these results suggest that resource-related variables can drive phenological differences among individuals and mediate population-level responses to larger-scale variables, such as climate anomalies. Consequently, a greater focus on the role of resource levels as endogenous cues for reproduction might help explain the frequent aseasonal phenological patterns observed among tropical plants, particularly those showing high intra-population asynchrony.     

La participación de personas con demencia en las reuniones del plan de atención individualizada: impacto en el bienestar y la calidad del cuidado

Introduction

An individualised intervention plan (IIP) offers a new paradigm in the care of the elderly with dementia, with the aim of increasing their quality of life through personalisation, respect for their freedom, and their participation in the decisions that affect their lives.

Objective

To evaluate the impact of the residential home patient with dementia and their quality of care when they take part in the interdisciplinary meeting in which their care plan is decided.

Material and methods

A total of 52 elderly patients with dementia took part in the study. They were distributed into two groups, one experimental (37 residents) and another control (15 residents). The Dementia Care Mapping (DCM) tool was used to assess the well-being and quality of care of the residents. This tool was used twice, before and after the intervention.

Results

The well-being of the resident, evaluated using the DCM, was similar before and after the intervention in the experimental group. No differences were observed either on comparing the control and experimental groups. However, some indicators of carer behaviour were different before and after the intervention, and when the control and experimental group were compared.

Conclusion

The inclusion of elderly persons with dementia in their IIP meeting had a positive effect in the interaction of the staff with the residents, but not on the well-being of the resident.     

Planificación anticipada de decisiones en las enfermedades crónicas avanzadas

Introduction

Advanced care planning (ACP) helps in make decisions on the health problems of people who have lost the capacity for informed consent. It has proven particularly useful in addressing the end of life. The aim of this study was to determine the prevalence of ACP in patients with severe chronic diseases.

Material and methods

Review of medical records of patients with dementia, amyotrophic lateral sclerosis, Parkinson's disease, chronic obstructive pulmonary disease or interstitial lung disease, heart failure, chronic kidney disease on dialysis and cancer, all in advanced stages. We collected data on living wills or registered prior decisions by the physician according to clinical planned.

Results

A total of 135 patients were studied. There was a record of ACP in 22 patients (16.3%). In most of them it was planned not to start any vital treatment in the event of high risk of imminent death and lacking the ability to make decisions. Only two patients were had a legal living will.

Conclusion

The registration of ACP is relatively low, and this can affect decision-making in accordance with the personal values of patients when they do not have the capacity to exercise informed consent.     

Utilisation des isotopes stables pour l’identification de l’origine du carbone dans la datation du charbon de bois du Paléolithique

Recent years have brought many results of radiocarbon dating the earliest periods of the Upper Palaeolithic that can bring light on the origins of figurative art by Sapiens or Neanderthals. These dates are often close to the limit of the field of radiocarbon dating; because they require measurements of the lowest amounts of radiocarbon, controls are particularly essential. Here we examine the case of the dating of charcoal, whose identification after decontamination is difficult. We suggest a method that does not require additional manipulation to determine whether carbon comes exclusively from charcoal: using the proportion of stable carbon isotopes 13C/12C which is often regarded as a signature (δ13C).     

Inhibiting PHGDH with NCT-503 reroutes glucose-derived carbons into the TCA cycle,independently of its on-target effect

The small-molecule inhibitor of phosphoglycerate dehydrogenase, NCT-503, reduces incorporation of glucose-derived carbons into serine in vitro. Here we describe an off-target effect of NCT-503 in neuroblastoma cell lines expressing divergent phosphoglycerate dehydrogenase (PHGDH) levels and single-cell clones with CRISPR-Cas9-directed PHGDH knockout or their respective wildtype controls. NCT-503 treatment strongly reduced synthesis of glucose-derived citrate in all cell models investigated compared to the inactive drug control and independent of PHGDH expression level. Incorporation of glucose-derived carbons entering the TCA cycle via pyruvate carboxylase was enhanced by NCT-503 treatment. The activity of citrate synthase was not altered by NCT-503 treatment. We also detected no change in the thermal stabilisation of citrate synthase in cellular thermal shift assays from NCT-503-treated cells. Thus, the direct cause of the observed off-target effect remains enigmatic. Our findings highlight off-target potential within a metabolic assessment of carbon usage in cells treated with the small-molecule inhibitor, NCT-503.