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Purpose Determine the effect of minute quantities of sub-visible aggregates on the in vitro immunogenicity of clinically relevant protein therapeutics. Methods Monoclonal chimeric (rituximab) and humanized (trastuzumab) antibodies were subjected to fine-tuned stress conditions to achieve low levels (<3% of total protein) of sub-visible aggregates. The effect of stimulating human dendritic cells (DC) and CD4 + T cells with the aggregates was measured in vitro using cytokine secretion, proliferation and confocal microscopy. Results Due to its intrinsic high clinical immunogenicity, aggregation of rituximab had minimal effects on DC activation and T cell responses compared to monomeric rituximab. However, in the case of trastuzumab (low clinical immunogenicity) small quantities of aggregates led to potent CD4 + T cell proliferation as a result of strong cytokine and co-stimulatory signals derived from DC. Consistent with this, confocal studies showed that stir-stressed rituximab was rapidly internalised and associated with late endosomes of DC. Conclusions These data link minute amounts of aggregates with activation of the innate immune response, involving DC, resulting in T cell activation. Thus, when protein therapeutics with little or no clinical immunogenicity, such as trastuzumab, contain minute amounts of sub-visible aggregates, they are associated with significantly increased potential risk of clinical immunogenicity.

Most protein therapeutics have the potential to induce undesirable immune responses in patients. Many patients develop anti-therapeutic antibodies, which can affect the safety and efficacy of the therapeutic protein, particularly if the response is neutralizing. There are a variety of factors that influence the immunogenicity of protein therapeutics and, in particular, the presence of B- and T-cell epitopes is considered to be of importance. In silico tools to identify the location of both B- and T-cell epitopes and to assess the potential for immunogenicity have been developed, and such tools provide an alternative to more complex in vitro or in vivo immunogenicity assays. This article reviews computational epitope prediction methods and also the use of manually curated databases containing experimentally derived epitope data. However, due to the complexities of the molecular interactions involved in epitope recognition by the immune system, the heterogeneity of key proteins in human populations and the adaptive nature of the immune response, in silico methods have not yet achieved a level of accuracy that enables them to be used as stand-alone tools for predicting clinical immunogenicity. Computational methods, particularly with regard to T-cell epitopes, only consider a limited number of events in the process of epitope formation and therefore routinely over-predict the number of epitopes within a molecule. Epitope databases such as the Immune Epitope Database (IEDB) and the proprietary T Cell Epitope Database™ (TCED™) have reached a size and level of organization that increases their utility; however, they are not exhaustive. These methods have greatest utility as an adjunct to in vitro assays where they can be used either to reduce the amount and complexity of the in vitro screening, or they can be used as tools to analyze the sequence of the identified epitope in order to locate amino acids critical for its properties.

Many chromatin features play critical roles in regulating gene expression. A complete understanding of gene regulation will require the mapping of specific chromatin features in small samples of cells at high resolution. Here we describe Cleavage Under Targets and Tagmentation (CUT&Tag), an enzyme-tethering strategy that provides efficient high-resolution sequencing libraries for profiling diverse chromatin components. In CUT&Tag, a chromatin protein is bound in situ by a specific antibody, which then tethers a protein A-Tn5 transposase fusion protein. Activation of the transposase efficiently generates fragment libraries with high resolution and exceptionally low background. All steps from live cells to sequencing-ready libraries can be performed in a single tube on the benchtop or a microwell in a high-throughput pipeline, and the entire procedure can be performed in one day. We demonstrate the utility of CUT&Tag by profiling histone modifications, RNA Polymerase II and transcription factors on low cell numbers and single cells. Understanding gene regulation will require mapping specific chromain features in a small number of cells at high resolution. Here the authors describe CUT&Tag, which uses antibody-mediated tethering of Tn5 transposase to a chromatin protein to generate high resolution libraries.

BackgroundWrong-drug medication errors are common. Regulators screen drug names for confusability, but screening methods lack empirical validation. Previous work showed that psycholinguistic tests on pairs of drug names are associated with real-world error rates in chain pharmacies. However, regulators evaluate individual names not pairs, and individual names can be confused with multiple drugs (eg, hydroxyzine with hydralazine but also hydrocet, thorazine, hydrochlorothiazide). This study examines whether an individual drug name’s performance on psycholinguistic tests correlates with that name’s sum total error rate in the real world.MethodsNineteen pharmacists and 18 pharmacy technicians completed memory and perception tests assessing confusability of 77 drug names. Tests involved presenting a drug name to participants in conditions that hindered their ability to see, hear or remember the name. Participants typed the name they perceived and selected that name from a menu of alternatives. Error rates on the tests were assessed in relation to real-world rates, as reported by the patient safety organisation associated with a national pharmacy chain in the USA.ResultsMean error rate on the psycholinguistic tests was positively correlated with the log-adjusted real-world error rate (r=0.50, p<0.0001). Linear and mixed effects logistic regression analyses indicated that the lab-measured error rates significantly predicted the real-world error rates and vice versa.ConclusionsLab-based psycholinguistic tests are associated with real-world drug name confusion error rates. Previous work showed that such tests were associated with error rates of specific look-alike sound-alike pairs, and the current work showed that lab-based error rates are also associated with an individual drug’s overall error rate. Taken together, these studies validate the use of psycholinguistic tests in assessing the confusability of proposed drug names.

An In Vitro Comparative Immunogenicity Assessment (IVCIA) assay was evaluated as a tool for predicting the potential relative immunogenicity of biotherapeutic attributes. Peripheral blood mononuclear cells from up to 50 healthy naïve human donors were monitored up to 8 days for T-cell proliferation, the number of IL-2 or IFN-γ secreting cells, and the concentration of a panel of secreted cytokines. The response in the assay to 10 monoclonal antibodies was found to be in agreement with the clinical immunogenicity, suggesting that the assay might be applied to immunogenicity risk assessment of antibody biotherapeutic attributes. However, the response in the assay is a measure of T-cell functional activity and the alignment with clinical immunogenicity depends on several other factors. The assay was sensitive to sequence variants and could differentiate single point mutations of the same biotherapeutic. Nine mAbs that were highly aggregated by stirring induced a higher response in the assay than the original mAbs before stirring stress, in a manner that did not match the relative T-cell response of the original mAbs. In contrast, mAbs that were glycated by different sugars (galactose, glucose, and mannose) showed little to no increase in response in the assay above the response to the original mAbs before glycation treatment. The assay was also used successfully to assess similarity between multiple lots of the same mAb, both from the same manufacturer and from different manufacturers (biosimilars). A strategy for using the IVCIA assay for immunogenicity risk assessment during the entire lifespan development of biopharmaceuticals is proposed.

Lactobacillus delbrueckii ssp. bulgaricus (L. bulgaricus) is a representative of the group of lactic acid-producing bacteria, mainly known for its worldwide application in yogurt production. The genome sequence of this bacterium has been determined and shows the signs of ongoing specialization, with a substantial number of pseudogenes and incomplete metabolic pathways and relatively few regulatory functions. Several unique features of the L. bulgaricus genome support the hypothesis that the genome is in a phase of rapid evolution. (i) Exceptionally high numbers of rRNA and tRNA genes with regard to genome size may indicate that the L. bulgaricus genome has known a recent phase of important size reduction, in agreement with the observed high frequency of gene inactivation and elimination; (ii) a much higher GC content at codon position 3 than expected on the basis of the overall GC content suggests that the composition of the genome is evolving toward a higher GC content; and (iii) the presence of a 47.5-kbp inverted repeat in the replication termination region, an extremely rare feature in bacterial genomes, may be interpreted as a transient stage in genome evolution. The results indicate the adaptation of L. bulgaricus from a plant-associated habitat to the stable protein and lactose-rich milk environment through the loss of superfluous functions and protocooperation with Streptococcus thermophilus.

BackgroundDrug name confusion is a common type of medication error and a persistent threat to patient safety. In the USA, roughly one per thousand prescriptions results in the wrong drug being filled, and most of these errors involve drug names that look or sound alike. Prior to approval, drug names undergo a variety of tests to assess their potential for confusability, but none of these preapproval tests has been shown to predict real-world error rates.ObjectivesWe conducted a study to assess the association between error rates in laboratory-based tests of drug name memory and perception and real-world drug name confusion error rates.MethodsEighty participants, comprising doctors, nurses, pharmacists, technicians and lay people, completed a battery of laboratory tests assessing visual perception, auditory perception and short-term memory of look-alike and sound-alike drug name pairs (eg, hydroxyzine/hydralazine).ResultsLaboratory test error rates (and other metrics) significantly predicted real-world error rates obtained from a large, outpatient pharmacy chain, with the best-fitting model accounting for 37% of the variance in real-world error rates. Cross-validation analyses confirmed these results, showing that the laboratory tests also predicted errors from a second pharmacy chain, with 45% of the variance being explained by the laboratory test data.ConclusionsAcross two distinct pharmacy chains, there is a strong and significant association between drug name confusion error rates observed in the real world and those observed in laboratory-based tests of memory and perception. Regulators and drug companies seeking a validated preapproval method for identifying confusing drug names ought to consider using these simple tests. By using a standard battery of memory and perception tests, it should be possible to reduce the number of confusing look-alike and sound-alike drug name pairs that reach the market, which will help protect patients from potentially harmful medication errors.

Scanning for links to autism Autism is a highly heritable neurodevelopmental disorder, and yet very few specific susceptibility genes have been identified to date. A genome-wide scan using half a million genome-wide SNPs (single nucleotide polymorphisms) in a common set of 1,031 multiplex autism families has now revealed significant linkage and association to autism. The linkage regions identified provide targets for rare variation screening while the discovery of a single novel association, between SEMA5A and TAS2R1 on chromosome 5p15. The expression of SEMA5A was found to be reduced in brains from autistic patients, further confirmation that it is an autism susceptibility gene. Autism is a highly heritable neurodevelopmental disorder, and yet few specific susceptibility genes have been identified to date. A linkage and association mapping study using half a million genome-wide single nucleotide polymorphisms is now described in a common set of 1,031 multiplex autism families. The linkage regions identified provide targets for rare variation screening whereas the discovery of a single novel association, SEMA5A , demonstrates the action of common variants. Although autism is a highly heritable neurodevelopmental disorder, attempts to identify specific susceptibility genes have thus far met with limited success 1 . Genome-wide association studies using half a million or more markers, particularly those with very large sample sizes achieved through meta-analysis, have shown great success in mapping genes for other complex genetic traits. Consequently, we initiated a linkage and association mapping study using half a million genome-wide single nucleotide polymorphisms (SNPs) in a common set of 1,031 multiplex autism families (1,553 affected offspring). We identified regions of suggestive and significant linkage on chromosomes 6q27 and 20p13, respectively. Initial analysis did not yield genome-wide significant associations; however, genotyping of top hits in additional families revealed an SNP on chromosome 5p15 (between SEMA5A and TAS2R1 ) that was significantly associated with autism ( P = 2 × 10 -7 ). We also demonstrated that expression of SEMA5A is reduced in brains from autistic patients, further implicating SEMA5A as an autism susceptibility gene. The linkage regions reported here provide targets for rare variation screening whereas the discovery of a single novel association demonstrates the action of common variants.

Understanding gene regulation will require mapping specific chromain features in a small number of cells at high resolution. Here the authors describe CUT&Tag, which uses antibody-mediated tethering of Tn5 transposase to a chromatin protein to generate high resolution libraries.

Pediatric AIDS Clinical Trials Group protocol 316 was an international, multicenter, placebo-controlled trial comparing single-dose oral nevirapine (200 mg to mother and 2 mg/kg to infant) with placebo in human immunodeficiency virus (HIV)–infected pregnant women receiving standard antiretroviral therapy. This substudy evaluated the emergence of nevirapine-resistance mutations at 6 weeks postpartum in a subgroup of participants. Maternal risk factors for the emergence of nevirapine-resistance mutations were evaluated. Mutations associated with nevirapine resistance were detectable at delivery, prior to receipt of study drug, in 5 (2.3%) of 217 women. Fourteen (15%; 95% confidence interval, 8%–23%) of 95 women who received intrapartum nevirapine developed a nevirapine-resistance mutation 6 weeks postpartum. The most common mutation was K103N, which was present in 10 women. The risk for development of a new nevirapine-resistance mutation did not correlate with CD4 cell count or HIV-1 RNA load at delivery or with type of antepartum antiretroviral therapy. The risk of nevirapine resistance should be considered when determining the risks or benefits of intrapartum nevirapine in women receiving antepartum antiretroviral therapy