Development of a semi-automated MHC-associated peptide proteomics (MAPPs) method using streptavidin bead-based immunoaffinity capture and nano LC-MS/MS to support immunogenicity risk assessment in drug development.

Major histocompatibility complex (MHC)-Associated Peptide Proteomics (MAPPs) is an ex vivo method used to assess the immunogenicity risk of biotherapeutics. MAPPs can identify potential T-cell epitopes within the biotherapeutic molecule. Using adalimumab treated human monocyte derived dendritic cells (DCs) and a pan anti-HLA-DR antibody (Ab), we systematically automated and optimized biotin/streptavidin (SA)-capture antibody coupling, lysate incubation with capture antibody, as well as the washing and elution steps of a MAPPs method using functionalized magnetic beads and a KingFisher Magnetic Particle processor. Automation of these steps, combined with capturing using biotinylated-Ab/SA magnetic beads rather than covalently bound antibody, improved reproducibility as measured by minimal inter-and intra-day variability, as well as minimal analyst-to-analyst variability. The semi-automated MAPPs workflow improved sensitivity, allowing for a lower number of cells per analysis. The method was assessed using five different biotherapeutics with varying immunogenicity rates ranging from 0.1 to 48% ADA incidence in the clinic. Biotherapeutics with ≥10%immunogenicity incidence consistently presented more peptides (1.8-28 fold) and clusters (10-21 fold) compared to those with <10% immunogenicity incidence. Our semi-automated MAPPs method provided two main advantages over a manual workflow- the robustness and reproducibility affords confidence in the epitopes identified from as few as 5 to 10 donors and the method workflow can be readily adapted to incorporate different capture Abs in addition to anti-HLA-DR. The incorporation of semi-automated MAPPs with biotinylated-Ab/SA bead-based capture in immunogenicity screening strategies allows the generation of more consistent and reliable data, helping to improve immunogenicity prediction capabilities in drug development. MHC associated peptide proteomics (MAPPs), Immunogenicity risk assessment, in vitro/ex vivo, biotherapeutics, Major Histocompatibility Complex Class II (MHC II), LC-MS, Immunoaffinity Capture, streptavidin magnetic beads.

Nutritional Assessment of Lactarius drassinus and L. controversus from the Cold Desert Region of the Northwest Himalayas for Their Potential as Food Supplements.

Kargil is a cold desert with hostile ecological conditions such as low temperature and precipitation, as well as difficult terrains. However, several wild mushrooms thrive well under such an extreme environment. Despite their abundance, the chemical composition of indigenous mushrooms has not been explored. This study aimed to assess the potential of two wild edible mushrooms from Kargil, Lactarius drassinus and Lactarius controversus, as food supplements by evaluating their nutritional and nutraceutical properties. Nutritional attributes such as total protein, available carbohydrates, soluble sugars, and vitamins were found to be high in the mushroom species. Furthermore, high mineral accumulation and relatively lower antinutrient concentrations resulted in higher bioavailabilities of Zn, Fe, Ca, and Mg. Gas-chromatography-mass-spectrometry-based metabolite profiling revealed that although the two mushroom species showed similar metabolite compositions, their relative concentrations differed. Sugars were the predominant compounds identified in both the species, with sugar alcohols being the major contributor. The second most abundant class of compound in L. drassinus was amino acids, with 5-oxoproline as the major contributor. On the other hand, fatty acids were the second most abundant compounds in L. controversus, with high oleic and linoleic acid concentrations. In the ultra-performance-liquid-chromatography-based quantification of phenolic compounds, chlorogenic acid was found to be highest in in terms of its concentration in both the mushrooms studied, followed by quercetin dihydrate and gallic acid in L. drassinus and L. controversus, respectively. Moreover, high antioxidant activities attributable to their high phenol, flavonoid, and carotenoid concentrations were observed. Overall, the two mushrooms offer well-balanced sources of nutritional and nutraceutical compounds, making them healthy foods.

Assessment of KRAS G12C Target Engagement by a Covalent Inhibitor in Tumor Biopsies Using an Ultra-Sensitive Immunoaffinity 2D-LC-MS/MS Approach.

KRAS is one of the most frequently mutated oncogenes, with KRAS G12C recently becoming an actionable target for small molecule intervention. GDC-6036 is an investigational KRAS G12C inhibitor that acts by irreversibly binding to the switch II pocket of KRAS G12C when in the inactive GDP-bound state, thereby blocking GTP binding and activation. Assessing target engagement is an essential component of clinical drug development, helping to demonstrate mechanistic activity, guide dose selection, understand pharmacodynamics as it relates to clinical response, and explore resistance. Here, we report the development of an ultra-sensitive approach for assessing KRAS G12C engagement. Immunoaffinity enrichment with a commercially available anti-RAS antibody was combined with a targeted 2D-LC-MS/MS technique to quantify both free and GDC-6036-bound KRAS G12C proteins. A KRAS G12C-positive non-small cell lung cancer xenograft model was dosed with GDC-6036 to assess the feasibility of this assay for analyzing small core needle biopsies. As predicted, dose-dependent KRAS G12C engagement was observed. To date, a sensitivity of 0.08 fmol/µg of total protein has been achieved for both free and GDC-6036-bound KRAS G12C with as little as 4 µg of total protein extracted from human tumor samples. This sub-fmol/µg level of sensitivity provides a powerful potential approach to assess covalent inhibitor target engagement at the site of action using core needle tumor biopsies from clinical studies.

IQ consortium perspective: complementary LBA and LC-MS in protein therapeutics bioanalysis and biotransformation assessment.

Increasingly diverse large molecule modalities have driven the need for complex bioanalysis and biotransformation assessment involving both traditional ligand-binding assays (LBA) and more recent hybrid immunoaffinity LC-MS platforms. Given the scientific expertise in LBA and LC-MS typically resides in different functions within the industry, this has presented operational challenges for an integrated approach for bioanalysis and biotransformation assessment. Encouragingly, over time, the industry has recognized the complementary value of the two platforms. This has not been an easy transition as organizational structures vary widely within the industry. However, there are tremendous benefits in adopting fully integrated strategies for biopharma. This IQ consortium paper presents current perspectives across the biopharma industry. It highlights the technical and operational challenges in current large molecule bioanalysis, the value of collaborations across LBA and LC-MS, and scientific expertise for fully integrated strategies for bioanalysis and biotransformation.

2019 White Paper on Recent Issues in Bioanalysis: Chromatographic Assays (Part 1 - Innovation in Small Molecules and Oligonucleotides & Mass Spectrometric Method Development Strategies for Large Molecule Bioanalysis).

The 2019 13th Workshop on Recent Issues in Bioanalysis (WRIB) took place in New Orleans, LA, USA on April 1-5, 2019 with an attendance of over 1000 representatives from pharmaceutical/biopharmaceutical companies, biotechnology companies, contract research organizations and regulatory agencies worldwide. WRIB was once again a 5-day, week-long event - a full immersion week of bioanalysis, biomarkers, immunogenicity and gene therapy. As usual, it was specifically designed to facilitate sharing, reviewing, discussing and agreeing on approaches to address the most current issues of interest including both small- and large-molecule bioanalysis involving LCMS, hybrid LBA/LCMS, LBA cell-based/flow cytometry assays and qPCR approaches. This 2019 White Paper encompasses recommendations emerging from the extensive discussions held during the workshop, and is aimed to provide the bioanalytical community with key information and practical solutions on topics and issues addressed, in an effort to enable advances in scientific excellence, improved quality and better regulatory compliance. Due to its length, the 2019 edition of this comprehensive White Paper has been divided into three parts for editorial reasons. This publication (Part 1) covers the recommendations on Innovation in Small Molecules and Oligonucleotides & Mass Spec Method Development Strategies for Large Molecules Bioanalysis. Part 2 (2018 FDA BMV Guidance, 2019 ICH M10 BMV Draft Guideline and regulatory agencies' input on bioanalysis, biomarkers, immunogenicity and gene therapy) and Part 3 (New Insights in Biomarkers Assays Validation, Current & Effective Strategies for Critical Reagent Management, Flow Cytometry Validation in drug discovery & development & CLSI H62, Interpretation of the 2019 FDA Immunogenicity Guidance and The Gene Therapy Bioanalytical Challenges) are published in volume 11 of Bioanalysis, issues 23 and 24 (2019), respectively.

Custom-Designed Affinity Capture LC-MS F(ab')2 Assay for Biotransformation Assessment of Site-Specific Antibody Drug Conjugates.

Affinity capture liquid chromatography-mass spectrometry (LC-MS) intact antibody assay has been widely used for direct drug-to-antibody ratio (DAR) and catabolite characterization of antibody-drug conjugates (ADCs). However, the intact mass spectra of new ADCs, which incorporate new types of linkers and payloads other than maytansines and auristatins, are more complex than those examined previously. The current method has showed some limitations in elucidating certain structural modifications. Herein, we report an alternative analytical approach for ADCs, such as THIOMAB antibody-drug conjugates (TDCs), where the linker drugs are site-specifically conjugated in the Fab region. The newly developed affinity capture LC-MS F(ab')2 assay incorporates affinity capture of human IgGs via binding to the Fab region, followed by on-bead IdeS digestion to remove the Fc domain specifically and uniformly. The resulting F(ab')2 (∼100 kDa) fragments contain the key ADC biotransformation information, such as drug-to-antibody ratio and drug metabolism and are more readily analyzed by electrospray ionization LC-MS than the intact ADC (∼150 kDa). The reduced size of analytes results in improved mass spectral sensitivity and resolution. In addition, the reduced and optimized sample preparation time, for example, rapid removal of the Fc fragment by IdeS digestion, minimizes assay artifacts of drug metabolism and skewed DAR profiles that may result from the prolonged incubation times (e.g., overnight enzymatic treatment for Fc deglycosylation). The affinity capture LC-MS F(ab')2 assay provides more detailed and accurate information on ADC biotransformations in vivo, enabling analysis of low-dose, labile, and complex site-specific ADCs with linker-drug conjugated in the Fab region.

Effectiveness and cost-effectiveness of mindfulness-based cognitive therapy compared with maintenance antidepressant treatment in the prevention of depressive relapse or recurrence (PREVENT): a randomised controlled trial.

BACKGROUND: Individuals with a history of recurrent depression have a high risk of repeated depressive relapse or recurrence. Maintenance antidepressants for at least 2 years is the current recommended treatment, but many individuals are interested in alternatives to medication. Mindfulness-based cognitive therapy (MBCT) has been shown to reduce risk of relapse or recurrence compared with usual care, but has not yet been compared with maintenance antidepressant treatment in a definitive trial. We aimed to see whether MBCT with support to taper or discontinue antidepressant treatment (MBCT-TS) was superior to maintenance antidepressants for prevention of depressive relapse or recurrence over 24 months. METHODS: In this single-blind, parallel, group randomised controlled trial (PREVENT), we recruited adult patients with three or more previous major depressive episodes and on a therapeutic dose of maintenance antidepressants, from primary care general practices in urban and rural settings in the UK. Participants were randomly assigned to either MBCT-TS or maintenance antidepressants (in a 1:1 ratio) with a computer-generated random number sequence with stratification by centre and symptomatic status. Participants were aware of treatment allocation and research assessors were masked to treatment allocation. The primary outcome was time to relapse or recurrence of depression, with patients followed up at five separate intervals during the 24-month study period. The primary analysis was based on the principle of intention to treat. The trial is registered with Current Controlled Trials, ISRCTN26666654. FINDINGS: Between March 23, 2010, and Oct 21, 2011, we assessed 2188 participants for eligibility and recruited 424 patients from 95 general practices. 212 patients were randomly assigned to MBCT-TS and 212 to maintenance antidepressants. The time to relapse or recurrence of depression did not differ between MBCT-TS and maintenance antidepressants over 24 months (hazard ratio 0·89, 95% CI 0·67-1·18; p=0·43), nor did the number of serious adverse events. Five adverse events were reported, including two deaths, in each of the MBCT-TS and maintenance antidepressants groups. No adverse events were attributable to the interventions or the trial. INTERPRETATION: We found no evidence that MBCT-TS is superior to maintenance antidepressant treatment for the prevention of depressive relapse in individuals at risk for depressive relapse or recurrence. Both treatments were associated with enduring positive outcomes in terms of relapse or recurrence, residual depressive symptoms, and quality of life. FUNDING: National Institute for Health Research (NIHR) Health Technology Assessment (HTA) programme, and NIHR Collaboration for Leadership in Applied Health Research and Care South West Peninsula.

Effectiveness of PhysioDirect telephone assessment and advice services for patients with musculoskeletal problems.

STUDY QUESTION: Are PhysioDirect services, based on initial telephone assessment and advice from a physiotherapist, as effective as usual care involving patients waiting for a face-to-face appointment? SUMMARY ANSWER: Patients allocated to PhysioDirect received treatment more quickly than those allocated to usual care, and had equivalent clinical outcomes.

A pragmatic randomised controlled trial of 'PhysioDirect' telephone assessment and advice services for patients with musculoskeletal problems: economic evaluation.

OBJECTIVES: To compare the cost-effectiveness of PhysioDirect with usual physiotherapy care for patients with musculoskeletal problems. DESIGN: (1) Cost-consequences comparing cost to the National Health Service (NHS), to patients, and the value of lost productivity with a range of outcomes. (2) Cost-utility analysis comparing cost to the NHS with Quality-Adjusted Life Years (QALYs). SETTING: Four physiotherapy services in England. PARTICIPANTS: Adults (18+) referred by their general practitioner or self-referred for physiotherapy. INTERVENTIONS: PhysioDirect involved telephone assessment and advice followed by face-to-face care if needed. Usual care patients were placed on a waiting list for face-to-face care. PRIMARY AND SECONDARY OUTCOMES: Primary clinical outcome: physical component summary from the SF-36v2 at 6 months. Also included in the cost-consequences: Measure Yourself Medical Outcomes Profile; a Global Improvement Score; response to treatment; patient satisfaction; waiting time. Outcome for the cost-utility analysis: QALYs. RESULTS: 2249 patients took part (1506 PhysioDirect; 743 usual care). (1) Cost-consequences: there was no evidence of a difference between the two groups in the cost of physiotherapy, other NHS services, personal costs or value of time off work. Outcomes were also similar. (2) Cost-utility analysis based on complete cases (n=1272). Total NHS costs, including the cost of physiotherapy were higher in the PhysioDirect group by £19.30 (95% CI -£37.60 to £76.19) and there was a QALY gain of 0.007 (95% CI -0.003 to 0.016). The incremental cost-effectiveness ratio was £2889 and the net monetary benefit at λ=£20 000 was £117 (95% CI -£86 to £310). CONCLUSIONS: PhysioDirect may be a cost-effective alternative to usual physiotherapy care, though only with careful management of staff time. Physiotherapists providing the service must be more fully occupied than was possible under trial conditions: consideration should be given to the scale of operation, opening times of the service and flexibility in the methods used to contact patients.

Effectiveness of PhysioDirect telephone assessment and advice services for patients with musculoskeletal problems: pragmatic randomised controlled trial.

OBJECTIVES: To assess the clinical effectiveness, effect on waiting times, and patient acceptability of PhysioDirect services in patients with musculoskeletal problems, compared with usual care. DESIGN: Pragmatic randomised controlled trial to assess equivalence in clinical effectiveness. Patients were individually randomised in a 2:1 ratio to PhysioDirect or usual care. SETTING: Four physiotherapy services in England. PARTICIPANTS: Adults (aged ≥ 18 years) referred by general practitioners or self referred for musculoskeletal physiotherapy. INTERVENTIONS: PhysioDirect services invited patients to telephone a physiotherapist for initial assessment and advice, followed by face-to-face physiotherapy if necessary. Usual care involved patients joining a waiting list for face-to-face treatment. MAIN OUTCOME MEASURES: Numbers of appointments, waiting time for treatment, and non-attendance rates. Primary outcome was physical health (SF-36v2 physical component score) at six months. Secondary outcomes included four other measures of health outcome, mental component score and scales from the SF-36v2, time lost from work, and patient satisfaction and preference. Participants were not blind to allocation, but outcome data were collected blind to allocation. RESULTS: Of 1506 patients allocated to PhysioDirect and 743 to usual care, 85% provided primary outcome data at six months (1283 and 629 patients, respectively). PhysioDirect patients had fewer face-to-face appointments than usual care patients (mean 1.91 v 3.11; incidence rate ratio 0.59 (95% confidence interval 0.53 to 0.65)), a shorter waiting time (median 7 days v 34 days; arm time ratio 0.32 (0.29 to 0.35)), and lower rates of non-attendance (incidence rate ratio 0.55 (0.41 to 0.73)). After six months' follow-up, the SF-36v2 physical component score was equivalent between groups (adjusted difference in means -0.01 (-0.80 to 0.79)). Health outcome measures suggested a trend towards slightly greater improvement in the PhysioDirect arm at six week follow-up and no difference at six months. There was no difference in time lost from work. PhysioDirect patients were no more satisfied with access to physiotherapy than usual care patients, but had slightly lower satisfaction overall at six months (difference in satisfaction -3.8% (-7.3% to -0.3%); P=0.031). PhysioDirect patients were more likely than usual care patients to prefer PhysioDirect in future. No adverse events were detected. CONCLUSIONS: PhysioDirect is equally clinically effective compared with usual care, provides faster access to physiotherapy, and seems to be safe. However, it could be associated with slightly lower patient satisfaction. TRIAL REGISTRATION: Current Controlled Trials ISRCTN55666618.

2012 white paper on recent issues in bioanalysis and alignment of multiple guidelines.

Over 400 professionals representing pharmaceutical companies, CROs, and multiple regulatory agencies participated in the 6th Workshop on Recent Issues in Bioanalysis (WRIB). Like the previous sessions, this event was in the format of a practical, focused, highly interactive and informative workshop aiming for high-quality, improved regulatory compliance and scientific excellence. Numerous 'hot' topics in bioanalysis of both small and large molecules were shared and discussed, leading to consensus and recommendations among panelists and attendees representing the bioanalytical community. The major outcome of this year's workshop was the noticeable alignment of multiple bioanalytical guidance/guidelines from different regulatory agencies. This represents a concrete step forward in the global harmonization of bioanalytical activities. The present 2012 White Paper acts as a practical and useful reference document that provides key information and solutions on several topics and issues in the constantly evolving world of bioanalysis.

Emerging phytopathogen Macrophomina phaseolina: biology, economic importance and current diagnostic trends.

Macrophomina phaseolina (Tassi) Goid. is an important phytopathogenic fungus, infecting a large number of plant species and surviving for up to 15 years in the soil as a saprophyte. Although considerable research related to the biology and ecology of Macrophomina has been conducted, it continues to cause huge economic losses in many crops. Research is needed to improve the identification and characterization of genetic variability within their epidemiological and pathological niches. Better understanding of the variability within the pathogen population for traits that influence fitness and soil survival will certainly lead to improved management strategies for Macrophomina. In this context, the present review discusses various biological aspects and distribution of M. phaseolina throughout the world and their importance to different plant species. Accurate identification of the fungus has been aided with the use of nucleic acid-based molecular techniques. The development of PCR-based methods for identification and detection of M. phaseolina are highly sensitive and specific. Early diagnosis and accurate detection of pathogens is an essential step in plant disease management as well as quarantine. The progress in the development of various molecular tools used for the detection, identification and characterization of Macrophomina isolates were also discussed.

Cost-effectiveness of therapist-delivered online cognitive-behavioural therapy for depression: randomised controlled trial.

BACKGROUND: Therapist-delivered online cognitive-behavioural therapy (CBT) has been found to be effective for depression in primary care. AIMS: To determine the cost-effectiveness of online CBT compared with usual care. METHOD: Economic evaluation at 8 months alongside a randomised controlled trial. Cost to the National Health Service (NHS), personal costs, and the value of lost productivity, each compared with outcomes based on the Beck Depression Inventory and quality-adjusted life-years (QALYs). Incremental analysis indicated the NHS cost per QALY gain. RESULTS: Online CBT was more expensive than usual care, although the outcomes for the CBT group were better. Cost per QALY gain based on complete case data was £17,173, and £10,083 when missing data were imputed. CONCLUSIONS: Online CBT delivered by a therapist in real time is likely to be cost-effective compared with usual care if society is willing to pay at least £20,000 per QALY; it could be a useful alternative to face-to-face CBT.

Therapist-delivered Internet psychotherapy for depression in primary care: a randomised controlled trial.

BACKGROUND: Despite strong evidence for its effectiveness, cognitive-behavioural therapy (CBT) remains difficult to access. Computerised programs have been developed to improve accessibility, but whether these interventions are responsive to individual needs is unknown. We investigated the effectiveness of CBT delivered online in real time by a therapist for patients with depression in primary care. METHODS: In this multicentre, randomised controlled trial, 297 individuals with a score of 14 or more on the Beck depression inventory (BDI) and a confirmed diagnosis of depression were recruited from 55 general practices in Bristol, London, and Warwickshire, UK. Participants were randomly assigned, by a computer-generated code, to online CBT in addition to usual care (intervention; n=149) or to usual care from their general practitioner while on an 8-month waiting list for online CBT (control; n=148). Participants, researchers involved in recruitment, and therapists were masked in advance to allocation. The primary outcome was recovery from depression (BDI score <10) at 4 months. Analysis was by intention to treat. This trial is registered, number ISRCTN 45444578. FINDINGS: 113 participants in the intervention group and 97 in the control group completed 4-month follow-up. 43 (38%) patients recovered from depression (BDI score <10) in the intervention group versus 23 (24%) in the control group at 4 months (odds ratio 2.39, 95% CI 1.23-4.67; p=0.011), and 46 (42%) versus 26 (26%) at 8 months (2.07, 1.11-3.87; p=0.023). INTERPRETATION: CBT seems to be effective when delivered online in real time by a therapist, with benefits maintained over 8 months. This method of delivery could broaden access to CBT. FUNDING: BUPA Foundation.

'PhysioDirect' telephone assessment and advice services for physiotherapy: protocol for a pragmatic randomised controlled trial.

BACKGROUND: Providing timely access to physiotherapy has long been a problem for the National Health Service in the United Kingdom. In an attempt to improve access some physiotherapy services have introduced a new treatment pathway known as PhysioDirect. Physiotherapists offer initial assessment and advice by telephone, supported by computerised algorithms, and patients are sent written self-management and exercise advice by post. They are invited for face-to-face treatment only when necessary. Although several such services have been developed, there is no robust evidence regarding clinical and cost-effectiveness, nor the acceptability of PhysioDirect. METHODS/DESIGN: This protocol describes a multi-centre pragmatic individually randomised trial, with nested qualitative research. The aim is to determine the effectiveness, cost-effectiveness, and acceptability of PhysioDirect compared with usual models of physiotherapy based on patients going onto a waiting list and receiving face-to-face care. PhysioDirect services will be established in four areas in England. Adult patients in these areas with musculoskeletal problems who refer themselves or are referred by a primary care practitioner for physiotherapy will be invited to participate in the trial. About 1875 consenting patients will be randomised in a 2:1 ratio to PhysioDirect or usual care. Data about outcome measures will be collected at baseline and 6 weeks and 6 months after randomisation. The primary outcome is clinical improvement at 6 months; secondary outcomes include cost, waiting times, time lost from work and usual activities, patient satisfaction and preference. The impact of PhysioDirect on patients in different age-groups and with different conditions will also be examined.Incremental cost-effectiveness will be assessed in terms of quality adjusted life years in relation to cost.Qualitative methods will be used to explore factors associated with the success or failure of the service, the acceptability of PhysioDirect to patients and staff, and ways in which the service could be improved. DISCUSSION: It is still relatively unusual to evaluate new forms of service delivery using randomised controlled trials. By combining rigorous trial methods with economic analysis of cost-effectiveness and qualitative research this study will provide robust evidence to inform decisions about the widespread introduction of PhysioDirect services. TRIAL REGISTRATION: Current Controlled Trials ISRCTN55666618.