Characterization of mAbs against Klebsiella pneumoniae type 3 fimbriae isolated in a target-independent phage display campaign.

We used phage display, antibody engineering, and high-throughput assays to identify antibody-accessible targets of Klebsiella pneumoniae. We report the discovery of monoclonal antibodies (mAbs) binding to type 3 fimbrial proteins, including MrkA. We found that anti-MrkA mAbs were cross-reactive to a diverse panel of K. pneumoniae clinical isolates, representing different O-serotypes. mAbs binding to MrkA have previously been described and have been shown to provide prophylactic protection, although only modest protection when dosed therapeutically in vivo in a murine lung infection model. Here, we used a combination of binding and opsonophagocytic killing studies using a high-content imaging platform to provide a possible explanation for the modest therapeutic efficacy in vivo reported in that model. Our work shows that expression of K. pneumoniae type 3 fimbriae in in vitro culture is not homogenous within a bacterial population. Instead, sub-populations of bacteria that do, and do not, express type 3 fimbriae exist. In a high-content opsonophagocytic killing assay, we showed that MrkA-targeting antibodies initially promote killing by macrophages; however, over time, this effect is diminished. We hypothesize the reason for this is that bacteria not expressing MrkA can evade opsonophagocytosis. Our data support the fact that MrkA is a conserved, immunodominant protein that is antibody accessible on the surface of K. pneumoniae and suggest that additional studies should evaluate the potential of using anti-MrkA antibodies in different stages of K. pneumoniae infection (different sites in the body) as well as against K. pneumoniae biofilms in the body during infection and associated with medical devices.IMPORTANCEThere is an unmet, urgent need for the development of novel antimicrobial therapies for the treatment of Klebsiella pneumoniae infections. We describe the use of phage display, antibody engineering, and high-throughput assays to identify antibody-accessible targets of K. pneumoniae. We discovered monoclonal antibodies (mAbs) binding to the type 3 fimbrial protein MrkA. The anti-MrkA mAbs were found to be highly cross-reactive, binding to all K. pneumoniae strains tested from a diverse panel of clinical isolates, and were active in an opsonophagocytic killing assay at pM concentrations. MrkA is important for biofilm formation; thus, our data support further exploration of the use of anti-MrkA antibodies for preventing and/or controlling K. pneumoniae in biofilms and during infection.

Pilot study using machine learning to improve estimation of physical abuse prevalence.

BACKGROUND: International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) codes have been shown to underestimate physical abuse prevalence. Machine learning models are capable of efficiently processing a wide variety of data and may provide better estimates of abuse. OBJECTIVE: To achieve proof of concept applying machine learning to identify codes associated with abuse. PARTICIPANTS AND SETTING: Children <5 years, presenting to the emergency department with an injury or abuse-specific ICD-10-CM code and evaluated by the child protection team (CPT) from 2016 to 2020 at a large Midwestern children's hospital. METHODS: The Pediatric Health Information System (PHIS) and the CPT administrative databases were used to identify the study sample and injury and abuse-specific ICD-10-CM codes. Subjects were divided into abused and non-abused groups based on the CPT's evaluation. A LASSO logistic regression model was constructed using ICD-10-CM codes and patient age to identify children likely to be diagnosed by the CPT as abused. Performance was evaluated using repeated cross-validation (CV) and Reciever Operator Characteristic curve. RESULTS: We identified 2028 patients evaluated by the CPT with 512 diagnosed as abused. Using diagnosis codes and patient age, our model was able to accurately identify patients with confirmed PA (mean CV AUC = 0.87). Performance was still weaker for patients without existing ICD codes for abuse (mean CV AUC = 0.81). CONCLUSIONS: We built a model that employs injury ICD-10-CM codes and age to improve accuracy of distinguishing abusive from non-abusive injuries. This pilot modelling endeavor is a steppingstone towards improving population-level estimates of abuse.

Physical abuse re-reporting during the COVID-19 pandemic: The kids are not okay.

BACKGROUND: Child physical abuse (PA) is a significant societal concern with limited research into predictors of re-reports. OBJECTIVE: Our research explores correlations between sociodemographic variables and re-reported PA. Our aim was to characterize populations at higher risk and identify changes in presentation during the COVID-19 pandemic. PARTICIPANTS AND SETTING: This retrospective descriptive study focused on 238 patients with re-reports of PA made by a pediatric hospital from January 2019 through April 2021. METHODS: We analyzed sociodemographic information and details of reports made to child protective services (CPS) obtained from the electronic health record. RESULTS: Females were 2.5 years older than males (mean 11.0 and 8.5 years, respectively) (p < .001, 95%CI 1.21-3.76). Males were more likely to have observable injuries (OR 2.61, p < .001) and a CPS response (OR = 2.70, p = .003). Patients categorized as "Other" races were less likely to have observable injuries (OR = 0.32, p = .006). Presentation changed during the pandemic: a quadrupling of re-reports by behavioral health clinicians caused the percentage of reports made by them to increase significantly (OR = 3.46, p < .001) and the mean age increased by 2.0 years (8.2 years before, 10.2 years during) (p = .009, 95%CI 0.5-3.5), though females remained approximately 2.2 years older than males (p = .003, 95%CI 0.8-3.7). CONCLUSIONS: Males experienced higher rates of re-reported PA and were younger at the time of re-report. Changes to presentation during the pandemic suggest an increase in PA among older children. Future research should further explore differences in sex/race, while current prevention efforts should focus on children receiving behavioral health care.

The Deterioration Risk Index: Developing and Piloting a Machine Learning Algorithm to Reduce Pediatric Inpatient Deterioration.

OBJECTIVES: Develop and deploy a disease cohort-based machine learning algorithm for timely identification of hospitalized pediatric patients at risk for clinical deterioration that outperforms our existing situational awareness program. DESIGN: Retrospective cohort study. SETTING: Nationwide Children's Hospital, a freestanding, quaternary-care, academic children's hospital in Columbus, OH. PATIENTS: All patients admitted to inpatient units participating in the preexisting situational awareness program from October 20, 2015, to December 31, 2019, excluding patients over 18 years old at admission and those with a neonatal ICU stay during their hospitalization. INTERVENTIONS: We developed separate algorithms for cardiac, malignancy, and general cohorts via lasso-regularized logistic regression. Candidate model predictors included vital signs, supplemental oxygen, nursing assessments, early warning scores, diagnoses, lab results, and situational awareness criteria. Model performance was characterized in clinical terms and compared with our previous situational awareness program based on a novel retrospective validation approach. Simulations with frontline staff, prior to clinical implementation, informed user experience and refined interdisciplinary workflows. Model implementation was piloted on cardiology and hospital medicine units in early 2021. MEASUREMENTS AND MAIN RESULTS: The Deterioration Risk Index (DRI) was 2.4 times as sensitive as our existing situational awareness program (sensitivities of 53% and 22%, respectively; p < 0.001) and required 2.3 times fewer alarms per detected event (121 DRI alarms per detected event vs 276 for existing program). Notable improvements were a four-fold sensitivity gain for the cardiac diagnostic cohort (73% vs 18%; p < 0.001) and a three-fold gain (81% vs 27%; p < 0.001) for the malignancy diagnostic cohort. Postimplementation pilot results over 18 months revealed a 77% reduction in deterioration events (three events observed vs 13.1 expected, p = 0.001). CONCLUSIONS: The etiology of pediatric inpatient deterioration requires acknowledgement of the unique pathophysiology among cardiology and oncology patients. Selection and weighting of diverse candidate risk factors via machine learning can produce a more sensitive early warning system for clinical deterioration. Leveraging preexisting situational awareness platforms and accounting for operational impacts of model implementation are key aspects to successful bedside translation.

Prioritizing Hormone Therapy Over Vigabatrin as the First Treatment for Infantile Spasms: A Quality Improvement Initiative.

BACKGROUND AND OBJECTIVES: Infantile spasms (IS) are early childhood seizures with potentially devastating consequences. Standard therapies (adrenocorticotropic hormone [ACTH], high-dose prednisolone, and vigabatrin) are strongly recommended as the first treatment for IS. Although this recommendation comes without preference for one standard therapy over another, early remission rates are higher with hormone therapy (ACTH and high-dose prednisolone) when compared with vigabatrin. Using quality improvement (QI) methodology that included hormone therapy as the first treatment, we sought to increase the percentage of children with new-onset nontuberous sclerosis complex (TSC)-associated IS achieving 3-month electroclinical remission from a mean of 53.8% to ≥70%. METHODS: This was an observational consecutive sample cohort study at a single academic tertiary care hospital that compared a prospective intervention cohort (May 2019-January 2022, N = 57) with a retrospective baseline cohort (November 2015-April 2019, N = 67). Our initiative addressed key drivers such as the routine use of vigabatrin over hormone therapy as first treatment and the common initiation of a second treatment after 14 days for initial nonresponders. We included consecutive children without TSC presenting with new-onset IS diagnosed and treated between ages 2 and 24 months. We displayed our primary outcome and process measures as control charts in which the centerline is the quarterly (previous 3 months) mean based on statistical process control methodology. RESULTS: QI interventions that included the standardization of hormone therapy as the first treatment resulted in higher rates of 3-month remission, rising from 53.8% (baseline cohort) to 75.9% (intervention cohort). Process measure results included an increased rate of children receiving hormone therapy as first treatment (mean, 44.6%-100%) and a decreased number of days to both clinical follow-up after first treatment (mean, of 16.3-12.6 days) and starting a second treatment within 14 days for initial nonresponders (mean, 36.3-17.2 days). DISCUSSION: For children with IS, improved rates of 3-month electroclinical remission can be achieved with QI methodology. Implementation of similar QI initiatives at other centers may likewise improve local remission rates.

Phenotypic whole-cell screening identifies a protective carbohydrate epitope on Klebsiella pneumoniae.

The increasing global occurrence of recalcitrant multi-drug resistant Klebsiella pneumoniae infections warrants the investigation of alternative therapy options, such as the use of monoclonal antibodies (mAbs). We used a target-agnostic phage display approach to K. pneumoniae bacteria lacking bulky, highly variable surface polysaccharides in order to isolate antibodies targeting conserved epitopes among clinically relevant strains. One antibody population contained a high proportion of unique carbohydrate binders, and biolayer interferometry revealed these antibodies bound to lipopolysaccharide (LPS). Antibodies that bound to O1 and O1/O2 LPS were identified. Antibodies were found to promote opsonophagocytic killing by human monocyte-derived macrophages and clearance of macrophage-associated bacteria when assessed using high-content imaging. One antibody, B39, was found to protect mice in a lethal model of K. pneumoniae pneumonia against both O1 and O2 strains when dosed therapeutically. High-content imaging, western blotting and fluorescence-activated cell sorting were used to determine binding to a collection of clinical K. pneumoniae O1 and O2 strains. The data suggests B39 binds to D-galactan-I and D-galactan-II of the LPS of O1 and O2 strains. Thus, we have discovered an mAb with novel binding and functional activity properties that is a promising candidate for development as a novel biotherapeutic for the treatment and prevention of K. pneumoniae infections.

Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli.

Cattle are the main reservoirs of Shiga toxin producing Escherichia coli (STEC), a major foodborne pathogen associated with acute enteric disease and hemolytic-uremic syndrome in humans. A total of 397 beef and dairy cattle from 5 farms were included in this study, of which 660 samples were collected for 16S rRNA gene sequencing. The microbiota of farms with a high-STEC prevalence (HSP) had greater richness compared to those of farms with a low-STEC prevalence (LSP). Longitudinal analyses showed STEC-shedders from LSP farms had higher microbiome diversity; meanwhile, changes in the microbiome composition in HSP farms were independent of the STEC shedding status. Most of the bacterial genera associated with STEC shedding in dairy farms were also correlated with differences in the percentage of forage in diet and risk factors of STEC carriage such as days in milk, number of lactations, and warm temperatures. Identifying factors that alter the gut microbiota and enable STEC colonization in livestock could lead to novel strategies to prevent fecal shedding and the subsequent transmission to humans.

A receptor for the complement regulator factor H increases transmission of trypanosomes to tsetse flies.

Persistent pathogens have evolved to avoid elimination by the mammalian immune system including mechanisms to evade complement. Infections with African trypanosomes can persist for years and cause human and animal disease throughout sub-Saharan Africa. It is not known how trypanosomes limit the action of the alternative complement pathway. Here we identify an African trypanosome receptor for mammalian factor H, a negative regulator of the alternative pathway. Structural studies show how the receptor binds ligand, leaving inhibitory domains of factor H free to inactivate complement C3b deposited on the trypanosome surface. Receptor expression is highest in developmental stages transmitted to the tsetse fly vector and those exposed to blood meals in the tsetse gut. Receptor gene deletion reduced tsetse infection, identifying this receptor as a virulence factor for transmission. This demonstrates how a pathogen evolved a molecular mechanism to increase transmission to an insect vector by exploitation of a mammalian complement regulator.

Structure of the trypanosome transferrin receptor reveals mechanisms of ligand recognition and immune evasion.

To maintain prolonged infection of mammals, African trypanosomes have evolved remarkable surface coats and a system of antigenic variation1. Within these coats are receptors for macromolecular nutrients such as transferrin2,3. These must be accessible to their ligands but must not confer susceptibility to immunoglobulin-mediated attack. Trypanosomes have a wide host range and their receptors must also bind ligands from diverse species. To understand how these requirements are achieved, in the context of transferrin uptake, we determined the structure of a Trypanosoma brucei transferrin receptor in complex with human transferrin, showing how this heterodimeric receptor presents a large asymmetric ligand-binding platform. The trypanosome genome contains a family of around 14 transferrin receptors4, which has been proposed to allow binding to transferrin from different mammalian hosts5,6. However, we find that a single receptor can bind transferrin from a broad range of mammals, indicating that receptor variation is unlikely to be necessary for promiscuity of host infection. In contrast, polymorphic sites and N-linked glycans are preferentially found in exposed positions on the receptor surface, not contacting transferrin, suggesting that transferrin receptor diversification is driven by a need for antigenic variation in the receptor to prolong survival in a host.

A single dose of antibody-drug conjugate cures a stage 1 model of African trypanosomiasis.

Infections of humans and livestock with African trypanosomes are treated with drugs introduced decades ago that are not always fully effective and often have severe side effects. Here, the trypanosome haptoglobin-haemoglobin receptor (HpHbR) has been exploited as a route of uptake for an antibody-drug conjugate (ADC) that is completely effective against Trypanosoma brucei in the standard mouse model of infection. Recombinant human anti-HpHbR monoclonal antibodies were isolated and shown to be internalised in a receptor-dependent manner. Antibodies were conjugated to a pyrrolobenzodiazepine (PBD) toxin and killed T. brucei in vitro at picomolar concentrations. A single therapeutic dose (0.25 mg/kg) of a HpHbR antibody-PBD conjugate completely cured a T. brucei mouse infection within 2 days with no re-emergence of infection over a subsequent time course of 77 days. These experiments provide a demonstration of how ADCs can be exploited to treat protozoal diseases that desperately require new therapeutics.

Survival of Mycobacterium bovis during forage ensiling.

OBJECTIVE To determine whether Mycobacterium bovis remains viable in ensiled forages. SAMPLE Alfalfa, mixed mostly grass, and corn silages. PROCEDURES For each of 10 sampling days, six 250-g replicate samples of each feedstuff were created and placed in a film pouch that could be vacuum sealed to simulate the ensiling process. Within each set of replicate samples, 4 were inoculated with 10 mL of mycobacterial liquid culture medium containing viable M bovis and 2 were inoculated with 10 mL of sterile mycobacterial liquid culture medium (controls) on day 0. Pouches were vacuum sealed and stored in the dark at room temperature. On the designated sampling day, 1 control pouch was submitted for forage analysis, and the other pouches were opened, and forage samples were obtained for M bovis culture and analysis with a PCR assay immediately and 24 hours later. RESULTS None of the control samples had positive M bovis culture or PCR assay results. Among M bovis-inoculated samples, the organism was not cultured from alfalfa and corn silage for > 2 days but was cultured from mixed mostly grass silage for 28 days after inoculation and ensiling initiation. Mycobacterium bovis DNA was detected by PCR assay in samples of all 3 feedstuffs throughout the 112-day observation period. CONCLUSIONS AND CLINICAL RELEVANCE Results suggested that properly ensiled forages would be an unlikely source for M bovis transmission to cattle. Further research is necessary to determine whether ensiling kills M bovis or forces it to become dormant and, if the latter, elucidate the conditions that cause it to revert to an infectious state.

Phenotypic screening-the fast track to novel antibody discovery.

The majority of antibody therapeutics have been isolated from target-led drug discovery, where many years of target research preceded drug program initiation. However, as the search for validated targets becomes more challenging and target space becomes increasingly competitive, alternative strategies, such as phenotypic drug discovery, are gaining favour. This review highlights successful examples of antibody phenotypic screens that have led to clinical drug candidates. We also review the requirements for performing an effective antibody phenotypic screen, including antibody enrichment and target identification strategies. Finally, the future impact of phenotypic drug discovery on antibody drug pipelines will be discussed.

Comparing the Genetic Diversity and Antimicrobial Resistance Profiles of Campylobacter jejuni Recovered from Cattle and Humans.

Campylobacter jejuni, a leading cause of gastroenteritis in humans, is a foodborne pathogen that can reside in chickens, pigs, and cattle. Because resistance to fluoroquinolones and macrolides, which are commonly used to treat human infections, has emerged in C. jejuni, it is imperative to continously monitor resistance patterns and examine the genetic variation in strains from human infections and animal reservoirs. Our previous study of C. jejuni from human campylobacteriosis cases showed a significantly higher rate of tetracycline resistance compared to national trends, and identified multilocus sequence type (ST)-982 and a history of cattle contact to be associated with tetracycline resistance. To further investigate these associations, we conducted a cross-sectional study to determine the frequency of antimicrobial resistance and examine the genetic diversity of C. jejuni recovered from 214 cattle at three Michigan herds. Overall, the prevalence of C. jejuni was 69.2% (range: 58.6-83.8%) for the three farms, and 83.7% (n = 113) of isolates were resistant to one or more antimicrobials. Resistance to only tetracycline predominated among the cattle isolates (n = 89; 65.9%) with most resistant strains belonging to ST-459 (96.5%) or ST-982 (86.4%). Among the 22 STs identified, STs 459 and 982 were more prevalent in one feedlot, which reported the use of chlortetracycline in feed upon arrival of a new herd. PCR-based fingerprinting demonstrated that the ST-982 isolates from cattle and humans had identical banding patterns, suggesting the possibility of interspecies transmission. Resistance to macrolides (1.5%) and ciprofloxacin (16.3%) was also observed; 14 of the 22 ciprofloxacin resistant isolates represented ST-1244. Together, these findings demonstrate a high prevalence of antimicrobial resistant C. jejuni in cattle and identify associations with specific genotypes. Continuous monitoring and identification of risk factors for resistance emergence are imperative to develop novel methods aimed at decreasing pathogen persistence in food animal reservoirs and the frequency of resistant infections in humans.

Patient-centered design criteria for wearable seizure detection devices.

INTRODUCTION: Epilepsy is a common neurological condition. Seizure diary reports and patient- or caregiver-reported seizure counts are often inaccurate and underestimated. Many caregivers express stress and anxiety about the patient with epilepsy having seizures when they are not present. Therefore, a need exists for the ability to recognize and/or detect a seizure in the home setting. However, few studies have inquired on detection device features that are important to patients and their caregivers. METHODS: A survey instrument utilizing a population of patients and caregivers was created to obtain information on the design criteria most desired for patients with epilepsy in regard to wearable devices. RESULTS: One thousand one hundred sixty-eight responses were collected. Respondents thought that sensors for muscle signal (61.4%) and heart rate (58.0%) would be most helpful followed by the O2 sensor (41.4%). There was more interest in these three sensor types than for an accelerometer (25.5%). There was very little interest in a microphone (8.9%), galvanic skin response sensor (8.0%), or a barometer (4.9%). Based on a rating scale of 1-5 with 5 being the most important, respondents felt that "detecting all seizures" (4.73) is the most important device feature followed by "text/email alerts" (4.53), "comfort" (4.46), and "battery life" (4.43) as an equally important group of features. Respondents felt that "not knowing device is for seizures" (2.60) and "multiple uses" (2.57) were equally the least important device features. Average ratings differed significantly across age groups for the following features: button, multiuse, not knowing device is for seizures, alarm, style, and text ability. The p-values were all<0.002. Eighty-two point five percent of respondents [95% confidence interval: 80.0%, 84.7%] were willing to pay more than $100 for a wearable seizure detection device, and 42.8% of respondents [95% confidence interval: 39.8%, 45.9%] were willing to pay more than $200. CONCLUSIONS: Our survey results demonstrated that patients and caregivers have design features that are important to them in regard to a wearable seizure detection device. Overall, the ability to detect all seizures rated highest among respondents which continues to be an unmet need in the community with epilepsy in regard to seizure detection. Additional uses for a wearable were not as important. Based on our results, it is important that an alert (via test and/or email) for events be a portion of the system. A reasonable price point appears to be around $200 to $300. An accelerometer was less important to those surveyed when compared with the use of heart rate, oxygen saturation, or muscle twitches/signals. As further products become developed for use in other health arenas, it will be important to consider patient and caregiver desires in order to meet the need and address the gap in devices that currently exist.

Phenotypic screening reveals TNFR2 as a promising target for cancer immunotherapy.

Antibodies that target cell-surface molecules on T cells can enhance anti-tumor immune responses, resulting in sustained immune-mediated control of cancer. We set out to find new cancer immunotherapy targets by phenotypic screening on human regulatory T (Treg) cells and report the discovery of novel activators of tumor necrosis factor receptor 2 (TNFR2) and a potential role for this target in immunotherapy. A diverse phage display library was screened to find antibody mimetics with preferential binding to Treg cells, the most Treg-selective of which were all, without exception, found to bind specifically to TNFR2. A subset of these TNFR2 binders were found to agonise the receptor, inducing iκ-B degradation and NF-κB pathway signalling in vitro. TNFR2 was found to be expressed by tumor-infiltrating Treg cells, and to a lesser extent Teff cells, from three lung cancer patients, and a similar pattern was also observed in mice implanted with CT26 syngeneic tumors. In such animals, TNFR2-specific agonists inhibited tumor growth, enhanced tumor infiltration by CD8+ T cells and increased CD8+ T cell IFN-γ synthesis. Together, these data indicate a novel mechanism for TNF-α-independent TNFR2 agonism in cancer immunotherapy, and demonstrate the utility of target-agnostic screening in highlighting important targets during drug discovery.

Factors Associated with Shiga Toxin-Producing Escherichia coli Shedding by Dairy and Beef Cattle.

UNLABELLED: Shiga toxin-producing Escherichia coli (STEC) is an important foodborne pathogen that can cause hemorrhagic colitis and hemolytic-uremic syndrome. Cattle are the primary reservoir for STEC, and food or water contaminated with cattle feces is the most common source of infections in humans. Consequently, we conducted a cross-sectional study of 1,096 cattle in six dairy herds (n = 718 animals) and five beef herds (n = 378 animals) in the summers of 2011 and 2012 to identify epidemiological factors associated with shedding. Fecal samples were obtained from each animal and cultured for STEC. Multivariate analyses were performed to identify risk factors associated with STEC positivity. The prevalence of STEC was higher in beef cattle (21%) than dairy cattle (13%) (odds ratio [OR], 1.76; 95% confidence interval [CI], 1.25, 2.47), with considerable variation occurring across herds (range, 6% to 54%). Dairy cattle were significantly more likely to shed STEC when the average temperature was >28.9°C 1 to 5 days prior to sampling (OR, 2.5; 95% CI, 1.25, 4.91), during their first lactation (OR, 1.8; 95% CI, 1.1, 2.8), and when they were <30 days in milk (OR, 3.9; 95% CI, 2.1, 7.2). These data suggest that the stress or the negative energy balance associated with lactation may result in increased STEC shedding frequencies in Michigan during the warm summer months. Future prevention strategies aimed at reducing stress during lactation or isolating high-risk animals could be implemented to reduce herd-level shedding levels and avoid transmission of STEC to susceptible animals and people. IMPORTANCE: STEC shedding frequencies vary considerably across cattle herds in Michigan, and the shedding frequency of strains belonging to non-O157 serotypes far exceeds the shedding frequency of O157 strains, which is congruent with human infections in the state. Dairy cattle sampled at higher temperatures, in their first lactation, and early in the milk production stage were significantly more likely to shed STEC, which could be due to stress or a negative energy balance. Future studies should focus on the isolation of high-risk animals to decrease herd shedding levels and the potential for contamination of the food supply.

Phenotypic screening: the future of antibody discovery.

Most antibody therapeutics have been isolated from high throughput target-based screening. However, as the number of validated targets diminishes and the target space becomes increasingly competitive, alternative strategies, such as phenotypic screening, are gaining momentum. Here, we review successful phenotypic screens, including those used to isolate antibodies against cancer and infectious agents. We also consider exciting advances in the expression and phenotypic screening of antibody repertoires in single cell autocrine systems. As technologies continue to develop, we believe that antibody phenotypic screening will increase further in popularity and has the potential to provide the next generation of therapeutic antibodies.

Identification of anti-tumour biologics using primary tumour models, 3-D phenotypic screening and image-based multi-parametric profiling.

BACKGROUND: Monolayer cultures of immortalised cell lines are a popular screening tool for novel anti-cancer therapeutics, but these methods can be a poor surrogate for disease states, and there is a need for drug screening platforms which are more predictive of clinical outcome. In this study, we describe a phenotypic antibody screen using three-dimensional cultures of primary cells, and image-based multi-parametric profiling in PC-3 cells, to identify anti-cancer biologics against new therapeutic targets. METHODS: ScFv Antibodies and designed ankyrin repeat proteins (DARPins) were isolated using phage display selections against primary non-small cell lung carcinoma cells. The selected molecules were screened for anti-proliferative and pro-apoptotic activity against primary cells grown in three-dimensional culture, and in an ultra-high content screen on a 3-D cultured cell line using multi-parametric profiling to detect treatment-induced phenotypic changes. The targets of molecules of interest were identified using a cell-surface membrane protein array. An anti-CUB domain containing protein 1 (CDCP1) antibody was tested for tumour growth inhibition in a patient-derived xenograft model, generated from a stage-IV non-small cell lung carcinoma, with and without cisplatin. RESULTS: Two primary non-small cell lung carcinoma cell models were established for antibody isolation and primary screening in anti-proliferative and apoptosis assays. These assays identified multiple antibodies demonstrating activity in specific culture formats. A subset of the DARPins was profiled in an ultra-high content multi-parametric screen, where 300 morphological features were measured per sample. Machine learning was used to select features to classify treatment responses, then antibodies were characterised based on the phenotypes that they induced. This method co-classified several DARPins that targeted CDCP1 into two sets with different phenotypes. Finally, an anti-CDCP1 antibody significantly enhanced the efficacy of cisplatin in a patient-derived NSCLC xenograft model. CONCLUSIONS: Phenotypic profiling using complex 3-D cell cultures steers hit selection towards more relevant in vivo phenotypes, and may shed light on subtle mechanistic variations in drug candidates, enabling data-driven decisions for oncology target validation. CDCP1 was identified as a potential target for cisplatin combination therapy.

Combining phenotypic and proteomic approaches to identify membrane targets in a 'triple negative' breast cancer cell type.

BACKGROUND: The continued discovery of therapeutic antibodies, which address unmet medical needs, requires the continued discovery of tractable antibody targets. Multiple protein-level target discovery approaches are available and these can be used in combination to extensively survey relevant cell membranomes. In this study, the MDA-MB-231 cell line was selected for membranome survey as it is a 'triple negative' breast cancer cell line, which represents a cancer subtype that is aggressive and has few treatment options. METHODS: The MDA-MB-231 breast carcinoma cell line was used to explore three membranome target discovery approaches, which were used in parallel to cross-validate the significance of identified antigens. A proteomic approach, which used membrane protein enrichment followed by protein identification by mass spectrometry, was used alongside two phenotypic antibody screening approaches. The first phenotypic screening approach was based on hybridoma technology and the second was based on phage display technology. Antibodies isolated by the phenotypic approaches were tested for cell specificity as well as internalisation and the targets identified were compared to each other as well as those identified by the proteomic approach. An anti-CD73 antibody derived from the phage display-based phenotypic approach was tested for binding to other 'triple negative' breast cancer cell lines and tested for tumour growth inhibitory activity in a MDA-MB-231 xenograft model. RESULTS: All of the approaches identified multiple cell surface markers, including integrins, CD44, EGFR, CD71, galectin-3, CD73 and BCAM, some of which had been previously confirmed as being tractable to antibody therapy. In total, 40 cell surface markers were identified for further study. In addition to cell surface marker identification, the phenotypic antibody screening approaches provided reagent antibodies for target validation studies. This is illustrated using the anti-CD73 antibody, which bound other 'triple negative' breast cancer cell lines and produced significant tumour growth inhibitory activity in a MDA-MB-231 xenograft model. CONCLUSIONS: This study has demonstrated that multiple methods are required to successfully analyse the membranome of a desired cell type. It has also successfully demonstrated that phenotypic antibody screening provides a mechanism for rapidly discovering and evaluating antibody tractable targets, which can significantly accelerate the therapeutic discovery process.

Improved drug-like properties of therapeutic proteins by directed evolution.

Many natural human proteins have functional properties that make them useful as therapeutic drugs. However, not all these proteins are compatible with large-scale manufacturing processes or sufficiently stable to be stored for long periods prior to use. In this study, we focus on small four-helix bundle proteins and employ ribosome display in conjunction with three parallel selection pressures to favour the isolation of variant proteins with improved expression, solubility and stability. This in vitro evolution strategy was applied to two human proteins with known drug development issues, granulocyte colony-stimulating factor (G-CSF) and erythropoietin (EPO). In the case of G-CSF, the soluble expression levels in Escherichia coli were improved 1000-fold, while for EPO the level of aggregation in an accelerated shelf-life study was reduced from over 80% to undetectable levels. These results exemplify the general utility of our in vitro evolution strategy for improving the drug-like properties of therapeutic proteins.