An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries.

Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of nine different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.

Rationalizing diverse binding mechanisms to the same protein fold: insights for ligand recognition and biosensor design.

The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem which could enable many practical applications of protein biosensors. In this work, we analyzed two engineer ed biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands. MD simulations indicate that both PYR1 protein-ligand complexes bind a single conformer of their target ligand that is close to the lowest free energy conformer. Computational design using a fixed conformer and rigid body orientation led to new WIN55,212-2 sensors with nanomolar limits of detection. This work reveals mechanisms by which the versatile PYR1 biosensor scaffold can bind diverse ligands. This work also provides computational methods to sample realistic ligand conformers and rigid body alignments that simplify the computational design of biosensors for novel ligands of interest.

An integrated technology for quantitative wide mutational scanning of human antibody Fab libraries.

Antibodies are engineerable quantities in medicine. Learning antibody molecular recognition would enable the in silico design of high affinity binders against nearly any proteinaceous surface. Yet, publicly available experiment antibody sequence-binding datasets may not contain the mutagenic, antigenic, or antibody sequence diversity necessary for deep learning approaches to capture molecular recognition. In part, this is because limited experimental platforms exist for assessing quantitative and simultaneous sequence-function relationships for multiple antibodies. Here we present MAGMA-seq, an integrated technology that combines multiple antigens and multiple antibodies and determines quantitative biophysical parameters using deep sequencing. We demonstrate MAGMA-seq on two pooled libraries comprising mutants of ten different human antibodies spanning light chain gene usage, CDR H3 length, and antigenic targets. We demonstrate the comprehensive mapping of potential antibody development pathways, sequence-binding relationships for multiple antibodies simultaneously, and identification of paratope sequence determinants for binding recognition for broadly neutralizing antibodies (bnAbs). MAGMA-seq enables rapid and scalable antibody engineering of multiple lead candidates because it can measure binding for mutants of many given parental antibodies in a single experiment.

Dynamics of SARS-CoV-2 Seroprevalence in a Large US population Over a Period of 12 Months.

Due to a combination of asymptomatic or undiagnosed infections, the proportion of the United States population infected with SARS-CoV-2 was unclear from the beginning of the pandemic. We previously established a platform to screen for SARS-CoV-2 positivity across a representative proportion of the US population, from which we reported that almost 17 million Americans were estimated to have had undocumented infections in the Spring of 2020. Since then, vaccine rollout and prevalence of different SARS-CoV-2 variants have further altered seropositivity trends within the United States population. To explore the longitudinal impacts of the pandemic and vaccine responses on seropositivity, we re-enrolled participants from our baseline study in a 6- and 12- month follow-up study to develop a longitudinal antibody profile capable of representing seropositivity within the United States during a critical period just prior to and during the initiation of vaccine rollout. Initial measurements showed that, since July 2020, seropositivity elevated within this population from 4.8% at baseline to 36.2% and 89.3% at 6 and 12 months, respectively. We also evaluated nucleocapsid seropositivity and compared to spike seropositivity to identify trends in infection versus vaccination relative to baseline. These data serve as a window into a critical timeframe within the COVID-19 pandemic response and serve as a resource that could be used in subsequent respiratory illness outbreaks.

Common framework mutations impact antibody interfacial dynamics and flexibility.

Introduction: With the flood of engineered antibodies, there is a heightened need to elucidate the structural features of antibodies that contribute to specificity, stability, and breadth. While antibody flexibility and interface angle have begun to be explored, design rules have yet to emerge, as their impact on the metrics above remains unclear. Furthermore, the purpose of framework mutations in mature antibodies is highly convoluted. Methods: To this end, a case study utilizing molecular dynamics simulations was undertaken to determine the impact framework mutations have on the VH-VL interface. We further sought to elucidate the governing mechanisms by which changes in the VH-VL interface angle impact structural elements of mature antibodies by looking at root mean squared deviations, root mean squared fluctuations, and solvent accessible surface area. Results and discussion: Overall, our results suggest framework mutations can significantly shift the distribution of VH-VL interface angles, which leads to local changes in antibody flexibility through local changes in the solvent accessible surface area. The data presented herein highlights the need to reject the dogma of static antibody crystal structures and exemplifies the dynamic nature of these proteins in solution. Findings from this work further demonstrate the importance of framework mutations on antibody structure and lay the foundation for establishing design principles to create antibodies with increased specificity, stability, and breadth.

Higher rates of all-cause mortality and resource utilization during episodes-of-care for diabetic foot ulceration.

AIMS: Our primary objective was to determine whether all-cause rates of mortality and resource utilization were higher during periods of diabetic foot ulceration. In support of this objective, a secondary objective was to develop and validate an episode-of-care model for diabetic foot ulceration. METHODS: We evaluated data from the Medicare Limited Data Set between 2013 and 2019. We defined episodes-of-care by clustering diabetic foot ulcer related claims such that the longest time interval between consecutive claims in any cluster did not exceed a duration which was adjusted to match two aspects of foot ulcer episodes that are well-established in the literature: healing rate at 12 weeks, and reulceration rate following healing. We compared rates of outcomes during periods of ulceration to rates immediately following healing to estimate incidence ratios. RESULTS: The episode-of-care model had a minimum mean relative error of 4.2% in the two validation criteria using a clustering duration of seven weeks. Compared to periods after healing, all-cause inpatient admissions were 2.8 times more likely during foot ulcer episodes and death was 1.5 times more likely. CONCLUSIONS: A newly-validated episode-of-care model for diabetic foot ulcers suggests an underappreciated association between foot ulcer episodes and all-cause resource utilization and mortality.

Regulatory Approved Monoclonal Antibodies Contain Framework Mutations Predicted From Human Antibody Repertoires.

Monoclonal antibodies (mAbs) are an important class of therapeutics used to treat cancer, inflammation, and infectious diseases. Identifying highly developable mAb sequences in silico could greatly reduce the time and cost required for therapeutic mAb development. Here, we present position-specific scoring matrices (PSSMs) for antibody framework mutations developed using baseline human antibody repertoire sequences. Our analysis shows that human antibody repertoire-based PSSMs are consistent across individuals and demonstrate high correlations between related germlines. We show that mutations in existing therapeutic antibodies can be accurately predicted solely from baseline human antibody sequence data. We find that mAbs developed using humanized mice had more human-like FR mutations than mAbs originally developed by hybridoma technology. A quantitative assessment of entire framework regions of therapeutic antibodies revealed that there may be potential for improving the properties of existing therapeutic antibodies by incorporating additional mutations of high frequency in baseline human antibody repertoires. In addition, high frequency mutations in baseline human antibody repertoires were predicted in silico to reduce immunogenicity in therapeutic mAbs due to the removal of T cell epitopes. Several therapeutic mAbs were identified to have common, universally high-scoring framework mutations, and molecular dynamics simulations revealed the mechanistic basis for the evolutionary selection of these mutations. Our results suggest that baseline human antibody repertoires may be useful as predictive tools to guide mAb development in the future.

Lower extremity reamputation in people with diabetes: a systematic review and meta-analysis.

In this study, we determined the reamputation-free survival to both limbs and to the contralateral limb only following an index amputation of any-level and assessed whether reamputation rates have changed over time. We completed a systematic search using PubMed and screened a total of 205 articles for data on reamputation rates. We reported qualitative characteristics of 56 studies that included data on reamputation rates and completed a meta-analysis on 22 of the studies which enrolled exclusively participants with diabetes. The random-effects meta-analysis fit a parametric survival distribution to the data for reamputations to both limbs and to the contralateral limb only. We assessed whether there was a temporal trend in the reamputation rate using the Mann-Kendall test. Incidence rates were high for reamputation to both limbs and to the contralateral limb only. At 1 year, the reamputation rate for all contralateral and ipsilateral reamputations was found to be 19% (IQR=5.1%-31.6%), and at 5 years, it was found to be 37.1% (IQR=27.0%-47.2%). The contralateral reamputation rate at 5 years was found to be 20.5% (IQR=13.3%-27.2%). We found no evidence of a trend in the reamputation rates over more than two decades of literature analyzed. The incidence of lower extremity reamputation is high among patients with diabetes who have undergone initial amputations secondary to diabetes, and rates of reamputation have not changed over at least two decades.

Investigating correlates of athletic identity and sport-related injury outcomes: a scoping review.

OBJECTIVES: To conduct a scoping review that (1) describes what is known about the relationship between athletic identity and sport-related injury outcomes and (2) describes the relationship that an injury (as an exposure) has on athletic identity (as an outcome) in athletes. DESIGN: Scoping review. PARTICIPANTS: A total of n=1852 athletes from various sport backgrounds and levels of competition. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary measure used within the studies identified was the Athletic Identity Measurement Scale. Secondary outcome measures assessed demographic, psychosocial, behavioural, physical function and pain-related constructs. RESULTS: Twenty-two studies were identified for inclusion. Samples were dominated by male, Caucasian athletes. The majority of studies captured musculoskeletal injuries, while only three studies included sport-related concussion. Athletic identity was significantly and positively associated with depressive symptom severity, sport performance traits (eg, ego-orientation and mastery-orientation), social network size, physical self-worth, motivation, rehabilitation overadherence, mental toughness and playing through pain, as well as injury severity and functional recovery outcomes. Findings pertaining to the association that an injury (as an exposure) had on athletic identity (as an outcome) were inconsistent and limited. CONCLUSIONS: Athletic identity was most frequently associated with psychosocial, behavioural and injury-specific outcomes. Future research should seek to include diverse athlete samples (eg, women, athletes of different races, para-athletes) and should continue to reference theoretical injury models to inform study methodologies and to specify variables of interest for further exploration.

Recurrence rates suggest delayed identification of plantar ulceration for patients in diabetic foot remission.

INTRODUCTION: Foot ulcers are a common and costly complication of diabetes, and delays in treatment can result in impaired healing, infection, hospitalization, and lower extremity amputation. RESEARCH DESIGN AND METHODS: We aimed to determine whether patterns in plantar diabetic foot ulcer (DFU) recurrence coincided with typical intervals between routine preventive care appointments, which would suggest that delays exist between ulcer development and identification. We completed an analysis of existing data from two multicenter studies in 300 total participants. We analyzed unadjusted counts of DFU binned in weekly intervals and defined 'exam periods' as intervals from 2 to 4 weeks, from 6 to 8 weeks, within 1 week of 3 months and within 1 week of 6 months. We tested whether recurrence rates during exam periods were equivalent to rates outside exam periods. We estimated the delay between DFU development and DFU identification such that the rate of development would have been constant. RESULTS: During exam periods, a total of 43 DFUs were identified (43/86=50%) despite the fact that these periods represent only 23.5% of follow-up in aggregate. Accounting for censoring, the annualized incidence during exam periods was 0.68 DFU/year (CI 0.48 to 0.89) in contrast to 0.25 DFU/year (CI 0.18 to 0.32) outside exam periods (incidence ratio=2.8, CI 1.8 to 4.3). We estimated delays between DFU occurrence and identification to average 15.3 days (IQR 7.4-23.7 days). CONCLUSIONS: These findings have potential implications for practice, particularly related to the value of telehealth and in-home monitoring of patients in diabetic foot remission. Additionally, there are implications for study design, which should consider the impact of interval censoring and attempt to control for confounders related to frequency and timing of exams.

Lower resource utilization for patients with healed diabetic foot ulcers during participation in a prevention program with foot temperature monitoring.

INTRODUCTION: We assessed the impact of a diabetic foot ulcer prevention program incorporating once-daily foot temperature monitoring on hospitalizations, emergency department and outpatient visits, and rates of diabetic foot ulcer recurrence and lower extremity amputations for patients with recently healed foot ulcers. RESEARCH DESIGN AND METHODS: In this retrospective analysis of real-world data, we enrolled 80 participants with a healed diabetic foot ulcer in a year-long foot ulcer recurrence prevention program. Four outpatient centers within a large integrated healthcare system in the USA contributed to enrollment. We evaluated diabetic foot-related outcomes and associated resource utilization for participants during three periods: the 2 years before the program, the year during the program, and after the program ended. We reported unadjusted resource utilization rates during the program and the periods before and after it. We then adjusted rates of outcomes in each phase using an interrupted time series approach, explicitly controlling for overall trends in resource utilization and recurrence during the three periods. RESULTS: Our unadjusted data showed high initial rates of resource utilization and recurrence before enrollment in the program, followed by lower rates during the program, and higher rates of resource utilization and similar rates of recurrence in the period following the end of the program. The adjusted data showed lower rates of hospitalizations (relative risk reduction (RRR)=0.52; number needed to treat (NNT)=3.4), lower extremity amputations (RRR=0.71; NNT=6.4), and outpatient visits (RRR=0.26; absolute risk reduction (ARR)=3.5) during the program. We also found lower rates of foot ulcer recurrence during the program in the adjusted data, particularly for wounds with infection or greater than superficial depth (RRR=0.91; NNT=4.4). CONCLUSIONS: We observed lower rates of healthcare resource utilization for high-risk participants during enrollment in a diabetic foot prevention program incorporating once-daily foot temperature monitoring. TRIAL REGISTRATION NUMBER: NCT04345016.

Use of a Remote Temperature Monitoring Mat for the Early Identification of Foot Ulcers.

INTRODUCTION: Diabetic foot ulcers (DFUs) are responsible for considerable morbidity, mortality, and cost. Remote temperature monitoring (RTM) is an evidenced-based and recommended component of standard foot care for at-risk patients. Although previous research has demonstrated the value of RTM for foot ulcer prevention, its benefits related to the early identification of diabetic foot complications may be underappreciated. OBJECTIVE: This article presents a case series supporting the use of RTM for early identification of DFUs. MATERIALS AND METHODS: The cases of 4 veteran patients who presented consecutively with inflammation, which was detected by a telemedicine temperature monitoring mat, are reported. The authors collected subjective history from each patient via telephone outreach and triaged these patients according to standard diabetic foot care recommendations. RESULTS: Each patient required a clinical exam prompted by the mat and the patient's subjective history. In each case, the patient required callus debridement upon which a pre-ulcerative lesion or partial-thickness wound was discovered. The DFUs in these 4 cases healed quickly and without complication. In 2 of the cases, the outreach prompted by the mat reestablished specialist foot care after a prolonged period without routine exam. CONCLUSIONS: In each of these cases, the RTM mat detected inflammation accompanying a preulcerative lesion or a partial-thickness wound, allowing for timely intervention and treatment, including debridement and offloading, which may have the potential to improve care and reduce morbidity, mortality, and costs.

Accuracy of a foot temperature monitoring mat for predicting diabetic foot ulcers in patients with recent wounds or partial foot amputation.

AIMS: To assess the accuracy of once-daily foot temperature monitoring for predicting foot ulceration in diabetic patients with recent wounds and partial foot amputation, complications previously perceived as challenging. METHODS: We completed a planned analysis of existing data from a recent study in 129 participants with a previously-healed diabetic foot ulcer. We considered four cohorts: all participants, participants with partial foot amputation, participants with a recent wound, and participants without partial foot amputation and without a recent wound. We reported the prediction specificity, lead time, and annualized alert frequency in each cohort at maximum sensitivity. We assessed the two potentially challenging cohorts for non-inferior accuracy relative to the control cohort using Delong's method. RESULTS: We report non-inferior predictive accuracy in each of the two potentially-challenging cohorts relative to the control cohort (⍺ < 0.05). The alert lead time was similar across these cohorts, ranging from 33 to 42 days. CONCLUSIONS: Once-daily foot temperature monitoring is no less accurate for predicting foot ulceration in those with recent wounds and partial foot amputations than in those without these complications. These results support expanded practice of once-daily foot temperature monitoring, which may result in improved patient outcomes and reduced healthcare resource utilization.

Ulcer metastasis? Anatomical locations of recurrence for patients in diabetic foot remission.

BACKGROUND: The "cancer analogy" is powerful for communicating risk to and organizing care for patients with diabetic foot syndrome. One potentially underappreciated similarity between cancer and foot ulcers is that both can recur at anatomical locations distinct from the primary occurrence, albeit with different physiological mechanisms. Few studies have characterized the location of diabetic foot ulcer recurrence, and these have been limited by considering only the first recurrent wound following a recent-healed wound. We therefore characterized the anatomical locations at which diabetic foot ulcers are likely to recur considering multiple wounds during follow-up and the locations of all prior wounds documented in the participant's history. METHODS: We completed a secondary analysis of existing data from a 129 participant multi-center study of participants in diabetic foot remission. The primary outcome was plantar foot ulceration, and each participant was followed for 34 weeks or until withdrawing consent, allowing characterization of all wounds occurring. We stratified the anatomical locations of wounds prior to the trial by the following outcome categories during the trial: no recurrence, recurrence to the same anatomical location, recurrence to a different anatomical location on the same foot, and recurrence to the contralateral foot. RESULTS: A large percentage (48%) of wounds recurred to the contralateral foot, and the proportion of subsequent foot ulcer to the contralateral limb was largely unaffected by the anatomical location of foot ulcer prior to the study. Only 17% of prior diabetic foot ulcers were followed by recurrence to the same anatomical location. Rates of recurrence remained high during treatment of a wound (0.41 foot ulcer/ulcer-year). Participants had documented wounds to 2.2 distinct anatomical locations on average, and more than 60% of participants had wounds to more than one plantar location by the end of the study. CONCLUSIONS: Given the significant morbidity, mortality, and resource utilization associated with foot ulcer recidivism, quality and evidenced-based preventive care is essential. Our results better characterize the burden of recurrence and to what anatomy recurrence is most likely. These insights may benefit providers and patients alike for the provision of high-quality preventive care thereby resulting in reduced morbidity, mortality, and cost. TRIAL REGISTRATION: The study providing the data for this secondary analysis was registered on ClinicalTrials.gov (NCT02647346) on January 6, 2016. The study was retrospectively registered.

Non-invasive MRI quantification of cerebrospinal fluid dynamics in amyotrophic lateral sclerosis patients.

BACKGROUND: Developing novel therapeutic agents to treat amyotrophic lateral sclerosis (ALS) has been difficult due to multifactorial pathophysiologic processes at work. Intrathecal drug administration shows promise due to close proximity of cerebrospinal fluid (CSF) to affected tissues. Development of effective intrathecal pharmaceuticals will rely on accurate models of how drugs are dispersed in the CSF. Therefore, a method to quantify these dynamics and a characterization of differences across disease states is needed. METHODS: Complete intrathecal 3D CSF geometry and CSF flow velocities at six axial locations in the spinal canal were collected by T2-weighted and phase-contrast MRI, respectively. Scans were completed for eight people with ALS and ten healthy controls. Manual segmentation of the spinal subarachnoid space was performed and coupled with an interpolated model of CSF flow within the spinal canal. Geometric and hydrodynamic parameters were then generated at 1 mm slice intervals along the entire spine. Temporal analysis of the waveform spectral content and feature points was also completed. RESULTS: Comparison of ALS and control groups revealed a reduction in CSF flow magnitude and increased flow propagation velocities in the ALS cohort. Other differences in spectral harmonic content and geometric comparisons may support an overall decrease in intrathecal compliance in the ALS group. Notably, there was a high degree of variability between cases, with one ALS patient displaying nearly zero CSF flow along the entire spinal canal. CONCLUSION: While our sample size limits statistical confidence about the differences observed in this study, it was possible to measure and quantify inter-individual and cohort variability in a non-invasive manner. Our study also shows the potential for MRI based measurements of CSF geometry and flow to provide information about  the hydrodynamic environment of the spinal subarachnoid space. These dynamics may be studied further to understand the behavior of CSF solute transport in healthy and diseased states.