Adapting recombinant bacterial alkaline phosphatase for nucleotide exchange of small GTPases

The small GTPase Rat sarcoma virus proteins (RAS) are key regulators of cell growth and involved in 20-30% of cancers. RAS switches between its active state and inactive state via exchange of GTP (active) and GDP (inactive). Therefore, to study active protein, it needs to undergo nucleotide exchange to a non-hydrolysable GTP analog. Calf intestine alkaline phosphatase bound to agarose beads (CIP-agarose) is regularly used in a nucleotide exchange protocol to replace GDP with a non-hydrolysable analog. Due to pandemic supply problems and product shortages, we found the need for an alternative to this commercially available product. Here we describe how we generated a bacterial alkaline phosphatase (BAP) with an affinity tag bound to an agarose bead. This BAP completely exchanges the nucleotide in our samples, thereby demonstrating an alternative to the commercially available product using generally available laboratory equipment.

A Top-Down Proteomic Assay to Evaluate KRAS4B-Compound Engagement

Development of new targeted inhibitors for oncogenic KRAS mutants may benefit from insight into how a given mutation influences the accessibility of protein residues and how compounds interact with mutant or wild-type KRAS proteins. Targeted proteomic analysis, a key validation step in the KRAS inhibitor development process, typically involves both intact mass- and peptide-based methods to confirm compound localization or quantify binding. However, these methods may not always provide a clear picture of the compound binding affinity for KRAS, how specific the compound is to the target KRAS residue, and how experimental conditions may impact these factors. To address this, we have developed a novel top-down proteomic assay to evaluate in vitro KRAS4B-compound engagement while assessing relative quantitation in parallel. We present two applications to demonstrate the capabilities of our assay: maleimide-biotin labeling of a KRAS4BG12D cysteine mutant panel and treatment of three KRAS4B proteins (WT, G12C, and G13C) with small molecule compounds. Our results show the time- or concentration-dependence of KRAS4B-compound engagement in context of the intact protein molecule while directly mapping the compound binding site.

Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties

KRAS, the most frequently mutated oncogene in human cancer, produces two isoforms, KRAS4a and KRAS4b, through alternative splicing. These isoforms differ in exon 4, which encodes the final 15 residues of the G-domain and hypervariable regions (HVRs), vital for trafficking and membrane localization. While KRAS4b has been extensively studied, KRAS4a has been largely overlooked. Our multidisciplinary study compared the structural and functional characteristics of KRAS4a and KRAS4b, revealing distinct structural properties and thermal stability. Position 151 influences KRAS4a's thermal stability, while position 153 affects binding to RAF1 CRD protein. Nuclear magnetic resonance analysis identified localized structural differences near sequence variations and provided a solution-state conformational ensemble. Notably, KRAS4a exhibits substantial transcript abundance in bile ducts, liver, and stomach, with transcript levels approaching KRAS4b in the colon and rectum. Functional disparities were observed in full-length KRAS variants, highlighting the impact of HVR variations on interaction with trafficking proteins and downstream effectors like RAF and PI3K within cells.

RAS-dependent RAF-MAPK hyperactivation by pathogenic RIT1 is a therapeutic target in Noonan syndrome-associated cardiac hypertrophy

RIT1 is a RAS guanosine triphosphatase (GTPase) that regulates different aspects of signal transduction and is mutated in lung cancer, leukemia, and in the germline of individuals with Noonan syndrome. Pathogenic RIT1 proteins promote mitogen-activated protein kinase (MAPK) hyperactivation; however, this mechanism remains poorly understood. Here, we show that RAF kinases are direct effectors of membrane-bound mutant RIT1 necessary for MAPK activation. We identify critical residues in RIT1 that facilitate interaction with membrane lipids and show that these are necessary for association with RAF kinases and MAPK activation. Although mutant RIT1 binds to RAF kinases directly, it fails to activate MAPK signaling in the absence of classical RAS proteins. Consistent with aberrant RAF/MAPK activation as a driver of disease, we show that pathway inhibition alleviates cardiac hypertrophy in a mouse model of RIT1 mutant Noonan syndrome. These data shed light on the function of pathogenic RIT1 and identify avenues for therapeutic intervention.

Methods of policy monitoring in physical activity promotion: a systematic review across different levels of government

Background

Even though the importance of policy monitoring in public health has increased in the last decades, there is still a lack of understanding what different approaches of policy monitoring exist and which methodology they employ. In order to address this research gap, this review attempts to provide a comprehensive overview about the methods of policy monitoring in the field of physical activity promotion.

Methods

A systematic search was conducted in five scientific databases, using the terms “physical activity”, “policy” and “monitoring” and their variations. In total, 12.963 studies were identified and, after the elimination of duplicates, screened independently by two reviewers. During full text analysis, information on the methods applied for policy monitoring was extracted and studies were categorized based on their key characteristics (monitoring tool, policy level, and setting).

Results

The search yielded in a total of 112 studies that were structured into seven categories: Report Cards on Physical Activity for Children and Youth, HEPA Monitoring Framework, HEPA Policy Audit Tool, national policies, subnational policies, school setting, and childcare setting. Across all categories, policy monitoring focused mainly on national level policies in a single country. Differences were identified with regards to the level of government involvement which allowed to differentiate between research-driven approaches (little or no government involvement), government-driven approaches (led by governments), and co-production approaches (strong collaboration between researchers and governments).

Conclusions

Research-driven, government-driven and co-production approaches have different strengths and weaknesses with regards to the monitoring of policies. Awareness needs to be raised regarding the implications of these approaches, and more research is needed to analyse the impact of policy monitoring on policy-making in public health.

The development of the Physical Activity Environment Policy Index (PA-EPI): a tool for monitoring and benchmarking government policies and actions to improve physical activity

Background

Insufficient physical activity (PA) is a global issue for health. A multifaceted response, including government action, is essential to improve population levels of PA. The purpose of this study was to develop the ‘Physical Activity Environment Policy Index’ (PA-EPI) monitoring framework to assess government policies and actions for creating a healthy PA environment.

Methods

An iterative process was undertaken. This involved a review of policy documents from authoritative organisations, a policy audit of four European countries, and systematic reviews of scientific literature. This was followed by an online consultation with academic experts (N = 101; 20 countries, 72% response rate), and policymakers (N = 40, 4 EU countries). During this process, consensus workshops where quantitative and qualitative data alongside theoretical and pragmatic considerations were used to inform PA-EPI development.

Results

The PA-EPI is conceptualised as a two-component ‘policy’ and ‘infrastructure support’ framework. The two components comprise eight policy and seven infrastructure support domains. The policy domains are education, transport, urban design, healthcare, public education (including mass media), sport-for-all, workplaces and community. The infrastructure support domains are leadership, governance, monitoring and intelligence, funding and resources, platforms for interaction, workforce development, and health-in-all-policies. Forty-five ‘good practice statements’ (GPS) or indicators of ideal good practice within each domain concludes the PA-EPI. A potential eight-step process for conducting the PA-EPI is described.

Conclusions

Once pre-tested and piloted in several countries of various sizes and income levels, the PA-EPI GPS will evolve into benchmarks established by governments at the forefront of creating and implementing policies to address inactivity.

Structure of the SHOC2-MRAS-PP1C complex provides insights into RAF activation and Noonan syndrome

SHOC2 acts as a strong synthetic lethal interactor with MEK inhibitors in multiple KRAS cancer cell lines. SHOC2 forms a heterotrimeric complex with MRAS and PP1C that is essential for regulating RAF and MAPK-pathway activation by dephosphorylating a specific phosphoserine on RAF kinases. Here we present the high-resolution crystal structure of the SHOC2-MRAS-PP1C (SMP) complex and apo-SHOC2. Our structures reveal that SHOC2, MRAS, and PP1C form a stable ternary complex in which all three proteins synergistically interact with each other. Our results show that dephosphorylation of RAF substrates by PP1C is enhanced upon interacting with SHOC2 and MRAS. The SMP complex forms only when MRAS is in an active state and is dependent on SHOC2 functioning as a scaffolding protein in the complex by bringing PP1C and MRAS together. Our results provide structural insights into the role of the SMP complex in RAF activation and how mutations found in Noonan syndrome enhance complex formation, and reveal new avenues for therapeutic interventions.

Insights into the Cross Talk between Effector and Allosteric Lobes of KRAS from Methyl Conformational Dynamics

KRAS is the most frequently mutated RAS protein in cancer patients, and it is estimated that about 20% of the cancer patients in the United States carried mutant RAS proteins. To accelerate therapeutic development, structures and dynamics of RAS proteins had been extensively studied by various biophysical techniques for decades. Although 31P NMR studies revealed population equilibrium of the two major states in the active GMPPNP-bound form, more complex conformational dynamics in RAS proteins and oncogenic mutants subtly modulate the interactions with their downstream effectors. We established a set of customized NMR relaxation dispersion techniques to efficiently and systematically examine the ms-μs conformational dynamics of RAS proteins. This method allowed us to observe varying synchronized motions that connect the effector and allosteric lobes in KRAS. We demonstrated the role of conformational dynamics of KRAS in controlling its interaction with the Ras-binding domain of the downstream effector RAF1, the first kinase in the MAPK pathway. This allows one to explain, as well as to predict, the altered binding affinities of various KRAS mutants, which was neither previously reported nor apparent from the structural perspective.

RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity

RAS proteins are molecular switches that interact with effector proteins when bound to guanosine triphosphate, stimulating downstream signaling in response to multiple stimuli. Although several canonical downstream effectors have been extensively studied and tested as potential targets for RAS-driven cancers, many of these remain poorly characterized. In this study, we undertook a biochemical and structural approach to further study the role of Sin1 as a RAS effector. Sin1 interacted predominantly with KRAS isoform 4A in cells through an atypical RAS-binding domain that we have characterized by X-ray crystallography. Despite the essential role of Sin1 in the assembly and activity of mTORC2, we find that the interaction with RAS is not required for these functions. Cells and mice expressing a mutant of Sin1 that is unable to bind RAS are proficient for activation and assembly of mTORC2. Our results suggest that Sin1 is a bona fide RAS effector that regulates downstream signaling in an mTORC2-independent manner.

Undiagnosed SARS-CoV-2 seropositivity during the first 6 months of the COVID-19 pandemic in the United States

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates in the United States and elsewhere. To address this, we analyzed seropositivity in 9089 adults in the United States who had not been diagnosed previously with COVID-19. Individuals with characteristics that reflected the U.S. population (n = 27,716) were selected by quota sampling from 462,949 volunteers. Enrolled participants (n = 11,382) provided medical, geographic, demographic, and socioeconomic information and dried blood samples. Survey questions coincident with the Behavioral Risk Factor Surveillance System survey, a large probability-based national survey, were used to adjust for selection bias. Most blood samples (88.7%) were collected between 10 May and 31 July 2020 and were processed using ELISA to measure seropositivity (IgG and IgM antibodies against SARS-CoV-2 spike protein and the spike protein receptor binding domain). The overall weighted undiagnosed seropositivity estimate was 4.6% (95% CI, 2.6 to 6.5%), with race, age, sex, ethnicity, and urban/rural subgroup estimates ranging from 1.1% to 14.2%. The highest seropositivity estimates were in African American participants; younger, female, and Hispanic participants; and residents of urban centers. These data indicate that there were 4.8 undiagnosed SARS-CoV-2 infections for every diagnosed case of COVID-19, and an estimated 16.8 million infections were undiagnosed by mid-July 2020 in the United States.

Mapping a Pandemic: SARS-CoV-2 Seropositivity in the United States

Asymptomatic SARS-CoV-2 infection and delayed implementation of diagnostics have led to poorly defined viral prevalence rates. To address this, we analyzed seropositivity in US adults who have not previously been diagnosed with COVID-19. Individuals with characteristics that reflect the US population (n = 11,382) and who had not previously been diagnosed with COVID-19 were selected by quota sampling from 241,424 volunteers (ClinicalTrials.gov NCT04334954). Enrolled participants provided medical, geographic, demographic, and socioeconomic information and 9,028 blood samples. The majority (88.7%) of samples were collected between May 10th and July 31st, 2020. Samples were analyzed via ELISA for anti-Spike and anti-RBD antibodies. Estimation of seroprevalence was performed by using a weighted analysis to reflect the US population. We detected an undiagnosed seropositivity rate of 4.6% (95% CI: 2.6 - 6.5%). There was distinct regional variability, with heightened seropositivity in locations of early outbreaks. Subgroup analysis demonstrated that the highest estimated undiagnosed seropositivity within groups was detected in younger participants (ages 18-45, 5.9%), females (5.5%), Black/African American (14.2%), Hispanic (6.1%), and Urban residents (5.3%), and lower undiagnosed seropositivity in those with chronic diseases. During the first wave of infection over the spring/summer of 2020 an estimate of 4.6% of adults had a prior undiagnosed SARS-CoV-2 infection. These data indicate that there were 4.8 (95% CI: 2.8-6.8) undiagnosed cases for every diagnosed case of COVID-19 during this same time period in the United States, and an estimated 16.8 million undiagnosed cases by mid-July 2020.

Standardization of ELISA protocols for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling

The extent of SARS-CoV-2 infection throughout the United States population is currently unknown. High quality serology is key to avoiding medically costly diagnostic errors, as well as to assuring properly informed public health decisions. Here, we present an optimized ELISA-based serology protocol, from antigen production to data analyses, that helps define thresholds for IgG and IgM seropositivity with high specificities. Validation of this protocol is performed using traditionally collected serum as well as dried blood on mail-in blood sampling kits. Archival (pre-2019) samples are used as negative controls, and convalescent, PCR-diagnosed COVID-19 patient samples serve as positive controls. Using this protocol, minimal cross-reactivity is observed for the spike proteins of MERS, SARS1, OC43 and HKU1 viruses, and no cross reactivity is observed with anti-influenza A H1N1 HAI. Our protocol may thus help provide standardized, population-based data on the extent of SARS-CoV-2 seropositivity, immunity and infection.

Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection.

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Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parameters.

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Two versions of RBD show different sensitivity in serology assays.

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Yields of greater than 50 mg/l obtained under optimal conditions.

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Magnetic bead purification technology improves throughput of protein production.

Improved production of SARS-CoV-2 spike receptor-binding domain (RBD) for serology assays

The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein is a commonly used antigen for serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Different versions of the RBD protein have been developed and utilized in assays, with higher sensitivity attributed to particular forms of the protein. To improve the yield of these high-sensitivity forms of RBD and support the increased demand for this antigen in serology assays, we investigated several protein expression variables including DNA elements such as promoters and signal peptides, cell culture expression parameters, and purification processes. Through this investigation, we developed a simplified and robust purification strategy that consistently resulted in high levels of the high-sensitivity form of RBD and demonstrated that a carboxyterminal tag is responsible for the increased sensitivity in the ELISA. These improved reagents and processes produce high-quality proteins which are functional in serology assays and can be used to investigate seropositivity to SARS-CoV-2 infection. Highlights: Improved yields of SARS-CoV-2 spike RBD through modification of DNA constructs and purification parametersTwo versions of RBD show different sensitivity in serology assaysYields of greater than 50 mg/l obtained under optimal conditionsMagnetic bead purification technology improves throughput of protein production.

Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays

The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.

Systematic review examining the evidence for impact of school policies on physical activity

Background

Epidemiological evidence has demonstrated that physical activity can have substantive health benefits for children and young people. The 'Policy Evaluation Network' is a multi-disciplinary research network across 7 European countries and New Zealand aimed at building capacity and evaluating the level of impact of policy interventions for promoting healthy lifestyles. The Toronto Charter identified 'whole-of-school' programmes as one of seven key investments for promotion of PA. This paper presents results of a SLR, designed to assess the level of evidence for policies within the school setting that contribute directly or indirectly to increasing PA.

Methods

Researchers searched six online databases for scientific literature regarding PA policy interventions in the school setting using key concepts of policy, school, PA and evaluation. Risk of bias will be assessed with tools appropriate to the design of the studies considered. Evidence of actual or potential positive PA outcomes arising directly or indirectly from policy actions will be catalogued.

Results

Preliminary searches identified 2327 unique scientific articles. 1938 (83.3%) were excluded on first reading and 189 (8.8%) were included for full text analysis. Initial findings suggest that organisational policies, for example avoiding overcrowding in playgrounds during school breaks, may be a promising policy action. Detailed analysis revealing other potential policy actions supported by evidence will be presented (SLR in progress).

Conclusions

Preliminary findings suggest that few studies link policy actions in the school setting to PA outcomes. However, studies that have investigated the effects of changes to the school environment on PA levels may provide evidence for policy actions. Preliminary recommendations include strengthening the evidence base for school-based PA policy by supporting studies into the effects of particular policy or legislative changes on PA outcomes.

Key messages

School physical activity policies are an underappreciated public health intervention. More studies should link policy changes to physical activity outcomes.

Sub-national structures matter when evaluating physical activity promotion: Lessons from Germany

Background

Public policies are increasingly acknowledged as important part of promoting physical activity (PA). However, especially in states with sub-national administrative structures such as Germany, national and sub-national approaches differ considerably. In Germany, sport for all (SfA) promotion is mostly organized at sub-national level, which is usually not covered in national evaluations. Knowledge of these structures helps to understand national outcomes, enables comparisons and learning within and between countries, and assists in identifying support structures for effective PA promotion.

Methods

Data were collected in the PEN Policy Evaluation Network project. In addition to the WHO HEPA PAT, a questionnaire was sent to the sports representatives of the 16 federal states. Responses of 11 state representatives were included and overarching issues were identified using inductive thematic analysis.

Results

PA promotion in Germany is organized in three areas: SfA, professional sports and school sports. SfA promotion at sub-national level is assigned to different administrative bodies (ministries, senate administration, state chancellery) and policy areas: culture, health and care, home affairs with various aspects, education, social affairs and family. The priorities of the federal states are more diverse and specific compared to the national level. There is an overlap in the topics: urban planning, cycling, health prevention and targeting children. Cooperation mechanisms and partners vary between federal states, but some partners are active at sub-national and national level.

Conclusions

The results provide an insight into the complexity of PA and especially SfA promotion at sub-national level in Germany. Our results suggest that a broader range of approaches is used in the 16 German states than national overviews would suggest. These particularities must be taken into account when assessing and comparing the results from different countries.

Key messages

The promotion of SfA at German sub-national level is much more diverse than represented at national level evaluations. Knowledge of sub-national structures enables the understanding of national outcomes, the promotion of cross-national learning and the identification of supportive structures for effective PA promotion.

Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD

CRAF activation requires binding to membrane-anchored and active GTP-bound RAS. Whereas its RAS-binding domain (RBD) contains the main binding interface to the RAS G domain, its cysteine-rich domain (CRD) is responsible for association to anionic lipid-rich membranes. Both RAF domains are connected by a short linker, and it remains unclear if the two domains act independently or if one domain can impact the function of the other. Here, we used a combination of coarse-grained and all-atom molecular dynamics simulations of a CRAF RBD-CRD construct to investigate the dynamics of the RBD when it is tethered to CRD that is anchored to a POPC:POPS model membrane. First, we show that the RBD positioning is very dynamic with a preferential localization near the membrane surface. Next, we show that membrane-localized RBD has its RAS-binding interface mostly inaccessible because of its proximity to the membrane. Several positively charged residues in this interface were identified from simulations as important for driving RBD association to the membrane. Surface plasmon resonance (SPR) measurements confirmed that mutations of these RBD residues reduced the liposome partitioning of RBD-CRD. Last, simulations indicated that the presence of RBD near the membrane led to a local enrichment of anionic lipids that could potentially enhance the membrane affinity of the entire RBD-CRD construct. This was supported by SPR measurements that showed stronger liposome partitioning of RBD-CRD relative to CRD alone. These findings thus suggest that the RBD and CRD have synergistic effects on their membrane dynamics, with CRD bringing RBD closer to the membrane that impacts its accessibility to RAS and with RBD causing local anionic lipid enrichment that enhances the overall affinity between the membrane and RBD-CRD. These mechanisms have potential implications on the order of events of the interactions between RAS and CRAF at the membrane.

Optimizing high-yield production of SARS-CoV-2 soluble spike trimers for serology assays

The SARS-CoV-2 spike trimer is the primary antigen for several serology assays critical to determining the extent of SARS-CoV-2 exposure in the population. Until stable cell lines are developed to increase the titer of this secreted protein in mammalian cell culture, the low yield of spike protein produced from transient transfection of HEK293 cells will be a limiting factor for these assays. To improve the yield of spike protein and support the high demand for antigens in serology assays, we investigated several recombinant protein expression variables by altering the incubation temperature, harvest time, chromatography strategy, and final protein manipulation. Through this investigation, we developed a simplified and robust purification strategy that consistently yields 5 mg of protein per liter of expression culture for two commonly used forms of the SARS-CoV-2 spike protein. We show that these proteins form well-behaved stable trimers and are consistently functional in serology assays across multiple protein production lots.

Standardization of enzyme-linked immunosorbent assays for serosurveys of the SARS-CoV-2 pandemic using clinical and at-home blood sampling

The extent of SARS-CoV-2 infection throughout the United States population is currently unknown. High quality serology is a key tool to understanding the spread of infection, immunity against the virus, and correlates of protection. Limited validation and testing of serology assays used for serosurveys can lead to unreliable or misleading data, and clinical testing using such unvalidated assays can lead to medically costly diagnostic errors and improperly informed public health decisions. Estimating prevalence and clinical decision making is highly dependent on specificity. Here, we present an optimized ELISA-based serology protocol from antigen production to data analysis. This protocol defines thresholds for IgG and IgM for determination of seropositivity with estimated specificity well above 99%. Validation was performed using both traditionally collected serum and dried blood on mail-in blood sampling kits, using archival (pre-2019) negative controls and known PCR-diagnosed positive patient controls. Minimal cross-reactivity was observed for the spike proteins of MERS, SARS1, OC43 and HKU1 viruses and no cross reactivity was observed with anti-influenza A H1N1 HAI titer during validation. This strategy is highly specific and is designed to provide good estimates of seroprevalence of SARS-CoV-2 seropositivity in a population, providing specific and reliable data from serosurveys and clinical testing which can be used to better evaluate and understand SARS-CoV-2 immunity and correlates of protection.

Abstract A10: Quantitative biophysical analysis defining key components modulating KRAS recruitment to the plasma membrane

The KRAS fraction in the plasma membrane (PM) correlates with activation of the MAPK pathway and subsequent cellular proliferation. Understanding KRAS interaction with the PM constitutes a challenge given the complexity of the cellular environment. To gain insight on key components necessary for KRAS signal transduction at the membrane, we make use of reconstituted liposomes and giant unilamellar vesicles as synthetic membranes. Using surface plasmon resonance (SPR) spectroscopy, we demonstrate that KRAS and RAF1 domains interact with these membranes primarily through electrostatic interactions with negatively charged lipids reinforced by additional interactions involving phosphatidyl ethanolamine and cholesterol. RAF1 52-188 (RBDCRD) interacts with the membrane significantly more strongly than the isolated RBD or CRD domains and synergizes KRAS membrane partitioning. Calmodulin and PDE6 delta, but not galectin3, passively sequester KRAS and prevent it from binding to the PM. RAF1 RBDCRD interacts with membranes preferentially at non-raft lipids domains. The carboxyterminal O-methylation is crucial for KRAS membrane localization. These results contribute to a better understanding of how KRAS-membrane interaction can be tuned by multiple factors.

Citation Format: Bindu Lakshman, Simon Messing, Eva M. Schmid, Jeffrey D. Clogston, William K. Gillette, Dominic Esposito, Bailey Kessing, Daniel A. Fletcher, Dwight V. Nissley, Frank McCormick, Andrew G. Stephen, Frantz L. Jean-Francois. Quantitative biophysical analysis defining key components modulating KRAS recruitment to the plasma membrane [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr A10.

Abstract PR08: Biochemical and structural analysis of the neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases

Neurofibromin is the 320-kilodalton protein product of the NF1 gene that is mutated in the Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to abrogation of the GTPase-activating activity of the protein, leading to aberrant signaling through the RAS-MAPK pathway. Very little is known about the function of the majority of the NF1 protein—to date, only the GAP domain and a region containing a Sec-PH motif have detailed structural information. To better understand the role of this large protein, we have carried out a series of biochemical and biophysical studies that clearly show that full-length NF1 protein exists primarily as a dimer. Data from in vivo experiments confirmed that this dimerization also occurs in cells, and presumably has biologic implications. A model was generated from negative-stain EM data that suggests that NF1 monomers form both intermolecular contacts to form dimers and intramolecular contacts that stabilize the individual monomers. Deletion analysis permitted us to map these two interacting domains to different parts of the NF1 protein, and crosslinking studies coupled with mass spectrometry helped to identify regions of possible interaction. In addition, introduction of point mutations observed in patients with NF diseases caused a dramatic decrease in the stability of proteins both in vitro and in vivo, potentially arguing for a rationale for loss of NF1 activity by these single mutations.

This abstract is also being presented as Poster A03.

Citation Format: Mukul Sherekar, Sae-Won Han, Simon Messing, Matthew Drew, Xiaoying Ye, William Gillette, Puneet Juneja, Hugh O’Neill, Christopher Stanley, Arvind Ramanathan, Natalia de Val, Claire Lorenzo, Frank McCormick, Dominic Esposito. Biochemical and structural analysis of the neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases [abstract]. In: Proceedings of the AACR Special Conference on Targeting RAS-Driven Cancers; 2018 Dec 9-12; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2020;18(5_Suppl):Abstract nr PR08.

Fully Processed Recombinant KRAS4b: Isolating and Characterizing the Farnesylated and Methylated Protein

Protein prenylation is a key modification that is responsible for targeting proteins to intracellular membranes. KRAS4b, which is mutated in 22% of human cancers, is processed by farnesylation and carboxymethylation due to the presence of a 'CAAX' box motif at the C-terminus. An engineered baculovirus system was used to express farnesylated and carboxymethylated KRAS4b in insect cells and has been described previously. Here, we describe the detailed, practical purification and biochemical characterization of the protein. Specifically, affinity and ion exchange chromatography were used to purify the protein to homogeneity. Intact and native mass spectrometry was used to validate the correct modification of KRAS4b and to verify nucleotide binding. Finally, membrane association of farnesylated and carboxymethylated KRAS4b to liposomes was measured using surface plasmon resonance spectroscopy.

Biochemical and structural analyses reveal that the tumor suppressor neurofibromin (NF1) forms a high-affinity dimer

Neurofibromin is a tumor suppressor encoded by the NF1 gene, which is mutated in Rasopathy disease neurofibromatosis type I. Defects in NF1 lead to aberrant signaling through the RAS–mitogen-activated protein kinase pathway due to disruption of the neurofibromin GTPase-activating function on RAS family small GTPases. Very little is known about the function of most of the neurofibromin protein; to date, biochemical and structural data exist only for its GAP domain and a region containing a Sec-PH motif. To better understand the role of this large protein, here we carried out a series of biochemical and biophysical experiments, including size-exclusion chromatography–multiangle light scattering (SEC-MALS), small-angle X-ray and neutron scattering, and analytical ultracentrifugation, indicating that full-length neurofibromin forms a high-affinity dimer. We observed that neurofibromin dimerization also occurs in human cells and likely has biological and clinical implications. Analysis of purified full-length and truncated neurofibromin variants by negative-stain EM revealed the overall architecture of the dimer and predicted the potential interactions that contribute to the dimer interface. We could reconstitute structures resembling high-affinity full-length dimers by mixing N- and C-terminal protein domains in vitro. The reconstituted neurofibromin was capable of GTPase activation in vitro, and co-expression of the two domains in human cells effectively recapitulated the activity of full-length neurofibromin. Taken together, these results suggest how neurofibromin dimers might form and be stabilized within the cell.

Abstract 1768: Biochemical and structural analysis of the Neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases

Neurofibromin is the 320 kilodalton protein product of the NF1 gene which is mutated in the Rasopathy disease Neurofibromatosis Type I. Defects in NF1 lead to abrogation of the GTPase activating activity of the protein, leading to aberrant signaling through the RAS-MAPK pathway. Very little is known about the function of the majority of the NF1 protein—to date only the GAP domain and a region containing a Sec-PH motif have detailed structural information. To better understand the role of this large protein, we have carried out a series of biochemical and biophysical studies which clearly show that full length NF1 protein exists primarily as a dimer. Data from in vivo experiments confirmed that this dimerization also occurs in cells, and presumably has biological implications. A model was generated from negative-stain EM data which suggests that NF1 monomers form both intermolecular contacts to form dimers and intramolecular contacts which stabilize the individual monomers. Deletion analysis permitted us to map these two interacting domains to different parts of the NF1 protein, and crosslinking studies coupled with mass spectrometry helped to identify regions of possible interaction. In addition, introduction of point mutations observed in patients with NF diseases caused a dramatic decrease in the stability of proteins both in vitro and in vivo, potentially arguing for a rationale for loss of NF1 activity by these single mutations

Citation Format: Mukul Sherekar, Sae-Won Han, Simon Messing, Matthew Drew, William Gillette, Claire Lorenzo, Frank McCormick, Dominic Esposito. Biochemical and structural analysis of the Neurofibromin (NF1) protein and a potential role for protein destabilization in Rasopathy diseases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1768.

KRAS Prenylation Is Required for Bivalent Binding with Calmodulin in a Nucleotide-Independent Manner

Deregulation of KRAS4b signaling pathway has been implicated in 30% of all cancers. Membrane localization of KRAS4b is an essential step for the initiation of the downstream signaling cascades that guide various cellular mechanisms. KRAS4b plasma membrane (PM) binding is mediated by the insertion of a prenylated moiety that is attached to the terminal carboxy-methylated cysteine, in addition to electrostatic interactions of its positively charged hypervariable region with anionic lipids. Calmodulin (CaM) has been suggested to selectively bind KRAS4b to act as a negative regulator of the RAS/mitogen-activated protein kinase (MAPK) signaling pathway by displacing KRAS4b from the membrane. However, the mechanism by which CaM can recognize and displace KRAS4b from the membrane is not well understood. In this study, we employed biophysical and structural techniques to characterize this mechanism in detail. We show that KRAS4b prenylation is required for binding to CaM and that the hydrophobic pockets of CaM can accommodate the prenylated region of KRAS4b, which might represent a novel CaM-binding motif. Remarkably, prenylated KRAS4b forms a 2:1 stoichiometric complex with CaM in a nucleotide-independent manner. The interaction between prenylated KRAS4b and CaM is enthalpically driven, and electrostatic interactions also contribute to the formation of the complex. The prenylated KRAS4b terminal KSKTKC-farnesylation and carboxy-methylation is sufficient for binding and defines the minimal CaM-binding motif. This is the same region implicated in membrane and phosphodiesterase6-δ binding. Finally, we provide a structure-based docking model by which CaM binds to prenylated KRAS4b. Our data provide new insights into the KRAS4b-CaM interaction and suggest a possible mechanism whereby CaM can regulate KRAS4b membrane localization.

Quantitative biophysical analysis defines key components modulating recruitment of the GTPase KRAS to the plasma membrane

The gene encoding the GTPase KRAS is frequently mutated in pancreatic, lung, and colorectal cancers. The KRAS fraction in the plasma membrane (PM) correlates with activation of the mitogen-activated protein kinase (MAPK) pathway and subsequent cellular proliferation. Understanding KRAS's interaction with the PM is challenging given the complexity of the cellular environment. To gain insight into key components necessary for KRAS signal transduction at the PM, we used synthetic membranes such as liposomes and giant unilamellar vesicles. Using surface plasmon resonance (SPR) spectroscopy, we demonstrated that KRAS and Raf-1 proto-oncogene Ser/Thr kinase (RAF1) domains interact with these membranes primarily through electrostatic interactions with negatively charged lipids reinforced by additional interactions involving phosphatidyl ethanolamine and cholesterol. We found that the RAF1 region spanning RBD through CRD (RBDCRD) interacts with the membrane significantly more strongly than the isolated RBD or CRD domains and synergizes KRAS partitioning to the membrane. We also found that calmodulin and phosphodiesterase 6 delta (PDE6δ), but not galectin3 previously proposed to directly interact with KRAS, passively sequester KRAS and prevent it from partitioning into the PM. RAF1 RBDCRD interacted with membranes preferentially at nonraft lipid domains. Moreover, a C-terminal O-methylation was crucial for KRAS membrane localization. These results contribute to a better understanding of how the KRAS-membrane interaction is tuned by multiple factors whose identification could inform drug discovery efforts to disrupt this critical interaction in diseases such as cancer.

Validity and Responsiveness of Generic Preference-based HRQOL Instruments in Chronic Epilepsy

Generic, preference-based instruments are recommended for assessing health-related quality of life (HRQOL) in cost-utility analyses (CUA). We aimed to determine which instrument is the most appropriate for CUA of epilepsy care, using established psychometric criteria. We compared validity and responsiveness of EQ5D (using both UK and US preferences), visual analog scale (VAS), Health Utilities Index Mark II (HUI-2) and Mark III (HUI-3) and SF6D in 165 adults evaluated for epilepsy surgery. SF6D had the strongest or next-strongest associations with seizure severity and seizure control. It was not associated with education or IQ. Only SF6D and HUI-3 discriminated between patients with and without seizures 2 years after baseline evaluation. SF6D was most or next-most responsive to being seizure-free for 2 years, in most responsiveness analyses. VAS was also responsive, but showed less evidence of validity. The QOLIE-89, an epilepsy-targeted profile instrument, had stronger evidence for validity and responsiveness than the preference instruments. SF6D has several key psychometric advantages over four other preference instruments in CUAs of epilepsy care. This may reflect better coverage of HRQOL dimensions affected by epilepsy, greater sensitivity at the upper end of the HRQOL continuum, or both. These findings may not generalize to other chronic conditions.

Validation and psychometric properties of Chinese version of SF-36 in patients with hypertension, coronary heart diseases, chronic gastritis and peptic ulcer

BACKGROUND

The SF-36 is widely used as a significant health outcome or quality of life indicator and validated in many languages versions including Chinese. But the Chinese version of the SF-36 (CSF-36) is rarely used for those patients with hypertension, coronary heart diseases, chronic gastritis and peptic ulcer in China. Therefore, the CSF-36 needs to be validated in patients with chronic diseases.

OBJECTIVES

This paper is aimed to validate the CSF-36 using an in-patient sample of four chronic diseases from mainland China, with focusing on psychometric properties.

METHODS

The CSF-36 was used in a longitudinal study consisting of 534 patients in these four chronic disease groups. The psychometric properties of the scale were evaluated by indicators such as validity and reliability coefficients Cronbach α, Pearson r, standardized response mean employing correlational analyses, multi-trait scaling analysis, t-tests, factor analyses and structural equation models.

RESULTS

Test-retest reliability coefficients for all domains were higher than 0.80 with a range of 0.83 to 0.96; the internal consistency (α) for most domains was higher than 0.70. Five of the eight domains as well as the Physical and Mental Health subscale summaries all had statistically significant changes after treatment with the SRM ranging from 0.18 to 0.28.

CONCLUSION

The CSF-36 showed good validity and reliability but small responsiveness when used in patients. It is a good and useful instrument for patients with chronic disease at some situations.

A laparoscopic approach reduces short-term complications and length of stay following ileocolic resection in Crohn's disease: an analysis of outcomes from the NSQIP database

AIM

Studies to date examining the impact of laparoscopy in resection for Crohn's disease on short-term morbidity have been limited by small study populations. The aim of this study was to establish the impact of the operative approach (laparoscopic or open) on outcomes after ileocolic resection for Crohn's disease.

METHOD

Ileocolic resections for Crohn's disease were identified using Current Procedural Terminology (CPT) and International Classification of Disease, Ninth Revision, Clinical Modification (ICD-9-CM) codes from the National Surgical Quality Improvement Program (NSQIP) database (2005-2009). Complications were categorized as major (organ system damage and systemic sepsis) or minor (incisional and urinary infections). Multivariate 30-day outcomes and length of stay were determined using linear models adjusting for patient characteristics, comorbidities and operative approach.

RESULTS

Of 1917 ileocolic resections, 644 (34%) were performed laparoscopically. At baseline, the open group was significantly older, had more comorbidities, higher American Society of Anesthesiology (ASA) classes, and more intra-operative transfusions (all variables, P<0.05). On multivariate analysis, laparoscopic ileocolic resections were associated with a decrease in major (OR=0.629, 95% CI: 0.430-0.905, P=0.014) and minor (OR=0.576, 95% CI: 0.405-0.804, P=0.002) complications compared with open resections. Laparoscopy was associated with a significant reduction in adjusted length of stay compared with the open approach (-1.08±0.29 days, P=0.0002).

CONCLUSION

After adjusting for comorbidities and perioperative factors, such as preoperative sepsis, higher ASA class and higher transfusion rates in the open group, laparoscopic ileocolic resection for Crohn's disease was found to be a safer choice than the open approach, resulting in fewer complications and length of stay. All other things being equal, such patients should be offered the laparoscopic approach as a first-choice option.

It's the procedure not the patient: the operative approach is independently associated with an increased risk of complications after rectal prolapse repair

AIM

This study compares 30-day outcomes following rectal prolapse repair, examining potential surgical and patient factors associated with perioperative complications.

METHOD

Using the NSQIP database, patients with rectal prolapse were categorized by surgical approach to repair (perineal or abdominal) and abdominal cases were further subdivided by procedure (resection compared with rectopexy alone). Univariate and multivariate analyses compared major and minor complication rates between the groups.

RESULTS

Of 1275 patients, the perineal group (n=706, 55%) was older, with more comorbidity, than those undergoing an abdominal procedure. There were fewer minor (odd ratio (OR)=0.35; 95% confidence interval (CI), 0.20-0.60; P=0.0038) and major complications (OR=0.46; 95% CI, 0.31-0.80; P=0.0038) in the perineal compared with the abdominal cohort. There was a significant increase in major complications amongst patients undergoing a resection compared with rectopexy only (OR=2.15; 95% CI, 1.10-4.41; P=0.0299). There was no difference in major complications between abdominal rectopexy and a perineal approach, but the latter had a lower chance of minor complications (OR=0.47; 95% CI, 0.24-0.94; P=0.0287).

CONCLUSION

A perineal approach is safer than an abdominal approach to the treatment of rectal prolapse. Regarding an abdominal operation, rectopexy has fewer major complications than resection.

Effects of pioglitazone on fasting and postprandial levels of lipid and hemostatic variables in overweight non-diabetic patients with coronary artery disease

OBJECTIVES

To evaluate the effects of pioglitazone on insulin sensitivity and levels of biomarkers associated with thrombotic risk in overweight and obese, non-diabetic subjects with coronary artery disease.

BACKGROUND

Little information is available regarding the effects of thiazolidinediones in the absence of diabetes. Further, although postprandial hyperlipemia is a risk factor for cardiovascular diseases, there is limited information about the postprandial effects.

METHODS

Twenty overweight and obese, non-diabetic patients with coronary artery disease were enrolled in a randomized, placebo-controlled, double-blind study. Subjects were on atorvastatin for the duration of the study and received either placebo or pioglitazone (45 mg day(-1)) for 12 weeks and then crossed over to the alternative therapy for an additional 12 weeks. Insulin sensitivity, fasting and postprandial levels of lipid, hemostatic, and inflammatory variables were measured, and endothelial function was assessed.

RESULTS

Insulin sensitivity improved from 0.03 micromol kg(-1) x min pM(-1) on placebo to 0.04 on pioglitazone (P = 0.0002), and there were decreases in fasting levels of factor (F) VII:C (102 +/- 17% to 92 +/- 18%, P = 0.001), FVII:Ag (68 +/- 12% to 60 +/- 14%, P = 0.01) and in von Willebrand factor (VWF) (174 +/- 94% to 142 +/- 69%, P = 0.01). Pioglitazone lowered postprandial levels of FVII:Ag, FVII:C, plasminogen activator inhibitor-1, VWF, and triglycerides, and increased high-density lipoproteins (+9%, P = 0.02).

CONCLUSIONS

Pioglitazone improves insulin sensitivity and favorably modifies fasting and postprandial lipid, hemostatic and inflammatory markers of the metabolic syndrome in overweight and obese non-diabetic patients with coronary artery disease.

Health care costs decline after successful epilepsy surgery

BACKGROUND

Surgery is an effective, high-cost procedure used increasingly to treat refractory epilepsy. For surgery to be cost-effective, long-term cost savings from reduced health care use should provide some offset to the initial costs of evaluation and surgery. There is little information about how health care costs are affected by evaluation and surgery.

OBJECTIVE

To determine whether health care costs change when seizures become controlled after surgery.

METHODS

Health care costs for the 2 years prior to surgical evaluation and for 2 years afterward were calculated from medical records of 68 subjects with temporal lobe epilepsy (TLE) participating in a multicenter observational study. Costs were compared among patients who did not have surgery, patients who had persisting seizures after surgery, and patients who were seizure free after surgery.

RESULTS

Antiepileptic drugs (AEDs) accounted for more than half of the costs of care in the pre-evaluation period. Total costs for seizure-free patients had declined 32% by 2 years following surgery due to less use of AEDs and inpatient care. Costs did not change in patients with persisting seizures, whether they had surgery or not. In the 18 to 24 months following evaluation, epilepsy-related costs were $2,068 to $2,094 in patients with persisting seizures vs $582 in seizure-free patients.

CONCLUSIONS

Costs remain stable over 2 years post-evaluation in patients with temporal lobe epilepsy whose seizures persist, but patients who become seizure free after surgery use substantially less health care than before surgery. Further cost reductions in seizure-free patients can be expected as antiepileptic drugs are successfully eliminated.

Is skin biopsy a predictor of transition to symptomatic HIV neuropathy?: A longitudinal study

OBJECTIVE

To investigate whether serially assessed epidermal nerve fiber (ENF) density and quantitative sensory thresholds (QSTs) are associated with the clinical transition from HIV infection with no neuropathy or asymptomatic neuropathy to symptomatic distal sensory neuropathy (SDSP).

BACKGROUND

Identifying predictors of transition to SDSP would enable identification of subjects at enhanced risk for development of HIV-SDSP and facilitate intervention studies with the ultimate goal of disease prevention. Asymptomatic signs of sensory dysfunction in the feet have been shown to be weakly predictive of SDSP; however, bedside evaluation of small sensory fibers is limited. Abnormality of these fibers may play an important role in the genesis of SDSP.

METHODS

Fifty-eight HIV-infected subjects underwent serial clinical, virologic, immunologic, skin biopsy, and QST assessments. Cox proportional hazards modeling was used to examine the associations of serial ENF density and QST assessments with the risk of development of SDSP among the subset of 26 subjects who had asymptomatic or no neuropathy at study entry.

RESULTS

Median follow-up was 2.9 years (range 6 months to 4.5 years) during which 19 of 26 subjects transitioned to SDSP. Using a model where ENF density and QST measures from the study visit before potential transition were examined, a lower leg ENF density, a higher cooling threshold, and a higher heat pain threshold for minimal pain (HP 0.5) were associated with a greater risk of SDSP in univariate analyses. In multiple regression analyses, leg ENF density but not QST measures were significantly associated with SDSP. A leg ENF density of 10 fibers/mm or less conferred a 14-fold greater risk of SDSP than a leg ENF density greater than 10 fibers/mm.

CONCLUSIONS

Measures of small sensory fibers (leg epidermal nerve fiber density, cooling and heat pain thresholds) seem to be associated with transition to symptomatic HIV-associated distal sensory neuropathy 6 to 12 months later.

A clinical rating scale for Batten disease: Reliable and relevant for clinical trials

BACKGROUND

Batten disease (juvenile neuronal ceroid lipofuscinosis [JNCL]) is an autosomal recessive neurodegenerative disorder characterized by blindness, seizures, and relentless decline in cognitive, motor, and behavioral function. Onset is in the early school years, with progression to death typically by late adolescence. Development of a clinical instrument to quantify severity of illness is a prerequisite to eventual assessment of experimental therapeutic interventions.

OBJECTIVE

To develop a clinical rating instrument to assess motor, behavioral, and functional capability in JNCL.

METHODS

A clinical rating instrument, the Unified Batten Disease Rating Scale (UBDRS), was developed by the authors to assess motor, behavioral, and functional capability in JNCL. Children with verified JNCL were evaluated independently by three neurologists. Intraclass correlation coefficients (ICCs) were used to estimate the interrater reliability for total scores in each domain. Interrater reliability for scale items was assessed with weighted kappa statistics.

RESULTS

Thirty-one children with confirmed JNCL (10 boys, 21 girls) were evaluated. The mean age at symptom onset was 6.1 +/- 1.6 years, and the mean duration of illness was 9.0 +/- 4.4 years. The ICCs for the domains were as follows: motor = 0.83, behavioral = 0.68, and functional capability = 0.85.

CONCLUSIONS

The Unified Batten Disease Rating Scale (UBDRS) is a reliable instrument that effectively tests for neurologic function in blind and demented patients. In its current form, the UBDRS is useful for monitoring the diverse clinical findings seen in Batten disease.

Broad support sought for emerging specialty of orofacial pain

The American Dental Association is considering giving the emerging field of orofacial pain full status as a new dental specialty. Many recent advances in the neuroscience of orofacial pain have lead to treatments by orofacial pain dentists that provide significant relief for patients with chronic disorders. However, access to this care has been limited, leaving many patients to continue to suffer. Recent efforts to improve this situation by developing the field into a specialty have received broad support among dentists and have increased awareness of the benefits this field can provide for dentists and their patients.

Arthrographically assisted splint therapy: a 6-month follow-up

After repositioning splint therapy, 51 patients were evaluated for a minimum of 6 months. Forty-five (88%) of the patients were considered to have been treated successfully, whereas six (12%) patients required surgery to correct meniscal displacement. A detailed analysis of signs and symptoms before and after splint treatment is in progress.