A cost-consequence model of using the 21-gene assay to identify patients with early-stage node-positive breast cancer who benefit from adjuvant chemotherapy in the Netherlands.

BACKGROUND: Patients with early-stage hormone receptor positive, human epidermal growth factor receptor-2 (HER2) negative invasive breast cancer with 1-3 positive lymph nodes (N1) often undergo surgical excisions followed by adjuvant chemotherapy (ACT). Many patients have no benefit from ACT and receive unnecessary, costly treatment often associated with short- and long-term adverse events (AEs). Gene expression profiling (GEP) assays, such as the 21-gene assay (i.e. the Oncotype DX assay), can identify patients at higher risk for recurrence who may benefit from ACT. However, the budgetary consequence of using the Oncotype DX assay versus no GEP testing in the Netherlands is unknown. Our study therefore assessed it using a cost-consequence model. METHODS: A validated model was used to create the N1 model. The model compared the costs and consequences of using the Oncotype DX assay versus no GEP testing and MammaPrint, and subsequent ACT use with corresponding costs for chemotherapy, treatment of AEs, productivity losses, GEP testing, and treatment of recurrences, according to the Oncotype DX results. The model time horizon was 5 years. RESULTS: Costs for the total population amounted to €8.0 million (M), €16.2 M, and €9.5 M, and cost per patient amounted to €13,540, €27,455, and €16,154 for using the Oncotype DX assay, no GEP testing, and MammaPrint, respectively. Total cost savings of using the Oncotype DX assay amounted to €8.2 M versus no GEP testing and €1.5 M versus MammaPrint. Using the Oncotype DX assay would result in fewer patients receiving ACT and thus fewer AEs, sick days, and hospitalizations, leading to overall cost savings compared with no GEP testing and MammaPrint. CONCLUSIONS: Implementing Oncotype DX testing in this population can prevent unnecessary overtreatment, reducing clinical and economic burden on the patient and Dutch healthcare system.

Early-stage invasive breast cancer patients often undergo surgery followed by adjuvant chemotherapy. However, many of these patients have no benefit from adjuvant chemotherapy and thus receive unnecessary and costly treatment often associated with side-effects. Patients who may benefit from adjuvant chemotherapy can be identified by analyzing the genomic profile of the patients' tumors using a molecular diagnostic test called the 21-gene assay (also known as Oncotype DX assay). However, the budgetary consequences of using Oncotype DX for this purpose in the Netherlands are currently unknown and, therefore, assessed using a health-economic model. The model compared the costs and consequences of using the Oncotype DX assay versus no molecular diagnostic testing and an alternative molecular diagnostic test called MammaPrint. The three diagnostic testing strategies resulted in different costs in terms of several different costing categories and were compared with one another. The total costs were lowest for the diagnostic strategy using the Oncotype DX assay, as it would result in fewer patients receiving adjuvant chemotherapy compared with no molecular diagnostic testing and MammaPrint. Implementing the Oncotype DX assay as a molecular diagnostic test can identify the right patient who benefits from chemotherapy (prevent over- and undertreatment) and lead to cost-savings, reducing the clinical and economic burden on the patient and Dutch healthcare system.

AlphaFold accurately predicts distinct conformations based on the oligomeric state of a de novo designed protein.

Using the molecular modeling program Rosetta, we designed a de novo protein, called SEWN0.1, which binds the heterotrimeric G protein Gαq. The design is helical, well-folded, and primarily monomeric in solution at a concentration of 10 µM. However, when we solved the crystal structure of SEWN0.1 at 1.9 Å, we observed a dimer in a conformation incompatible with binding Gαq . Unintentionally, we had designed a protein that adopts alternate conformations depending on its oligomeric state. Recently, there has been tremendous progress in the field of protein structure prediction as new methods in artificial intelligence have been used to predict structures with high accuracy. We were curious if the structure prediction method AlphaFold could predict the structure of SEWN0.1 and if the prediction depended on oligomeric state. When AlphaFold was used to predict the structure of monomeric SEWN0.1, it produced a model that resembles the Rosetta design model and is compatible with binding Gαq , but when used to predict the structure of a dimer, it predicted a conformation that closely resembles the SEWN0.1 crystal structure. AlphaFold's ability to predict multiple conformations for a single protein sequence should be useful for engineering protein switches.

Associations Between Online Pornography Consumption and Sexual Dysfunction in Young Men: Multivariate Analysis Based on an International Web-Based Survey.

BACKGROUND: Expanding access to the internet has resulted in more and earlier consumption of online pornography. At the same time, a higher prevalence of erectile dysfunction (ED) among young men is seen. Increased pornography consumption has been suggested as a possible explanation for this rise. OBJECTIVE: The aim of this study was to better understand associations between problematic pornography consumption (PPC) and ED. METHODS: A 118-item survey was published online, and data collection took place between April 2019 and May 2020. Of the 5770 men who responded, the responses from 3419 men between 18 years old and 35 years old were analyzed. The survey used validated questionnaires such as the Cyber Pornography Addiction Test (CYPAT), International Index of Erectile Function (IIEF-5), and Alcohol Use Disorders Identification Test-Concise (AUDIT-C). The estimated amount of porn watching was calculated. Univariable and multivariable analyses were performed. For the multivariable analysis, a logistic regression model using a directed acyclic graph was used. RESULTS: According to their IIEF-5 scores, 21.48% (444/2067) of our sexually active participants (ie, those who attempted penetrative sex in the previous 4 weeks) had some degree of ED. Higher CYPAT scores indicating problematic online pornography consumption resulted in a higher probability of ED, while controlling for covariates. Masturbation frequency seemed not to be a significant factor when assessing ED. CONCLUSIONS: This prevalence of ED in young men is alarmingly high, and the results of this study suggest a significant association with PPC. TRIAL REGISTRATION: Research Registry researchregistry5111; https://tinyurl.com/m45mcaa2.

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and extended. Its advantages are its performance and interoperability between broad modeling capabilities. Here we review tools developed in the last 5 years, including over 80 methods. We discuss improvements to the score function, user interfaces and usability. Rosetta is available at http://www.rosettacommons.org.

Structure of an anti-PEG antibody reveals an open ring that captures highly flexible PEG polymers.

Polyethylene glycol (PEG) is a polymer routinely used to modify biologics and nanoparticles to prolong blood circulation and reduce immunogenicity of the underlying therapeutic. However, several PEGylated therapeutics induce the development of anti-PEG antibodies (APA), leading to reduced efficacy and increased adverse events. Given the highly flexible structure of PEG, how APA specifically bind PEG remains poorly understood. Here, we report a crystal structure illustrating the structural properties and conformation of the APA 6-3 Fab bound to the backbone of PEG. The structure reveals an open ring-like sub-structure in the Fab paratope, whereby PEG backbone is captured and then stabilized via Van der Waals interactions along the interior and exterior of the ring paratope surface. Our finding illustrates a strategy by which antibodies can bind highly flexible repeated structures that lack fixed conformations, such as polymers. This also substantially advances our understanding of the humoral immune response generated against PEG.

Engineering Polymer-Binding Bispecific Antibodies for Enhanced Pretargeted Delivery of Nanoparticles to Mucus-Covered Epithelium.

Mucus represents a major barrier to sustained and targeted drug delivery to mucosal epithelium. Ideal drug carriers should not only rapidly diffuse across mucus, but also bind the epithelium. Unfortunately, ligand-conjugated particles often exhibit poor penetration across mucus. In this work, we explored a two-step "pretargeting" approach through engineering a bispecific antibody that binds both cell-surface ICAM-1 and polyethylene glycol (PEG) on the surface of nanoparticles, thereby effectively decoupling cell targeting from particle design and formulation. When tested in a mucus-coated Caco-2 culture model that mimics the physiological process of mucus clearance, pretargeting increased the amount of PEGylated particles binding to cells by around 2-fold or more compared to either non-targeted or actively targeted PEGylated particles. Pretargeting also markedly enhanced particle retention in mouse intestinal tissues. Our work underscores pretargeting as a promising strategy to improve the delivery of therapeutics to mucosal surfaces.

Computational Design of Protein Linkers.

Naturally occurring proteins often consist of multiple distinct domains joined by linker regions. Similarly, the ability to combine globular protein domains through engineered linkers would allow the creation of a wide variety of complex and useful multifunctional proteins. Recent advances in computational design of protein structures have enabled highly accurate design of novel protein structures. In this chapter we outline a computational protocol for the de novo design of protein linkers, and apply this protocol to the design of a helical linker between two rigid protein domains.

UbSRD: The Ubiquitin Structural Relational Database.

The structurally defined ubiquitin-like homology fold (UBL) can engage in several unique protein-protein interactions and many of these complexes have been characterized with high-resolution techniques. Using Rosetta's structural classification tools, we have created the Ubiquitin Structural Relational Database (UbSRD), an SQL database of features for all 509 UBL-containing structures in the PDB, allowing users to browse these structures by protein-protein interaction and providing a platform for quantitative analysis of structural features. We used UbSRD to define the recognition features of ubiquitin (UBQ) and SUMO observed in the PDB and the orientation of the UBQ tail while interacting with certain types of proteins. While some of the interaction surfaces on UBQ and SUMO overlap, each molecule has distinct features that aid in molecular discrimination. Additionally, we find that the UBQ tail is malleable and can adopt a variety of conformations upon binding. UbSRD is accessible as an online resource at rosettadesign.med.unc.edu/ubsrd.

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.

Computational protein design has found great success in engineering proteins for thermodynamic stability, binding specificity, or enzymatic activity in a 'single state' design (SSD) paradigm. Multi-specificity design (MSD), on the other hand, involves considering the stability of multiple protein states simultaneously. We have developed a novel MSD algorithm, which we refer to as REstrained CONvergence in multi-specificity design (RECON). The algorithm allows each state to adopt its own sequence throughout the design process rather than enforcing a single sequence on all states. Convergence to a single sequence is encouraged through an incrementally increasing convergence restraint for corresponding positions. Compared to MSD algorithms that enforce (constrain) an identical sequence on all states the energy landscape is simplified, which accelerates the search drastically. As a result, RECON can readily be used in simulations with a flexible protein backbone. We have benchmarked RECON on two design tasks. First, we designed antibodies derived from a common germline gene against their diverse targets to assess recovery of the germline, polyspecific sequence. Second, we design "promiscuous", polyspecific proteins against all binding partners and measure recovery of the native sequence. We show that RECON is able to efficiently recover native-like, biologically relevant sequences in this diverse set of protein complexes.

Data in support of UbSRD: The Ubiquitin Structural Relational Database.

This article provides information to support the database article titled "UbSRD: The Ubiquitin Structural Relational Database" (Harrison et al., 2015) [1] . The ubiquitin-like homology fold (UBL) represents a large family that encompasses both post-translational modifications, like ubiquitin (UBQ) and SUMO, and functional domains on many biologically important proteins like Parkin, UHRF1 (ubiquitin-like with PDB and RING finger domains-1), and Usp7 (ubiquitin-specific protease-7) (Zhang et al., 2015; Rothbart et al., 2013; Burroughs et al., 2012; Wauer et al., 2015) [2], [3], [4], [5]. The UBL domain can participate in several unique protein-protein interactions (PPI) since protein adducts can be attached to and removed from amino groups of lysine side chains and the N-terminus of proteins. Given the biological significance of UBL domains, many have been characterized with high-resolution techniques, and for UBQ and SUMO, many protein complexes have been characterized. We identified all the UBL domains in the PDB and created a relational database called UbSRD (Ubiquitin Structural Relational Database) by using structural analysis tools in the Rosetta (Leaver et al., 2013; O'Meara et al., 2015; Leaver-fay et al., 2011) [1], [6], [7], [8]. Querying UbSRD permitted us to report many quantitative properties of UBQ and SUMO recognition at different types interfaces (noncovalent: NC, conjugated: CJ, and deubiquitanse: DB). In this data article, we report the average number of non-UBL neighbors, secondary structure of interacting motifs, and the type of inter-molecular hydrogen bonds for each residue of UBQ and SUMO. Additionally, we used PROMALS3D to generate a multiple sequence alignment used to construct a phylogram for the entire set of UBLs (Pei and Grishin, 2014) [9]. The data described here will be generally useful to scientists studying the molecular basis for recognition of UBQ or SUMO.

Identification and characterization of the chicken galanin receptor GalR2 and a novel GalR2-like receptor (GalR2-L).

In mammals, the neuropeptide galanin exerts a variety of physiological roles in the neuroendocrine system through its interactions with three galanin receptor subtypes (GalR1, GalR2 and GalR3). However, little is known about the characteristics of galanin receptors in birds, and it is only recently that avian GalR1 and a novel GalR1-like receptor were first identified in chickens. In this study, we report the cDNA cloning and characterization of the other two chicken galanin receptors, the galanin type II receptor (cGalR2) and a novel GalR2-like receptor (GalR2-L), which share high degrees of similarity in sequence identity, gene structure and signaling properties. cGalR2 and cGalR2-L cDNAs encode two putative receptors of 371 and 370 amino acids, in which they show considerable amino acid sequence identities (65-67%, and 53-55%, respectively) with the mammalian GalR2. RT-PCR assays revealed that cGalR2 and cGalR2-L mRNA were widely expressed in the adult chicken tissues including the whole brain, intestine, lung, ovary, pituitary and different regions of the oviduct. As assayed with different luciferase reporter systems, chicken galanin (cGal 1-29) and human galanin-like peptide (hGALP 1-60) were demonstrated to stimulate the luciferase activities in Chinese hamster ovary cells expressing cGalR2 and cGalR2-L through the activations of cAMP/PKA, Ca(2+)/calcineurin and MAPK/ERK signaling pathways, hence suggesting that both receptors are functionally coupled to the G(s) and G(q) proteins. Furthermore, the previously identified cGalR1 and cGalR1-L were found to be solely coupled to the G(i/o) proteins, and the hGALP (1-60) exhibited only a low potency to cGalR1, cGalR1-L, cGalR2 and cGalR2-L activations.

Fluctuation symmetries for work and heat.

We consider a particle dragged through a medium at constant temperature as described by a Langevin equation with a time-dependent potential. The time dependence is specified by an external protocol. We give conditions on potential and protocol under which the fluctuations of the dissipative work satisfy an exact symmetry for all times. We also present counterexamples to that fluctuation theorem when our conditions are not satisfied. Finally, we consider the dissipated heat, which differs from the work by a temporal boundary term. We explain why there is a correction to the standard fluctuation theorem due to the unboundedness of that temporal boundary. However, the corrected fluctuation relation has again a general validity.