Unveiling the proteome-wide autoreactome enables enhanced evaluation of emerging CAR T cell therapies in autoimmunity.

Given the global surge in autoimmune diseases, it is critical to evaluate emerging therapeutic interventions. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leveraged advances in programmable-phage immunoprecipitation methodology to explore the modulation, or lack thereof, of autoantibody profiles, proteome-wide, in both health and disease. Using a custom set of over 730,000 human-derived peptides, we demonstrated that each individual, regardless of disease state, possesses a distinct and complex constellation of autoreactive antibodies. For each individual, the set of resulting autoreactivites constituted a unique immunological fingerprint, or "autoreactome," that was remarkably stable over years. Using the autoreactome as a primary output, we evaluated the relative effectiveness of various immunomodulatory therapies in altering autoantibody repertoires. We found that therapies targeting B cell maturation antigen (BCMA) profoundly altered an individual's autoreactome, while anti-CD19 and anti-CD20 therapies had minimal effects. These data both confirm that the autoreactome comprises autoantibodies secreted by plasma cells and strongly suggest that BCMA or other plasma cell-targeting therapies may be highly effective in treating currently refractory autoantibody-mediated diseases.

Sex and gender essentialism in textbooks.

Several widely used high school biology texts depart from established science.

Humane genomics education can reduce racism.

Moving instruction "beyond Mendel" can counter inaccurate, essentialist views.

Identification of a small molecule for enhancing lentiviral transduction of T cells.

Genetic modification of cells using viral vectors has shown huge therapeutic benefit in multiple diseases. However, inefficient transduction contributes to the high cost of these therapies. Several transduction-enhancing small molecules have previously been identified; however, some may be toxic to the cells or patient, otherwise alter cellular characteristics, or further increase manufacturing complexity. In this study, we aimed to identify molecules capable of enhancing lentiviral transduction of T cells from available small-molecule libraries. We conducted a high-throughput flow-cytometry-based screen of 27,892 compounds, which subsequently was narrowed down to six transduction-enhancing small molecules for further testing with two therapeutic lentiviral vectors used to manufacture GSK's clinical T cell therapy products. We demonstrate enhanced transduction without a negative impact on other product attributes. Furthermore, we present results of transcriptomic analysis, suggesting alteration of ribosome biogenesis, resulting in reduced interferon response, as a potential mechanism of action for the transduction-enhancing activity of the lead compound. Finally, we demonstrate the ability of the lead transduction enhancer to produce a comparable T cell product using a 3-fold reduction in vector volume in our clinical manufacturing process, resulting in a predicted 15% reduction in the overall cost of goods.

Motor Competence Among Irish Adolescents: An Investigation of Sex Differences and Relatedness Between Fundamental Movement Skills and Functional Movement.

In prior research, Irish youth displayed poor motor competence across fundamental movement skills (FMS) and functional movements (FM). Our purpose in this study was to compare FMS and FM across male and female Irish adolescents and to determine whether there are associations between these movement domains. We collected data on 373 adolescents (178 females; M age = 14.38, SD = 0.87 years) from six Irish secondary schools, including motor competence testing of 10 FMS, and 7 FM. Overall levels of motor competence of both FMS and FM were low, and certain levels of dysfunctional movement were high. We observed significant sex-based differences in both FMS and FM, and there was a moderate association between FMS and FM that warrants further investigation. There is a need for societal intervention and policy changes to address low levels of motor competence among adolescent youth.

Unveiling the autoreactome: Proteome-wide immunological fingerprints reveal the promise of plasma cell depleting therapy.

The prevalence and burden of autoimmune and autoantibody mediated disease is increasing worldwide, yet most disease etiologies remain unclear. Despite numerous new targeted immunomodulatory therapies, comprehensive approaches to apply and evaluate the effects of these treatments longitudinally are lacking. Here, we leverage advances in programmable-phage immunoprecipitation (PhIP-Seq) methodology to explore the modulation, or lack thereof, of proteome-wide autoantibody profiles in both health and disease. We demonstrate that each individual, regardless of disease state, possesses a distinct set of autoreactivities constituting a unique immunological fingerprint, or "autoreactome", that is remarkably stable over years. In addition to uncovering important new biology, the autoreactome can be used to better evaluate the relative effectiveness of various therapies in altering autoantibody repertoires. We find that therapies targeting B-Cell Maturation Antigen (BCMA) profoundly alter an individual's autoreactome, while anti-CD19 and CD-20 therapies have minimal effects, strongly suggesting a rationale for BCMA or other plasma cell targeted therapies in autoantibody mediated diseases.

Mendelian or Multifactorial? Current Undergraduate Genetics Assessments Focus on Genes and Rarely Include the Environment.

Undergraduate genetics courses have historically focused on simple genetic models, rather than taking a more multifactorial approach where students explore how traits are influenced by a combination of genes, the environment, and gene-by-environment interactions. While a focus on simple genetic models can provide straightforward examples to promote student learning, they do not match the current scientific understanding and can result in deterministic thinking among students. In addition, undergraduates are often interested in complex human traits that are influenced by the environment, and national curriculum standards include learning objectives that focus on multifactorial concepts. This research aims to discover to what extent multifactorial genetics is currently being assessed in undergraduate genetics courses. To address this, we analyzed over 1,000 assessment questions from a commonly used undergraduate genetics textbook; published concept assessments; and open-source, peer-reviewed curriculum materials. Our findings show that current genetics assessment questions overwhelmingly emphasize the impact of genes on phenotypes and that the effect of the environment is rarely addressed. These results indicate a need for the inclusion of more multifactorial genetics concepts, and we suggest ways to introduce them into undergraduate courses.

Unwrapping a full temporal cycle in time domain thermoreflectance for enhanced measurement sensitivity in thermally insulating materials.

Time delayed pump-probe measurement techniques, such as Time Domain Thermoreflectance (TDTR), have opened up a wealth of opportunities for metrology at ultra-fast timescales and nanometer length scales. For nanoscale thermal transport measurements, typical thermal lifetimes used to measure thermal conductivity and thermal boundary conductance span from sub-picosecond to ∼6 nanoseconds. In this work, we demonstrate a simple rearrangement and validation of a configuration that allows access to the entire 12.5 ns time delay available in the standard pulse train. By reconfiguring a traditional TDTR system so that the pump and probe arrive concurrently when the delay stage reaches its midpoint, followed by unwrapping the temporal scan, we obtain a dataset that is bounded only by the oscillator repetition rate. Sensitivity analysis along with conducted measurements shows that great increases in measurement sensitivity are available with this approach, particularly for thin films with low thermal conductivities.

Photoacoustic imaging of posterior periodontal pocket using a commercial hockey-stick transducer.

SIGNIFICANCE: Photoacoustic imaging has shown advantages over the periodontal probing method in measuring the periodontal probing depth, but the large size of conventional photoacoustic transducers prevents imaging of the more posterior teeth. AIM: Our aim is to develop a photoacoustic imaging system to image the more posterior periodontal pocket. APPROACH: We report a clinical "hockey-stick"-style transducer integrated with fibers for periodontal photoacoustic imaging. Cuttlefish ink labeled the periodontal pocket as the photoacoustic contrast agent. RESULTS: We characterized the imaging system and then measured the pocket depth of 35 swine teeth. Three raters evaluated the performance of the hockey-stick transducer. The measurements between the Williams probing (gold standard) and the photoacoustic methods were blinded but highly correlated. We showed a bias of ∼0.3 mm for the imaging-based technique versus Williams probing. The minimum inter-reliability was over 0.60 for three different raters of varying experience, suggesting that this approach to measure the periodontal pocket is reproducible. Finally, we imaged three pre-molars of a human subject. We could access more upper and posterior teeth than conventional linear transducers. CONCLUSIONS: The unique angle shape of the hockey-stick transducer allows it to image more posterior teeth than regular linear transducers. This study demonstrated the ability of a hockey-stick transducer to measure the periodontal pocket via photoacoustic imaging.

Peptide-Induced Fractal Assembly of Silver Nanoparticles for Visual Detection of Disease Biomarkers.

We report the peptide-programmed fractal assembly of silver nanoparticles (AgNPs) in a diffusion-limited aggregation (DLA) mode, and this change in morphology generates a significant color change. We show that peptides with specific repetitions of defined amino acids (i.e., arginine, histidine, or phenylalanine) can induce assembly and coalescence of the AgNPs (20 nm) into a hyperbranched structure (AgFSs) (∼2 µm). The dynamic process of this assembly was systematically investigated, and the extinction of the nanostructures can be modulated from 400 to 600 nm by varying the peptide sequences and molar ratio. According to this rationale, two strategies of SARS-CoV-2 detection were investigated. The activity of the main protease (Mpro) involved in SARS-CoV-2 was validated with a peptide substrate that can bridge the AgNPs after the proteolytic cleavage. A sub-nanomolar limit of detection (0.5 nM) and the capacity to distinguish by the naked eye in a wide concentration range (1.25-30 nM) were achieved. Next, a multichannel sensor-array based on multiplex peptides that can visually distinguish SARS-CoV-2 proteases from influenza proteases in doped human samples was investigated.

Ending genetic essentialism through genetics education.

Genetic concepts are regularly used in arguments about racial inequality. This review summarizes research about the relationship between genetics education and a particular form of racial prejudice known as genetic essentialism. Genetic essentialism is a cognitive form of prejudice that is used to rationalize inequality. Studies suggest that belief in genetic essentialism among genetics students can be increased or decreased based on what students learn about human genetics and why they learn it. Research suggests that genetics education does little to prevent the development of genetic essentialism, and it may even exacerbate belief in it. However, some forms of genetics education can avert this problem. In particular, if instructors teach genetics to help students understand the flaws in genetic essentialist arguments, then it is possible to reduce belief in genetic essentialism among biology students. This review outlines our knowledge about how to accomplish this goal and the research that needs to be done to end genetic essentialism through genetics education.

Photoacoustic monitoring of angiogenesis predicts response to therapy in healing wounds.

Chronic wounds are a major health problem that cause the medical infrastructure billions of dollars every year. Chronic wounds are often difficult to heal and cause significant discomfort. Although wound specialists have numerous therapeutic modalities at their disposal, tools that could three dimensional-map wound bed physiology and guide therapy do not exist. Visual cues are the current standard but are limited to surface assessment; clinicians rely on experience to predict response to therapy. Photoacoustic (PA) ultrasound (US) is a non-invasive, hybrid imaging modality that can solve these major limitations. PA relies on the contrast generated by haemoglobin in blood which allows it to map local angiogenesis, tissue perfusion and oxygen saturation-all critical parameters for wound healing. This work evaluates the use of PA-US to monitor angiogenesis and stratify patients responding versus not-responding to therapy. We imaged 19 patients with 22 wounds once a week for at least 3 weeks. Our findings suggest that PA imaging directly visualises angiogenesis. Patients responding to therapy showed clear signs of angiogenesis and an increased rate of PA increase (p = 0.002). These responders had a significant and negative correlation between PA intensity and wound size. Hypertension was correlated to impaired angiogenesis in non-responsive patients. The rate of PA increase and hence the rate of angiogenesis was able to predict healing times within 30 days from the start of monitoring (power = 88%, alpha = 0.05). This early response detection system could help inform management and treatment strategies while improving outcomes and reducing costs.

Effects of an 8-Week Intervention Targeting the Veridicality of Actual and Perceived Motor Competence Among Irish Adolescents in Project FLAME.

High levels of perceived motor competence and low levels of actual motor competence in youth populations have been reported world-wide. Both perceived and actual motor competence have been deemed independent correlates of health and physical activity (PA) behavior, and past research has indicated that their alignment may be linked to more consistent PA. Moreover, there is potential for a movement-based intervention to strengthen the alignment between perceived and actual motor competence, perhaps then guiding future health, PA, and community sport engagement globally. Thus, the objective of this study was to investigate the effectiveness of an 8-week movement-based intervention on increasing the alignment (i.e., veridicality) between PMC and AMC among Irish adolescent youth. We collected data on adolescents (n = 324; females = 149; M age = 14.5, SD = 0.88 years) across six second-level schools in Ireland, including measurements of actual and perceived, motor competence at pre- and post-intervention. We observed low levels of actual in contrast to high levels of perceived motor competence. We found a small but significant veridical alignment between perceived and actual motor competence, but there was no intervention effect on alignment. Future research should prioritize a longer intervention duration that targets student learning and understanding in order to develop veridical perceptions in adolescents that might sustain their participation in PA.

Deep profiling of protease substrate specificity enabled by dual random and scanned human proteome substrate phage libraries.

Proteolysis is a major posttranslational regulator of biology inside and outside of cells. Broad identification of optimal cleavage sites and natural substrates of proteases is critical for drug discovery and to understand protease biology. Here, we present a method that employs two genetically encoded substrate phage display libraries coupled with next generation sequencing (SPD-NGS) that allows up to 10,000-fold deeper sequence coverage of the typical six- to eight-residue protease cleavage sites compared to state-of-the-art synthetic peptide libraries or proteomics. We applied SPD-NGS to two classes of proteases, the intracellular caspases, and the ectodomains of the sheddases, ADAMs 10 and 17. The first library (Lib 10AA) allowed us to identify 104 to 105 unique cleavage sites over a 1,000-fold dynamic range of NGS counts and produced consensus and optimal cleavage motifs based position-specific scoring matrices. A second SPD-NGS library (Lib hP), which displayed virtually the entire human proteome tiled in contiguous 49 amino acid sequences with 25 amino acid overlaps, enabled us to identify candidate human proteome sequences. We identified up to 104 natural linear cut sites, depending on the protease, and captured most of the examples previously identified by proteomics and predicted 10- to 100-fold more. Structural bioinformatics was used to facilitate the identification of candidate natural protein substrates. SPD-NGS is rapid, reproducible, simple to perform and analyze, inexpensive, and renewable, with unprecedented depth of coverage for substrate sequences, and is an important tool for protease biologists interested in protease specificity for specific assays and inhibitors and to facilitate identification of natural protein substrates.

High-resolution epitope mapping of anti-Hu and anti-Yo autoimmunity by programmable phage display.

Paraneoplastic neurological disorders are immune-mediated diseases understood to manifest as part of a misdirected anti-tumor immune response. Paraneoplastic neurological disorder-associated autoantibodies can assist with diagnosis and enhance our understanding of tumor-associated immune processes. We designed a comprehensive library of 49-amino-acid overlapping peptides spanning the entire human proteome, including all splicing isoforms and computationally predicted coding regions. Using this library, we optimized a phage immunoprecipitation and sequencing protocol with multiple rounds of enrichment to create high-resolution epitope profiles in serum and cerebrospinal fluid (CSF) samples from patients suffering from two common paraneoplastic neurological disorders, the anti-Yo (n = 36 patients) and anti-Hu (n = 44 patients) syndromes. All (100%) anti-Yo patient samples yielded enrichment of peptides from the canonical anti-Yo (CDR2 and CDR2L) antigens, while 38% of anti-Hu patients enriched peptides deriving from the nELAVL (neuronal embryonic lethal abnormal vision like) family of proteins, the anti-Hu autoantigenic target. Among the anti-Hu patient samples that were positive for nELAVL, we noted a restricted region of immunoreactivity. To achieve single amino acid resolution, we designed a novel deep mutational scanning phage library encoding all possible single-point mutants targeting the reactive nELAVL region. This analysis revealed a distinct preference for the degenerate motif, RLDxLL, shared by ELAVL2, 3 and 4. Lastly, phage immunoprecipitation sequencing identified several known autoantigens in these same patient samples, including peptides deriving from the cancer-associated antigens ZIC and SOX families of transcription factors. Overall, this optimized phage immunoprecipitation sequencing library and protocol yielded the high-resolution epitope mapping of the autoantigens targeted in anti-Yo and anti-Hu encephalitis patients to date. The results presented here further demonstrate the utility and high-resolution capability of phage immunoprecipitation sequencing for both basic science and clinical applications and for better understanding the antigenic targets and triggers of paraneoplastic neurological disorders.

Investigating the Age-Related Association between Perceived Motor Competence and Actual Motor Competence in Adolescence.

Irish adolescents have been found to possess high perceptions of motor competence. However, there is an evidential value to investigating the strength of the relationship between adolescent perceptions of motor competence and their low levels of actual motor competence. The purpose of this research was to gather data on the fundamental, functional, and perceived motor competence in adolescents, differentiated by year group, to discern if participants could assess their perceptions of ability. Data were collected on adolescents (N = 373; mean age: 14.38 ± 0.87 years; 47.7% female) across six second-level schools in Ireland, including measurements of fundamental movement skills, functional movement, and perceived motor competence. Poor levels of fundamental and functional movement were observed, with significant differences between year groups detected. Participants in 1st year scored the highest in overall fundamental movement skills; however, for overall functional movement, 3rd-year participants scored highest. High levels of perceived motor competence were reported across the entire sample. These scores did not align with actual motor competence, nor did any alignment between these measurements improve with aging, countering theorized age-related associations. Future research should target low levels of actual motor competence while emphasizing the cognitive aspects of movement to ensure greater accuracy between actual and perceived motor competence.

Correction to Identification of Quinoline-Based RIP2 Kinase Inhibitors with an Improved Therapeutic Index to the hERG Ion Channel.

[This corrects the article DOI: 10.1021/acsmedchemlett.8b00344.].

Materials as Machines.

Machines are systems that harness input power to extend or advance function. Fundamentally, machines are based on the integration of materials with mechanisms to accomplish tasks-such as generating motion or lifting an object. An emerging research paradigm is the design, synthesis, and integration of responsive materials within or as machines. Herein, a particular focus is the integration of responsive materials to enable robotic (machine) functions such as gripping, lifting, or motility (walking, crawling, swimming, and flying). Key functional considerations of responsive materials in machine implementations are response time, cyclability (frequency and ruggedness), sizing, payload capacity, amenability to mechanical programming, performance in extreme environments, and autonomy. This review summarizes the material transformation mechanisms, mechanical design, and robotic integration of responsive materials including shape memory alloys (SMAs), piezoelectrics, dielectric elastomer actuators (DEAs), ionic electroactive polymers (IEAPs), pneumatics and hydraulics systems, shape memory polymers (SMPs), hydrogels, and liquid crystalline elastomers (LCEs) and networks (LCNs). Structural and geometrical fabrication of these materials as wires, coils, films, tubes, cones, unimorphs, bimorphs, and printed elements enables differentiated mechanical responses and consistently enables and extends functional use.