bluuebunny/crossref_metadata_2025 huggingface dataset:
Gastric Alimetry®improves patient phenotyping in gastroduodenal disorders compared to gastric emptying scintigraphy alone
Authors: Wang William Jiaen , Foong Daphne , Calder Stefan , Schamberg Gabriel , Varghese Chris , Tack Jan , Xu William , Daker Charlotte , Carson Daniel , Waite Stephen , Hayes Thomas , Du Peng , Abell Thomas L. , Parkman Henry P. , Huang I-Hsuan , Fernandes Vivian , Andrews Christopher N. , Gharibans Armen A. , Ho Vincent , O’Grady Greg
Published: May 2023

Objectives

Gastric emptying testing (GET) assesses gastric motility, however is non-specific and insensitive for neuromuscular disorders. Gastric Alimetry® (GA) is a new medical device combining non-invasive gastric electrophysiological mapping and validated symptom profiling. This study assessed patient-specific phenotyping using GA compared to GET.

Methods

Patients with chronic gastroduodenal symptoms underwent simultaneous GET and GA, comprising a 30-minute baseline,99mTC-labelled egg meal, and 4-hour postprandial recording. Results were referenced to normative ranges. Symptoms were profiled in the validated GA App and phenotyped using rule-based criteria based on their relationships to the meal and gastric activity: i) sensorimotor; ii) continuous; and iii) other.

Results

75 patients were assessed; 77% female. Motility abnormality detection rates were:GET22.7% (14 delayed, 3 rapid);GA spectral analysis33.3% (14 low rhythm stability / low amplitude; 5 high amplitude; 6 abnormal frequency);combined yield42.7%. In patients with normal spectral analysis,GA symptom phenotypesincluded: sensorimotor 17% (where symptoms strongly paired with gastric amplitude; median r=0.61); continuous 30%; other 53%. GA phenotypes showed superior correlations with GCSI, PAGI-SYM, and anxiety scales, whereas Rome IV Criteria did not correlate with psychometric scores (p>0.05).

Delayed emptying was not predictive of specific GA phenotypes.

Conclusions

GA improves patient phenotyping in chronic gastroduodenal disorders in the presence and absence of motility abnormalities with improved correlation with symptoms and psychometrics compared to gastric emptying status and Rome IV criteria. These findings have implications for the diagnostic profiling and personalized management of gastroduodenal disorders.

Study Highlights

1) WHAT IS KNOWN

Chronic gastroduodenal symptoms are common, costly and greatly impact on quality of life

There is a poor correlation between gastric emptying testing (GET) and symptoms

Gastric Alimetry® is a new medical device combining non-invasive gastric electrophysiological mapping and validated symptom profiling

2) WHAT IS NEW HERE

Gastric Alimetry generates a 1.5x higher yield for motility abnormalities than GET

With symptom profiling, Gastric Alimetry identified 2.7x more specific patient categories than GET

Gastric Alimetry improves clinical phenotyping, with improved correlation with symptoms and psychometrics compared to GET
Statistical haemoglobin thresholds to define anaemia across the lifecycle
Authors: Braat Sabine , Fielding Katherine , Han Jiru , Jackson Victoria E. , Zaloumis Sophie , Xu Jessica Xu Hui , Moir-Meyer Gemma , Blaauwendraad Sophia M. , Jaddoe Vincent W.V. , Gaillard Romy , Parkin Patricia C. , Borkhoff Cornelia M. , Keown-Stoneman Charles D.G. , Birken Catherine S. , Maguire Jonathon L. ,   Genes & Health Research Team, Bahlo Melanie , Davidson Eliza , Pasricha Sant-Rayn
Published: May 2023

Detection of anaemia is critical for clinical medicine and public health. Current WHO values that define anaemia are statistical thresholds (5thcentile) set over 50 years ago, and are presently <110g/L in children 6-59 months, <115g/L in children 5-11 years, <110g/L in pregnant women, <120g/L in children 12-14 years of age, <120g/L in non-pregnant women, and <130g/L in men. Haemoglobin is sensitive to iron and other nutrient deficiencies, medical illness and inflammation, and is impacted by genetic conditions; thus, careful exclusion of these conditions is crucial to obtain a healthy reference population. We identified data sources from which sufficient clinical and laboratory information was available to determine an apparently healthy reference sample. Individuals were excluded if they had any clinical or biochemical evidence of a condition that may diminish haemoglobin concentration. Discrete 5thcentiles were estimated along with two-sided 90% confidence intervals and estimates combined using a fixed-effect approach. Estimates for the 5thcentile of the healthy reference population in children were similar between sexes. Thresholds in children 6-23 months were 104.4g/L [90% CI 103.5, 105.3]; in children 24-59 months were 110.2g/L [109.5, 110.9]; and in children 5-11 years were 114.1g/L [113.2, 115.0]. Thresholds diverged by sex in adolescents and adults. In females and males 12-17 years, thresholds were 122.2g/L [121.3, 123.1] and 128.2 [126.4, 130.0], respectively. In adults 18-65 years, thresholds were 119.7g/L [119.1, 120.3] in non-pregnant females and 134.9g/L [134.2, 135.6] in males. Limited analyses indicated 5thcentiles in first-trimester pregnancy of 110.3g/L [109.5, 111.0] and 105.9g/L [104.0, 107.7] in the second trimester. All thresholds were robust to variations in definitions and analysis models. Using multiple datasets comprising Asian, African, and European ancestries, we did not identify novel high prevalence genetic variants that influence haemoglobin concentration, other than variants in genes known to cause important clinical disease, suggesting non-clinical genetic factors do not influence the 5thcentile between ancestries. Our results directly inform WHO guideline development and provide a platform for global harmonisation of laboratory, clinical and public health haemoglobin thresholds.
Long-term optical imaging of the spinal cord in awake, behaving animals
Authors: Ahanonu Biafra , Crowther Andrew , Kania Artur , Casillas Mariela Rosa , Basbaum Allan
Published: May 2023

Advances in optical imaging approaches and fluorescent biosensors have enabled an understanding of the spatiotemporal and long-term neural dynamics in the brain of awake animals. However, methodological difficulties and the persistence of post-laminectomy fibrosis have greatly limited similar advances in the spinal cord. To overcome these technical obstacles, we combinedin vivoapplication of fluoropolymer membranes that inhibit fibrosis; a redesigned, cost-effective implantable spinal imaging chamber; and improved motion correction methods that together permit imaging of the spinal cord in awake, behaving mice, for months to over a year. We also demonstrate a robust ability to monitor axons, identify a spinal cord somatotopic map, conduct Ca2+imaging of neural dynamics in behaving animals responding to pain-provoking stimuli, and observe persistent microglial changes after nerve injury. The ability to couple neural activity and behavior at the spinal cord level will drive insights not previously possible at a key location for somatosensory transmission to the brain.
The adiponectin analogue ALY688-SR attenuates diaphragm fibrosis, atrophy and mitochondrial stress in a mouse model of Duchenne muscular dystrophy
Authors: Bellissimo Catherine A. , Gandhi Shivam , Castellani Laura N. , Murugathasan Mayoorey , Delfinis Luca J. , Thuhan Arshdeep , Garibotti Madison C. , Seo Yeji , Rebalka Irena A. , Sweeney Gary , Hawke Thomas J. , Abdul-Sater Ali A. , Perry Christopher G.R.
Published: May 2023

Fibrosis is associated with respiratory and limb muscle atrophy in Duchenne muscular dystrophy (DMD). Current standard of care partially delays the progression of this myopathy but there remains an unmet need to develop additional therapies. Adiponectin receptor agonism has emerged as a possible therapeutic target to lower inflammation and improve metabolism inmdxmouse models of DMD but the degree to which fibrosis and atrophy are prevented remain unknown. Here, we demonstrate that the recently developed slow-release peptidomimetic adiponectin analogue ALY688-SR prevents fibrosis and fibre type-specific atrophy in diaphragm of D2.mdxmice treated from days 7-28 of age. ALY688-SR also lowered IL-6mRNA but increased IL-6 and TGF-β protein contents in diaphragm, suggesting dynamic inflammatory remodeling. ALY688-SR alleviated mitochondrial redox stress by decreasing complex I-stimulated H2O2emission. Treatment also loweredin vitrodiaphragm force production in diaphragm suggesting a complex relationship between adiponectin receptor activity, muscle remodeling and force generating properties during the very early stages of disease progression in D2.mdxmice. In tibialis anterior, the modest fibrosis at this young age was not altered by treatment, and atrophy was not apparent at this young age. These results demonstrate that short-term treatment of ALY688-SR partially prevents fibrosis and atrophy in the more disease-apparent diaphragm of young D2.mdxmice in relation to lower mitochondrial redox stress. These results provide a foundation for the exploration of slow-release adiponectin-based therapies to prevent fibrosis and atrophy in Duchenne muscular dystrophy.
Prudent burrow-site selection in a landscape of fear
Authors: Torsekar Viraj R. , Lajmi Aparna , Hawlena Dror
Published: May 2023

Prey should select safer breeding sites over riskier sites of otherwise similar habitats. This preference, however, may differ between conspecifics of different competitive abilities if the costs of intraspecific competition overpower the benefits of breeding in a safer site. Our goal was to test this hypothesis by exploring the burrow-site selection of different-sized desert isopods (Hemilepistus reaumuri) near and away from a scorpion burrow. We found that larger females are more likely to occupy burrows than smaller females, regardless of whether these burrows were close or away from scorpion burrows. We also found that larger females stayed longer in safer burrows and that smaller females tended to stay longer in riskier sites even in the absence of direct competition, implying a prudent burrow-site selection. We found no association between male size and the tendency to occupy or to spend time in a burrow, regardless of whether these burrows were close or away from scorpion burrows. Our work highlights the need to consider intraspecific competition when exploring how predators regulate prey behavior.
The Structural Role of N170 in Substrate-assisted Deacylation in KPC-2 β-Lactamase
Authors: Parwana Diksha , Gu Jing , Chen Shuang , Bethel Christopher R. , Marshall Emma , Hujer Andrea M. , Bonomo Robert A. , Haider Shozeb
Published: May 2023

The amino acid substitutions inKlebsiella pneumoniaecarbapenemase 2 (KPC-2) that have arisen in the clinic are observed to lead to the development of resistance to ceftazidime-avibactam, a preferred treatment for KPC bearing Gram-negative bacteria. Specific substitutions in the omega loop (R164-D179) results in changes in the structure and function of the enzyme, leading to alterations in substrate specificity, decreased stability, and more recently observed, increased resistance to ceftazidime/avibactam. Using accelerated rare-event sampling well-tempered metadynamics simulations, we explored in detail the structural role of R164 and D179 variants that are described to confer ceftazidime/avibactam resistance. The buried conformation of D179 substitutions produce a pronounced structural disorder in the omega loop - more than R164 mutants, where the crystallographic omega loop structure remains mostly intact. Our findings also reveal that the conformation of N170 plays an underappreciated role impacting drug binding and restricting deacylation. The results further support the hypothesis that KPC-2 D179 variants employ substrate-assisted catalysis for ceftazidime hydrolysis, involving the ring amine of the aminothiazole group to promote deacylation and catalytic turnover. Moreover, the shift in the WT conformation of N170 contributes to reduced deacylation and altered spectrum of enzymatic activity.
Causal evidence that herpes zoster vaccination prevents a proportion of dementia cases
Authors: Eyting Markus , Xie Min , Heß Simon , Heß Simon , Geldsetzer Pascal
Published: May 2023

The root causes of dementia are still largely unclear, and the medical community lacks highly effective preventive and therapeutic pharmaceutical agents for dementia despite large investments into their development. There is growing interest in the question if infectious agents play a role in the development of dementia, with herpesviruses attracting particular attention. To provide causal as opposed to merely correlational evidence on this question, we take advantage of the fact that in Wales eligibility for the herpes zoster vaccine (Zostavax) for shingles prevention was determined based on an individual’s exact date of birth. Those born before September 2 1933 were ineligible and remained ineligible for life, while those born on or after September 2 1933 were eligible to receive the vaccine. By using country-wide data on all vaccinations received, primary and secondary care encounters, death certificates, and patients’ date of birth in weeks, we first show that the percentage of adults who received the vaccine increased from 0.01% among patients who were merely one week too old to be eligible, to 47.2% among those who were just one week younger. Apart from this large difference in the probability of ever receiving the herpes zoster vaccine, there is no plausible reason why those born just one week prior to September 2 1933 should differ systematically from those born one week later. We demonstrate this empirically by showing that there were no systematic differences (e.g., in pre-existing conditions or uptake of other preventive interventions) between adults across the date-of-birth eligibility cutoff, and that there were no other interventions that used the exact same date-of-birth eligibility cutoff as was used for the herpes zoster vaccine program. This unique natural randomization, thus, allows for robust causal, rather than correlational, effect estimation. We first replicate the vaccine’s known effect from clinical trials of reducing the occurrence of shingles. We then show that receiving the herpes zoster vaccine reduced the probability of a new dementia diagnosis over a follow-up period of seven years by 3.5 percentage points (95% CI: 0.6 – 7.1, p=0.019), corresponding to a 19.9% relative reduction in the occurrence of dementia. Besides preventing shingles and dementia, the herpes zoster vaccine had no effects on any other common causes of morbidity and mortality. In exploratory analyses, we find that the protective effects from the vaccine for dementia are far stronger among women than men. Randomized trials are needed to determine the optimal population groups and time interval for administration of the herpes zoster vaccine to prevent or delay dementia, as well as to quantify the magnitude of the causal effect when more precise measures of cognition are used. Our findings strongly suggest an important role of the varicella zoster virus in the etiology of dementia.
Pathformer: a biological pathway informed Transformer integrating multi-omics data for disease diagnosis and prognosis
Authors: Liu Xiaofan , Tao Yuhuan , Cai Zilin , Bao Pengfei , Ma Hongli , Li Kexing , Li Mengtao , Zhu Yunping , Lu Zhi John
Published: May 2023

Multi-omics data provide a comprehensive view of gene regulation at multiple levels, which is helpful in achieving accurate diagnosis of complex diseases like cancer. To integrate various multi-omics data of tissue and liquid biopsies for disease diagnosis and prognosis, we developed a biological pathway informed Transformer, Pathformer. It embeds multi-omics input with a compacted multi-modal vector and a pathway-based sparse neural network. Pathformer also leverages criss-cross attention mechanism to capture the crosstalk between different pathways and modalities. We first benchmarked Pathformer with 18 comparable methods on multiple cancer datasets, where Pathformer outperformed all the other methods, with an average improvement of 6.3%-14.7% in F1 score for cancer survival prediction and 5.1%-12% for cancer stage prediction. Subsequently, for cancer prognosis prediction based on tissue multi-omics data, we used a case study to demonstrate the biological interpretability of Pathformer by identifying key pathways and their biological crosstalk. Then, for cancer early diagnosis based on liquid biopsy data, we used plasma and platelet datasets to demonstrate Pathformer’s potential of clinical applications in cancer screen. Moreover, we revealed deregulation of interesting pathways (e.g., scavenger receptor pathway) and their crosstalk in cancer patients’ blood, providing new candidate targets for cancer microenvironment study.
Endogenous pathology in tauopathy mice progresses via brain networks
Authors: Ramirez Denise M.O. , Whitesell Jennifer D. , Bhagwat Nikhil , Thomas Talitha L. , Ajay Apoorva D. , Nawaby Ariana , Delatour Benoît , Bay Sylvie , LaFaye Pierre , Knox Joseph E. , Harris Julie A. , Meeks Julian P. , Diamond Marc I.
Published: May 2023

Neurodegenerative tauopathies are hypothesized to propagate via brain networks. This is uncertain because we have lacked precise network resolution of pathology. We therefore developed whole-brain staining methods with anti-p-tau nanobodies and imaged in 3D PS19 tauopathy mice, which have pan-neuronal expression of full-length human tau containing the P301S mutation. We analyzed patterns of p-tau deposition across established brain networks at multiple ages, testing the relationship between structural connectivity and patterns of progressive pathology. We identified core regions with early tau deposition, and used network propagation modeling to determine the link between tau pathology and connectivity strength. We discovered a bias towards retrograde network-based propagation of tau. This novel approach establishes a fundamental role for brain networks in tau propagation, with implications for human disease.

One-Sentence Summary

Novel whole brain imaging of p-tau deposition reveals retrograde-dominant network propagation in a tauopathy mouse model.
Acoustically-Targeted Measurement of Transgene Expression in the Brain
Authors: Seo Joon Pyung , Trippett James S. , Huang Zhimin , Wang Ryan Z. , Lee Sangsin , Szablowski Jerzy O.
Published: May 2023

Gene expression is a critical component of brain physiology and activity, but monitoring this expression in the living brain represents a significant challenge. Here, we introduce a new paradigm called Recovery of Markers through InSonation (REMIS) for noninvasive measurement of gene expression in the brain with cell-type, spatial, and temporal specificity. Our approach relies on engineered protein markers that are designed to be expressed in neurons and exit into the interstitium. By applying ultrasound to targeted brain regions, these markers are released into the bloodstream, where they can be readily detected using biochemical techniques. REMIS can noninvasively confirm gene delivery and measure endogenous signaling in specific brain sites through a simple insonation and a subsequent blood test. Using REMIS, we successfully measured chemogenetic induction of neuronal activity in ultrasound-tar-geted brain regions. REMIS recovery of markers is reliable and demonstrated improved recovery of markers from the brain into the blood in every tested animal. Overall, our work establishes a noninvasive, spatially-specific means of monitoring gene delivery outcomes and endogenous signaling in mammalian brains, opening up possibilities for brain research and noninvasive monitoring of gene therapies in the brain.
Design of optimal labeling patterns for optical genome mapping via information theory
Authors: Nogin Yevgeni , Bar-Lev Daniella , Hanania Dganit , Detinis Zur Tahir , Ebenstein Yuval , Yaakobi Eitan , Weinberger Nir , Shechtman Yoav
Published: May 2023

Optical genome mapping (OGM) is a technique that extracts partial genomic information from optically imaged and linearized DNA fragments containing fluorescently labeled short sequence patterns. This information can be used for various genomic analyses and applications, such as the detection of structural variations and copy-number variations, epigenomic profiling, and microbial species identification. Currently, the choice of labeled patterns is based on the available bio-chemical methods, and is not necessarily optimized for the application. In this work, we develop a model of OGM based on information theory, which enables the design of optimal labeling patterns for specific applications and target organism genomes. We validated the model through experimental OGM on human DNA and simulations on bacterial DNA. Our model predicts up to 10-fold improved accuracy by optimal choice of labeling patterns, which may guide future development of OGM bio-chemical labeling methods and significantly improve its accuracy and yield for applications such as epigenomic profiling and cultivation-free pathogen identification in clinical samples.
Thalamic contributions to psychosis susceptibility: Evidence from co-activation patterns accounting for intra-seed spatial variability (μCAPs)
Authors: Delavari Farnaz , Sandini Corrado , Kojovic Nada , Saccaro Luigi F. , Eliez Stephan , Van De Ville Dimitri , Bolton Thomas A. W.
Published: May 2023

The temporal variability of the thalamus in functional networks may provide valuable insights into the pathophysiology of schizophrenia. To address the complexity of the role of the thalamic nuclei in psychosis, we introduced micro-co-activation patterns (μCAPs) by employing this method on the human genetic model of schizophrenia 22q11.2 deletion syndrome (22q11.2DS). Participants underwent resting-state functional MRI and a data-driven iterative process resulting in the identification of six whole-brain μCAPs with specific activity patterns within the thalamus. Unlike conventional methods, μCAPs extract dynamic spatial patterns that reveal partially overlapping and non-mutually exclusive functional subparts. Thus, the μCAPs method detects finer foci of activity within the initial seed region, retaining valuable and clinically relevant temporal and spatial information. We found that a μCAP showing co-activation of the mediodorsal thalamus with brain-wide cortical regions was significantly less frequent in patients with 22q11.2DS, and its occurrence negatively correlated with the severity of positive psychotic symptoms. Additionally, the activity within the auditory-visual cortex and their respective geniculate nuclei were expressed in two different μCAPs. One of these auditory-visual μCAPs co-activated with salience areas, while the other co-activated with the default mode network (DMN). A significant shift of occurrence from the salience+visuo-auditory-thalamus to the DMN+visuo-auditory-thalamus μCAP was observed in patients with 22q11.2DS. Thus, our findings support existing research on the gatekeeping role of the thalamus for sensory information in the pathophysiology of psychosis and revisit the evidence of geniculate nuclei hyperconnectivity with the audio-visual cortex in 22q11.2DS in the context of dynamic functional connectivity as specific hyper-occurrence of these circuits with the task negative brain networks.
Setdb1-loss induces type-I interferons and immune clearance of melanoma
Authors: McGeary Meaghan K. , Damsky William , Daniels Andrew , Song Eric , Micevic Goran , Huet-Calderwood Clotilde , Lou Hua Jane , Paradkar Sateja , Kaech Susan , Calderwood David A. , Turk Benjamin E. , Iwasaki Akiko , Bosenberg Marcus W.
Published: May 2023

Despite recent advances in the treatment of melanoma, many patients with metastatic disease still succumb to their disease. To identify tumor-intrinsic modulators of immunity to melanoma, we performed a whole-genome CRISPR screen in melanoma and identified multiple components of the HUSH complex, includingSetdb1, as hits. We found that loss ofSetdb1leads to increased immunogenicity and complete tumor clearance in a CD8+ T-cell dependent manner. Mechanistically, loss ofSetdb1causes de-repression of endogenous retroviruses (ERVs) in melanoma cells and triggers tumor-cell intrinsic type-I interferon signaling, upregulation of MHC-I expression, and increased CD8+ T-cell infiltration. Furthermore, spontaneous immune clearance observed inSetdb1-/-tumors results in subsequent protection from other ERV-expressing tumor lines, supporting the functional anti-tumor role of ERV-specific CD8+ T-cells found in theSetdb1-/-microenvironment. Blocking the type-I interferon receptor in mice grafted withSetdb1-/-tumors decreases immunogenicity by decreasing MHC-I expression, leading to decreased T-cell infiltration and increased melanoma growth comparable to Setdb1wttumors. Together, these results indicate a critical role forSetdb1and type-I interferons in generating an inflamed tumor microenvironment, and potentiating tumor-cell intrinsic immunogenicity in melanoma. This study further emphasizes regulators of ERV expression and type-I interferon expression as potential therapeutic targets for augmenting anti-cancer immune responses.
Foxp3 depends on Ikaros for control of regulatory T cell gene expression and function
Authors: Thomas Rajan M. , Pahl Matthew C. , Wang Liqing , Grant Struan F. A. , Hancock Wayne W. , Wells Andrew D.
Published: May 2023

Ikaros is a transcriptional factor required for conventional T cell development, differentiation, and anergy. While the related factors Helios and Eos have defined roles in regulatory T cells (Treg), a role for Ikaros has not been established. To determine the function of Ikaros in the Treg lineage, we generated mice with Treg-specific deletion of the Ikaros gene (Ikzf1). We find that Ikaros cooperates with Foxp3 to establish a major portion of the Treg epigenome and transcriptome. Ikaros-deficient Treg exhibit Th1-like gene expression with abnormal expression of IL-2, IFNg, TNFa, and factors involved in Wnt and Notch signaling. WhileIkzf1-Treg-cko mice do not develop spontaneous autoimmunity, Ikaros-deficient Treg are unable to control conventional T cell-mediated immune pathology in response to TCR and inflammatory stimuli in models of IBD and organ transplantation. These studies establish Ikaros as a core factor required in Treg for tolerance and the control of inflammatory immune responses.
Antigen spacing on protein nanoparticles influences antibody responses to vaccination
Authors: Ellis Daniel , Dosey Annie , Boyoglu-Barnum Seyhan , Park Young-Jun , Gillespie Rebecca , Syeda Hubza , Tsybovsky Yaroslav , Murphy Michael , Pettie Deleah , Matheson Nick , Chan Sidney , Ueda George , Fallas Jorge A. , Carter Lauren , Graham Barney S. , Veesler David , Kanekiyo Masaru , King Neil P.
Published: May 2023

Immunogen design approaches aim to control the specificity and quality of antibody responses to enable the creation of next-generation vaccines with improved potency and breadth. However, our understanding of the relationship between immunogen structure and immunogenicity is limited. Here we use computational protein design to generate a self-assembling nanoparticle vaccine platform based on the head domain of influenza hemagglutinin (HA) that enables precise control of antigen conformation, flexibility, and spacing on the nanoparticle exterior. Domain-based HA head antigens were presented either as monomers or in a native-like closed trimeric conformation that prevents exposure of trimer interface epitopes. These antigens were connected to the underlying nanoparticle by a rigid linker that was modularly extended to precisely control antigen spacing. We found that nanoparticle immunogens with decreased spacing between closed trimeric head antigens elicited antibodies with improved hemagglutination inhibition (HAI) and neutralization potency as well as binding breadth across diverse HAs within a subtype. Our “trihead” nanoparticle immunogen platform thus enables new insights into anti-HA immunity, establishes antigen spacing as an important parameter in structure-based vaccine design, and embodies several design features that could be used to generate next-generation vaccines against influenza and other viruses.

HIGHLIGHTS

Computational design of a closed trimeric HA head (“trihead”) antigen platform.

Design of a rigid, extendable linker between displayed antigen and underlying protein nanoparticle enables precise variation of antigen spacing.

Decreased antigen spacing of triheads elicits antibodies with the highest HAI, neutralizing activity, and cross-reactivity.

Changes to antigen spacing alter epitope specificities of vaccine-elicited antibodies.
Efficient calculation of orientation-dependent lipid dynamics from membrane simulations
Authors: Doktorova Milka , Khelashvili George , Brown Michael F
Published: May 2023

Molecular dynamics simulations of lipid membranes have become increasingly impactful in biophysics because they offer atomistic resolution of structural fluctuations in relation to their functional outputs. Yet quantitative characterization of multiscale processes is a formidable challenge due to the distribution of motions that evade analysis of discrete simulation data. Here we investigate the efficient calculation of CH bond relaxation rates from membrane simulations. Widely used computational approaches offer numerical simplicity but fall short of capturing crucial aspects of the orientation dependence of the dynamics. To circumvent this problem, we introduced a robust framework based on liquid crystal theory which considers explicitly the CH bond motions with respect to the director axis (bilayer normal). Analysis of the orientation dependence of the dynamics shows excellent agreement with experiment, illustrating how the ordering potential affects the calculated relaxation rates. Furthermore, a fit-based resampling of the autocorrelation function of the bond fluctuations validates the new approach for low-temporal resolution data. The recovered relaxation rates indicate that at short timescales, both with and without cholesterol, the local motions of CH bonds describe the bilayer microviscosity and resemble liquid hydrocarbons. Our results establish the critical role of the orientational anisotropy in analysis of membrane simulations, explain fundamental aspects of lipid dynamics, and provide guidelines for extracting information that can be compared to experimental data.
Implementation of the PrAISED (Promoting Activity, Independence and Stability in Early Dementia) intervention in practice: a mixed methods study
Authors: Adams Emma J , Burgon Clare , Lock Juliette , Smith Helen , Vickers Robert , Tucker Rachael , Timmons Stephen , Orton Elizabeth , Goldberg Sarah E , Gladman John , Masud Tahir , Harwood Rowan H
Published: May 2023

There is a paucity of evidence relating to the implementation of dementia care. The Promoting Activity, Independence and Stability in Early Dementia (PrAISED) intervention is a newly developed 12-month, home-based, individually tailored rehabilitation programme, delivered by therapists and rehabilitation support workers, with a focus on strength, balance, physical activity and activities of daily living. The aim of this study was to identify what is required to implement PrAISED, or similar interventions, in routine clinical practice. PrAISED was delivered as a pilot service in one National Health Service organisation in England. Patient characteristics and the number and duration of visits were recorded by intervention delivery staff. Quantitative data were explored using descriptive statistics. Semi-structured interviews were conducted with seven members of staff delivering the PrAISED service (two managers, five delivery staff) and eight members of staff from other sites involved in the PrAISED Randomised Controlled Trial (RCT) (four managers, four delivery staff). The Consolidated Framework for Implementation Research was used to inform interview guides and conduct a codebook thematic analysis. Adaptations were needed to deliver PrAISED as a service and referrals were lower than expected. Five themes were identified from interviews relating to the pilot service: operational processes; workforce capacity; referral; intervention delivery and patient impact. A further six themes were identified regarding the wider implementation of dementia therapy programmes: the need for support post-dementia diagnosis; acceptability; effective delivery; reach/referral; intervention design and adaptability; and intervention materials and training. There is a need for interventions like PrAISED to fill a gap in support immediately post-dementia diagnosis. Future implementation will require attention to the identification of intervention funding; leadership and management; time to establish operational processes; therapists with appropriate skills and experience; providing training and resources to support intervention delivery; defining patient eligibility and referral processes; and maintaining fidelity of the intervention.
Hypoxia modulates P-glycoprotein (P-gp) and breast cancer resistance protein (BCRP) drug transporters in brain endothelial cells of the developing human blood-brain barrier
Authors: Mughis Hafsah , Lye Phetcharawan , Imperio Guinever E. , Bloise Enrrico , Matthews Stephen G.
Published: May 2023

P-glycoprotein (P-gp) and Breast Cancer Resistance Protein (BCRP) are two multidrug resistance (MDR) transporters expressed at the blood-brain barrier (BBB). They confer protection against entry of harmful molecules into the fetal brain. The fetus develops under relatively low oxygen concentrations; however, pregnancy disorders (including pre-eclampsia) may lead to even lower intrauterine oxygen levels. We investigated the effects of hypoxia on transporter expression and activity in human fetal brain endothelial cells (hfBECs) isolated in early and mid-gestation. Results indicate decreased BCRP protein and activity under hypoxia in early-gestation hfBECs. Mid-gestation hfBECs exhibited an increase in P-gp and BCRP activity following hypoxia. Results suggest a hypoxia-induced reduction in fetal brain protection in early-pregnancy, but a potential increase in transporter-mediated protection at the BBB during mid-gestation. This would modify accumulation of various key P-gp and BCRP physiological and pharmacological substrates in the developing fetal brain and may play a role in the pathogenesis of neurodevelopmental disorders commonly associated within uterohypoxia.
Transcriptional reprogramming by IL-2 variant generates metabolically active stem-like T cells
Authors: Ortiz-Miranda Yaquelin , Masid Maria , Jiménez-Luna Cristina , Montalvo Bereau Galia Magela , Muller Tania , Rayroux Nicolas , Cribioli Elisabetta , Corría-Osorio Jesús , Carrasco Hope Helen , Vuillefroy de Silly Romain , Seijo Bili , Ginefra Pierpaolo , León Kalet , Vannini Nicola , Ho Ping-Chih , Crespo Isaac , Hatzimanikatis Vassily , Irving Melita , Coukos George
Published: May 2023

Interleukin-2 receptor (IL-2R)-mediated intracellular signaling is a key regulator of T-cell fate decisions. While the potent signals generated by IL-2 engagement execute effector differentiation, elevated metabolic activities and rapid cellular expansion, IL-15 binding induces a stemness/memory phenotype and a quiescent metabolic state. Here, we demonstrate that weak but sustained signaling generated by a non-IL-2Rα-binding variant of IL-2 (IL-2v) drive proliferation/metabolic and stemness transcriptional programs, thereby reprogramming CD8+T cells into a hybrid ‘metabolically active stem-like state’. We further show that IL-2v-induced T cells are capable of superior engraftment, persistence, and tumor control when utilized in adoptive cell therapy. Taken together, our study highlights the ability to fine-tune cytokine engagement of cognate receptors in order to generate therapeutically relevant T-cell states and further reveals the metabolic plasticity of the T-cell memory program.
Molecular dynamics of the interaction between the ALS/FTD-associated (GGGGCC)n RNA G-quadruplex structure and the three RRM domains of hnRNP H
Authors: Cava Marvin Jericho , Billones Junie B , Galipon Josephine
Published: May 2023

Hexanucleotide repeat expansions (HRE), located in the first intron of chromosome 9 open reading frame 72 (C9orf72) are the most common genetic abnormality associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Presence of the HRE may cause various effects to neuronal cells, leading to pathogenicity. One of these is the sequestration of RNA-binding proteins by three-quartet parallel RNA G-quadruplexes (RG4s) formed from repeated (GGGGCC)n sequences on the sense transcripts of the HRE. Multiple studies imply a major role of the sequestration of heterogeneous nuclear ribonucleoprotein H (hnRNP H) in the pathology of ALS/FTD. In this study, molecular docking and molecular dynamics (MD) were used to simulate the interaction of the three RNA recognition motifs (RRMs) of hnRNP H with the RG4. Molecular Mechanics with Generalised Born and Surface Area Solvation (MM-GBSA) and hydrogen bonding analyses of MD simulations were performed. The MM-GBSA analyses revealed that Arg29, Arg150, and Arg299 are important contributors to the binding, consistent with previous observations of arginine-mediated binding of protein to RNA. In addition, our results point to a previously unknown role of the stretch of residues from Lys72 to Tyr82 on hnRNP H for binding the (GGGGCC)n RG4, forming a hydrogen bonding hotspot. Interestingly, the identified residues are not located in the beta sheet, as would be expected of RRMs in general, suggesting that the binding of hnRNP H to this pathological RG4 may be specifically targeted. This has implications for futurein vitrostudies including but not limited to mutational analysis of these mentioned residues as well as drug development to prevent the sequestration of hnRNP H in ALS/FTD.
Macrophage-specific lipid nanoparticle therapy blocks the lung’s mechanosensitive immunity due to macrophage-epithelial interactions
Authors: Mthunzi Liberty , Islam Mohammad N , Gusarova Galina A , Bhattacharya Sunita , Karolewski Brian , Bhattacharya Jahar
Published: May 2023

The lung’s mechanosensitive immune response, which occurs when pulmonary alveoli are overstretched, is a major impediment to ventilation therapy for hypoxemic respiratory failure. The cause is not known. We tested the hypothesis that alveolar stretch causes stretch of alveolar macrophages (AMs), leading to the immune response. In lungs viewed by optical imaging, sessile AMs expressed gap junctional protein connexin-43 (Cx43), and they communicated with the alveolar epithelium through gap junctions. Alveolar hyperinflation increased Ca2+in the AMs but did not stretch the AMs. The Ca2+response, and concomitant TNFα secretion by AMs were blocked in mice with AM-specific deletion of Cx43. The AM responses, as also lung injury due to mechanical ventilation at high tidal volume, were inhibited by AM-specific delivery of lipid nanoparticles containing Xestospongin C, which blocked the induced Ca2+increases. We conclude, Cx43- and Ca2+-dependent AM-epithelial interactions determine the lung’s mechanosensitive immunity, providing a basis for therapy for ventilator- induced lung injury.
Estimating gross transcription rates from RNA level fluctuation data and the effects of sampling time intervals
Authors: Xu Zhongneng , Asakawa Shuichi
Published: May 2023

Transcription rates are key biological parameters, but the estimation of transcription rates from RNA level fluctuation data by current methods is still problematic, considering in particular the derived relationship between RNA fragments from different samples and the neglect of the effects of sampling time intervals. Based on defining the gross transcription rate as the amount of converted complete nascent RNA divided by time, the present study developed an algorithm that calculated the cumulative transcription amount and RNA abundance at each time point by simulating moving windows to estimate gross transcription rates from RNA level fluctuation data and explore the effects of sampling time intervals on the estimation. The results showed that the gross transcription rates could be calculated from RNA level fluctuation data with the models fitting the experimental data well. In the analysis of 384 yeast genes, the genes with the highest gross transcription rates mainly played roles in cell division regulation and DNA replication, and the gene utilizing the most cellular resources for gene expression during the experiment was YNR016c, whose main functions are fatty acid biosynthesis and transporting proteins into the nucleus. The shapes of the RNA level curves affected the estimation of gross transcription rates, and the crests and valleys of the RNA level curves responded to higher gross transcription rates. Different scenarios of sampling time intervals could change the shapes of the RNA level curves, resulting in different estimation values of gross transcription rates. Given the potential applications of the present method, further improvements are expected.
Noncanonical TRAIL Signaling Promotes Myeloid-Derived Suppressor Cell Abundance and Tumor Progression in Cholangiocarcinoma
Authors: Loeuillard Emilien , Li Binbin , Stumpf Hannah E. , Yang Jingchun , Willhite Jessica , Tomlinson Jennifer L. , Wang Juan , Rohakhtar Fred Rakhshan , Simon Vernadette A. , Graham Rondell P. , Smoot Rory L. , Dong Haidong , Ilyas Sumera I.
Published: May 2023

Proapoptotic tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) signaling as a cause of cancer cell death is a well-established mechanism. However, TRAIL-receptor (TRAIL-R) agonists have had very limited anticancer activity in humans, challenging the concept of TRAIL as a potent anticancer agent. Herein, we demonstrate that TRAIL+cancer cells can leverage noncanonical TRAIL signaling in myeloid-derived suppressor cells (MDSCs) promoting their abundance in murine cholangiocarcinoma (CCA). In multiple immunocompetent syngeneic, orthotopic murine models of CCA, implantation of TRAIL+murine cancer cells intoTrail-r-/-mice resulted in a significant reduction in tumor volumes compared to wild type mice. Tumor bearingTrail-r-/-mice had a significant decrease in the abundance of MDSCs due to attenuation of MDSC proliferation. Noncanonical TRAIL signaling with consequent NF-κB activation in MDSCs facilitated enhanced MDSC proliferation. Single cell RNA sequencing and cellular indexing of transcriptomes and epitopes by sequencing (CITE-Seq) of CD45+cells in murine tumors from three distinct immunocompetent CCA models demonstrated a significant enrichment of an NF-κB activation signature in MDSCs. Moreover, MDSCs were resistant to TRAIL-mediated apoptosis due to enhanced expression of cellular FLICE inhibitory protein (cFLIP), an inhibitor of proapoptotic TRAIL signaling. Accordingly, cFLIP knockdown sensitized murine MDSCs to TRAIL-mediated apoptosis. Finally, cancer cell-restricted deletion ofTrailsignificantly reduced MDSC abundance and murine tumor burden. In summary, our findings define a noncanonical TRAIL signal in MDSCs and highlight the therapeutic potential of targeting TRAIL+cancer cells for the treatment of a poorly immunogenic cancer.
A bioinformatics tool for identifying intratumoral microbes from the ORIEN dataset
Authors: Wang Cankun , Ma Anjun , McNutt Megan E. , Hoyd Rebecca , Wheeler Caroline E. , Robinson Lary A. , Chan Carlos H.F. , Zakharia Yousef , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Denko Nicholas , Tinoco Gabriel , Husain Marium , Jin Ning , Osman Afaf E.G. , Eljilany Islam , Tan Aik Choon , Coleman Samuel S. , Denko Louis , Riedlinger Gregory , Schneider Bryan P. , Spakowicz Daniel , Ma Qin
Published: May 2023

Evidence supports significant interactions among microbes, immune cells, and tumor cells in at least 10–20% of human cancers, emphasizing the importance of further investigating these complex relationships. However, the implications and significance of tumor-related microbes remain largely unknown. Studies have demonstrated the critical roles of host microbes in cancer prevention and treatment responses. Understanding interactions between host microbes and cancer can drive cancer diagnosis and microbial therapeutics (bugs as drugs). Computational identification of cancer-specific microbes and their associations is still challenging due to the high dimensionality and high sparsity of intratumoral microbiome data, which requires large datasets containing sufficient event observations to identify relationships, and the interactions within microbial communities, the heterogeneity in microbial composition, and other confounding effects that can lead to spurious associations. To solve these issues, we present a bioinformatics tool, MEGA, to identify the microbes most strongly associated with 12 cancer types. We demonstrate its utility on a dataset from a consortium of 9 cancer centers in the Oncology Research Information Exchange Network (ORIEN). This package has 3 unique features: species-sample relations are represented in a heterogeneous graph and learned by a graph attention network; it incorporates metabolic and phylogenetic information to reflect intricate relationships within microbial communities; and it provides multiple functionalities for association interpretations and visualizations. We analyzed 2704 tumor RNA-seq samples and MEGA interpreted the tissue-resident microbial signatures of each of 12 cancer types. MEGA can effectively identify cancer-associated microbial signatures and refine their interactions with tumors.

SIGNIFICANCE

Studying the tumor microbiome in high-throughput sequencing data is challenging because of the extremely sparse data matrices, heterogeneity, and high likelihood of contamination. We present a new deep-learning tool, microbial graph attention (MEGA), to refine the organisms that interact with tumors.