bluuebunny/crossref_metadata_2025 huggingface dataset:
Allosteric degraders induce CRL5ASB8mediated degradation of XPO1
Authors: Hudman-Wing Casey Elizabeth , Fung Ho Yee Joyce , Cagatay Tolga , Kwanten Bert , Niesman Ashley B. , Gharghabi Mehdi , Permentier Brecht , Shakya Binita , Shacham Sharon , Landesman Yosef , Lapalombella Rosa , Daelemans Dirk , Chook Yuh Min
Published: October 2024

The nuclear export receptor Exportin 1 (XPO1/CRM1) is often overexpressed in cancer cells resulting in aberrant localization of many cancer-related protein cargoes. The XPO1 inhibitor and cancer drug selinexor (KPT-330), and its analog KPT-185, block XPO1-cargo binding thereby restoring cargo localization. Selinexor binding induces cullin-RING E3 ubiquitin ligase (CRL) substrate receptor ASB8-mediated XPO1 degradation. Here we reveal the mechanism of inhibitor-XPO1 engagement by CRL5ASB8. Cryogenic electron microscopy (cryo-EM) structures show ASB8 binding to a large surface of selinexor/KPT-185-XPO1 that includes a three-dimensional degron unique to the drug-bound exportin. The structure explains weak XPO1-ASB8 binding in the absence of selinexor/KPT-185 that is unproductive for proteasomal degradation, and the substantial affinity increase upon selinexor/KPT-185 conjugation, which results in CRL5ASB8-mediated XPO1 ubiquitination. In contrast to previously characterized small molecule degraders, which all act as molecular glues, selinexor/KPT-185 binds extensively to XPO1 but hardly contacts ASB8. Instead, selinexor/KPT-185 binds XPO1 and stabilizes a unique conformation of the NES/inhibitor-binding groove that binds ASB8. Selinexor/KPT-185 is an allosteric degrader. We have explained how drug-induced protein degradation is mediated by a CRL5 system through an allosteric rather than a molecular glue mechanism, expanding the modes of targeted protein degradation beyond the well-known molecular glues of CRL4.
Tuning Insulin Receptor Signaling UsingDe NovoDesigned Agonists
Authors: Wang Xinru , Cardoso Sarah , Cai Kai , Venkatesh Preetham , Hung Albert , Ng Michelle , Hall Catherine , Coventry Brian , Lee David , Chowhan Rishabh , Gerben Stacey , Li Jie , An Weidong , Hon Mara , Accili Domenico , Bai Xiaochen , Choi Eunhee , Baker David
Published: October 2024

Binding of insulin to the insulin receptor (IR) induces conformational changes in the extracellular portion of the receptor that lead to activation of the intracellular kinase domain and the AKT and MAPK pathways, and downstream modulation of glucose metabolism and cell proliferation. We reasoned that designed agonists that induce different conformational changes in the receptor might induce different downstream responses, which could be useful both therapeutically and to shed light on how extracellular conformation is coupled to intracellular signaling. We usedde novoprotein design to first generate binders to individual IR extracellular domains, and then to fuse these together in different orientations and with different conformational flexibility. We describe a series of synthetic agonists that signal through the IR that differ from insulin and from each other in the induction of receptor autophosphorylation, MAPK activation, intracellular trafficking, and cell proliferation. We identify designs that are more potent than insulin causing much longer lasting reductions in glucose levels, and that retain signaling activity on disease-causing receptor mutants that do not respond to insulin. These results inform our understanding of how changes in receptor conformation and dynamics are transmitted to downstream signaling, and our synthetic agonists have considerable therapeutic potential for diabetes and severe insulin resistance syndromes.

Highlights

Computational design yielded super agonists, partial agonists, and antagonists of IR.

De novoagonists induce a distinct IR active conformation.

Designed agonists tune IR signaling by modulating conformational dynamics of activated IR.

Designed agonists are more potent than insulin, reducing glucose levels longer and activating disease-causing IR mutants.
Antibody-Fab and -Fc features promoteMycobacterium tuberculosisrestriction
Authors: Grace Patricia S. , Peters Joshua M. , Sixsmith Jaimie , Lu Richard , Luedeman Corinne , Fenderson Brooke A. , Vickers Andrew , Slein Matthew D. , Irvine Edward B. , McKitrick Tanya , Wei Mo-Hui , Cummings Richard D. , Wallace Aaron , Cavacini Lisa A. , Choudhary Alok , Proulx Megan K. , Sundling Christopher , Källenius Gunilla , Reljic Rajko , Ernst Joel D. , Casadevall Arturo , Locht Camille , Pinter Abraham , Sasseti Christopher M. , Bryson Bryan D. , Fortune Sarah M. , Alter Galit
Published: October 2024

Mycobacterium tuberculosis (Mtb),the causative agent of tuberculosis (TB), is a leading cause of death by an infectious disease globally, with no efficacious vaccine. Antibodies are implicated inMtbcontrol, but the mechanisms of antibody action remain poorly understood. We assembled a library of TB monoclonal antibodies (mAb) and screened for the ability to restrictMtbin mice, identifying protective antibodies targeting known and novel antigens. To dissect the mechanism of mAb-mediatedMtbrestriction, we optimized a protective lipoarabinomannan-specific mAb through Fc-swapping.In vivoanalysis of these Fc-variants revealed a critical role for Fc-effector function inMtbrestriction. Restrictive Fc-variants altered distribution ofMtbacross innate immune cells. Single-cell transcriptomics highlighted distinctly activated molecular circuitry within innate immune cell subpopulations, highlighting early activation of neutrophils as a key signature of mAb-mediatedMtbrestriction. Therefore, improved antibody-mediated restriction ofMtbis associated with reorganization of the tissue-level immune response to infection and depends on the collaboration of antibody Fab and Fc.
Transgenerational effects alter the fitness consequences and genetic architecture of phenotypic plasticity and its regulatory pathways
Authors: Bogan Samuel N. , Strader Marie E. , Hofmann Gretchen E.
Published: October 2024

Parental exposure to environmental stress can influence phenotypic plasticity by offspring developing under that stressor. Transgenerational effects may also reshape natural selection on developmental plasticity by influencing its fitness consequences and expression of its genetic variation. We tested these hypotheses in the purple sea urchinStrongylocentrotus purpuratus, an invertebrate exposed to coastal upwelling (periods of low temperature and pH impacting biomineralization and performance). We conditioned parents and larvae to experimental upwelling and integrated RNA-seq, phenotyping of body size and biomineralization, and measured fitness-correlated traits in a quantitative genetic experiment. Larvae developing under upwelling induced widespread differential expression (DE), decreased biomineralization, and reduced body size. We detected fitness benefits for increased biomineralization and reduced size under upwelling indicative of adaptive plasticity, but only when larvae were spawned from parents exposed to upwelling. Larval DE was largely associated with adaptive phenotypic plasticity. Negative genetic correlation in DE was abundant between genes associated with adaptive plasticity. However, genetic correlations in DE associated with body size plasticity were significantly more positive in larvae from upwelling-exposed parents. These results show that transgenerational effects modify the fitness landscape and genetic architecture of phenotypic plasticity and its regulatory pathways.
Addressing domain shift in deep learning: Challenges and insights from plant disease diagnosis and flower recognition
Authors: Sun Jianqiang
Published: October 2024

Deep learning models have demonstrated potential in plant disease diagnosis and flower recognition; however, their real-world application is hindered by domain shift—where models trained on one dataset underperform when tested on datasets collected in different conditions. This study assessed the cross-dataset generalization of deep learning models, including ResNet, EfficientNet, Inception, and MobileNet, using multiple tomato disease and flower datasets. While models achieved high accuracy when trained and validated on the same dataset, their performance declined significantly when evaluated on different datasets, underscoring the impact of domain variability. This performance degradation was consistent across all model architectures, suggesting that domain shift cannot be addressed through model architecture alone. The results emphasize the need for more diverse and representative datasets to mitigate variability in agricultural data and enhance the practical utility of deep learning models in agricultural applications.
Thermal Adaptation of Cytosolic Malate Dehydrogenase Revealed by Deep Learning and Coevolutionary Analysis
Authors: Shukla D , Martin J , Morcos F , Potoyan DA
Published: October 2024

Protein evolution has produced enzymes that maintain stability and function across various thermal environments. While sequence variation, structural dynamics, and intermolecular interactions are known to influence an enzyme’s thermal adaptation, how these factors collectively govern stability and function across diverse temperatures remains unresolved. Cytosolic malate dehydrogenase (cMDH), a citric acid cycle enzyme, is an ideal model for studying these mechanisms due to its temperature-sensitive flexibility and broad presence in species from diverse thermal environments. In this study, we employ techniques inspired by deep learning and statistical mechanics to uncover how sequence variation and structural dynamics shape patterns of cMDH’s thermal adaptation. By integrating coevolutionary models with variational autoencoders (VAE), we generate a latent generative landscape (LGL) of cMDH sequence space, enabling us to explore evolutionary pathways and predict fitness using direct coupling analysis (DCA). Structural predictions via AlphaFold and molecular dynamics simulations further illuminate how variations in hydrophobic interactions and conformational flexibility contribute to the thermal stability of warm- and cold-adapted cMDH orthologs. The integrative computational framework employed in this study provides powerful insights into protein adaptation at both sequence and structural levels, offering new perspectives on the evolution of thermal stability and creating avenues for the rational design of proteins with optimized thermal properties for biotechnological applications.
Long-Term Effects of Working Memory Retrieval From Prioritized and Deprioritized States
Authors: Born Frieda , Spitzer Bernhard
Published: October 2024

Which factors determine whether information temporarily held in working memory (WM) is transferred to long-term memory (LTM)? Previous work has shown that retrieving (“testing”) memories from LTM can benefit their future LTM recall. Here, we examined the extent to which a benefit for subsequent LTM may also occur after retrieval from WM, depending on whether the WM contents were retrieved from a prioritized or deprioritized state. In three experiments, we combined variants of a novel visual WM paradigm with a subsequent surprise LTM recall test. We found a LTM benefit of WM testing both for prioritized and deprioritized WM contents, which, interestingly, was stronger for the deprioritized information. This pattern showed similarly across experiments with different priority manipulations. Subsequent LTM benefits generally occurred after WM testing with a recall-like test format (continuous report), but not after simple WM comparisons against a probe. The surprisingly larger LTM benefit for deprioritized WM contents may reflect enhanced encoding of the participants’ own subjective WM report – as opposed to the originally presented sample information – into LTM.
Tunneling Nanotubes Between Bone Marrow Stromal Cells Support Transmitophagy and Resistance to Apoptosis in Myeloma
Authors: Solimando Antonio Giovanni , Di Palma Francesco , Desantis Vanessa , Vacca Angelo , Svelto Maria , Pisani Francesco
Published: October 2024

Here we show that under oxygen-glucose deprivation (OGD), multiple myeloma cells transfer dysfunctional mitochondria to bone marrow stromal cells (BMSCs) for degradation (transmitophagy). These mitochondria are then transferred between BMSCs via tunneling nanotubes contributing to myeloma survival in OGD.
Reporter CRISPR screens deciphercis- andtrans-regulatory principles at theXistlocus
Authors: Schwämmle Till , Noviello Gemma , Kanata Eleni , Froehlich Jonathan J. , Bothe Melissa , Altay Aybuge , Scouarnec Jade , Feng Vivi-Yun , Vingron Martin , Schulz Edda G.
Published: October 2024

Developmental genes are controlled by an ensemble ofcis-acting regulatory elements (REs), which in turn respond to multipletrans-acting transcription factors (TFs). Understanding how acis-regulatory landscape integrates information from many dynamically expressed TFs has remained a challenge. We develop a combined CRISPR-screening approach using endogenous RNA and RE-reporters as readouts. Applied to theXistlocus, crucial for X-chromosome inactivation in females, this method allows us to comprehensively identify Xist-controlling TFs and map their TF-RE wiring. We find a group of transiently expressed TFs that regulate proximal REs, driving the binary activation of Xist expression. These basal activators are more highly expressed in cells with two X chromosomes, potentially driving female-specific Xist upregulation. A second set of developmental TFs is upregulated later during differentiation and targets distal REs. This regulatory axis is crucial to achieve high levels of Xist RNA, which is necessary for X-chromosome inactivation. Our findings support a model for developmental gene regulation in which factors targeting proximal REs drive binary ON-OFF decisions, while factors interacting with distal REs control the transcription output.
Aligning Funding Models with Clinical Practice: Phases of Neonatal Care and the Link with Activity-Based Funding
Authors: Mordaunt Dylan A
Published: October 2024

Objective

To explore the potential impact of partitioning neonatal unit funding into acute and sub-acute/non-acute care (SNAP) types, within a level 6 neonatal unit under the Independent Health and Aged Care Pricing Authority (IHACPA) National Efficient Price (NEP) Funding Model.

Methods

In a 12-month retrospective cohort from our neonatal unit, we simulated the effect of a care type change to SNAP. We then explored the trend in this activity type over the past 20 years.

Results

341 patients with a length of stay greater than 10 days were identified from FY 2021-22. Modelling estimates that between 51 and 175 episodes could have a SNAP opportunity. When moderated, this corresponds with an uplift of between AUD $0.3 - 1.7M, based on 2023-24 value and NEP price.

Conclusions

Utilisation of a SNAP care-type change has the potential for a considerable uplift in funding for level 6 neonatal units, supporting service sustainability. This may be of use for other units, whilst the neonatal funding model continues to be reviewed and optimized by IHACPA. Implementation in our context, would require changes to both local and state funding management systems, as well as alterations in the Electronic Medical Record (EMR).
Pilot randomized controlled trial of acetylsalicylic acid to reduce cerebral microembolism in Chagas heart failure
Authors: Castello-Branco Renan Carvalho , de Santana Cárita Victoria Carvalho , Botelho Victor L. P. P. , deSousa Paulo R. S. P. , Nunes Maria C.P. , Furie Karen L. , Oliveira-Filho Jamary
Published: October 2024

Background

Chagas disease is an important cause of heart failure (HF) and stroke, affecting over six million people. High intensity transient signals (HITS) are detected on transcranial Doppler (TCD) in patients with Chagas disease, but the effect of antithrombotic treatment on HITS is unknown. The aim of this study was to evaluate whether acetylsalicylic acid (ASA) reduces the frequency and number of HITS in patients with chagasic HF.

Methods

Proof-of-principle pilot prospective, randomized, open and blinded endpoint clinical trial (PROBE), where patients with both Chagas and HITS were randomized 2:1 to ASA 300 mg for seven days and standard HF treatment or standard HF treatment alone (control group). The primary outcome was the proportion of HITS after one week, analyzed using chi-squared test.

Results

373 patients with HF were evaluated, HITS occurred in 22/190 (12%) chagasic patients and in 16/183 (8%) non-chagasic patients (p=0.531). Twelve of the 22 (54%) chagasic patients were randomized to treatment with ASA (n = 8) or without ASA (n = 4). Two patients in the control group (50%) persisted with HITS after 7 days of treatment, compared to none in the ASA group, p=0.028. Median number of HITS decreased from 3.5 to 0 with ASA (p=0.012) and 4.0 to 0.5 in the control group (p=0.095), with no significant between-group difference (p=0.262). No adverse events were reported.

Conclusion

In this pilot clinical trial, ASA reduced the proportion of HITS in patients with Chagas disease HF.
Exploring the Decisional Needs of Patients living with Subacromial Pain Syndrome: a qualitative needs assessment study
Authors: Bengtsen Samantha Charmaine , Zadro Joshua Robert , Rathleff Michael Skovdal , Foster Nadine E , Thomsen Janus Laust , Olesen Jens Lykkegaard , Søndergaard Jens , Lyng Kristian Damgaard
Published: October 2024

Background

There are a variety of different treatments for patients living with subacromial pain syndrome (SAPS). All treatments have small to moderate effect sizes, and it is challenging when healthcare practitioners and patients need to decide on which treatment options to choose. The aim of this study was to explore and understand the decisional needs of patients with SAPS, to inform and support the decision-making process.

Methods

A qualitative research study, using semi-structured individual interviews with patients with SAPS. The interview guide was informed by the Ottawa Decision Support Framework (ODSF), previous research related to treatment decision-making, other decisional needs assessment studies, and inputs from patients with SAPS and healthcare practitioners. Data were analysed by using reflexive thematic text analysis and ODSF. The analysis was conducted in NVivo 12.

Results

We invited 22 participants of which 17 (age 22-71 years) took part in the study. We found three main themes related to individual decisional needs in the context of decision-making: 1) The necessity of certainty and adequate information as fundamental prerequisites for effective decision-making, 2) The importance of person-centred care to achieve a desirable decision, and 3) The need for a supportive environment to facilitate adaptation and acceptance of the decision.

Conclusion

The decision-making process faced by patients with SAPS is complex and involves several decisional needs. Our findings highlight the importance of healthcare professionals identifying and addressing patients’ decisional needs in consultations with patients with SAPS.

Implications

Our study provides guidance to clinical practice in terms of increased understanding of the decisional needs experienced by patients with SAPS. Furthermore, these results should inform future development of decision aids for patients with SAPS.

Highlights

Subacromial pain syndrome is a complex condition, demanding a thorough decision-making process

We identified several concrete decisional needs through the Ottawa Decision Support Framework and further provided in-depth knowledge on key themes related to certainty, patient-centeredness, and support.

Our study provides information of designing a decision aid supporting shared decision-making in future studies.
Pre-pandemic national immunisation programme strength and health workforce capacity improved routine immunisation resilience during the COVID-19 pandemic
Authors: Evans Beth , Kaiser Laurent , Keiser Olivia , Jombart Thibaut
Published: October 2024

Background

The adverse impact of the COVID-19 pandemic on Routine Immunisation (RI) coverage has been well-documented: most countries experienced backsliding or stagnation in coverage. Qualitative surveys indicated potential causes of such declines, including reduced health care seeking behaviour, lockdowns, and overwhelmed health systems.

Methods

We investigate determinants of RI resilience during COVID-19 at a national level for 119 countries from 2020 to 2022, using publicly available data on pre-pandemic immunisation programme performance, health workforce capacity, health systems strength, health financing, global health security preparedness, COVID-19 burden, COVID-19 containment, economic, and health policy responses, population mobility changes, and country wealth. We employ a mixed methods approach: stepwise linear regression based on a causal inference framework, and Random Forest regression to identify potential nonlinear interactions and collinear effects.

Results

We provide evidence that stronger pre-pandemic immunisation programmes and more health workers, once above minimum thresholds (about 83% Diphtheria-Tetanus-Pertussis third-dose coverage and 60 health workers per 10,000 population), are associated with improved RI resilience. Random Forest analysis suggests health financing and health system strength impact RI resilience. COVID-19 vaccinations and pandemic policies were not associated with RI coverage changes, implying – reassuring – these acute responses did not interrupt routine services. In addition to these findings, a large fraction of variation in pandemic RI resilience remains unexplained, highlighting the need for further research on RI performance determinants.

Conclusion

Our findings underscore the role of robust immunisation programmes and sufficiently sized health workforces in mitigating RI disruption during global health crises once above minimum thresholds. Reassuringly, we do not find evidence that COVID-19 vaccination campaigns nor pandemic containment policies impacted RI performance – counter to qualitative survey indications. We encourage continued efforts to identify RI disruption determinants to inform the evidence base for public health practitioners globally.
“Trained Immunity” from BCG Vaccination andMycobacteriumspp. Exposure may be Linked to Reduced Early Childhood (<5-Year-olds) Brain and CNS Cancer Incidences
Authors: Singh Samer , Singh Rakesh K.
Published: October 2024

Globally, with improvements in general hygiene, the incidence of early childhood (0-4Y-olds/<5Y-olds) brain and central nervous system (BCNS) cancers is increasing. Although immunological underpinning is suspected, the identification of protective variables in most BCNS cancer cases remains elusive. Extant hypotheses suggest a role for progressively diminishing exposure to common microbes/pathogens in the rise of childhood cancers in industrialized countries with improved hygiene. Natural exposure to common microbes/pathogens and childhood vaccinations help train the developing immune system of children to respond appropriately to future infections and maintain a healthy immune system. Considering the established role of childhood vaccinations in augmenting immunity, including “trained immunity,” their protective role in pediatric cancers can be surmised. However, a lack of definitive theoretical and practical frameworks to explain conflicting observations has impaired progress. When we analyzed the epidemiological data of European region countries with different childhood vaccination policies but more similar socioeconomic conditions, access to medical services, and genetic makeup as compared to other parts of the world, the coverage of seven major childhood (0-1Y-olds) vaccines was not significantly associated with BCNS cancer incidences in the same cohort of 0-4Y-olds (2020). However, interestingly, prevailing tuberculin immunoreactivity, a surrogate for the existence of heterologous cell-mediated immunity resulting from exposure toMycobacteriumspp., including Bacille Calmette-Guérin (BCG) vaccination, for these populations, is found consistently negatively correlated with the BCNS cancer incidence in 0-4Y-olds for countries mandating neonatal BCG vaccination [r(24): -0.7226, p-value:<0.0001]. Neonatal immune system priming by BCG and boosting by exposure to environmentalMycobacteriumspp. appear protective in 0-4Y-olds. Exploration of BCNS cancer incidence and prevailing immune correlates in matched cohorts, along with prospective randomized controlled trials, may be warranted to confirm the impact of childhood vaccinations and boosters (including natural exposure) on early childhood BCNS cancer incidence.

STATEMENT OF SIGNIFICANCE

The discovery of preventive variables/interventions for early childhood (<5Y-old) brain and other CNS (BCNS) cancers is highly desirable. The early childhood BCNS cancer incidence rates in countries with differential childhood vaccination coverage and policies display a strong negative correlation withMycobacteriumspp. exposure chances/frequency in neonatal BCG-vaccinated children. A potentially protective cause- and-effect relationship with timelyMycobacteriumspp. exposures (BCGs and/or environmental) seems likely. An assessment of the biological and translational aspects of current observations is warranted.
A flexible multi-sensor device enabling handheld sensing of heart sounds by untrained users
Authors: McDonald Andrew , Nussbaumer Maximilian , Rathnayake Nirmani , Steeds Richard , Agarwal Anurag
Published: October 2024

Heart valve disease has a large and growing burden, with a prognosis worse than many cancers. Screening with a traditional stethoscope is underutilised, often inaccurate even in skilled hands, and requires time-consuming, intimate examinations. Here, we present a handheld device to enable untrained users to record high-quality heart sounds without the need to undress. The device incorporates multiple high-sensitivity sensors embedded in a flexible substrate, placed at key chest locations by the user. To address challenges from localised heart sound vibrations and noise interference, we developed time-frequency signal quality algorithms that automatically select the best sensor in the device and reject recordings with insufficient diagnostic quality. A validation study demonstrates the device’s effectiveness across a diverse range of body types, with multiple sensors significantly increasing the likelihood of a successful recording. The device has the potential to enable accurate, accessible, low-cost heart disease screening.
When Two plus Four Does Not Equal Six: Combining Computational and Functional Evidence Towards Classification of BRCA1 Key Domain Missense Substitutions.
Authors: Pew Scott T , Wiffler Madison B , Thomas Alun , Boyle Julie L , Cline Melissa S , Camp Nicola J , Goldgar David E , Tavtigian Sean V
Published: October 2024

Classification of genetic variants remains an obstacle to realizing the full potential of clinical genetic sequencing. Because of their ability to interrogate large numbers of variants, multiplexed assays of variant effect (MAVEs) and computational tools are viewed as a critical part of the solution to variant classification uncertainty. However, the (joint) performance of these assays and tools on novel variants has not been established. Transformation of the qualitative classification guidelines developed by the American College of Medical Genetics and Genomics (ACMG) into a quantitative Bayesian point system enables empirical validation of strength of evidence assigned to evidence criteria. Here, we derived a maximum likelihood estimate (MLE) model that converts frequentist odds ratios calculated from case-control data to proportions pathogenic and applied this model to functional assays, alone and in combination with, computational tools across several domains of BRCA1. Furthermore, we defined exceptionally conserved ancestral residues (ECARs) and interrogated the performance of assays and tools at these residues in BRCA1. We found that missense substitutions in BRCA1 that fall at ECARs are disproportionately likely to be pathogenic with effect sizes similar to that of protein truncating variants. In contrast, for substitutions falling at non-ECAR positions, concordant predictions of pathogenicity from functional assay and computational tool fail to meet the additive assumptions of strength in ACMG guidelines. Thus, collectively, we conclude that strengths of evidence assigned by expert opinion in the ACMG guidelines are not universally applicable and require empirical validation.
Associations of PFASs and Pesticides with Lung Function Changes from Adolescence to Young Adulthood in the ESPINA study
Authors: Kornher Kayleigh , Gould Carlos F. , Manzano Jomel Meeko , Baines Katie , Kayser Georgia , Tu Xin , Suarez-Torres Jose , Martinez Danilo , Suarez-Lopez Jose R
Published: October 2024

Per- and polyfluoroalkyl substances (PFASs) and pesticides are ubiquitous environmental exposures with increasingly recognized adverse health outcomes; however, their impact on lung function, particularly in combination, remains poorly understood. We included 381 adolescent participants from a prospective cohort study in Ecuador who underwent measurements of serum PFAS (perfluorooctanoic acid [PFOA], perfluorooctanesulfonic acid [PFOS] and perfluorononanoic acid [PFNA]) and urinary herbicides (glyphosate, 2,4D) and fungicides (ethylene thiourea) and had spirometric measurements in either 2016 or 2022. We characterized the association between each PFAS or pesticide and each lung function measure in log-log models estimated via ordinary least squares regression. We used quantile g-computation to assess the association of the mixture of PFAS and pesticides with lung function outcomes. After accounting for multiple hypothesis testing, and in models adjusting for household income, parental education, and exposure to tobacco, we found that, individually, PFOA, glyphosate, and ETU were associated with slight increases in FEV1/FVC between 2016 and 2022. No other individual associations were significant. In mixtures analyses, a one quartile increase in all PFASs and pesticides simultaneously was also not associated with statistically significant changes in lung function outcomes after accounting for multiple hypothesis testing. In large part, we do not provide evidence for associations of PFAS and herbicide and fungicide pesticides with lung function among adolescents in moderate-to-high-altitude agricultural communities in Ecuador.
Distinct proteomic signatures in Ethiopians predict acute and long-term sequelae of COVID-19
Authors: Wolday Dawit , Gebrehiwot Abrha G. , Rameto Muhammed Ahmed , Abdella Saro , Gebreegziabxier Atsbeha , Amogne Wondwossen , de Wit Tobias F. Rinke , Hailu Messay , Tollera Getachew , Tasew Geremew , Tessema Masresha , Miller Matthew , Mukhreji Manali , Gillgrass Amy , Bowdish Dawn M.E. , Kaushic Charu , Verschoor Chris P.
Published: October 2024

Little is known about the acute and long-term sequelae of COVID-19 and its pathophysiology in African patients, who are known to have a distinct immunological profile compared to Caucasian populations. Here, we established proteomic signatures to define severe outcomes of acute COVID-19 and determined whether proteome signatures during the first week of acute illness predict the risk of post-acute sequelae of COVID-19 (Long COVID) in a low-income country (LIC) setting. Using the Olink inflammatory panel, we measured the expression of 92 proteins in the plasma of COVID-19 patients (n=55) and non-COVID-19 individuals (n=23). We identified distinct inflammatory proteomic signatures in acute severe COVID-19 individuals (n=22) compared to asymptomatic or mild/moderate COVID-19 cases (n=33), and non-COVID-19 controls. Levels of SLAMF1, CCL25, IL2RB, IL10RA, IL15RA, IL18 and CST5 were significantly upregulated in patients with critical COVID-19 illness compared to individuals negative for COVID-19. The cohort was followed for an average of 20 months, and 23 individuals developed Long COVID, based on the WHO’s case definition, while 32 COVID-19 patients recovered fully. Whereas upregulated levels of SLAMF1, TNF, TSLP, IL15RA, IL18, ADA, CXCL9, CXCL10, IL17C, and NT3 at the acute phase of the illness were associated with increased Long COVID risk, upregulated expression of TRANCE was associated with a reduced risk of developing Long COVID. Proteomic expression levels of SLAMF1, IL15RA, and IL18 associated with critical illness during the acute phase of COVID-19 also predicted Long COVID risk. Unravelling the pathophysiology of severe acute COVID-19 and Long COVID before its advent may contribute to designing novel interventions for diagnosing, treating, and monitoring of SARS-CoV-2 infection and its associated acute and long-term consequences.
Elucidation and functional characterization of natural sweetener biosynthesis in hortensia species
Authors: Padmakumar Sarala Goutham , Engel Frauke , Hartmann Anja , von Wirén Nicolaus , Hajirezaei Mohammad-Reza
Published: October 2024

Among the various coumarins found in Hydrangea species, the bioactive dihydroisocoumarin known as phyllodulcin (PD) stands out as a non-caloric, high-intensity sweetener, which is up to 800 times sweeter than sucrose. Additionally, PD possesses notable medicinal properties, including antifungal, anti-ulcer, and anti-inflammatory effects. PD also plays several plant-specific roles, such as defending against phytopathogens, responding to abiotic and biotic stresses and regulating hormones. However, the biological function and biosynthetic pathway of PD in Hydrangea remain unexplored. This study employs targeted metabolomic and transcriptomic approaches to uncover the regulatory mechanisms and identify potential candidate genes involved in the biosynthesis of PD. 14 out of 182 different Hydrangea accessions, exhibiting varying levels of PD, were selected for detailed analysis. Accessions ofH. macrophyllawith high PD levels displayed distinct metabolite profiles compared to those with low PD concentrations. Specifically, pathways involving caffeic acid, ferulic acid, and their derivatives, such as scopolin, scopoletin, esculetin, and fraxetin, were predominant in accessions with low PD concentrations. Conversely, the metabolism of phenylalanine, umbelliferone, p-coumaric acid, naringenin, resveratrol, and Thn C was more active in accessions containing PD. Correlation analysis between PD and these metabolites offered valuable insights into their interrelationships. Transcriptome analysis revealed specific genes involved in phenylpropanoid biosynthesis, flavonoid biosynthesis, and stilbene biosynthesis pathways that are crucial for PD biosynthesis. Moreover, the identification of cyclase and ketoreductase genes, which were up regulated in accessions with high PD, provided further understanding of the biosynthetic pathway leading to PD. Finally, based on metabolite levels and gene expression data, a hypothetical pathway from resveratrol to Thn C was proposed, suggesting its potential involvement in PD biosynthesis.

Highlight

The metabolic and transcriptomic analysis led to the identification of specific metabolites and genes that are involved in the biosynthesis of dihydrisocoumarin.
Computational Insights into Membrane Disruption by Cell-Penetrating Peptides
Authors: Catalina-Hernandez Eric , Aguilella-Arzo Marcel , Peralvarez-Marin Alex , Lopez-Martin Mario
Published: October 2024

Cell-penetrating peptides (CPPs) can translocate into cells without inducing cytotoxicity. The internalization process implies several steps at different time scales ranging from microseconds to minutes. We combine adaptive Steered Molecular Dynamics (aSMD) with conventional Molecular Dynamics (cMD) to observe equilibrium and non-equilibrium states to study the early mechanisms of peptide-bilayer interaction leading to CPPs internalization. We define three membrane compositions representing bilayer sections, neutral lipids (i.e. upper leaflet), neutral lipids with cholesterol (i.e hydrophobic core), and neutral/negatively charged lipids with cholesterol (i.e. lower leaflet) to study the energy barriers and disruption mechanisms of Arg9, MAP, and TP2, representing cationic, amphiphilic, and hydrophobic CPPs, respectively. Cholesterol and negatively charged lipids increase the energetic barriers for peptide bilayer crossing. TP2 interacts with the bilayer by hydrophobic insertion, while Arg9 and MAP disrupt the bilayer by forming transient or stable pores. Collectively, these findings underscore the significance of innovative computational approaches in studying membrane-disruptive peptides, more specifically, in harnessing their potential for cell penetration.
A phosphoramidate modification of FUDR, NUC-3373, causes DNA damage and DAMPs release from colorectal cancer cells, potentiating lymphocyte-induced cell death
Authors: Read Oliver J. , Bré Jennifer , Zhang Ying , Mullen Peter , Elshani Mustafa , Harrison David J.
Published: October 2024

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide with 5-FU still the primary chemotherapeutic of choice. With the increasing use of immunotherapies, much research is focused on the ability to make tumours more immunogenic, thereby rationalising combination with immunotherapy. Here we investigate whether NUC-3373, a phosphoramidate transformation of FUDR, enhances immunogenicity in CRC cell lines and facilitates lymphocyte mediated cell deathin vitro. At sub IC50doses NUC-3373 upregulates damage associate molecular patterns (DAMPs) in both HCT116 and SW480 cells and increases surface expression of MHCII and PD-L1. Pre-treatment with NUC-3373 and subsequent coculture with NK-92 MI natural killer cells caused an increase in LAMP1 expression (degranulation), production of IFN-ψ, and NK-mediated cytotoxicity compared to vehicle controls. Cocultures with patient-derived PBMCs with heterologous CRC cells pre-treated with NUC-3373 demonstrated increased cell death compared to both vehicle controls and monocultures of CRC cells exposed to NUC-3373. Lastly, the PD-1 immune checkpoint inhibitor nivolumab showed synergistic activity when HCT116 cells were pre-treated with NUC-3373. To conclude, we show that NUC-3373 can modulate immune signaling and may therefore facilitate immune mediated tumour cell death.
Genomic and epigenomic maps of mouse centromeres and pericentromeres
Authors: Chaudhry Gitika , Chen Jinguye , Snipes Lucy , Bahl Smriti , Packiaraj Jenika , Lin Xuan , Thakur Jitendra
Published: October 2024

Satellite DNA makes up ∼11% of the mouse genome, predominantly located in centromeric and pericentric regions, which are crucial for chromosome segregation. While comprehensive assemblies of these regions have been established in the human genome, they are still lacking in the mouse genome. In this study, we used PacBio long-read sequencing, CUT&RUN sequencing, DNA methylation analysis, and RNA sequencing to generate genomic and epigenomic maps of these regions. We find that centromeric regions are primarily occupied by 120-mer Minor satellites, with other Minor Satellite length variants, 112-mers and 112-64-dimers, localized at centromere-pericentric junctions. Pericentromeric regions are mainly composed of homogeneous Major satellites, while pericentric-chromosomal junctions contain a higher density of divergent satellites. Additionally, the density of non-satellite repeats increases progressively from centromeres to pericentromeres, and further toward chromosomal arm junctions. We found that 120-mer Minor satellites in the core centromere are highly enriched with CENP-A, while the 112-mers and 112-64-dimers show lower CENP-A levels. Homogeneous Major satellites are more enriched with H3K9me3 heterochromatin, whereas divergent Major satellites are preferentially associated with H3K27me3. Furthermore, DNA methylation levels are lower in centromeres compared to pericentric regions. We also observed that only a small subset of satellites is transcribed into RNA, particularly regions exhibiting lower DNA methylation density. Our comprehensive assembly and characterization of the genomic and epigenomic landscape of mouse centromeric and pericentric regions have major implications for satellite biology and ongoing mouse telomere-to-telomere (T2T) assembly efforts.
Rare-Event Sampling using a Reinforcement Learning-Based Weighted Ensemble Method
Authors: Yang Darian T. , Goldberg Alex M. , Chong Lillian T.
Published: October 2024

Despite the power of path sampling strategies in enabling simulations of rare events, such strategies have not reached their full potential. A common challenge that remains is the identification of a progress coordinate that captures the slow relevant motions of a rare event. Here we have developed a weighted ensemble (WE) path sampling strategy that exploits reinforcement learning to automatically identify an effective progress coordinate among a set of potential coordinates during a simulation. We apply our WE strategy with reinforcement learning to three benchmark systems: (i) an egg carton-shaped toy potential, (ii) an S-shaped toy potential, and (iii) a dimer of the HIV-1 capsid protein (C-terminal domain). To enable rapid testing of the latter system at the atomic level, we employed discrete-state synthetic molecular dynamics trajectories using a generative, fine-grained Markov state model that was based on extensive conventional simulations. Our results demonstrate that using concepts from reinforcement learning with a weighted ensemble of trajectories automatically identifies relevant progress coordinates among multiple candidates at a given time during a simulation. Due to the rigorous weighting of trajectories, the simulations maintain rigorous kinetics.
MANGIFERIN AS A POTENTIAL INHIBITOR OF TRANSTHYRETIN FIBRILLOGENESIS
Authors: Grudinina N.A. , Petukhov M.G. , Shaldzhyan A.A. , Zabrodskaya Y.A. , Gavrilova N.V. , Morozkina S.N. , Egorov V.V.
Published: October 2024

By usingin silicomolecular docking, we predicted a high potential of mangiferin to inhibit transthyretin amyloidogenesis. Subsequently, we tested this prediction in anin vitrosystem. The study involved testing effect of mangiferrin in a system that included isolated and purified recombinant transthyretin under fibrillogenesis conditions and a detection assay based on the fluorescent dye thioflavin T, characteristic of amyloid fibrils. The conditions for fibrillogenesis of this protein at neutral pH values were established. Using the developed test system, it was shown that mangiferin is able to inhibit abnormal transthyretin fibrillogenesis.
Genome-wide studies define new genetic mechanisms of IgA vasculitis
Authors: Liu Lili , Zhu Li , Monteiro-Martins Sara , Griffin Aaron , Vlahos Lukas J. , Fujita Masashi , Berrouet Cecilia , Zanoni Francesca , Marasa Maddalena , Zhang Jun Y. , Zhou Xu-jie , Caliskan Yasar , Akchurin Oleh , Al-Akash Samhar , Jankauskiene Augustina , Bodria Monica , Chishti Aftab , Esposito Ciro , Esposito Vittoria , Claes Donna , Tesar Vladimir , Davis Thomas K. , Samsonov Dmitry , Kaminska Dorota , Hryszko Tomasz , Zaza Gianluigi , Flynn Joseph T. , Iorember Franca , Lugani Francesca , Rizk Dana , Julian Bruce A. , Hidalgo Guillermo , Kallash Mahmoud , Biancone Luigi , Amoroso Antonio , Bono Luisa , Mani Laila-Yasmin , Vogt Bruno , Lin Fangming , Sreedharan Raji , Weng Patricia , Ranch Daniel , Xiao Nianzhou , Quiroga Alejandro , Matar Raed Bou , Rheault Michelle N. , Wenderfer Scott , Selewski Dave , Lundberg Sigrid , Silva Cynthia , Mason Sherene , Mahan John D. , Vasylyeva Tetyana L. , Mucha Krzysztof , Foroncewicz Bartosz , Pączek Leszek , Florczak Michał , Olszewska Małgorzata , Gradzińska Agnieszka , Szczepańska Maria , Machura Edyta , Badeński Andrzej , Krakowczyk Helena , Sikora Przemysław , Kwella Norbert , Miklaszewska Monika , Drożdż Dorota , Zaniew Marcin , Pawlaczyk Krzysztof , Siniewicz-Luzeńczyk Katarzyna , Bomback Andrew S. , Appel Gerald B. , Izzi Claudia , Scolari Francesco , Materna-Kiryluk Anna , Mizerska-Wasiak Malgorzata , Berthelot Laureline , Pillebout Evangeline , Monteiro Renato C. , Novak Jan , Green Todd Jason , Smoyer William E. , Hastings M. Colleen , Wyatt Robert J. , Nelson Raoul , Martin Javier , González-Gay Miguel A. , De Jager Philip L. , Köttgen Anna , Califano Andrea , Gharavi Ali G. , Zhang Hong , Kiryluk Krzysztof
Published: October 2024

IgA vasculitis (IgAV) is a pediatric disease with skin and systemic manifestations. Here, we conducted genome, transcriptome, and proteome-wide association studies in 2,170 IgAV cases and 5,928 controls, generated IgAV-specific maps of gene expression and splicing from blood of 255 pediatric cases, and reconstructed myeloid-specific regulatory networks to define disease master regulators modulated by the newly identified disease driver genes. We observed significant association at theHLA-DRB1(OR=1.55, P=1.1×10−25) and fine-mapped specific amino-acid risk substitutions in DRβ1. We discovered two novel non-HLA loci:FCAR(OR=1.51, P=1.0×10−20) encoding a myeloid IgA receptor FcαR, andINPP5D(OR=1.34, P=2.2×10−09) encoding a known inhibitor of FcαR signaling. TheFCARrisk locus co-localized with a cis-eQTL increasingFCARexpression; the risk alleles disrupted aPRDM1binding motif within a myeloid enhancer ofFCAR. Another risk locus was associated with a higher genetically predicted levels of plasma IL6R. TheIL6Rrisk haplotype carried a missense variant contributing to accelerated cleavage of IL6R into a soluble form. Using systems biology approaches, we prioritized IgAV master regulators co-modulated byFCAR,INPP5DandIL6Rin myeloid cells. We additionally identified 21 shared loci in a cross-phenotype analysis of IgAV with IgA nephropathy, including novel lociPAID4, WLS, andANKRD55.
Biallelic variants inMRPL49cause variable clinical presentations, including sensorineural hearing loss, leukodystrophy, and ovarian insufficiency
Authors: Thomas Huw B. , Demain Leigh A.M. , Cabrera-Orefice Alfredo , Schrauwen Isabelle , Shamseldin Hanan E. , Rea Alessandro , Bharadwaj Thashi , Smith Thomas B. , Oláhová Monika , Thompson Kyle , He Langping , Kaur Namanpreet , Shukla Anju , Abukhalid Musaad , Ansar Muhammad , Rehman Sakina , Riazuddin Saima , Abdulwahab Firdous , Smith Janine M. , Stark Zornitza , Carrera Samantha , Yue Wyatt W. , Munro Kevin J. , Alkuraya Fowzan S. , Jamieson Peter , Ahmed Zubair M. , Leal Suzanne M. , Taylor Robert W. , Wittig Ilka , O’Keefe Raymond T. , Newman William G.
Published: October 2024

Combined oxidative phosphorylation deficiency (COXPD) is a rare multisystem disorder which is clinically and genetically heterogeneous. Genome sequencing identified biallelicMRPL49variants in individuals from five unrelated families with presentations ranging from Perrault syndrome (primary ovarian insufficiency and sensorineural hearing loss) to severe childhood onset of leukodystrophy, learning disability, microcephaly and retinal dystrophy. Complexome profiling of fibroblasts from affected individuals revealed reduced levels of the small and, a more pronounced reduction of, the large mitochondrial ribosomal subunits. There was no evidence of altered mitoribosomal assembly. The reductions in levels of OXPHOS enzyme complexes I and IV are consistent with a form of COXPD associated with biallelicMRPL49variants, expanding the understanding of how disruption of the mitochondrial ribosomal large subunit results in multi-system phenotypes.