bluuebunny/crossref_metadata_2025 huggingface dataset:
Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma
Authors: Margalit Sapir , Tulpová Zuzana , Michaeli Yael , Detinis Zur Tahir , Deek Jasline , Louzoun-Zada Sivan , Nifker Gil , Grunwald Assaf , Scher Yuval , Schütz Leonie , Weinhold Elmar , Gnatek Yehudit , Omer Dorit , Dekel Benjamin , Friedman Eitan , Ebenstein Yuval
Published: October 2022

Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily characterized by short-read sequencing. We present a method for simultaneous profiling of long-range genetic/epigenetic changes in matched cancer samples. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer. Most ccRCC cases demonstrate somatic genomic alterations involving the short arm of chromosome 3 (3p), most often targeting the von Hippel–Lindau (VHL) gene. Aiming to identify somatic alterations that characterize early stage ccRCC, we performed comprehensive genetic, cytogenetic and epigenetic analyses comparing ccRCC tumor to adjacent non-tumorous tissue. Optical genome mapping identified genomic aberrations such as structural and copy number variations, complementing exome-sequencing results. Single-molecule methylome and hydroxymethylome mapping revealed multiple differential regions, some of them known to be associated with ccRCC pathogenesis. Among them, metabolic pathways were significantly enriched. Moreover, significant global epigenetic differences were detected between the tumor and the adjacent non-tumorous tissue, and a correlation between epigenetic signals and gene expression was found. This is the first reported comparison of a human tumor and a matched tissue by optical genome/epigenome mapping, revealing well-established and novel somatic aberrations.
Engineering a Universal Dengue Virus Vaccine using a Virus-Like Particle Scaffold
Authors: Basore Danielle A. , Barcellona Carolyn M. , Jordan Thomas B. , Crone Donna E. , Isern Sharon , Michael Scott F. , Bystroff Christopher
Published: October 2022

The authors have withdrawn their manuscript as it was submitted and made public without the full consent of all the authors. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.”
Coevolution of species colonization rates controls food-chain length in spatially structured food webs
Authors: Calcagno Vincent , David Patrice , Jarne Philippe , Massol François
Published: October 2022

The complexity of food webs and how it depends on environmental variables is a long-standing question in ecology. Food-chain length depends on many factors, such as productive space, disturbance and spatial processes. It is not clear though how food-chain length should vary with adaptive evolutionary changes of the constitutive species. Assuming that each trophic level is subject to a competition-colonization trade-off, we model the adaptive evolution of their colonization rates and its consequences on equilibrium occupancies and food-chain length. When colonization rates are allowed to evolve, longer food chains can persist. Extinction, perturbation and habitat loss all affect the evolutionary-stable colonization rates, but trade-off strength (costs of dispersal) has a major role: weaker trade-offs yield longer chains. Our results suggest a strong link between within-trophic level competition, spatial occupancies and food-chain length. Although these eco-evo dynamics partly alleviate the constraint on food-chain length in metacommunities, we show it is no magic bullet: the highest, most vulnerable, trophic levels are also those that least benefit from evolution. Our model generates qualitative predictions regarding how trait evolution affects the response of communities to disturbance and habitat loss. This highlights the importance of eco-evolutionary dynamics at metacommunity level in determining food-chain length.
Virulence Network of Interacting Influenza-Host Protein Domains
Authors: Ng Teng Ann , Rashid Shamima , Kwoh Chee Keong
Published: October 2022

There exist several databases that provide virus-host protein interactions. While most provide curated records of interacting virus-host protein pairs, information on the strain-specific virulence factors or protein domains involved, is lacking. Some databases offer incomplete coverage of Influenza strains because of the need to sift through vast amounts of literature (including those of major viruses including HIV and Dengue, besides others). None have offered complete, strain specific protein-protein interaction records for the Influenza A group of viruses.

In this paper, we present a comprehensive network of predicted domain-domain interaction(s) (DDI) between Influenza A virus (IAV) and mouse host proteins, that will allow the systematic study of disease factors by taking the virulence information (lethal dose) into account. From a previously published dataset of lethal dose studies of IAV infection in mice, we constructed an interacting domain network of mouse and viral protein domains as nodes with weighted edges. The edges were scored with the Domain Interaction Statistical Potential (DISPOT) to indicate putative DDI.

The virulence network can be easily navigated via a web browser, with the associated virulence information (LD50values) prominently displayed. The network will aid Influenza A disease modeling by providing strain-specific virulence levels with interacting protein domains. It can possibly contribute to computational methods for uncovering Influenza infection mechanisms mediated through protein domain interactions between viral and host proteins.
Remodeling of yeast vacuole membrane lipidomes from the log (1-phase) to stationary stage (2-phases)
Authors: Reinhard John , Leveille Chantelle L. , Cornell Caitlin E. , Merz Alexey J. , Klose Christian , Ernst Robert , Keller Sarah L.
Published: October 2022

Upon nutrient limitation, budding yeast ofSaccharomyces cerevisiaeshift from fast growth (the log stage) to quiescence (the stationary stage). This shift is accompanied by liquid-liquid phase separation in the membrane of the vacuole, an endosomal organelle. Recent work indicates that the resulting micron-scale domains in vacuole membranes enable yeast to survive periods of stress. An outstanding question is which molecular changes might cause this membrane phase separation. Here, we conduct lipidomics of vacuole membranes in both the log and stationary stages. Isolation of pure vacuole membranes is challenging in the stationary stage, when lipid droplets are in close contact with vacuoles. Immuno-isolation has previously been shown to successfully purify log-stage vacuole membranes with high organelle specificity, but it was not previously possible to immuno-isolate stationary stage vacuole membranes. Here, we develop Mam3 as a bait protein for vacuole immuno-isolation, and demonstrate low contamination by non-vacuolar membranes. We find that stationary stage vacuole membranes contain surprisingly high fractions of phosphatidylcholine lipids (∼50%), roughly twice as much as log-stage membranes. Moreover, in the stationary stage these lipids have higher melting temperatures, due to longer and more saturated acyl chains. Another surprise is that no significant change in sterol content is observed. These results fit within the predominant view that phase separation in membranes requires at least three types of molecules to be present: lipids with high melting temperatures, lipids with low melting temperatures, and sterols.

SIGNIFICANCE STATEMENT

When budding yeast shift from growth to quiescence, the membrane of one of their organelles (the vacuole) undergoes liquid-liquid phase separation. What changes in the membrane’s lipids cause this phase transition? Here, we conduct lipidomics of immuno-isolated vacuole membranes. We analyze our data in the context of lipid melting temperatures, inspired by observations that liquid-liquid phase separation in model membranes requires a mixture of lipids with high melting temperatures, lipids with low melting temperatures, and sterols. We find that phase-separated vacuole membranes have higher concentrations of PC lipids, and that those lipids have higher melting temperatures. To conduct our experiments, we developed a tagged version of a protein (Mam3) for immuno-isolation of vacuole membranes.
Photodynamic therapy in colorectal cancer using photosensitizers functionalized by arene-ruthenium complexes
Authors: Massoud Jacquie , Pinon Aline , Gallardo-Villagran Manuel , Paulus Lucie , Antoun Sayed , Diab-Assaf Mona , Therrien Bruno , Liagre Bertrand
Published: October 2022

Colorectal cancer (CRC) is one of the most frequently diagnosed cancers worldwide and one of the main causes of cancer deaths in the global population. First-line treatment usually includes surgical procedures followed by combination chemotherapy. Despite the improvements in CRC treatments, the mortality rate remains very high, leading consequently to conventional treatment resistance. Several therapies were enrolled to this content in a way to find the best solutions for this disease. Photodynamic therapy (PDT) using photosensitizers (PS) presents itself as an original innovative therapeutic strategy that strongly limits the undesirable side effects of conventional treatment. However, low physiological solubility and a lack of selectivity of PS towards tumor sites are the principal restrictions of their current clinical use. Indeed, drug delivery systems are currently a key issue in cancer therapy. To overcome the problem of solubility and stability of PS such as porphyrins and their derivatives, metallic assemblies based on arene-ruthenium (Ru) units have begun to attract considerable attention as PS delivery systems. The purpose of this study was to demonstrate firstly the interest in the vectorization of tetrapyridylporphin (TPyP-arene-Ru) and Zn-tetrapyridylporphin arene-ruthenium (Zn-TPyP-arene-Ru) metallacages to increase their solubility in biological media and then, consequently their anticancer efficacy in PDT. Secondly, to elucidate the anticancer mechanism as well as identify the cell death process mediated by these new vectorized PS. The results showed that the two PS-arene-Ru complexes have a strong photocytotoxic effect after photoactivation on human HCT116 and HT-29 colorectal cancer cell lines. TPyP-arene-Ru-PDT induced outstanding cytotoxicity when compared to the Zn-TPyP-arene-Ru analogue. The two complexes show no significant effect on proliferation in the dark. In addition, results demonstrated that these two PS-arene-Ru complexes-PDT induce an apoptotic process through the appearance of a sub-G1 peak, phosphatidylserines externalization, poly-ADP ribose polymerase (PARP) cleavage and DNA fragmentation. Thus, our data contribute to highlighting that the incorporation of porphyrins in Ru-based assemblies could be an efficient vectorized system to treat CRC by PDT.
SARS-CoV2 associated secretion of nanoLuciferase reports on virus and Virus-Like Particle production
Authors: Gullberg Rebekah C. , Frydman Judith
Published: October 2022

SARS-CoV2 is a positive-strand RNA virus in theCoronaviridaefamily that has caused world-wide morbidity and mortality. While much progress has been made we still need expanded rapid anti-virals. The top advanced antiviral candidates all target stages of RNA replication, leaving virus assembly an unexplored avenue of antiviral research. To address this gap, and explore the biochemical and cell biological features of viral assembly, we have employed an improved virus-like particle (VLP) system. We exploited the small nanoLuciferase protein for enhanced signal and surprisingly found that the protein itself appears to be packaged into both SARS CoV2 VLPs and virions and secreted from cells. Interestingly, nLuc is not co-secreted with dengue or Zika infection, suggesting the large virion of Coronavirus can encaspidate and secrete a cellularly expressed reporter protein. Our findings open the way for powerful new approaches to measure viral particle production, egress and viral entry mechanisms.
Tripartite interactions between filamentous Pf4 bacteriophage,Pseudomonas aeruginosa, and bacterivorous nematodes
Authors: Schwartzkopf Caleb M. , Robinson Autumn J. , Ellenbecker Mary , Faith Dominick R. , Brooks Diane M. , Lewerke Lincoln , Voronina Ekaterina , Dandekar Ajai A. , Secor Patrick R.
Published: October 2022

The opportunistic pathogenPseudomonas aeruginosaPAO1 is infected by the filamentous bacteriophage Pf4. Pf4 virions promote biofilm formation, protect bacteria from antibiotics, and modulate animal immune responses in ways that promote infection. Furthermore, strains cured of their Pf4 infection (ΔPf4) are less virulent in animal models of infection. Consistently, we find that strain ΔPf4 is less virulent in aCaenorhabditis elegansnematode infection model. However, our data indicate that PQS quorum sensing is activated and production of the pigment pyocyanin, a potent virulence factor, is enhanced in strain ΔPf4. The reduced virulence of ΔPf4 despite high levels of pyocyanin production may be explained by our finding thatC. elegansmutants unable to sense bacterial pigments through the aryl hydrocarbon receptor are more susceptible to ΔPf4 infection compared to wild-typeC. elegans. Collectively, our data support a model where suppression of quorum-regulated virulence factors by Pf4 allowsP. aeruginosato evade detection by innate host immune responses.

Author Summary

Pseudomonas aeruginosais an opportunistic bacterial pathogen that infects wounds, lungs, and medical hardware.P. aeruginosastrains are often themselves infected by a filamentous virus (phage) called Pf. At sites of infection, filamentous Pf virions are produced that promote bacterial colonization and virulence. Here, we report that strains ofP. aeruginosacured of their Pf infection are less virulent in aCaenorhabditis elegansnematode infection model. We also report that PQS quorum sensing and production of the virulence factor pyocyanin are enhanced inP. aeruginosastrains cured of their Pf infection. Compared to wild-typeC. elegans, nematodes unable to detect bacterial pigments via the aryl hydrocarbon receptor AhR were more susceptible to infection by Pf-freeP. aeruginosastrains that over-produce pyocyanin. Collectively, this study supports a model where Pf phage suppressP. aeruginosaPQS quorum sensing and reduce pyocyanin production, allowingP. aeruginosato evade AhR-mediated immune responses inC. elegans.
Discovering hub genes involved in the pathophysiological impact of COVID-19 on diabetes kidney disease by differential gene expression and interactome analysis
Authors: Osuna-Martínez Ulises , Aviña-Padilla Katia , Olimón-Andalón Vicente , Angulo-Rojo Carla , Guadrón-Llanos Alma , Rivas-Ferreira José Carlos , Urrea Francisco , Calderon-Zamora Loranda
Published: October 2022

Diabetic kidney disease (DKD) is a frequently chronic kidney pathology derived from diabetes comorbidity. This condition has irreversible damage, and its risk factor increases with SARS-CoV-2 infection. The prognostic outcome for diabetic patients with COVID-19 is dismal, even with intensive medical treatment. However, there is still scarce information on critical genes involved in the pathophysiological impact of COVID-19 on DKD. Herein, we characterize differential expression gene (DEG) profiles and determine hub genes undergoing transcriptional reprogramming in both disease conditions. Out of 995 DEGs, we identified 42 DEGs shared with COVID-19 pathways. Enrichment analysis elucidated that they are significantly induced with implications for immune and inflammatory responses. By performing a protein-protein interaction (PPI) network and applying topological methods, we determine the following five hub genesSTAT1, IRF7, ISG15, MX1, andOAS1. Then, by network deconvolution, we determine their co-expressed gene modules. Moreover, we validate the conservancy of their upregulation using the Coronascape database (DB). Finally, tissue-specific regulation of the five predictive hub genes indicates thatOAS1andMX1expression levels are lower in healthy kidney tissue. Altogether, our results suggest that these genes could play an essential role in developing severe outcomes of COVID-19 in DKD patients.
Real-time surveillance of international SARS-CoV-2 prevalence using systematic traveller arrival screening
Authors: Kucharski Adam J , Chung Kiyojiken , Aubry Maite , Teiti Iotefa , Teissier Anita , Richard Vaea , Russell Timothy W , Bos Raphaëlle , Olivier Sophie , Cao-Lormeau Van-Mai
Published: October 2022

Background

Effective COVID-19 response relies on good knowledge of infection dynamics, but owing to under-ascertainment and delays in symptom-based reporting, obtaining reliable infection data has typically required large dedicated local population studies. Although many countries implemented SARS-CoV-2 testing among travellers, interpretation of arrival testing data has typically been challenging because arrival testing data were rarely reported systematically, and pre-departure testing was often in place as well, leading to non-representative infection status among arrivals.

Methods

In French Polynesia, testing data were reported systematically with enforced pre-departure testing type and timing, making it possible to adjust for non-representative infection status among arrivals. Combining statistical models of PCR positivity with data on international travel protocols, we reconstructed estimates of prevalence at departure using only testing data from arrivals. We then applied this estimation approach to the USA and France, using data from over 220,000 tests from travellers arriving into French Polynesia between July 2020 and March 2022.

Findings

We estimated a peak infection prevalence at departure of 2.8% (2.3-3.6%) in France and 1.1% (0.81-3.1%) in the USA in late 2020/early 2021, with prevalence of 5.4% (4.8-6.1%) and 5.5% (4.6-6.6%) respectively estimated for the Omicron BA.1 waves in early 2022. We found that our infection estimates were a leading indicator of later reported case dynamics, as well as being consistent with subsequent observed changes in seroprevalence over time.

Interpretation

As well as elucidating previously unmeasured infection dynamics in these countries, our analysis provides a proof-of-concept for scalable tracking of global infections during future pandemics.

Funding

Wellcome (206250/Z/17/Z)
Cytosolic PCNA interacts with S100A8 and controls an inflammatory subset of neutrophils in COVID-19
Authors: de Oliveira Formiga Rodrigo , Pesenti Lucie , Ladjemi Maha Zohra , Frachet Philippe , Andrieu Muriel , Many Souganya , Karunanithy Vaarany , Bailly Karine , Dhôte Théo , Castel Manon , Rousseau Christophe , Starick Marick , da Rocha Edroaldo Lummertz , Lombardi Emilia Puig , Granger Vanessa , Chollet-Martin Sylvie , De Chaisemartin Luc , Mouthon Luc , Spiller Fernando , Hosmalin Anne , Hurtado-Nedelec Margarita , Martin Clémence , Pène Frédéric , Burgel Pierre-Regis , Tourneur Léa , Witko-Sarsat Véronique
Published: October 2022

Neutrophils are key players in the hyperinflammatory response upon SARS-CoV-2 infection. We have previously described that cytosolic proliferating cell nuclear antigen (PCNA) controls neutrophil survival and NADPH oxidase-dependent ROS production. We here show that both PCNA and S100A8 expression and interaction were elevated in neutrophils from patients with COVID-19 compared to healthy donors and this was correlated with disease severity. Increased PCNA expression was accompanied by a decreased apoptosis and increased NADPH-oxidase activity in neutrophils from COVID-19 patients compared to healthy donors. These effects, as well as the interaction between PCNA and S100A8, were potently counteracted by T2 amino alcohol (T2AA), a PCNA inhibitor, demonstrating that the PCNA scaffold orchestrated neutrophil activation. Notably, the interaction between PCNA-S100A8 was more intense in the CD16high-CD62Llowactivated neutrophil subset. We propose that PCNA-S100A8 complex acts as potential driver for neutrophil dysregulation in COVID-19 and show for the first time that the PCNA scaffold is a decisive component of both neutrophil activation and heterogeneity.
Analysis of fatality among COVID-19 cases in Mexican pregnant women: a cross-sectional study
Authors: Padilla-Raygoza Nicolás , Gallardo-Luna María de Jesús , Flores-Vargas Gilberto , Navarro-Olivos Efrain , Magos-Vázquez Francisco J. , Lara-Lona Elia , Díaz-Martínez Daniel A.
Published: October 2022

This study aims to analyze the fatality of cases confirmed by COVID-19 among pregnant women in Mexico. It is a cross-sectional and analytical study. We used the registries from pregnant women available in the open database of the National Epidemiological Surveillance System from the General Directorate of Epidemiology. We showed descriptive statistics for all the variables. A suspected case of COVID-19 is any person who presented the following signs and symptoms: fever, headache, cough, and others. A confirmed case is any suspected case with a positive RT-PCR test result. We computed OR and 95% confidence intervals to estimate the effect of independent variables on dying from COVID-19. Also, it was calculated the Case Fatality Ratio (CFR) among pregnant women. The alpha value was fixed at 0.05 as a threshold to show statistical significance. The CFR was 1.09%. For confirmed cases, the average age among those who died was higher than among those who did not die (P <0.05). The average time between the onset of symptoms and registration in the system was higher for those who died (P <0.05). Among the deceased, 76.97% had pneumonia. For the 40-49 years age group, the effect on death was statistically significant (OR 4.97, CI95% 1.77 – 17.85). Outpatient care had a protective effect on dying (OR 0.04, CI95% 0.02 – 0.09). Pneumonia was highly associated with death (OR 8.68, CI95% 5.72 – 13.6). Co-morbidities did not affect dying while considering them in a multivariable logistic regression model. Among pregnant women, smoking has little effect on death by COVID-19. The CFR was low compared with the rest of the Mexican population. The co-morbidities had a low prevalence among pregnant women. Since the reproductive age span is young age, pregnant women have two protective factors for COVID-19 detected so far: being young and woman.
Presence of ventriculoperitoneal and lumbar shunts stimulate long lasting non-inflammatory changes in the cerebrospinal fluid distinct from the response to bacterial infection
Authors: Cuff Simone M. , Merola Joseph P. , Eberl Matthias , Gray William P.
Published: October 2022

Ventriculoperitoneal (VP) shunts are effective at relieving hydrocephalus but are prone to malfunction. There are two hypotheses as to how shunts may malfunction independently of mechanical failure or blockage by debris from initial placement. The first is that the presence of a foreign object results in cells migrating into and colonising the shunt. The second is that the shunts contain either small numbers of live bacteria or residual bacterial products from manufacture or handling, triggering an inflammatory response that attracts cells to the site which go on to cause malfunctions. The presence of bacteria can be difficult to definitively rule in or out, given that they are capable of forming biofilms which poses challenges for isolation and microbiological culture. In this study, we measured 91 soluble immunological molecules and 91 soluble neurological molecules in CSF of patients with VP shunts and compared them to both patients without shunts and those with bacterial infection to determine whether there is an ongoing inflammatory response to shunting. We find that shunts elicit a soluble signature of neural wound healing and cell migration proteins that is distinct from the inflammatory signature of patients with neurological infection. This appears to represent a long-term response, persisting for at least 5 years in one patient.
Personalized Mood Prediction from Patterns of Behavior Collected with Smartphones
Authors: Balliu Brunilda , Douglas Chris , Seok Darsol , Shenhav Liat , Wu Yue , Chatzopoulou Doxa , Kaiser William , Chen Victor , Kim Jennifer , Deverasetty Sandeep , Arnaudova Inna , Gibbons Robert , Congdon Eliza , Craske Michelle G. , Freimer Nelson , Halperin Eran , Sankararaman Sriram , Flint Jonathan
Published: October 2022

Over the last ten years, there has been considerable progress in using digital behavioral phenotypes, captured passively and continuously from smartphones and wearable devices, to infer depressive mood. However, most digital phenotype studies suffer from poor replicability, often fail to detect clinically relevant events, and use measures of depression that are not validated or suitable for collecting large and longitudinal data. Here, we report high-quality longitudinal validated assessments of depressive mood from computerized adaptive testing paired with continuous digital assessments of behavior from smartphone sensors for up to 40 weeks on 183 individuals experiencing mild to severe symptoms of depression. We apply a combination of cubic spline interpolation and idiographic models to generate individualized predictions of future mood from the digital behavioral phenotypes, achieving high prediction accuracy of depression severity up to three weeks in advance (R2:2 80%) and a 65.7% reduction in the prediction error over a baseline model which predicts future mood based on past depression severity alone. Finally, our study verified the feasibility of obtaining high-quality longitudinal assessments of mood from a clinical population and predicting symptom severity weeks in advance using passively collected digital behavioral data. Our results indicate the possibility of expanding the repertoire of patient-specific behavioral measures to enable future psychiatric research.
Spleen stiffness can predict liver decompensation and survival in patients with cirrhosis
Authors: Karagiannakis Dimitrios S , Voulgaris Theodoros , Markakis George , Lakiotaki Dimitra , Michailidou Elisavet , Cholongitas Evangelos , Papatheodoridis George
Published: October 2022

Background/Aim

Liver stiffness measurement (LSM) has been predicting liver decompensation and survival in cirrhotics. The aim of our study was to investigate if spleen stiffness measurement (SSM) by 2D-Shear Wave Elastography could predict better the probability of decompensation and mortality, compared to LSM and other parameters.

Methods

Consecutive cirrhotic patients were recruited between 1/2017-12/2021. LSM and SSM were performed at baseline and epidemiological, clinical and laboratory data were collected. Clinical events were recorded every 3 months.

Results

Totally, 177 patients were followed for a mean period of 31±18 months. In Cox regression analysis, only SSM was independently associated with the probability of decompensation (HR: 1.063, 95% CI: 1.009-1.120; p=0.021), offering an AUROC of 0.710 (p=0.003) for predicting 1-year liver decompensation (NPV: 81.1% for the cut-off point of 37 kPa). The occurrence of death/liver transplantation was independently associated only with higher SSM (HR: 1.043; 95% CI:1.003-1.084; p=0.034). The AUROC of SSM for predicting 1-year death/liver transplantation was 0.72 (p=0.006), (NPV: 95% for the cut-off of 38.8 kPa). The performance of SSM to predict the 1-year death/liver transplantation increased in high-risk patients (CTP: B/C plus MELD >10 plus LSM >20 kPa) giving an AUROC of 0.80 (p<0.001). Only 1/26 high-risk patients with SSM <38.8 kPa died during the first year of follow-up (NPV: 96.4%).

Conclusions

SSM was the only factor independently associated with the probability of decompensation and occurrence of death, showing better diagnostic accuracy for the prediction of 1-year decompensation or death compared to LSM and MELD score.
Use of artificial intelligence on retinal images to accurately predict the risk of cardiovascular event (CVD-AI)
Authors: Vaghefi Ehsan , Squirrell David , Yang Song , An Songyang , Marshall John
Published: October 2022

Purpose

To create and evaluate the accuracy of an artificial intelligence platform capable of using only retinal fundus images to predict both an individual’s overall 10 year Cardiovascular Disease (CVD) risk and the relative contribution of the component risk factors that comprise this risk (CVD-AI).

Methods

The UK Biobank and the US-based AREDS 1 datasets were obtained and used for this study. The UK Biobank data was used for training, validation and testing, while the AREDS 1 dataset was used as an external testing dataset. Overall, we used 110,272 fundus images from 55,118 patient visits. A series of models were trained to predict the risk of CVD against available labels in the UK Biobank dataset.

Results

In both the UK Biobank testing dataset and the external validation dataset (AREDS 1), the 10-year CV risk scores generated by CVD-AI were significantly higher for patients who had suffered an actual CVD event when compared to patients who did not experience a CVD event. In the UK Biobank dataset the median 10-year CVD risk for those individuals who experienced a CVD was higher than those who did not (4.9% [ICR 2.9-8%] v 2.3% [IQR 4.3-1.3%] P<0.01.]. Similar results were observed in the AREDS 1 dataset The median 10-year CVD risk for those individuals who experienced a CVD event was higher than those who did not (6.2% [ICR 3.2%-12.9%] v 2.2% [IQR 3.9-1.3%] P<0.01

Conclusion

Retinal photography is inexpensive and as fully automated, inexpensive camera systems are now widely available, minimal training is required to acquire them. As such, AI enabled retinal image-based CVD risk algorithms like CVD-AI will make cardiovascular health screening more affordable and accessible. CVD-AI’s unique ability to assess the relative contribution of the components that comprise an individual’s overall risk could inform personalized treatment decisions based on the specific needs of an individual, thereby increasing the likelihood of positive health outcomes.
Essential role of the amino-terminal region of Drosha for the Microprocessor function
Authors: Prabhakar Amit , Hu Song , Tang Jin , Ghatpande Prajakta , Lagna Giorgio , Jiang Xuan , Hata Akiko
Published: October 2022

The ribonuclease (RNase) III enzyme Drosha enables processing of microRNA (miRNA) primary transcripts (pri-miRNAs) and control of ribosomal protein (RP) biogenesis by the Microprocessor. The extensively studied carboxyl-terminal half of Drosha is sufficient to crop pri-miRNAs in vitro, but the function of the evolutionarily conserved Drosha amino-terminal region (NTR) is unknown, despite it harboring mutations linked to a hereditary vascular disorder. Here, we provide evidence that, when replacing the endogenous Drosha, a mutant missing the NTR (ΔN-Drosha) fails to associate with endogenous pri-miRNAs and to support the expression of all miRNAs, except the miR-183 cluster. Surprisingly, Argonaute2 (Ago2) associates with and cleaves pri-miR-183 in ΔN-Drosha cells and in Drosha-depleted cells. ΔN-Drosha is also unable to inhibit RP biogenesis upon serum starvation. Thus, Drosha NTR is essential for pri-miRNA processing and RP biogenesis in vivo, and Ago2 can process the miR-183 cluster in the absence of Drosha.
Alterations in platelet proteome signature and impaired platelet integrin αIIbβ3activation in patients with COVID-19
Authors: Goudswaard Lucy J. , Williams Christopher M. , Khalil Jawad , Burley Kate L. , Hamilton Fergus , Arnold David , Milne Alice , Lewis Phil A. , Heesom Kate J. , Mundell Stuart J. , Davidson Andrew D. , Poole Alastair W. , Hers Ingeborg
Published: October 2022

Background

Patients with coronavirus disease-19 (COVID-19) are at increased risk of thrombosis, which is associated with altered platelet function and coagulopathy, contributing to excess mortality.

Objectives

We aimed to characterise the mechanism of altered platelet function in COVID-19 patients.

Methods

The platelet proteome, platelet functional responses and platelet-neutrophil aggregates were compared between patients hospitalised with COVID-19 and healthy control subjects using Tandem Mass Tag (TMT) proteomic analysis, Western blotting and flow cytometry.

Results

COVID-19 patients showed a different profile of platelet protein expression (858 altered out of 5773 quantified). Levels of COVID-19 plasma markers were enhanced in COVID-19 platelets. Gene ontology (GO) pathway analysis demonstrated that levels of granule secretory proteins were raised, whereas some platelet activation proteins, such as the thrombopoietin receptor and PKCα, were lowered. Basally, COVID-19 platelets showed enhanced phosphatidylserine (PS) exposure, with unaltered integrin αIIbβ3activation and P-selectin expression. Agonist-stimulated integrin αIIbβ3activation and PS exposure, but not P-selectin expression, were significantly decreased in COVID-19 patients. COVID-19 patients had high levels of platelet-neutrophil aggregates, even under basal conditions, compared to controls. This interaction was disrupted by blocking P-selectin, demonstrating that platelet P-selectin is critical for the interaction.

Conclusions

Overall, our data suggests the presence of two platelet populations in patients with COVID-19: one with circulating platelets with an altered proteome and reduced functional responses and another with P-selectin expressing neutrophil-associated platelets. Platelet driven thromboinflammation may therefore be one of the key factors enhancing the risk of thrombosis in COVID-19 patients.

Essentials

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COVID-19 patient platelet function and platelet proteins were compared with healthy controls

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Proteomic analysis of platelets indicated that COVID-19 decreased platelet activation proteins

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Agonist induced PS exposure and integrin αIIbβ3activation were impaired in COVID-19

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COVID-19 led to maximal levels of P-selectin dependent platelet-neutrophil aggregates
Restoration of functional PAX6 in aniridia patient iPSC-derived ocular tissue models using repurposed nonsense suppression drugs
Authors: Lima Cunha Dulce , Eintracht Jonathan , Harding Philippa , Zhou Jo Huiqing , Moosajee Mariya
Published: October 2022

Aniridia is a rare, pan-ocular disease causing severe sight loss, with only symptomatic intervention offered to patients. Approximately 40% of aniridia patients present with heterozygous nonsense variants inPAX6, resulting in haploinsufficiency. Translational readthrough inducing compounds (TRIDs) have the ability to weaken the recognition of in-frame premature stop codons (PTCs), permitting full-length protein to be translated. We have established induced pluripotent stem cell (iPSC)-derived 3D optic cups and 2D limbal epithelial stem cell (LESC) models from an aniridia patient with a prevalentPAX6nonsense mutation. Bothin vitromodels show reduced PAX6 protein levels, mimicking the disease. Repurposed TRIDs amlexanox and 2,6-diaminopurine (DAP), and positive control compounds ataluren and G418 were tested for their efficiency. Amlexanox was identified as the most promising TRID, increasing full-length PAX6 levels in both models, and rescuing the disease phenotype through normalization of VSX2 and cell proliferation in the optic cups and reduction of ABCG2 protein andSOX10expression in LESC. This study highlights the significance of patient iPSC-derived cells as a new model system for aniridia and proposes amlexanox as a new putative treatment for nonsense-mediated aniridia.
Genetic analysis of a phenotypic loss in the mechanosensory entrainment of a circalunar clock
Authors: Briševac Dušica , Prakash Celine , Kaiser Tobias S.
Published: October 2022

Genetic variants underlying traits that become either non-adaptive or selectively neutral are expected to have altered evolutionary trajectories. Uncovering genetic signatures associated with phenotypic loss presents the opportunity to discover the molecular basis for the phenotype in populations where it persists. Here we study circalunar clocks in populations of marine midgeClunio marinus. The circalunar clock synchronizes development to the lunar phase, and it is set by moonlight and tidal cycles of mechanical agitation. Two out of ten studied populations have lost their sensitivity to mechanical agitation while preserving sensitivity to moonlight. Intriguingly, the F1 offspring of the two insensitive populations regained the sensitivity to mechanical entrainment, implying a genetically independent loss of the phenotype. By combining quantitative trait locus mapping and genome-wide screens, we explored the genetics of this phenotypic loss. QTL analysis suggested an oligogenic origin with one prevalent additive locus in one of the strains. In addition, it confirmed a distinct genetic architecture in the two insensitive populations. Genomic screens further uncovered several candidate genes underlying QTL regions. The strongest signal under the most prominent QTL contains a duplicatedSTAT1gene, which has a well-established role in development, andCG022363, an ortholog of theDrosophila melanogaster CG32100gene, which plays a role in gravitaxis. Our results support the notion that adaptive phenotypes have a complex genetic basis with mutations occurring at several loci. By dissecting the most prevalent signals, we started to reveal the molecular machinery responsible for the entrainment of the circalunar clock.
MR1-restricted T cell clonotypes are associated with ‘resistance’ toM.tuberculosisinfection
Authors: Cross Deborah L. , Layton Erik D. , Yu Krystle K.Q. , Smith Malisa T. , Aguilar Melissa S. , Li Shamin , Mayanja-Kizza Harriet , Stein Catherine M. , Boom W. Henry , Hawn Thomas R. , Bradley Philip , Newell Evan , Seshadri Chetan
Published: October 2022

T cells are required for a protective immune response against the human adapted pathogenMycobacterium tuberculosis(M.tb). We recently described a cohort of Ugandan household contacts of tuberculosis cases that appear to ‘resist’ M.tb infection (RSTRs) and showed that these individuals harbor IFN-γ independent T cell responses to M.tb-specific peptide antigens. However, T cells also recognize non-protein antigens via antigen presenting systems that are independent of genetic background, leading to their designation as donor-unrestricted T (DURT) cells. We used combinatorial tetramer staining and multi-parameter flow cytometry to comprehensively characterize the association between DURTs and ‘resistance’ to M.tb infection. We did not observe a difference in peripheral blood frequencies of invariant natural killer T (iNKT) cells, germline encoded mycolyl-reactive (GEM) T cells, or γδ T cells between RSTRs and matched controls with latent M.tb infection (LTBIs). However, we did observe a 1.65-fold increase in frequency of circulating MR1-restricted T (MR1T) cells among RSTRs in comparison with LTBI (p=0.03). Multi-modal single cell RNA-sequencing of 18,251 MR1T cells sorted from a subset of donors revealed 5150 clonotypes that expressed a common transcriptional program, the majority of which were private. Deep sequencing of the TCR-α repertoire revealed several DURT clonotypes that were expanded among RSTRs, including at least two MR1T clonotypes. Taken together, our data reveal unexpected donor-specific diversity in the TCR repertoire of human MR1T cells as well as associations between MR1 clonotypes and ‘resistance’ to M.tb infection.
PAR-4/LKB1 regulates intestinal cell number by restricting endoderm specification to the E lineage
Authors: Demouchy Flora , Nicolle Ophélie , Michaux Grégoire , Pacquelet Anne
Published: October 2022

The master kinase PAR-4/LKB1 appears as a major regulator of intestinal physiology. It is in particular mutated in the Peutz-Jeghers syndrome, an inherited disorder in which patients develop benign intestine polyps. Moreover, ectopic activation of PAR-4/LKB1 is sufficient to induce the polarized accumulation of apical and basolateral surface proteins and the formation of apical microvilli-like structures in intestinal epithelial cancer cell lines. InC. elegans, PAR-4 was shown to be required for the differentiation of intestinal cells. Here, we further examine the role of PAR-4 during intestinal development. We find that it is not required for the establishment of enterocyte polarity and plays only a minor role in brush border formation. By contrast,par-4mutants display severe deformations of the intestinal lumen as well as supernumerary intestinal cells, thereby revealing a novel function of PAR-4 in preventing intestinal hyperplasia. Importantly, we find that the ability of PAR-4 to control intestinal cell number does not involve the regulation of cell proliferation but is rather due to its ability to restrict the expression of intestinal cell fate factors to the E blastomere lineage. We therefore propose that PAR-4 is required to regulateC. elegansintestine specification.
Structural journey of an insecticidal pore-forming protein targeting western corn rootworm
Authors: Marini G. , Poland B. , Leininger C. , Lukoyanova N. , Spielbauer D. , Barry J. , Altier D. , Lum A. , Scolaro E. , Pérez Ortega C. , Yalpani N. , Sandahl G. , Mabry T. , Klever J. , Nowatzki T. , Zhao J-Z. , Sethi A. , Kassa A. , Crane V. , Lu A. , Nelson M.E. , Eswar N. , Topf M. , Saibil H.R.
Published: October 2022

Broad adoption of transgenic crops has revolutionized agriculture. However, resistance to insecticidal proteins by agricultural pests poses a continuous challenge to maintaining crop productivity and new proteins are urgently needed to replace existing transgenic traits. We identified an insecticidal membrane attack complex/perforin (MACPF) protein, Mpf2Ba1, with strong activity against western corn rootworm larvae and a novel site of action. By integrating X-ray crystallography, cryo-EM, and modelling, we determined monomeric, pre-pore and pore structures, revealing changes between structural states at atomic resolution. We discovered a monomer inhibition mechanism, a molecular “switch” associated with pre-pore activation/oligomerization upon gut fluid incubation and solved the highest resolution MACPF pore structure to-date. Our findings provide a mechanistic basis for Mpf2Ba1 effectiveness as an insecticidal protein with potential for biotechnology development.

One-Sentence Summary

The molecular mechanism of an insecticidal protein is revealed through 3D structures of the three main pore formation states
Model-driven approach for the production of butyrate from CO2/H2by a novel co-culture ofC. autoethanogenumandC. beijerinckii
Authors: Benito-Vaquerizo Sara , Nouse Niels , Schaap Peter J. , Hugenholtz Jeroen , Brul Stanley , Lopez-Contreras Ana , Martins dos Santos Vitor A. P. , Suarez-Diez Maria
Published: October 2022

One-carbon (C1) compounds are promising feedstocks for sustainable production of commodity chemicals. CO2is a particularly advantageous C1-feedstock since it is an unwanted industrial off-gas that can be converted to valuable products while reducing its atmospheric levels. Acetogens are known microorganisms that can grow on CO2/H2and syngas converting these substrates into ethanol and acetate. Co-cultivation of acetogens with microbes that can further process such products can expand the variety of products to, for example, medium chain fatty acids (MCFA) and longer chain alcohols. Solventogens are microorganisms known to produce MCFA and alcohols via the acetone, butanol and ethanol (ABE) fermentation in which acetate is a key metabolite. Thus, co-cultivation of a solventogen and acetogen in a consortium provides a potential platform to produce valuable chemicals from CO2.

In this study, metabolic modelling was implemented to design a new co-culture of an acetogen and a solventogen to produce butyrate from CO2/H2mixtures. The model-driven approach suggested the ability of the studied solventogenic species to grow on lactate/glycerol with acetate as co-substrate. This ability was confirmed experimentally by cultivation ofClostridium beijerinckiion these substrates in serum bottles and subsequently in pH-controlled bioreactors.

Community modelling also suggested that a novel microbial consortium consisting of the acetogenClostridium autoethanogenum,and the solventogenC. beijerinckiiwould be feasible and stable. On the basis of this prediction, a co-culture was experimentally established.C. autoethanogenumgrew on CO2/H2producing acetate and traces of ethanol. Acetate was in turn, consumed byC. beijerinckiitogether with lactate, producing butyrate. These results show that community modelling of metabolism is a valuable tool to guide the design of microbial consortia for the tailored production of chemicals from renewable resources.
AtSWEET13 transporter discriminates sugars by selective facial and positional substrate recognition
Authors: Weigle Austin T. , Shukla Diwakar
Published: October 2022

Transporters are targeted by endogenous metabolites and exogenous molecules to reach cellular destinations, but it is generally not understood how different substrate classes exploit the same transporter’s mechanism. Any disclosure of plasticity in transporter mechanism when treated with different substrates becomes critical for developing general selectivity principles in membrane transport catalysis. Using extensive molecular dynamics simulations with an enhanced sampling approach, we select theArabidopsissugar transporter AtSWEET13 as a model system to identify the basis for glucose versus sucrose molecular recognition and transport. We find that AtSWEET13 chemical selectivity originates from a conserved substrate facial selectivity demonstrated when committing alternate access, despite mono-/di-saccharides experiencing differing degrees of conformational and positional freedom throughout other stages of transport. In summary, our results point to a potentially generalizable finding that selectivity in transporters emerges from molecular recognition events occurring within regions distal from any conserved (non)functional binding sites.
The function of ethanol in olfactory associative behaviors inDrosophila melanogasterlarvae
Authors: Berger Michael , Yapıcı Barış , Scholz Henrike
Published: October 2022

Drosophila melanogasterlarvae develop on fermenting fruits with increasing ethanol concentrations. To address the relevance of ethanol in the behavioral response of the larvae, we analyzed the function of ethanol in the context of olfactory associative behavior inCanton Sandw1118larvae. The motivation of larvae to move toward or out of an ethanol-containing substrate depends on the ethanol concentration and the genotype. Ethanol in the substrate reduces the attraction to odorant cues in the environment. Relatively short repetitive exposures to ethanol, which are comparable in their duration to reinforcer representation in olfactory associative learning and memory paradigms, result in positive or negative association with the paired odorant or indifference to it. The outcome depends on the order in which the reinforcer is presented during training, the genotype and the presence of the reinforcer during the test. Independent of the order of odorant presentation during training,Canton Sandw1118larvae do not form a positive or negative association with the odorant when ethanol is not present in the test context. When ethanol is present in the test,w1118larvae show aversion to an odorant paired with a naturally occurring ethanol concentration of 5%. Our results provide insights into the parameters influencing olfactory associative behaviors using ethanol as a reinforcer inDrosophilalarvae and indicate that short exposures to ethanol might not uncover the positive rewarding properties of ethanol for developing larvae.