bluuebunny/crossref_metadata_2025 huggingface dataset:
Redesigning theDrosophilahistone gene cluster: An improved genetic platform for spatiotemporal manipulation of histone function
Authors: Crain Aaron T. , Nevil Markus , Leatham-Jensen Mary P. , Reeves Katherine B. , Matera A. Gregory , McKay Daniel J. , Duronio Robert J.
Published: April 2024

Mutating replication-dependent (RD) histone genes is an important tool for understanding chromatin-based epigenetic regulation. Deploying this tool in metazoan models is particularly challenging because RD histones in these organisms are typically encoded by many genes, often located at multiple loci. Such RD histone gene arrangements make the ability to generate homogenous histone mutant genotypes by site-specific gene editing quite difficult.Drosophila melanogasterprovides a solution to this problem because the RD histone genes are organized into a single large tandem array that can be deleted and replaced with transgenes containing mutant histone genes. In the last ∼15 years several different RD histone gene replacement platforms have been developed using this simple strategy. However, each platform contains weaknesses that preclude full use of the powerful developmental genetic capabilities available toDrosophilaresearchers. Here we describe the development of a newly engineered platform that rectifies many of these weaknesses. We used CRISPR to precisely delete the RD histone gene array (HisC), replacing it with a multifunctional cassette that permits site-specific insertion of either one or two synthetic gene arrays using selectable markers. We designed this cassette with the ability to selectively delete each of the integrated gene arrays in specific tissues using site-specific recombinases. We also present a method for rapidly synthesizing histone gene arrays of any genotype using Golden Gate cloning technologies. These improvements facilitate generation of histone mutant cells in various tissues at different stages ofDrosophiladevelopment and provide an opportunity to apply forward genetic strategies to interrogate chromatin structure and gene regulation.
Equilibrium Tension and Compression Mechanical Properties of the Human Uterus
Authors: Fang Shuyang , Duarte-Cordon Camilo A. , Fodera Daniella M. , Shi Lei , Chen Xiaowei , Advincula Arnold , Vink Joy , Hendon Christine , Myers Kristin M.
Published: April 2024

A successful pregnancy relies on the proper cellular, biochemical, and mechanical functions of the uterus. A comprehensive understanding of uterine mechanical properties during pregnancy is key to understanding different gynecological and obstetric disorders such as preterm birth, placenta accreta, leiomyoma, and endometriosis. This study sought to characterize the macro-scale equilibrium material behaviors of the human uterus in non-pregnancy and late pregnancy under both compressive and tensile loading. Fifty human uterine specimens from 16 patients (8 nonpregnant [NP] and 8 pregnant [PG]) were tested using spherical indentation and uniaxial tension coupled with digital image correlation (DIC). A three-level incremental load–hold protocol was applied to both tests. A microstructurally-inspired material model considering fiber architecture was applied to this dataset. Inverse finite element analysis (IFEA) was then performed to generate a single set of mechanical parameters to describe compressive and tensile behaviors. The freeze-thaw effect on uterine macro mechanical properties was also evaluated. PG tissue exhibits decreased overall stiffness and increased fiber network extensibility compared to NP uterine tissue. Under indentation, ground substance compressibility was similar between NP and PG uterine tissue. In tension, the fiber network of the PG uterus was found to be more extensible and dispersed than in nonpregnancy. Lastly, a single freeze-thaw cycle did not systematically alter the macro-scale material behavior of the human uterus.
Substrate-directed control of N-glycosylation in the endoplasmic reticulum calibrates signal reception at the cell-surface
Authors: Ma Mengxiao , Dubey Ramin , Jen Annie , Pusapati Ganesh V. , Shishkova Evgenia , Overmyer Katherine A. , Cormier-Daire Valérie , Aravind L. , Coon Joshua J. , Rohatgi Rajat
Published: April 2024

One-fifth of human proteins are N-glycosylated in the endoplasmic reticulum (ER) by two oligosaccharyltransferases, OST-A and OST-B. Contrary to the prevailing view of N-glycosylation as a housekeeping function, we identified an ER pathway that modulates the activity of OST-A. Genetic analyses linked OST-A to HSP90B1, an ER chaperone for membrane receptors, and CCCD134, an ER protein we identify as the first specificity factor for N-glycosylation. During its translocation into the ER, a N-terminal peptide in HSP90B1 functions as a pseudosubstrate inhibitor of OST-A and templates the assembly of specialized ER translocon complexes containing CCDC134. Unexpectedly, OST-A functions as a scaffold rather than an enzyme in this context, stabilizing HSP90B1 by preventing its hyperglycosylation and degradation. Disruption of this pathway impairs WNT signaling at the cell surface and causes the bone developmental disorder Osteogenesis Imperfecta. Thus, N-glycosylation can be regulated by ER factors to control cell-surface receptor signaling and tissue development.

One-Sentence Summary

N-glycosylation of asparagine residues on proteins can be regulated by specificity factors in the endoplasmic reticulum to control cell-surface signaling and tissue development.
Cell Simulation as Cell Segmentation
Authors: Jones Daniel C. , Elz Anna E. , Hadadianpour Azadeh , Ryu Heeju , Glass David R. , Newell Evan W.
Published: April 2024

Single-cell spatial transcriptomics promises a highly detailed view of a cell’s transcriptional state and microenvironment, yet inaccurate cell segmentation can render this data murky by misattributing large numbers of transcripts to nearby cells or conjuring nonexistent cells. We adopt methods from ab initio cell simulation to rapidly infer morphologically plausible cell boundaries that preserve cell type heterogeneity. Benchmarking applied to datasets generated by three commercial platforms show superior performance and computational efficiency of this approach compared with existing methods. We show that improved accuracy in cell segmentation aids greatly in detection of difficult to accurately segment tumor infiltrating immune cells such as neutrophils and T cells. Lastly, through improvements in our ability to delineate subsets of tumor infiltrating T cells, we show that CXCL13-expressing CD8+ T cells tend to be more closely associated with tumor cells than their CXCL13-negative counterparts in data generated from renal cell carcinoma patient samples.
An ingestible, battery-free, tissue-adhering robotic interface for non-invasive and chronic electrostimulation of the gut
Authors: Nan Kewang , Wong Kiwan , Li Dengfeng , Ying Binbin , McRae James C , Feig Vivian R , Wang Shubing , Yao Kuanming , Zhou Jingkun , Li Jian , Jenkins Joshua , Ishida Keiko , Kuosmanen Johannes , Madani Wiam Abdalla Mohammed , Hayward Alison , Ramadi Khalil , Yu Xinge , Traverso Giovanni
Published: April 2024

Ingestible electronics have the capacity to transform our ability to effectively diagnose and potentially treat a broad set of conditions. Current applications could be significantly enhanced by addressing poor electrode-tissue contact, lack of navigation, short dwell time, and limited battery life. Here we report the development of an ingestible, battery-free, and tissue-adhering robotic interface (IngRI) for non-invasive and chronic electrostimulation of the gut, which addresses challenges associated with contact, navigation, retention, and powering (C-N-R-P) faced by existing ingestibles. We show that near-field inductive coupling operating near 13.56 MHz was sufficient to power and modulate the IngRI to deliver therapeutically relevant electrostimulation, which can be further enhanced by a bio-inspired, hydrogel-enabled adhesive interface. In swine models, we demonstrated the electrical interaction of IngRI with the gastric mucosa by recording conductive signaling from the subcutaneous space. We further observed changes in plasma ghrelin levels, the “hunger hormone,” while IngRI was activatedin vivo, demonstrating its clinical potential in regulating appetite and treating other endocrine conditions. The results of this study suggest that concepts inspired by soft and wireless skin-interfacing electronic devices can be applied to ingestible electronics with potential clinical applications for evaluating and treating gastrointestinal conditions.
Effects of Age on Cross-Cultural Differences in the Neural Correlates of Memory Retrieval
Authors: Cho Isu , Leger Krystal R. , Valoumas Ioannis , Mair Ross W. , Goh Joshua Oon Soo , Gutchess Angela
Published: April 2024

Culture can shape memory, but little research investigates age effects. The present study examines the neural correlates of memory retrieval for old, new, and similar lures in younger and older Americans and Taiwanese. Results show that age and culture impact discrimination of old from new items. Taiwanese performed worse than Americans, with age effects more pronounced for Taiwanese. Americans activated the hippocampus for new more than old items, but pattern of activity for the conditions did not differ for Taiwanese, nor did it interact with age. The engagement of left inferior frontal gyrus (LIFG) differed across cultures. Patterns of greater activity for old (for Americans) or new (for Taiwanese) items were eliminated with age, particularly for older Americans. The results are interpreted as reflecting cultural differences in orientation to novelty vs. familiarity for younger, but not older, adults, with the LIFG supporting interference resolution at retrieval. Support is not as strong for cultural differences in pattern separation processes. Although Americans had higher levels of memory discrimination than Taiwanese and engaged the LIFG for correct rejections more than false alarms, the patterns of behavior and neural activity did not interact with culture and age. Neither culture nor age impacted hippocampal activity, which is surprising given the region’s role in pattern separation. The findings suggest ways in which cultural life experiences and concomitant information processing strategies can contribute to consistent effects of age across cultures or contribute to different trajectories with age in terms of memory.
FIGL1 attenuates meiotic interhomolog repair and is counteracted by RAD51 paralog XRCC2 and chromosome axis protein ASY1 during meiosis
Authors: Emmenecker Côme , Pakzad Simine , Ture Fatou , Guerin Julie , Hurel Aurelie , Chambon Aurelie , Girard Chloe , Mercier Raphael , Kumar Rajeev
Published: April 2024

Two recombinases, RAD51 and DMC1, catalyze meiotic break repair to ensure crossovers (COs) between homologous chromosomes (interhomolog) rather than between sisters (intersister). FIDGETIN-LIKE-1 (FIGL1) downregulates both recombinases. However, the understanding of FIGL1 functions in meiotic repair remains limited. Here, we discover new genetic interactions ofArabidopsis thaliana FIGL1that are importantin vivodeterminants of meiotic repair outcome. Infigl1, compromising the RAD51-dependent repair by either losing RAD51 paralogs (RAD51B or XRCC2) or RAD54 or inhibiting RAD51’s catalytic activity results in either unrepaired breaks or meiotic CO defects. Further, XRCC2 physically interacts with FIGL1 and partially counteracts FIGL1 for RAD51 focus formation. Our data support that RAD51-mediated repair mechanisms compensate for the FIGL1 dysfunction. FIGL1 is dispensable for intersister repair indmc1but is essential for meiotic repair completion in mutants with impaired DMC1 functions and interhomolog bias such asasy1. We show that FIGL1 attenuates interhomolog repair, and ASY1 counteracts FIGL1 to promote interhomolog recombination.
Spatial distribution of Tree-related Microhabitats in a primeval mountain forest: from natural patterns to landscape planning and forest management recommendations
Authors: Przepióra Fabian , Lewandowski Paweł , Ciach Michał
Published: April 2024

Tree-related Microhabitats (TreMs) are essential for sustaining forest biodiversity. Although TreMs represent ephemeral resources that are spread across the landscape, their spatial distribution within temperate forests remains poorly understood. To address this knowledge gap, we conducted a study on 90 sample plots (0.05 ha each) located in a primeval mountain European beechFagus sylvatica-dominated forest (Bieszczady Mountains, Carpathians). We explored the TreM profile with its link to habitat characteristics and described the spatial distribution of TreM indices. We identified 61 TreM types, with a mean richness of 19.7 ±4.9 SD TreM types per plot, a mean density of 740.7 ±292.5 SD TreM-bearing trees ha-1and a mean TreM diversity of 1.2 ±0.1 SD. The diameter and living status of trees (livingvsdead standing tree) were correlated with TreM richness on an individual tree. The stand structure, i.e. density and/or basal area of living and/or dead standing trees, and topographic conditions, i.e. slope exposure, were correlated with the TreM richness, density and diversity recorded on a study plot. We found no relationship between TreM richness, density and diversity and the presence of canopy gaps, which indicates that the influence of small-scale disturbances on the TreM profile is limited. However, our analysis revealed a clustered spatial pattern of TreM indices, with TreM-rich habitat patches (hot-spots) covering ∼20% of the forest. A moderate TreM richness, density and diversity dominated ∼60% of the forest, while TreM-poor habitat patches (cold-spots) covered ∼20%. Based on our findings, we advise the transfer of knowledge on the spatial distribution of TreMs from primeval to managed forests and advocate the ‘2:6:2’ triad rule: to allocate 20% of forests as strictly protected areas, to dedicate 60% to low-intensity forest management with the retention of large living trees and all dead standing trees, and to use the remaining 20% for intensive timber production. To ensure the continuance of the majority of TreM types, ≥ 55 living trees ha-1> 60 cm in diameter should be retained. Such an approach will maintain a rich and diverse TreM assemblage across a broad spatial scale, which in turn will support biodiversity conservation and ecosystem restoration in secondary or managed forests.

Highlights

Primeval mountain beech forest hosts rich and abundant TreM assemblage

Stand structure, slope exposure, but not canopy gaps mould TreM profiles

Habitat patches with high/low TreM indices are spatially clustered

Hot- and cold-spots each make up 20% of TreM richness, density and diversity

2:6:2 - the protected: managed forest ratio for maintaining the TreM assemblage
Descriptive Epidemiology of Kyasanur Forest Disease in Thirthahalli Taluk, Shivamogga, 2018-2022
Authors: Srividya KV , Bhavesh LR , Choudhary Sushma , Shewale Ajit , Pallavi DM , Padma MR , Tiwari Simmi
Published: April 2024

Background

Kyasanur Forest Disease (KFD) is a zoonotic viral disease caused by the Kyasanur Forest Disease Virus (KFDV), belongs to the family Flaviviridae, and is transmitted to humans through the bites of infected ticks, primarily in forested regions. Thirthahalli taluk from Shivamogga district of Karnataka has been reporting consistently high burden of KFD. We describe the epidemiology of KFD cases in Thirthahalli taluk including their temporal and spatial distribution, correlate KFD hot-spots with the number of cases and identify high-risk groups.

Methods

We conducted a retrospective analysis of KFD surveillance data obtained from district surveillance unit, Shivamogga, on human, tick and monkey data, of Thirthahalli taluk from November 2017 to May 2022, described epidemiology, calculated the annual and seasonal time-trend of cases and correlated number of cases with number of tick pools and/ or monkey carcass positive for KFDV. We report Pearson’s correlation coefficient. We performed spatial analysis to identify clustering patterns and describe the PHC-wise disease burden.

Results

Thirthahalli taluk reported 326 cases, all were lab-confirmed using either RT-PCR (93%) or IgM-ELISA (7%); with an annual incidence rate of 45.9 per 100,000 population, 58% in males and median age 40 (IQR 28-51) years. Most (71,5%) cases occurred from February to April, case fatality rate was 1.8%. The maximum number of cases occurred in the years 2019 (38%) and 2020 (44%) crossing the outbreak threshold. The populations coming under six Primary Health Centre (PHCs) reported 84% of all cases and reported all deaths. There was correlation between number of human cases in a PHC and tick pool positivity (r=0.62); and positive tick pools and positive monkey carcasses (r=0.71). Age groups with the highest average annual incidence were 45 to 49 years (8.4 per 100,000 population) and 50-54 years (8.1 per 100,000 population).

Conclusion

Thirthahalli taluk had an ongoing endemic transmission of KFD during the study period including two outbreaks in consecutive years. All deaths occurred in PHCs with a high case burden; occurrence of human cases per year was moderately correlated with tick pool positivity. Age groups most at risk for both the occurrence of the disease and mortality were middle-aged adult males. We recommend continued tick surveillance and monkey carcass testing to map disease hot-spots; and targeted interventions in high-burden PHCs and at-risk age groups for effective disease control.
Latent Tuberculosis Diagnostics: A Systematic Review What is the past, present, and future in the diagnosis of latent tuberculosis?
Authors: Kostoudi Sofia , Hammond Robert J H
Published: April 2024

Background

Tuberculosis (TB) is the second leading infectious killer after COVID-19 and the 13thleading cause of death worldwide. Latent tuberculosis (LTBI) has become a major pool of potential active tuberculosis cases and is propelling the TB global health burden further.

Objective

The creation and application of a diagnostic to effectively identify LTBI is vital. This systematic review aims to examine and analyze the present and proposed future diagnostics in the identification of latent tuberculosis.

Design

Systematic Review

Methods

PubMed and Scopus were scanned as primary databases during May 2022. Exclusion criteria for the papers scanned included patients with immunosuppression (due to HIV or treatment), pediatric TB, cancer and dialysis patients, pregnancy, IV drug users, animal models, papers published before 2005, co-infected patients, IBD and transplant patients, and finally secondary literature. Such criteria were incorporated due to the differences in TB immunology in these circumstances. 18 papers were included in this review and their risk of bias assessed using the QUADAS-2 guidelines. For analysis the papers’ sensitivities and specificities were examined. There was also a deeper look into the surrounding variables such as population differentiation, diagnostic technologies, clinical translation, and bias.

Findings

With thorough analysis of the data, it was determined that there are promising diagnostics for the precise identification of LTBI. Specifically, 2 studies one which used ELISA measuring the IgG response of LTBI and ATB patients when exposed to a combination of antigens and this resulted in a sensitivity and specificity of 93.33% and 93.10% respectively. The second study utilizes ESAT-6 SFC MSS (mean spot size) and the modified TBAg/PHA ratio diagnostic model to establish LTBI or ATB and using ROC curve analysis found a sensitivity of 90.12% and specificity of 91.02%.

Interpretation

To conclude, specific diagnostics still being examined in the preliminary phase could in the future be used as adjuncts to already present diagnostics for the diagnosis of LTBI based on their strong sensitivities and specificities.

No funding.

SUMMARY BOX

What is already known on this topic?

The WHO guidelines for diagnosing LTBI include TST and IGRA, but neither can distinguish LTBI from ATB therefore a new diagnostic must be proposed for the specific detection of LTBI

What this study adds

Our review reveals new two specific new diagnostic tools for the diagnosis of LTBI

How this study might affect research, practice, or policy

Our study can impact the future specific diagnosis of LTBI through proposing new ways of differentiating between ATB and LTBI and their possible further progression into clinical practice
Guiding principles for accelerating change through health inequities research and practice: A modified Delphi consensus process
Authors: Ahmed F. , Woodhead C. , Hossaini A. , Stanley N. , Ensum L. , Rhead R. , Onwumere J. , Mir G. , Dyer J. ,   HSE Collective, Hatch S.L.
Published: April 2024

Despite a preponderance of evidence, and considerable resources, health & social inequities persist and there is evidence of widening unfair differences in markers of health and care. While power imbalances created by broader structural and economic systems are major influencing factors, reform within health inequities research, policy and health and social care practice is key to both bottom-up and top-down change. We aimed to develop agreement for an iterative set of guiding principles underpinning ways of working for a newly formed Health and Social Equity Collective comprising researchers, community leaders, policymakers, and health and care professionals, seeking to address inequity by identifying and engaging the levers of change within and across institutions. The principles aim to inform a more inclusive and translational knowledge base through research practices, tackling entrenched inequalities in education, training, and capacity-building; and centring communities affected by health inequities through engagement and advocacy. We carried out a modified Delphi consensus process between March and September 2022 with Collective members and networks through online workshops and surveys. Out of 24 consensus statements developed and refined over a workshop and three successive survey rounds, we identified eleven key principles agreed upon by a majority of respondents. Two of these were rated high priority by over 75% of respondents, four by over 60% and five by over 50%. These could be grouped into three main topics detailing ways of working and change needed within: ‘Knowledge and framing of health and social inequities, and incorporation into practice’, ‘Community engagement, involvement and peer research’, and ‘Organisational culture change’. Given the pressing need to address inequities, these principles offer a grounding for future consensus building initiatives which also incorporate a wider diversity of perspectives, and which should be iteratively updated with ongoing learning from health equity initiatives nationally and internationally.
AI-based model for T1-weighted brain MRI diagnoses Amyotrophic Lateral Sclerosis
Authors: Turrisi Rosanna , Forzanini Federica , Stanziano Mario , Nigri Anna , Fedeli Davide , Giovanna Carrara , Laura Lequio , Manera Umberto , Moglia Cristina , Valentini Maria Consuelo , Calvo Andrea , Chiò Adriano , Barla Annalisa
Published: April 2024

Amyotrophic Lateral Sclerosis (ALS) is an incurable deadly motor neuron disease that causes the gradual deterioration of nerve cells in the spinal cord and brain. It impacts voluntary limb control and can result in breathing impairment. ALS diagnosis is often challenging due to its symptoms overlapping with other medical conditions and many tests must be performed to rule out other conditions, as easily identifiable biomarkers are still lacking. In this study, we explore T1-weighted (T1w) brain Magnetic Resonance Imaging (MRI), a non-invasive neuroimaging approach which has shown to be a reliable biomarker in many medical fields. Nonetheless, current literature on ALS diagnosis fails to retrieve evidence on how to identify biomarkers from T1w MRI.

In this paper, we leverage Artificial Intelligence (AI) methods to unveil the unexplored potential of T1w brain MRI for distinguishing ALS patients from those who have similar symptoms but different diseases (mimicking). We consider a retrospective single-center dataset of brain T1-weighted MRIs collected from 2010 to 2018 recruited from the Piemonte and Valle d’Aosta ALS register (PARALS). The collection includes 548 patients with ALS and 106 with mimicking diseases. Our goal is to develop and validate a ML diagnostic model based exclusively on T1w MRI distinguishing the two classes. First, we extract a set of radiomic features and two sets of Deep Learning (DL)-based features from MRI scans. Then, using each representation, we train 8 binary classifiers. The best results were obtained by combining DL-based features with SVM classifier, reaching an F1-score of 0.91, and a Precision of 0.88, a Recall of 0.94, and an AUC of 0.7 considering the ALS group as the positive class in the testing set.
Fertility decline in the later phase of the COVID-19 pandemic: The role of policy interventions, vaccination programmes, and economic uncertainty
Authors: Winkler-Dworak Maria , Zeman Kryštof , Sobotka Tomáš
Published: April 2024

BACKGROUND

During the COVID-19 pandemic, birth rates in most higher-income countries first briefly declined and then shortly recovered, showing no common trends afterwards until early 2022, when they unexpectedly dropped.

STUDY FOCUS

We analyse monthly changes in total fertility rates in higher-income countries during the COVID-19 pandemic, with a special focus on 2022, when birth rates declined in most countries. We consider three broader sets of explanatory factors: economic uncertainty, policy interventions restricting mobility and social activities outside the home, and the role of vaccination programmes.

STUDY DESIGN, DATA

This study uses population-wide data on monthly total fertility rates adjusted for seasonality and calendar effects provided in the Human Fertility Database (HFD, 2023). Births taking place between November 2020 and October 2022 correspond to conceptions occurring between February 2020 and January 2022, i.e., after the onset of the pandemic but prior to the Russian invasion of Ukraine. The data cover 26 countries, including 21 countries in Europe, the United States, Canada, Israel, Japan and the Republic of Korea.

METHODS

First, we provide a descriptive analysis of the monthly changes in the total fertility rate (TFR). Second, we estimate the effects of the explanatory factors on the observed fertility swings using linear fixed effects (within) regression models.

MAIN RESULTS

We find that birth trends during the COVID-19 pandemic were associated with economic uncertainty, as measured by increased inflation, the stringency of pandemic policy interventions, and the progression of the COVID-19 vaccination campaign, whereas unemployment did not show any link to fertility during the pandemic.

LIMITATIONS, REASONS FOR CAUTION

Our research is restricted to higher-income countries with relatively strong social support policies provided by the government as well as wide access to modern contraception. Our data do not allow analysing fertility trends by key characteristics, such as age, birth order and social status.

WIDER IMPLICATIONS OF THE FINDINGS

This is the first multi-country study of the drivers of birth trends in a later phase of the COVID-19 pandemic. In the past, periods following epidemics and health crises were typically associated with a recovery in fertility. In contrast, our results show that the gradual phasing out of pandemic containment measures, allowing increased mobility and a return to more normal work and social life, contributed to declining birth rates in most countries. In addition, our analysis indicates that some women avoided pregnancy during the initial vaccination roll-out.
Secondary deficiency of neuraminidase 1 contributes to CNS pathology in neurological mucopolysaccharidoses via hypersialylation of brain glycoproteins
Authors: Xu TianMeng , Heon-Roberts Rachel , Moore Travis , Dubot Patricia , Pan Xuefang , Guo Tianlin , Cairo Christopher W. , Holley Rebecca , Bigger Brian , Durcan Thomas M. , Levade Thierry , Ausseil Jerôme , Amilhon Bénédicte , Gorelik Alexei , Nagar Bhushan , Sturiale Luisa , Palmigiano Angelo , Röckle Iris , Thiesler Hauke , Hildebrandt Herbert , Garozzo Domenico , Pshezhetsky Alexey V.
Published: April 2024

Mucopolysaccharidoses (MPS) are lysosomal storage diseases caused by defects in catabolism of glycosaminoglycans. MPS I, II, III and VII are associated with lysosomal accumulation of heparan sulphate and manifest with neurological deterioration. Most of these neurological MPS currently lack effective treatments. Here, we report that, compared to controls, neuraminidase 1 (NEU1) activity is drastically reduced in brain tissues of neurological MPS patients and in mouse models of MPS I, II, IIIA, IIIB and IIIC, but not of other neurological lysosomal disorders not presenting with heparan sulphate storage. We further show that accumulated heparan sulphate disrupts the lysosomal multienzyme complex of NEU1 with cathepsin A (CTSA), β-galactosidase (GLB1) and glucosamine-6-sulfate sulfatase (GALNS) necessary to maintain enzyme activity, and that NEU1 deficiency is linked to partial deficiencies of GLB1 and GALNS in cortical tissues and iPSC-derived cortical neurons of neurological MPS patients. Increased sialylation of N-linked glycans in brain samples of human MPS III patients and MPS IIIC mice implicated insufficient processing of brain N-linked sialylated glycans, except for polysialic acid, which was reduced in the brains of MPS IIIC mice. Correction of NEU1 activity in MPS IIIC mice by lentiviral gene transfer ameliorated previously identified hallmarks of the disease, including memory impairment, behavioural traits, and reduced levels of the excitatory synapse markers VGLUT1 and PSD95. Overexpression of NEU1 also restored levels of VGLUT1-/PSD95-positive puncta in cortical neurons derived from iPSC of an MPS IIIA patient. Together, our data demonstrate that heparan sulphate-induced secondary NEU1 deficiency and aberrant sialylation of glycoproteins implicated in synaptogenesis, memory, and behaviour constitute a novel pathological pathway in neurological MPS spectrum crucially contributing to CNS pathology.

Graphical abstract
An integrated single-nucleus and spatial transcriptomics atlas reveals the molecular landscape of the human hippocampus
Authors: Thompson Jacqueline R. , Nelson Erik D. , Tippani Madhavi , Ramnauth Anthony D. , Divecha Heena R. , Miller Ryan A. , Eagles Nicholas J. , Pattie Elizabeth A. , Kwon Sang Ho , Bach Svitlana V. , Kaipa Uma M. , Yao Jianing , Hou Christine , Kleinman Joel E. , Collado-Torres Leonardo , Han Shizhong , Maynard Kristen R. , Hyde Thomas M. , Martinowich Keri , Page Stephanie C. , Hicks Stephanie C.
Published: April 2024

The hippocampus contains many unique cell types, which serve the structure’s specialized functions, including learning, memory and cognition. These cells have distinct spatial organization, morphology, physiology, and connectivity, highlighting the importance of transcriptome-wide profiling strategies that retain cytoarchitectural organization. Here, we generated spatially-resolved transcriptomics (SRT) and single-nucleus RNA-sequencing (snRNA-seq) data from adjacent tissue sections of the anterior human hippocampus in ten adult neurotypical donors to define molecular profiles for hippocampal cell types and spatial domains. Using non-negative matrix factorization (NMF) and label transfer, we integrated these data by defining gene expression patterns within the snRNA-seq data and inferring their expression in the SRT data. We identified NMF patterns that captured transcriptional variation across neuronal cell types and indicated that the response of excitatory and inhibitory postsynaptic specializations were prioritized in different SRT spatial domains. We used the NMF and label transfer approach to leverage existing rodent datasets, identifying patterns of activity-dependent transcription and subpopulations of dentate gyrus granule cells in our SRT dataset that may be predisposed to participate in learning and memory ensembles. Finally, we characterized the spatial organization of NMF patterns corresponding to non-cornu ammonispyramidal neurons and identified snRNA-seq clusters mapping to distinct regions of the retrohippocampus, to three subiculum layers, and to a population of presubiculum neurons. To make this comprehensive molecular atlas accessible to the scientific community, both raw and processed data are freely available, including through interactive web applications.
Functional genomics screens reveal a role for TBC1D24 and SV2B in antibody-dependent enhancement of dengue virus infection
Authors: Belmont Laura , Contreras Maya , Cartwright-Acar Catiana H. , Marceau Caleb D. , Agrawal Aditi , Levoir Lisa M. , Lubow Jay , Goo Leslie
Published: April 2024

Dengue virus (DENV) can hijack non-neutralizing IgG antibodies to facilitate its uptake into target cells expressing Fc gamma receptors (FcgR) - a process known as antibody-dependent enhancement (ADE) of infection. Beyond a requirement for FcgR, host dependency factors for this non-canonical infection route remain unknown. To identify cellular factors exclusively required for ADE, here, we performed CRISPR knockout screens in anin vitrosystem permissive to infection only in the presence of IgG antibodies. Validating our approach, a top hit was FcgRIIa, which facilitates binding and internalization of IgG-bound DENV but is not required for canonical infection. Additionally, we identified host factors with no previously described role in DENV infection, including TBC1D24 and SV2B, both of which have known functions in regulated secretion. Using genetic knockout andtrans-complemented cells, we validated a functional requirement for these host factors in ADE assays performed with monoclonal antibodies and polyclonal sera in multiple cell lines and using all four DENV serotypes. We show that knockout of TBC1D24 or SV2B impaired binding of IgG-DENV complexes to cells without affecting FcgRIIa expression levels. Thus, we identify cellular factors beyond FcgR that are required for ADE of DENV infection. Our findings represent a first step towards advancing fundamental knowledge behind the biology of ADE that can ultimately be exploited to inform vaccination and therapeutic approaches.
Assessing genome conservation on pangenome graphs with PanSel
Authors: Zytnicki Matthias
Published: April 2024

1

Motivation

With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a reference genome, augmented with variations. However, this major change requires new tools adapted to this data structure. Among the numerous questions that can be addressed to a pangenome graph is the search for conserved or divergent genes.

Results

In this article, we present a new tool, named PanSel, which computes a conservation score for each segment of the genome, and finds genomic regions that are significantly conserved, or divergent.

Availability

PanSel, written in C++11 with no dependency, is available athttps://github.com/mzytnicki/pansel.

Contact

matthias.zytnicki@inrae.fr
Multivalent Afadin Interaction Promotes IDR-Mediated Condensate Formation and Junctional Separation of Epithelial Cells
Authors: Kuno Shuhei , Nakamura Ryu , Otani Tetsuhisa , Togashi Hideru
Published: April 2024

In epithelial cells, cell-cell adhesion is mediated by the apical junctional complex (AJC), which consists of tight junctions (TJs) and adherens junctions (AJs) aligned from the apical to the basal axis. However, the mechanism of AJC formation on the apical side and the separation of these junctions within AJCs are poorly understood. We found that multivalent interactions of afadin with adhesion molecules and the cytoskeleton lead to condensate formation in an intrinsically disordered region (IDR)-dependent manner, which promotes efficient accumulation in the linear AJ during initial junction formation. Furthermore, we found that afadin and ZO-1 were able to induce different condensate formations in the cell and that these molecules were differentially distributed from each other. These properties of afadin explain how it strictly localizes to AJs in epithelial cells and is involved in regulating the segregation of AJ and TJ within the AJC.
Neurodegenerative fluid biomarkers are enriched in human cervical lymph nodes
Authors: Al-Diwani Adam , Provine Nicholas M , Murchison Andrew , Laban Rhiannon , Swann Owen J , Koychev Ivan , Sheerin Fintan , Da Mesquita Sandro , Heslegrave Amanda , Zetterberg Henrik , Klenerman Paul , Irani Sarosh R
Published: April 2024

In animal models, brain neurodegeneration biomarkers drain into cervical lymph nodes (CLNs). If this occurred in humans, CLNs may provide a readily accessible source of these biomarkers, draining the site of primary pathology. We tested this hypothesis in discovery and validation cohorts using ultrasound-guided fine needle aspiration (FNA).

We measured amyloid-beta 40 and 42, phospho-Tau-181, glial-fibrillary-acidic-protein, and neurofilament-light using single molecule array in CLN aspirates and plasma from: i) a discovery cohort of 25 autoimmune patients, and from ii) plasma, CLNs and capillary blood in four healthy volunteers, an optimisation-validation cohort.

FNA was well-tolerated by all participants. In both cohorts, all biomarkers were detected in all plasmas and CLNs, other than neurofilament-light (8/17 of discovery cohort). CLN biomarker concentrations were significantly greater than plasma concentrations for all except neurofilament-light, most markedly for phospho-Tau-181 (266 fold;P<0.02), whose CLN concentrations decreased with age (Spearmanr=-0.66,P=0.001).

This study presents the first evidence that neurodegenerative biomarkers are detectable in human CLNs. Raised CLN:plasma biomarker ratios suggest their concentration in CLNs, which may offer a sensitive compartment for minimally-invasive sampling in clinical trials. Further, age-associated phospho-Tau-181 reduction with age suggests FNA of CLNs may measure the integrity of brain lymphatic drainagein vivo.
Spatial mapping of dextran sodium sulphate-induced intestinal inflammation and its systemic effects
Authors: Adams Lauren , Rasid Orhan , Hulme Heather , Quon Tezz , Burchmore Richard , Milling Simon , Goodwin Richard J.A. , Wall Daniel M.
Published: April 2024

Inflammatory bowel disease (IBD) is a multifactorial disease and patients frequently experience extraintestinal manifestations affecting multiple sites. Causes of systemic inflammation remain poorly understood but molecules originating from the intestine likely play a role, with microbial and host small molecules polarizing host immune cells towards a pro- or anti-inflammatory phenotype. Using the dextran sodium sulphate (DSS) mouse model, which mimics the disrupted barrier function, microbial dysbiosis and immune cell dysregulation of IBD, we investigated metabolomic and phenotypic changes at intestinal and systemic sites. Using spatial biology approaches we mapped distribution and relative abundance of molecules and cell types across a range of tissues revealing significant changes in DSS-treated mice. Molecules identified as contributing to the statistical separation of treated from control mice were spatially localized within organs to determine their effects on cellular phenotypes through imaging mass cytometry. This spatial approach identified both intestinal and systemic molecular drivers of inflammation, including several not previously implicated in inflammation linked to IBD or the systemic effects of intestinal inflammation. Metabolic and inflammatory pathway interplay underpins systemic disease and determining drivers at the molecular level may aid the development of new targeted therapies.
Jumping DNA polymerases in bacteriophages
Authors: Yutin Natalya , Tolstoy Igor , Mutz Pascal , Wolf Yuri I , Krupovic Mart , Koonin Eugene V
Published: April 2024

Viruses with double-stranded (ds) DNA genomes in the realmDuplodnaviriashare a conserved structural gene module but show a broad range of variation in their repertoires of DNA replication proteins. Some of the duplodnaviruses encode (nearly) complete replication systems whereas others lack (almost) all genes required for replication, relying on the host replication machinery. DNA polymerases (DNAPs) comprise the centerpiece of the DNA replication apparatus. The replicative DNAPs are classified into 4 unrelated or distantly related families (A-D), with the protein structures and sequences within each family being, generally, highly conserved. More than half of the duplodnaviruses encode a DNAP of family A, B or C. We showed previously that multiple pairs of closely related viruses in the orderCrassviralesencode DNAPs of different families. Here we identify four additional groups of tailed phages in the classCaudoviricetesin which the DNAPs apparently were swapped on multiple occasions, with replacements occurring both between families A and B, or A and C, or between distinct subfamilies within the same family. The DNAP swapping always occurs “in situ”, without changes in the organization of the surrounding genes. In several cases, the DNAP gene is the only region of substantial divergence between closely related phage genomes, whereas in others, the swap apparently involved neighboring genes encoding other proteins involved in phage replication. We hypothesize that DNAP swapping is driven by selection for avoidance of host antiphage mechanisms targeting the phage DNAP that remain to be identified, and/or by selection against replicon incompatibility. In addition, we identified two previously undetected, highly divergent groups of family A DNAPs that are encoded in some phage genomes along with the main DNAP implicated in genome replication.
Transglutaminase 2 is an RNA-binding protein: Experimental verification and characterisation of a novel transglutaminase feature
Authors: Csaholczi Bianka , Csuth Anna Renáta , Korponay-Szabó Ilma Rita , Fésüs László , Király Róbert
Published: April 2024

Transglutaminase 2 (TG2) is a uniquely versatile protein with diverse catalytic activities, such as transglutaminase, protein disulfide isomerase, GTPase, protein kinase, and participates in several biological processes. According to information available in the RBP2GO database, TG2 can be an RNA-binding protein (RBP). RBPs participate in posttranscriptional gene expression regulation, influencing RNAs’ function, while RNA molecules can also modulate RBPs’ biological activity. Our goal was to confirm this novel character of TG2 in human umbilical cord vein endothelial cells (HUVEC), which physiologically express TG2.

First, UV cross-linked RNA-protein complexes were isolated from immortalised HUVEC using orthogonal organic phase separation. Compared with the RBP2GO database, mass spectrometry identified 392 potential RBPs, including TG2 and 20 novel, endothelium-related RBPs. Total RNA from HUVEC pulled down recombinant human TG2. Complex formation between TG2 and a 43-mer RNA molecule with a secondary structure as well as a homo-oligomeric single-stranded poly(dG), but not poly(dA), could be observed in magnetic RNA-protein pull-down experiments. Experiments with TG2 inhibitors NC9 and GTPγS, which stabilise its open and closed conformation, respectively, revealed that the open conformation of the enzyme favoured RNA-binding. Biolayer interferometry revealed a high binding affinity between TG2 and RNA with a KDvalue of 88 nM.

We propose that superficial residues on the catalytic core and C-terminal β-barrel domains, being in a hidden position in the closed TG2, are involved in RNA binding. Our study demonstrates TG2’s previously uncharacterised RNA-binding ability, opening new avenues for understanding its multi-functionality.

Graphical abstract

Transglutaminase 2 (TG2) is a unique multifunctional protein demonstrating large conformational changes. It has various transglutaminase and other catalytic and non-catalytic activities which show conformation dependency. Our study has characterised a novel, open conformation-related biological activity of TG2 and its RNA-binding ability.
RIPK3 promotes neuronal survival by suppressing excitatory neurotransmission during CNS viral infection
Authors: Estevez Irving , Buckley Benjamin D. , Panzera Nicholas , Lindman Marissa , Chou Tsui-Wen , McCourt Micheal , Vaglio Brandon J. , Atkins Colm , Firestein Bonnie L. , Daniels Brian P.
Published: April 2024

While recent work has identified roles for immune mediators in the regulation of neural activity, the capacity for cell intrinsic innate immune signaling within neurons to influence neurotransmission remains poorly understood. However, the existing evidence linking immune signaling with neuronal function suggests that modulation of neurotransmission may serve previously undefined roles in host protection during infection of the central nervous system. Here, we identify a specialized function for RIPK3, a kinase traditionally associated with necroptotic cell death, in preserving neuronal survival during neurotropic flavivirus infection through the suppression of excitatory neurotransmission. We show that RIPK3 coordinates transcriptomic changes in neurons that suppress neuronal glutamate signaling, thereby desensitizing neurons to excitotoxic cell death. These effects occur independently of the traditional functions of RIPK3 in promoting necroptosis and inflammatory transcription. Instead, RIPK3 promotes phosphorylation of the key neuronal regulatory kinase CaMKII, which in turn activates the transcription factor CREB to drive a neuroprotective transcriptional program and suppress deleterious glutamatergic signaling. These findings identify an unexpected function for a canonical cell death protein in promoting neuronal survival during viral infection through the modulation of neuronal activity, highlighting new mechanisms of neuroimmune crosstalk.
Unraveling the Molecular Landscape of Uterine Fibroids, Insights intoHMGA2and Stem Cell Involvement
Authors: Paul Emmanuel N. , Carpenter Tyler J. , Pavliscak Laura A. , Bennett Abigail Z. , Ochoa-Bernal Maria Ariadna , Fazleabas Asgerally T. , Teixeira Jose M.
Published: April 2024

Uterine fibroids are prevalent benign tumors in women that exhibit considerable heterogeneity in clinical presentation and molecular characteristics, necessitating a deeper understanding of their etiology and pathogenesis.HMGA2overexpression has been associated with fibroid development, yet its precise role remains elusive. Mutations in fibroids are mutually exclusive and largely clonal, suggesting that tumors originate from a single mutant cell. We explored a possible role forHMGA2overexpression in differentiated myometrial cells, hypothesizing its potential to induce a stem cell-like or dedifferentiating phenotype and drive fibroid development. Myometrial cells were immortalized and transduced with anHMGA2lentivirus to produce HMGA2hi cells.In vitrostem cell assays were conducted and RNA from HMGA2hi and control cells and fibroid-free myometrial and HMGA2 fibroid (HMGA2F) tissues were submitted for RNA-sequencing. HMGA2hi cells have enhanced self-renewal capacity, decreased proliferation, and have a greater ability to differentiate into other mesenchymal cell types. HMGA2hi cells exhibit a stem cell-like signature and share transcriptomic similarities with HMGA2F. Moreover, dysregulated extracellular matrix pathways are observed in both HMGA2hi cells and HMGA2F. Our findings suggest that HMGA2 overexpression drives myometrial cells to dedifferentiate into a more plastic phenotype and underscore a pivotal role for HMGA2 in fibroid pathogenesis.