bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomic and biological panoramas of non-muscle actinopathies
Authors: Di Donato Nataliya ,   NMA Consortium, Thom Andrew , Rump Andreas , Greve Johannes N. , Kropp Marcus , Cadiñanos Juan , Calabro Salvatore , Cathey Sara , Chung Brian , Cope Heidi , Costales Maria , Cuvertino Sara , Dinkel Philine , Erripi Kalliopi , Fry Andrew E. , Garavelli Livia , Guan Kaomei , Hoffjan Sabine , Janzarik Wibke G. , Koenig Matti , Kreimer Insa , Kuenzel Karolina , Mancini Grazia , Marin-Reina Purificacion , Meinhardt Andrea , Niehaus Indra , Pilz Daniela , Ricca Ivana , Simarro Fernando Santos , Schrock Evelin , Marquardt Anja , Taft Manuel H. , Tezcan Kamer , Thunström Sofia , Verhagen Judith , Verloes Alain , Wollnik Bernd , Krawitz Peter , Hsieh Tzung-Chien , Zeef Leo , Seifert Michael , Heide Michael , Lawrence Catherine B. , Roberts Neil , Manstein Dietmar , Woolf Adrian S. , Banka Siddharth
Published: August 2024

Background

Cytoskeletal non-muscle actin isoforms are the most abundant intracellular proteins and extensively interact with other molecules. Biological consequences and genotype-phenotype correlations of the variants in genes encoding these isoforms, ACTB and ACTG1, are not delineated.

Methods

Clinical data analysis from 290 individuals with pathogenic ACTB/ACTG1 variants; characterization of patient cells, mutant proteins, patient-derived iPSC-based models and mutant mice.

Results

We show that ACTB and ACTG1 variants have distinct clinical profiles. ACTB nonsense, frameshift and missense variants that lead to rapid protein degradation result in milder phenotypes. Heterozygous Actb knockout causes altered neuronal cell morphology and abnormal expression of actin-related genes in newborn mouse brains. Truncating ACTG1 variants are likely to be non-pathogenic, but chromosomal deletions encompassing ACTG1 and flanking genes may result in susceptibility to neurodevelopmental phenotypes. Subsets of disease-causing ACTB missense variants (MVs) result in more severe Type 1 Baraitser-Winter Cerebrofrontofacial (BWCFF1) or Deafness Dystonia syndromes. Pathogenic ACTG1 MVs cause BWCFF2 or isolated hearing loss. These amino acid substitutions are associated with dramatically dysregulated actin polymerization and depolymerization dynamics and, in induced pluripotent stem cells (iPSC) derived models, lead to neuronal migration defects. A significant subset of MVs result in disorders that cannot yet be classified into recognizable groups.

Conclusions

ACTB or ACTG1 variants and result in minimum eight mechanistically diverse non-muscle actinopathies. These results will improve their diagnosis and management, and pave the way for new treatment strategies. This study reflects the scale of collaborative clinical studies and multi-modal mechanistic studies required to dissect rare allelic disorders.
Likely cross-border introductions of MPXV Clade I into the Republic of the Congo from the Democratic Republic of the Congo
Authors: Yinda Claude Kwe , Koukouikila-Koussounda Félix , Mayengue Pembe Issamou , Elenga Golmard Reiche , Greene Benjamin , Ochwoto Missiani , Indolo Ghislain Dzeret , Thiécesse Mavoungou Yanne Vanessa , Eyenet Boussam Dachel Aymard , Vishnou Ampiri Bani Reize , Mapanguy Mfoutou Chastel Claujens , Kianguebeni Mbouala Yvanhe Deho , Ntoumi Francine , Kankou Jean-Médard , Munster Vincent J. , Niama Fabien Roch
Published: August 2024

Background

Mpox virus (MPXV) Clade I is endemic in several central African countries and characterized by severe disease and high mortality. Since October 2023, a large-scale Mpox outbreak has emerged in the Democratic Republic of the Congo (DRC), with 22,477 cases and 1,038 deaths reported as of May 26, 2024, and World Health organization (WHO) has declared mpox a public health emergency of international concern on august 14 2024. Twenty-three provinces in the DRC have been affected, 15 of which border another country, including the Republic of the Congo (RoC). The RoC is bordered by five of these affected provinces, increasing the risk of cross-border spread. In the RoC, Mpox cases have historically occurred in the endemic areas of the Likouala department in the north. Recently, suspected cases have emerged outside this region, and it is unclear if these cases are recent spillover events from the DRC outbreaks. Therefore, we performed molecular analyses of these cases in the RoC.

Methods

Samples were collected from suspected cases between January and April 29, 2024, in Likouala, Cuvette-Centralle, and Pointe-Noire. Blood samples, skin/oropharyngeal swabs or skin crusts were obtained for molecular diagnosis at the Laboratoire National de Santé Publique (LNSP), Brazzaville. MPXV sequences were obtained and analyzed using newly established Nanopore sequencing methodology and bioinformatic pipeline.

Findings

Phylogenetic analysis of sequences shows the clustering of MPXV sequences obtained from cases in RoC with sequences from the ongoing Mpox outbreak in the DRC. In addition, sequences from the RoC show multiple phylogenetic positioning suggesting the occurrence of multiple co-circulating strains in the human population.

Interpretation

The close genetic relatedness between sequences from RoC and those from DRC indicates a possible cross-border transmission of MPXV from DRC to RoC. These data highlight the need for implementation of expanded surveillance in countries bordering DRC and RoC, in combination with control measures focused at containing the current outbreaks in DRC and RoC to prevent escalation into a larger-scale epidemic.

Funding

This research was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH).
Qualitative assessment of the citizen science approach to foster public partnerships for pandemic preparedness and response in South and Southeast Asian countries
Authors: Kumar Dinesh , Hauter Ingo , Canlas Felipe C. , Sunaryoko Firli Yogiteten , Maharjan Gyanu Raja , Anowar Md. Mazharul , Khosa Harjyot , Tan Yi-Roe , Yap Peiling
Published: August 2024

Citizen science (CS) promotes the inclusion of diverse stakeholders and offers a scientific in-depth understanding of community engagement to build trust, increase knowledge, and facilitate policymaking. Study aimed to understand concepts, practices, approaches, and sustainability issues of CS among citizens in five South and Southeast Asian countries. Qualitative study from October 2022 to March 2023 was carried in Nepal, Bangladesh, India, Philippines, and Indonesia. In each country, four focus group discussions were conducted with an overall total of 130 participants. Content analysis and coding were carried out for narrative responses of participants. Across all countries, the participants collectively comprehended the term "research" while referring to CS. Participants also related social responsibility and capacity building of citizens to CS. In terms of their contributions to pandemic response, participants stated compliance with government guidelines, helping to create awareness, and providing necessary support and assistance. Participants value personal achievement, satisfaction, happiness, and a chance to build social capital while participating in CS activities. Participants were ready to actively contribute to CS activities and share their opinions with stakeholders such as policymakers and researchers but felt that a lack of personal confidence, ineffective communication, and insufficient translation of their opinions to actions could deter them. Creation of an organization or network, provision of budget for activities, incentives to participants, and transportation assistance were considered as resources needed for the sustainability of CS. Participants expressed their readiness for CS activities considering personal and social factors, while systemic support is needed for sustained participation.
Keratinocyte-Derived Exosomes in Painful Diabetic Neuropathy
Authors: Coy-Dibley James , Jayaraj Nirupa D. , Ren Dongjun , Pacifico Paola , Belmadani Abdelhak , Wang Yi-Zhi , Gebis Kamil K. , Savas Jeffrey N. , Paller Amy S. , Miller Richard J. , Menichella Daniela M.
Published: August 2024

Painful diabetic neuropathy (PDN) is a challenging complication of diabetes with patients experiencing a painful and burning sensation in their extremities. Existing treatments provide limited relief without addressing the underlying mechanisms of the disease. PDN involves the gradual degeneration of nerve fibers in the skin. Keratinocytes, the most abundant epidermal cell type, are closely positioned to cutaneous nerve terminals, suggesting the possibility of bi-directional communication. Exosomes are small extracellular vesicles released from many cell types that mediate cell to cell communication. The role of keratinocyte-derived exosomes (KDEs) in influencing signaling between the skin and cutaneous nerve terminals and their contribution to the genesis of PDN has not been explored. In this study, we characterized KDEs in a well-established high-fat diet (HFD) mouse model of PDN using primary adult mouse keratinocyte cultures. We obtained highly enriched KDEs through size exclusion chromatography and then analyzed their molecular cargo using proteomic analysis and small RNA sequencing. We found significant differences in the protein and microRNA content of HFD KDEs compared to KDEs obtained from control mice on a regular diet (RD), including pathways involved in axon guidance and synaptic transmission. Additionally, using anin vivoconditional extracellular vesicle (EV) reporter mouse model, we demonstrated that epidermal-originating GFP-tagged KDEs are retrogradely trafficked into the DRG neuron cell body. Overall, our study presents a potential novel mode of communication between keratinocytes and DRG neurons in the skin, revealing a possible role for KDEs in contributing to the axonal degeneration that underlies neuropathic pain in PDN. Moreover, this study presents potential therapeutic targets in the skin for developing more effective, disease-modifying, and better-tolerated topical interventions for patients suffering from PDN, one of the most common and untreatable peripheral neuropathies.
Predictive power of different Akkermansia phylogroups in clinical response to PD-1 blockade against non-small cell lung cancer
Authors: Fan Peixin , Ni Mi , Fan Yu , Ksiezarek Magdalena , Fan Peixin
Published: August 2024

Immune checkpoint blockade has emerged as a promising form of cancer therapy. However, only some patients respond to checkpoint inhibitors, while a significant proportion of patients do not, calling for the discovery of reliable biomarkers. Recent studies reported the importance of the gut microbiome in the clinical response to PD-1 blockade against advanced non-small cell lung cancer (NSCLC), highlighting Akkermansia muciniphila as a candidate biomarker. Motivated by the genomic and phenotypic differences across Akkermansia muciniphila strains and Akkermansia (Akk) phylogroups (AmIa, AmIb, AmII, AmIII and AmIV), we analyzed fecal metagenomic sequencing data from three publicly available NSCLC cohorts (n=425). Encouragingly, we found that patients' responses to PD-1 blockade are significantly different across different Akk phylogroups, highlighting the relatively stronger association between AmIa and positive response than the other phylogroups. We built a machine learning model based on Akk gene profiles, which improved the predictive power and shed light on a group of Akk genes that may be associated with the response to PD-1 blockade. In summary, our study underlines the benefits of high-resolution analysis of Akk genomes in the search for biomarkers that may improve the prediction of patients' responses to cancer immunotherapy.
Ionizable networks mediate pH-dependent allostery in SH2 signaling proteins
Authors: Van Dyck Papa Kobina , Piszkin Luke , Gorski Elijah A. , Nascimento Eduarda Tartarella , Abebe Joshua A. , Hoffmann Logan M. , Peng Jeffrey W. , White Katharine A.
Published: August 2024

Introduction

Transient intracellular pH dynamics1regulate mammalian proliferation2,3, migration4, and differentiation5. However, for many pH-dependent cell processes, the molecular mediators are unknown6. Prior work identified histidine residues as molecular switches in pH-sensitive proteins, but how other ionizable residues contribute to pH-dependent protein allostery is understudied. Here, we develop anin silicocomputational pipeline to identify putative pH-sensitive proteins and their molecular mechanisms. We first apply this pipeline to SHP2, a known pH-sensitive signaling protein with an uncharacterized molecular mechanism. We show wild-type SHP2 phosphatase activity is pH-sensitivein vitroand in cells, and mutation of identified H116 and E252 to non-titratable alanine residues abolishes pH-sensitive function. We also show that c-Src is a previously unrecognized pH-dependent kinase, and mutation of the identified ionizable network again abolishes pH-sensitive activity. Constant pH molecular dynamics simulations support a conserved allosteric mechanism of pH-dependent binding of inhibitory SH2 domains to the functional catalytic domains of SHP2 and c-Src. We apply our computational pipeline across SH2 domain-containing signaling proteins and identify evolutionarily conserved putative pH-sensing networks. Our results reveal that pH is an allosteric regulator of SH2 domain-containing signaling proteins providing insight into normal pH-dependent cell biology and diseases where pHi is dysregulated, such as cancer.
Type-B response regulators MaRR_B9 and MaRR_B12 coordinate cytokinin-mediated negative regulation of anthocyanin biosynthesis in banana fruits
Authors: Rajput Ruchika , Tyagi Shivi , Anchal Kumar , Singh Samar , Laxmi Ashverya , Misra Prashant , Pandey Ashutosh
Published: August 2024

Anthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. Comparing two banana varieties, grand naine (GN) and red banana (RB), which display significant contrast in anthocyanin pigmentation. Transcriptomic analysis of GN and RB peel and pulp tissue highlighted cytokinin-specific response regulators, MaRR_B9 and MaRR_B12, as regulators of anthocyanin biosynthesis. Through a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, dihydroflavanol reductase (MaDFR) and anthocyanidin synthase (MaANS). MaRR_B9 and MaRRB_12 interact with the promoters of MaDFR and MaANS, repressing the concerned genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, particularly that of the cyanidin derivative, along with altered expression patterns of MaDFR and MaANS. Thus, the present study identifies novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs for the genetic manipulation of anthocyanin content and thereby for the development of stress-resilient and nutritionally enriched crop plants.
Inflammatory Signatures of Microglia in the Mouse Model of Corticosterone-Induced Depression
Authors: Zhao Yanxiang , Huang Yingying , Cao Ying , Yang Jing
Published: August 2024

Microglia-mediated inflammation has been recognized as a key feature of major depressive disorder. Although hypercortisolemia commonly occurs in depressed patients and can be predictive of treatment response, how chronic exposure to this stress hormone influences microglia is incompletely characterized. Here, we exploited a standard mouse model of depressive-like behaviors induced by peripheral administration of corticosterone. Microglia in the prefrontal cortex of mice were profiled by bulk RNA sequencing, which exhibited the up-regulation of inflammatory markers. In addition, single-cell RNA sequencing identified distinct molecular patterns of microglial responses. Moreover, we revealed the elevation of Pu.1 and Irf8, the two central transcription factors governing microglia-mediated inflammation, in the prefrontal cortex and hippocampus of corticosterone-treated mice, which was similarly observed in the single-nucleus RNA sequencing dataset of depressed patients' microglia. These results have established inflammatory signatures of microglia in the mouse model recapitulating hypercortisolemia-related depression, providing new insights into diagnostic and therapeutic strategies.
Conventional therapy induces tumor immunoediting and modulates the immune contexture in colorectal cancer
Authors: Fotakis Georgios , Rieder Dietmar , Loncova Zuzana , Carollo Sandro , Klieser Eckhard , Neureiter Daniel , Huemer Florian , Hoegler Sandra , Tomberger Martina , Krogsdam Anne , Kenner Lukas , Ziegler Paul K. , Greil Richard , Weiss Lukas , Trajanoski Zlatko
Published: August 2024

Background

Cancer immunotherapies for patients with colorectal cancer (CRC) continue to lag behind other solid cancer types with the exception of 4% of patients with microsatellite-instable tumors. Thus, there is an urgent need to broaden the clinical benefit of checkpoint blockers to CRC by combining conventional therapies to sensitise tumors to immunotherapy. However, the impact of conventional drugs on immunoediting, potentially promoting the positive selection of less immunogenic variants, and on the tumor immune contexture in CRC, remain elusive.

Methods

We performed comprehensive multimodal profiling using longitudinal samples from metastatic CRC patients undergoing neoadjuvant therapy with mFOLFOX6 and Bevacizumab. Exome-sequencing, RNA-sequencing and multiplexed immunofluorescence imaging was carried out on tumor samples obtained before and after therapy and the data was analysed using established methods. The results of the analysis were extrapolated to publicly available datasets (TCGA and CPTAC). In order to identify a surrogate marker, an explainable artificial intelligence method was developed using a transformer-based analytical pipeline for the identification of features in Hematoxylin and Eosin (H&E) images associated with specific biological processes, followed by manual evaluation of highly informative tiles by a pathologist.

Results

Mutational profiles were highly modified and the level of genetic intertumoral heterogeneity between patients varied following treatment. Evolutionary analysis indicated eradication of some clones and dominant clonal prevalence of others, supporting the notion of pharmacologically-induced cancer immunoeditin. Post treatment samples showed upregulation of HLA class II genes, activation of differentiation and stemness pathways, and changes in the consensus molecular subtypes. The tumor immune contexture was characterised by increased densities of CD8+ and CD4+ T cells, but reduced T cell-tumor cell interactions (and increased T cell exhaustion. The AI-guided analyses of the H&E images pinpointed extracellular mucin deposits associated with stemness genes, suggesting a surrogate marker for routine pathological evaluation.

Conclusions

Conventional therapy induces immunoediting and modulates the immune contexture in metastatic CRC patients.
Latitudinal gradients in air density create “invisible topography” at sea level affecting animal flight costs
Authors: Shepard Emily L.C. , Garde Baptiste , Krishnan Krishnamoorthy , Fell Adam , Tatayah Vikash , Jones Carl G. , Cole Nik C. , Lempidakis Emmanouil
Published: August 2024

Regional patterns in wind underpin the low-cost migratory flyways of billions of birds and insects1-3, but how large-scale changes in temperature affect flight is unknown. Flight costs should increase with rising temperatures, because lift decreases as density decreases, whereas weight remains unchanged. The effects of air density on flight costs are well-established in the context of high-altitude movements and migration4-7. Here, we examine the impact of air density on low-flying birds, in relation to seasonal, regional and global changes in temperature. Using multi-sensor loggers, we find that air density was the most important predictor of wingbeat frequency in red-tailed tropicbirds (Phaethon rubricauda) breeding year-round in Mauritius. Lower air densities in the Austral summer were associated with a small but significant increase in mean wingbeat frequency, which translated to an estimated 1-2% increase in flight costs. The variation in flight costs increased by an order of magnitude when considered in space, rather than time, with flight costs varying by ≥ 10 % across the tropicbird’s range. Changes in air density can therefore be an important determinant of flight costs even when birds are operating close to sea-level. Indeed, mapping air density at sea-level revealed that global temperature gradients cause effective altitude to vary by >2 km when considered as seasonal averages. This “invisible topography” at sea-level could have influenced the biogeography of flight morphologies and life-history traits.
A molecular brain atlas reveals cellular shifts during the repair phase of stroke
Authors: Weber Rebecca Z , Achon Buil Beatriz , Rentsch Nora H , Bosworth Allison , Zhang Mingzi , Kisler Kassandra , Tackenberg Christian , Zlokovic Berislav V , Rust Ruslan
Published: August 2024

Ischemic stroke triggers a cascade of pathological events that affect multiple cell types and often lead to incomplete functional recovery. Despite advances in single-cell technologies, the molecular and cellular responses that contribute to long-term post-stroke impairment remain poorly understood. To gain better insight into the underlying mechanisms, we generated a single-cell transcriptomic atlas from distinct brain regions using a mouse model of permanent focal ischemia at one month post-injury. Our findings reveal cell- and region-specific changes within the stroke-injured and peri-infarct brain tissue. For instance, GABAergic and glutamatergic neurons exhibited upregulated genes in signaling pathways involved in axon guidance and synaptic plasticity, and downregulated pathways associated with aerobic metabolism. Using cell-cell communication analysis, we identified increased strength in predicted interactions within stroke tissue among both neural and non-neural cells via signaling pathways such as those involving collagen, protein tyrosine phosphatase receptor, neuronal growth regulator, laminin, and several cell adhesion molecules. Furthermore, we found a strong correlation between mouse transcriptome responses after stroke and those observed in human nonfatal brain stroke lesions. Common molecular features were linked to inflammatory responses, extracellular matrix organization, and angiogenesis. Our findings provide a detailed resource for advancing our molecular understanding of stroke pathology and for discovering therapeutic targets in the repair phase of stroke recovery.
Effective excitability captures network dynamics across development and phenotypes
Authors: Vinogradov Oleg , Giannakakis Emmanouil , Buendía Victor , Uysal Betül , Ron Shlomo , Weinreb Eyal , Schwarz Niklas , Lerche Holger , Moses Elisha , Levina Anna
Published: August 2024

Neuronal culturesin vitroare a versatile system for studying the fundamental properties of individual neurons and neuronal networks. Recently, this approach has gained attention as a precision medicine tool. Mature neuronal culturesin vitroexhibit synchronized collective dynamics called network bursting. If analyzed appropriately, this activity could offer insights into the network’s properties, such as its composition, topology, and developmental and pathological processes. A promising method for investigating the collective dynamics of neuronal networks is to map them onto simplified dynamical systems. This approach allows the study of dynamical regimes and the characteristics of the parameters that lead to data-consistent activity. We designed a simple biophysically inspired dynamical system and used Bayesian inference to fit it to a large number of recordings ofin vitropopulation activity. Even with a small number of parameters, the model showed strong inter-parameter dependencies leading to invariant bursting dynamics for many parameter combinations. We further validated this observation in our analytical solution. We found thatin vitrobursting can be well characterized by each of three dynamical regimes: oscillatory, bistable, and excitable. The probability of finding a data-consistent match in a particular regime changes with network composition and development. The more informative way to describe thein vitronetwork bursting is the effective excitability, which we analytically show to be related to the parameter-invariance of the model’s dynamics. We establish that the effective excitability can be estimated directly from the experimentally recorded data. Finally, we demonstrate that effective excitability reliably detects the differences between cultures of cortical, hippocampal, and human pluripotent stem cell-derived neurons, allowing us to map their developmental trajectories. Our results open a new avenue for the model-based description ofin vitronetwork phenotypes emerging across different experimental conditions.
Genomic Characterization of a Dog-Mediated Rabies Outbreak in El Pedregal, Arequipa, Peru
Authors: Salazar Renzo , Brunker Kirstyn , Díaz Elvis W , Zegarra Edith , Monroy Ynes , Baldarrago Gorky N , Borrini-Mayorí Katty , De la Puente-León Michaela , Kasaragod Sandeep , Levy Michael Z , Hampson Katie , Castillo-Neyra Ricardo
Published: August 2024

Background: Rabies, a re-emerging zoonosis with the highest known human case fatality rate, has been largely absent from Peru, except for endemic circulation in the Puno region on the Bolivian border and re-emergence in Arequipa City in 2015, where it has persisted. In 2021, an outbreak occurred in the rapidly expanding city of El Pedregal near Arequipa, followed by more cases in 2022 after nearly a year of epidemiological silence. While currently under control, questions persist regarding the origin of the El Pedregal outbreak and implications for maintaining rabies control in Peru. Methods: We sequenced 25 dog rabies virus (RABV) genomes from the El Pedregal outbreak (n=11) and Arequipa City (n=14) from 2021-2023 using Nanopore sequencing in Peru. Historical genomes from Puno (n=4, 2010-2012) and Arequipa (n=5, 2015-2019), were sequenced using an Illumina approach in the UK. In total, 34 RABV genomes were analyzed, including archived and newly obtained samples. The genomes were analyzed phylogenetically to understand the outbreak's context and origins. Results: Phylogenomic analysis identified two genetic clusters in El Pedregal: 2021 cases stemmed from a single introduction unrelated to Arequipa cases, while the 2022 sequence suggested a new introduction from Arequipa rather than persistence. In relation to canine RABV diversity in Latin America, all new sequences belonged to a new minor clade, Cosmopolitan Am5, sharing relatives from Bolivia, Argentina, and Brazil. Conclusion: Genomic insights into the El Pedregal outbreak revealed multiple introductions over a 2-year window. Eco-epidemiological conditions, including migratory worker patterns, suggest human-mediated movement drove introductions. Despite outbreak containment, El Pedregal remains at risk of dog-mediated rabies due to ongoing circulation in Arequipa, Puno, and Bolivia. Human-mediated movement of dogs presents a major risk for rabies re-emergence in Peru, jeopardizing regional dog-mediated rabies control. Additional sequence data is needed for comprehensive phylogenetic analyses.
Early immune response toCoccidioidesis characterized by robust neutrophil and fibrotic macrophage recruitment and differentiation
Authors: Miranda Nadia , Davalos Oscar A. , Sebastian Aimy , Rangel Margarita V. , Leon Nicole F. , Gorman Bria M. , Murugesh Deepa K. , Hum Nicholas R. , Loots Gabriela G. , Hoyer Katrina K. , Weilhammer Dina R.
Published: August 2024

Coccidioidomycosis, or Valley fever, is an emerging respiratory disease caused by soil dwelling fungi of theCoccidioidesgenus that is expected to spread from the southwest into the central U.S. by 2050. While 60% of infections are asymptomatic, the other 40% of patients experience a range of symptoms, from self-limiting pneumonia to life-threatening disseminated disease. The immunological events that underlie the progression to severe disease remain under defined. Here, we probed the early immune response toCoccidioidesusing a high dose of an attenuated strain ofC. posadasiiin a mouse model of infection coupled with single-cell RNA sequencing. At 24 hours post-infection, robust immune infiltration is detected in the lung, marked by high levels of inflammatory PD-L1+neutrophils and fungal-contact dependent pro-fibrotic Spp1+macrophages. These findings elucidate the early dynamics of the host response toCoccidioidesand provide a deeper understanding of host-pathogen interactions in the lung.

Importance

By examining early immune dynamics in the lungs, we uncover critical insights into how myeloid cells, particularly neutrophils and macrophages, are recruited and differentiated duringCoccidioidesinfection. The discovery of specific immune cell subsets, such as PD-L1+neutrophils and Spp1+macrophages, which are associated with inflammation and fibrosis, highlights potential targets for therapeutic intervention. These findings provide a deeper understanding of the host-pathogen interactions that occur duringCoccidioidesinfection, offering valuable directions for developing more effective treatments and preventive strategies against this increasingly prevalent disease.
Stress responses and dynamic equilibrium: Key determinants of aging in the C. elegans clk-1 mutant
Authors: Carracedo-Gonzalez Jose , Arellano-Carbajal Fausto , Garrido Etzel , Alvarez-Martinez Roberto
Published: August 2024

Systems biology is a helpful approach to study complex processes such as aging. Indeed, integrating experimental data with mathematical models and bioinformatics can help us to better understand the aging process.The long-lived mutants of C. elegans have generated extensive data about the molecular and cellular mechanisms involved in aging. Among these mutants, clk-1 is a well-studied gene that encodes for a ubiquitin precursor and exhibits a pleiotropic phenotype during aging, characterized by slow rate behaviors, high levels of mitochondrial ROS, autophagy induction, and metabolic changes. However, further elucidation is required to disentangle the relationship between these molecular changes and the phenotype (lifespan extension and changes in pharyngeal pumping, swimming, and defecation). We combined experimental data and modeling tools to represent the genetic interactions with a boolean network. We then inferred the differential equations for each node , following the boolean rules, to achieve a continuous approach. The results show that aak-2 (AMPK) is a critical gene for the long lifespan of clk-1, given its essential role in the induction of a stress response observed in the network attractors and the health condition and lifespan. To define the health condition of the strains (N2, clk-1, aak-2, and clk-1;aak-2), we propose a novel health index estimation based on the attrition of neuromuscular behaviors. We found that the attractor properties in the clk-1 mutant widely depend on a cyclic regulation for the stress response. From our findings, we infer that while stress responses can increase lifespan, health primarily relies on the amount of damage.
Predicting peptide properties from mass spectrometry data using deep attention-based multitask network and uncertainty quantification
Authors: Tariq Usman , Saeed Fahad
Published: August 2024

Database search algorithms reduce the number of potential candidate peptides against which scoring needs to be performed using a single (i.e. mass) property for filtering. While useful, filtering based on one property may lead to exclusion of non-abundant spectra and uncharacterized peptides – potentially exacerbating thestreetlighteffect. Here we presentProteoRift, a novel attention and multitask deep-network, which canpredictmultiple peptide properties (length, missed cleavages, and modification status) directly from spectra. We demonstrate thatProteoRiftcan predict these properties with up to 97% accuracy resulting in search-space reduction by more than 90%. As a result, our end-to-end pipeline is shown to exhibit 8x to 12x speedups with peptide deduction accuracy comparable to algorithmic techniques. We also formulate two uncertainty estimation metrics, which can distinguish between in-distribution and out-of-distribution data (ROC-AUC 0.99) and predict high-scoring mass spectra against correct peptide (ROC-AUC 0.94). These models and metrics are integrated in an end-to-end ML pipeline available athttps://github.com/pcdslab/ProteoRift.
Reexamining the essentiality of Pdi1 in yeast – APDI1knockout is viable inKomagataella phaffiiand still produces recombinant disulfide bonded proteins
Authors: Palma Arianna , Kowarz Viktoria , Gasser Brigitte
Published: August 2024

Protein disulfide isomerase 1 (Pdi1) and Ero1 form the main oxidative folding axis in the endoplasmic reticulum (ER). Despite having additional PDI family members, Pdi1 has long ago been determined to be essential in baker’s yeast and this concept was inferred to other yeast species. In this study, we reexamine the gene essentiality of Pdi1 in the methylotrophic yeastKomagataella phaffii. Strikingly, the absence of Pdi1 does not cause lethality, but even allows for folding and secretion of heterologous proteins in a homogeneous redox state. Remarkably, while sensitivity to externally added folding stressors, such as tunicamycin and DTT is increased inpdi1Δ knock-out cells, in non-stressed growth conditions they do not display upregulation of folding stress markers, such as the master chaperone Kar2 or the unfolded protein response regulator Hac1, suggesting homeostatic adaptation.
A stimulus-computable rational model of habituation in infants and adults
Authors: Raz Gal , Cao Anjie , Saxe Rebecca , Frank Michael C.
Published: August 2024

How do we decide what to look at and when to stop looking? Even very young infants engage in active visual selection, looking less and less as stimuli are repeated (habituation) and regaining interest when novel stimuli are subsequently introduced (dishabituation). The mechanisms underlying these looking time changes remain uncertain, however, due to limits on both the scope of existing formal models and the empirical precision of measurements of infant behavior. To address this, we developed the Rational Action, Noisy Choice for Habituation (RANCH) model, which operates over raw images and makes quantitative predictions of participants’ looking behaviors. In a series of pre-registered experiments, we exposed infants and adults to stimuli for varying durations and measured looking time to familiar and novel stimuli. We found that these data were well captured by RANCH. Using RANCH’s stimulus-computability, we also tested its out-of-sample predictions about the magnitude of dishabituation in a new experiment in which we manipulated the similarity between the familiar and novel stimulus. By framing looking behaviors as rational decision-making, this work identified how the dynamics of learning and exploration guide our visual attention from infancy through adulthood.
Coordinated cross-brain activity during accumulation of sensory evidence and decision commitment
Authors: Bondy Adrian G , Charlton Julie A , Luo Thomas Zhihao , Kopec Charles D , Stagnaro Wynne M , Venditto Sarah Jo C , Lynch Laura , Janarthanan Sanjeev , Oline Stefan N , Harris Timothy D , Brody Carlos D
Published: August 2024

Cognition is produced by the continuous interactions between many regions across the brain, but has typically been studied one brain region at a time. How signals in different regions coordinate to achieve a single coherent action remains unclear. Here, we address this question by characterizing the simultaneous interactions between up to 20 brain regions across the brain (10 targeted regions per hemisphere), of rats performing the "Poisson Clicks" task, a decision-making task that demands the gradual accumulation of momentary evidence. Using 8 Neuropixels probes in each animal, we recorded simultaneously in prefrontal cortex, striatum, motor cortex, hippocampus, amygdala, and thalamus. To assess decision-related interactions between regions, we quantified correlations of each region's "decision variable": moment-to-moment co-fluctuations along the axis in neural state space that best predicts the upcoming choice. This revealed a network of strongly correlated brain regions that include the dorsomedial frontal cortex (dmFC), anterior dorsal striatum (ADS), and primary motor cortex (M1), whose decision variables also led the rest of the brain. If coordinated activity within this subnetwork reflects an ongoing evidence accumulation process, these correlations should cease at the time of decision commitment. We therefore compared correlations before versus after "nTc", a recently reported estimator for the time of internal decision commitment. We found that correlations in the decision variables between different brain regions decayed to near-zero after nTc. Additionally, we found that choice-predictive activity steadily increased over time before nTc, but abruptly stopped growing at nTc, consistent with an evidence accumulation process that has stopped evolving at that time. Assessing nTc from the activity of individual regions revealed that nTc could be reliably detected earlier in M1 than other regions. These results show that evidence accumulation involves coordination within a network of frontal cortical and striatal regions, and suggests that termination of this process may initiate in M1.
S-adenosylmethionine metabolism buffering is regulated by glycine N-methyltransferase decrease via nuclear ubiquitin-proteasome system
Authors: Kashio Soshiro , Miura Masayuki
Published: August 2024

Metabolic homeostasis is essential for survival; however, many studies have focused on the fluctuations of these factors. Furthermore, while metabolic homeostasis depends on the balance between the production and consumption of metabolites, there have been limited investigations into the mechanisms regulating their consumption. S-adenosylmethionine (SAM) metabolism has diverse functions, including methylation, polyamine biosynthesis, and transsulfuration, making its regulation and control crucial. Recent studies have revealed the feedback regulation of SAM production; however, the mechanisms governing its consumption are still poorly understood.

In this study, we focused on the stability of SAM levels in the fat body (FB) ofDrosophila, which serves as a functional equivalent of the mammalian liver and adipose tissue, under conditions of SAM shortage, including nutrient deprivation. We found that glycine N-methyltransferase (Gnmt), a major SAM-consuming methyltransferase in the FB, decreased via the nuclear ubiquitin-proteasome system (UPS), along with the inhibition of SAM synthesis and starvation. Furthermore, the nuclear accumulation of Gnmt with age disrupts the mechanism that maintains a stable SAM level. Thus, the regulation of Gnmt levels through nuclear UPS-mediated degradation helps maintain SAM levels under SAM shortage conditions and during aging.

Significance Statement

S-adenosylmethionine (SAM) metabolism is crucial for diverse functions, which are mediated through methylation process. Although the feedback regulation of SAM production has been explored extensively, our understanding of the mechanism behind SAM consumption remains incomplete. Constant levels of SAM have been observed inDrosophilafat bodies even under conditions of SAM shortage, including nutrient deficiency and inhibition of SAM synthesis. SAM levels are controlled by the degradation of glycine N-methyltransferase (Gnmt), a cytosolic SAM-consuming enzyme, via the nuclear ubiquitin-proteasome system under conditions of SAM shortage. Additionally, the inhibition of Gnmt degradation by suppression of the nuclear UPS causes starvation tolerance. Considering that SAM accumulation promotes energy expenditurein vivo, the starvation-dependent mechanism of Gnmt degradation is important for energy homeostasis.
Quantitative Interpretation of Transverse Spin Relaxation by Translational Diffusion in Liquids Under Arbitrary Potentials
Authors: Okuno Yusuke
Published: August 2024

Intermolecular spin relaxation by translational motion of spin pairs have been widely used to study properties of the biomolecules in liquids. Notably, solvent paramagnetic relaxation enhancement (sPRE) arising from paramagnetic cosolutes has gained attentions for various applications, including the structural refinement of intrinsically disordered proteins, cosolute-induced protein denaturation, and the characterization of residue-specific effective near-surface electrostatic potentials (ENS). Among these applications, the transverse sPRE rate known as Γ2has been predominantly been interpreted empirically as being proportional to norm. In this study, we present a rigorous theoretical interpretation of Γ2that it is instead proportional to normand provide explicit formula for calculating normwithout any adjustable parameters. This interpretation is independent of the type or strength of interactions and can be broadly applied, including to the precise interpretation of ENS.
Conservation of gene expression patterns between the amniotic epithelium at birth and a newborn's nasal epithelium
Authors: Hancock David G , Agudelo-Romero Patricia , Kicic-Starcevich Elizabeth , Lim James , Iosifidis Thomas , Karpievitch Yuliya V , Zhang Guicheng , Martino David J , Kicic Anthony , Stick Stephen M
Published: August 2024

Background: Amniotic epithelial cells are foetal-derived stem cells, capable of differentiating into all three germ layers, including mature epithelial cell populations. However, the conservation between amniotic epithelium and other epithelial tissues has not been sufficiently explored. We hypothesised that the amniotic epithelium might serve as a surrogate tissue source for investigating transcriptional profiles in the respiratory epithelium of the newborn. We compared gene expression profiles and weighted gene co-expression network structure in paired amniotic and newborn nasal epithelial samples from 85 participants in the Airway Epithelium Respiratory Illnesses and Allergy (AERIAL) birth cohort. Results: In total, 11,867 genes (79.7%) were commonly expressed in both amniotic and nasal epithelium, with uniquely expressed genes (2,563 and 458, respectively) enriched for biological functions related to each tissue's specialist functions (e.g. developmental programs and ciliated cells, respectively). We observed a strong overlap in weighted gene co-expression network structure between both tissues, with ten co-expression modules identified in consensus network analysis. Genes commonly expressed in both tissues and/or found in the consensus network modules were enriched for biologically relevant gene signatures and pathway terms related to airway function. We also observed significant overlap in gene expression and network structure between the amniotic epithelium and published datasets of epithelial samples from the lower airway and other epithelial tissues including skin and oesophagus, suggesting a global epithelial signature. Conclusions: Overall, we observed significant overlap in gene expression and network structure between paired amniotic and nasal epithelial samples, supporting the potential of the amnion as a non-invasive and abundant tissue surrogate. Observed differences between tissues were related to each tissue's specialist functions, which remains an important consideration when assessing their overlap. Future studies aimed at investigating amnion-based biomarkers for respiratory exposures in utero and disease outcomes in childhood are needed to extend these results towards clinical translation.
Activation and Evasion of the FEAR Pathway by RNA Viruses
Authors: Rex Emily A. , Seo Dahee , Embry Aaron , Arulanandam Rozanne , Spinelli Marcus M. , Diallo Jean-Simon , Gammon Don B.
Published: August 2024

We recently identified theFACT-ETS-1AntiviralResponse (FEAR) pathway as an interferon-independent innate immune response that restricts DNA virus replication and is countered by poxvirus-encoded A51R proteins (Rexet al., 2024,Nature Microbiology). The human FEAR pathway is mediated by the FACT complex, consisting of hSpt16 and SSRP1 subunits, that remodels chromatin to activate expression of the antiviral transcription factor, ETS-1. To counter this pathway, poxvirus A51R proteins tether SUMOylated hSpt16 subunits to microtubules to prevent ETS-1 expression. While these observations indicate a role for the FEAR pathway in DNA virus restriction, it was unclear if RNA viruses interact with this pathway. Here, we show that RNA viruses are also restricted by the FEAR pathway, yet encode mechanisms distinct from poxviruses to counter this response. We show vesicular stomatitis virus (VSV), a rhabdovirus, utilizes its matrix (M) protein to promote proteasome-dependent degradation of SUMOylated hSpt16 and to block ETS-1 nuclear import. Strains encoding mutant M proteins that cannot antagonize the FEAR pathway exhibit replication defects in human cells that can be rescued by hSpt16 or ETS-1 depletion. Moreover, FACT inhibitor treatment enhanced the replication of oncolytic VSV strains encoding defective M proteins in restrictive cancer cells, suggesting FEAR pathway inhibition may improve oncolytic virotherapy. Strikingly, we provide evidence that the inability of VSV M to degrade SUMOylated Spt16 in lepidopteran insect cells results in abortive infection, suggesting VSV-Spt16 interactions influence virus host range. Lastly, we show that human and murine paramyxovirus target SUMOylated Spt16 proteins for degradation in human and murine cells utilizing a conserved N-terminal motif in their accessory “C” proteins. Collectively, our study illustrates that DNA and RNA viruses have independently evolved diverse mechanisms to antagonize SUMOylated host Spt16 proteins, underscoring the physiological importance of the FEAR pathway to antiviral immunity.
On the relationship between serotype, chemotype and genotype for Cryptococcus spp. including a method for including polysaccharide structure in strain characterization
Authors: Wear Maggie P. , Greengo Seth , McConnell Scott , Xu Alan , Lopes Livia Liporagi , Majumdar Ananya , Casadevall Arturo
Published: August 2024

Over the past eight decades the classification of cryptococcal strains has relied on the technologies available to discriminate among isolates, such as serology, exopolysaccharide (EPS) NMR, and most recently multi-locus sequencing, which yielded serotypes, chemotypes, and genotypes, respectively.  However, as one method superseded the other, the relationship between classification schemes became uncertain, resulting in assumptions that have not been rigorously validated. Here we compared the serotype, chemotype, and genotype as defined by multi-locus sequence typing (MLST) of 63 strains for which both serotype and chemotype characterization was available. None of the three strain typing methods were correlative with each other, although for about 50% of the strains there was correlation between chemotype and genotype. To address this, we updated the methodology of GXM motif categorization for cryptococcal strains through analyzing filter-isolated EPS by 1D [1H] NMR and assigning GXM motifs along with the O-acetylation level. The result is a facile method using minimally processed EPS material coupled with simple cryptococcal strain classification by GXM motif expression. While this method increases the correlation between MLST genotype and GXM motif expression, further studies to establish the polysaccharide regulatory genes in cryptococcus will be necessary to understand the polysaccharide differences. In summary, none of the current classification methods correlated with each other, indicating a dissociation between genotype and phenotype, which poses a challenge to the cryptococcal field for explaining how phenotypic characteristics arise and are maintained.