bluuebunny/crossref_metadata_2025 huggingface dataset:
Fever-like temperature bursts promote competence development via an HtrA-dependent pathway inStreptococcus pneumoniae
Authors: Maziero Mickaël , Lane David , Polard Patrice , Bergé Mathieu
Published: April 2023

Streptococcus pneumoniae(the pneumococcus) is well known for its ability to develop competence for natural DNA transformation. Competence development is regulated by an autocatalytic loop driven by variations in the basal level of transcription of thecomCDEandcomABoperons. These genes are part of the early gene regulon that controls expression of the late competence genes known to encode the apparatus of transformation. Several stressful conditions are known to promote competence development, although the induction pathways are remain poorly understood so far. To date there have been no reports of the response of the pneumococcal competence regulon to changes in the physical conditions of the environment, oxidative potential and temperature. Here we demonstrate that transient temperature elevation induces an immediate increase in the basal expression level of thecomCDEoperon and early genes that, in turn, stimulates its full induction, including that of the late competence regulon. This thermal regulation depends on the HtrA chaperone/protease and its proteolytic activity. We find that certain other competence induction stimuli are not conveyed by the HtrA-dependent pathway. This finding strongly supports that competence can be induced by any of several independent pathways and thus reinforces the view that competence is a general stress response system in the pneumococcus.

Authors’ summary

Streptococcus pneumoniaeis a commensal bacterium and an opportunistic pathogen of humans. Certain environmental stimuli, such as a variety of antibiotics targeting distinct cellular functions, trigger the induction of the distinct physiological state of competence, in which cells can, among other things, import and integrate external DNA. Competence is thus considered a general stress response in this highly adaptable species. To understand the role of competence in pneumococcal interaction with its host and in pathogenicity, we attempted to decipher the pathways that enable appropriate reactions to environmental stress, and have focused here on induction of competence by elevation of temperature to levels similar to that of a host in fever. We found that elevated temperature raises the basal expression level of the competence control operon, and thus lowers the threshold of transition to full competence induction. By genetic characterisation of the thermal induction pathway of competence, we demonstrated that the chaperone/protease HtrA is essential to relaying of the thermal signal but is not involved in transmitting other stimuli such as those arising from the presence of certain antibiotics. Our work supports the view that competence can be induced through various pathways in response to distinct aggressions, but also by fever-like bursts of temperature that the pneumococcus could face in its natural habitat.
Polymerization force-regulated actin filament-Arp2/3 complex interaction dominates self-adaptive cell migrations
Authors: Chen Xindong , Li Yuhui , Guo Ming , Xu Bowen , Ma Yanhui , Zhu Hanxing , Feng Xi-Qiao
Published: April 2023

Cells migrate by adapting their leading-edge behaviours to heterogeneous extracellular microenvironments (ECMs) during cancer invasions and immune responses. Yet it remains poorly understood how such complicated dynamic behaviours emerge from millisecond-scale assembling activities of protein molecules, which are hard to probe experimentally. To address this gap, we established a spatiotemporal “resistance-adaptive propulsion” theory based on the protein interactions between Arp2/3 complexes and polymerizing actin filaments, and a multiscale dynamic modelling system spanning from molecular proteins to the cell. Combining spatiotemporal simulations with experiments, we quantitatively find that cells can accurately self-adapt propulsive forces to overcome heterogeneous ECMs via a resistance-triggered positive feedback mechanism, dominated by polymerization-induced actin filament bending and the bending-regulated actin-Arp2/3 binding. However, for high resistance regions, resistance triggered a negative feedback, hindering branched filament assembly, which adapts cellular morphologies to circumnavigate the obstacles. Strikingly, the synergy of the two opposite feedbacks not only empowers cells with both powerful and flexible migratory capabilities to deal with complex ECMs, but also endows cells to use their intracellular proteins efficiently. In addition, we identify that the nature of cell migration velocity depending on ECM history stems from the inherent temporal hysteresis of cytoskeleton remodelling. We also quantitatively show that directional cell migration is dictated by the competition between the local stiffness of ECMs and the local polymerizing rate of actin network caused by chemotactic cues. Our results reveal that it is the polymerization force-regulated actin filament-Arp2/3 complex binding interaction that dominates self-adaptive cell migrations in complex ECMs, and we provide a predictive theory and a spatiotemporal multiscale modelling system at the protein level.
Limited Diffusion of Scientific Knowledge Forecasts Collapse
Authors: Kang Donghyun , Danziger Robert S. , Rehman Jalees , Evans James A.
Published: April 2023

Market bubbles emerge when asset prices are driven unsustainably higher than asset values and shifts in belief burst them. We demonstrate the same phenomenon for biomedical knowledge when promising research receives inflated attention. We predict deflationary events by developing a diffusion index that captures whether research areas have been amplified within social and scientific bubbles or have diffused and become evaluated more broadly. We illustrate our diffusion approach contrasting the trajectories of cardiac stem cell research and cancer immunotherapy. We then trace the diffusion of unique 28,504 subfields in biomedicine comprising nearly 1.9M papers and more than 80M citations and demonstrate that limited diffusion of biomedical knowledge anticipates abrupt decreases in popularity. Our analysis emphasizes that restricted diffusion, implying a socio-epistemic bubble, leads to dramatic collapses in relevance and attention accorded to scientific knowledge.
Light modulates task-dependent thalamo-cortical connectivity during an auditory attentional task
Authors: Paparella Ilenia , Campbell Islay , Sharifpour Roya , Beckers Elise , Berger Alexandre , Balda Aizpurua Jose Fermin , Koshmanova Ekaterina , Mortazavi Nasrin , Talwar Puneet , Degueldre Christian , Lamalle Laurent , Sherif Siya , Phillips Christophe , Maquet Pierre , Vandewalle Gilles
Published: April 2023

Exposure to blue wavelength light stimulates alertness and performance by modulating a widespread set of task-dependent cortical and subcortical areas. How light affects the crosstalk between brain areas to trigger this stimulating effect is not established. We recorded the brain activity of 19 healthy young participants (24.05±2.63; 12 women) while they completed an auditory attentional task in darkness or under an active (blue-enriched) or a control (orange) light, in an ultra-high-field 7 Tesla MRI scanner. We tested if light modulated the effective connectivity between an area of the posterior associative thalamus, encompassing the pulvinar, and the intraparietal sulcus (IPS), key areas in the regulation of attention. We found that only the blue-enriched light strengthened the connection from the posterior thalamus to the IPS. Our results provide the first empirical data supporting that blue wavelength light affects ongoing non-visual cognitive activity by modulating task-dependent information flow from subcortical to cortical areas.
Efficient and Robust Search of Microbial Genomes via Phylogenetic Compression
Authors: Břinda Karel , Lima Leandro , Pignotti Simone , Quinones-Olvera Natalia , Salikhov Kamil , Chikhi Rayan , Kucherov Gregory , Iqbal Zamin , Baym Michael
Published: April 2023

Comprehensive collections approaching millions of sequenced genomes have become central information sources in the life sciences. However, the rapid growth of these collections has made it effectively impossible to search these data using tools such as BLAST and its successors. Here, we present a technique called phylogenetic compression, which uses evolutionary history to guide compression and efficiently search large collections of microbial genomes using existing algorithms and data structures. We show that, when applied to modern diverse collections approaching millions of genomes, lossless phylogenetic compression improves the compression ratios of assemblies, de Bruijn graphs, andk-mer indexes by one to two orders of magnitude. Additionally, we develop a pipeline for a BLAST-like search over these phylogeny-compressed reference data, and demonstrate it can align genes, plasmids, or entire sequencing experiments against all sequenced bacteria until 2019 on ordinary desktop computers within a few hours. Phylogenetic compression has broad applications in computational biology and may provide a fundamental design principle for future genomics infrastructure.
Heritable changes of epialleles in maize can be triggered in the absence of DNA methylation
Authors: Liu Beibei , Yang Diya , Wang Dafang , Liang Chun , Wang Jianping , Lisch Damon , Zhao Meixia
Published: April 2023

Trans-chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions. Here, we compared DNA methylomes of F1 hybrids that are mutant for a small RNA biogenesis gene,Mop1(mediator of paramutation1) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in bothtrans-chromosomal methylation (TCM) andtrans-chromosomal demethylation (TCdM), most of which involved changes in CHH methylation. In more than 60% of these TCM differentially methylated regions (DMRs) in which small RNAs are available, no significant changes in the quantity of small RNAs were observed. Methylation at the CHH TCM DMRs was largely lost in themop1mutant, although the effects of this mutant varied depending on the location of the CHH DMRs. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that TCM and TCdM can be maintained in the subsequent generation, but that TCdM is more stable than TCM. Surprisingly, although increased CHH methylation in F1 plants did requireMop1, initiation of the changes in the epigenetic state of TCM DMRs did not require a functional copy of this gene, suggesting that initiation of these changes is not dependent on RNA-directed DNA methylation.
Reprogramming of lipid secretome in senescent synovial fibroblasts ameliorate osteoarthritis development
Authors: Hu Jiajie , Yu Dongsheng , Wu Dongmei , Wang Jiasheng , Cai Youzhi , Du Xiaotian , Ji Junfen , Ouyang Hongwei
Published: April 2023

Osteoarthritis (OA) is one of the most common causes of physical disability among older people and its incidence increases with age. Removal of the senescent cells (SNCs) delays OA pathologies, but little is known about the SNCs in OA synovium and their roles in OA pathogenesis. Here, we reported that RCAN1+IL1α+double-positive cells represent a senescent subset of synovial fibroblasts which accelerate cartilage degeneration via saturated fatty acids (SFAs). Using single-cell RNA sequencing and synovial organoids, we found that IL1α+ senescent synovial fibroblasts mainly located at lining layer of human OA synovium and promote cartilage degeneration. We performed genome-wide CRISPR/Cas9 screens to identify novel regulators of cell-surface bounded IL1α in senescent cells. RCAN1, which was a hit as positive regulator of IL1α, governs the cellular senescence and pro-degenerative senescence-associated secretory phenotype (SASP). Mechanistically, we found that RCAN1 mediated the secretion of SFAs from senescent synovial fibroblasts, which promote chondrocytes senescence and cartilage matrix degradation. Intra-articular delivery of synovium-targeted anti-Rcan1 siRNA ameliorates the development of post-traumatic OA in mice, while reducing of SNCs accumulation in synovium and increasing cartilage regeneration. Last, co-culture experiments of human OA cartilage explant with synovial organoids confirmed that RCAN1 silencing in human synovial fibroblasts suppressed chondrocyte senescence and cartilage degradation. Thus, our study revealed a pro-degenerative interaction between RCAN1+IL1α+senescent synovial fibroblasts and chondrocytes through secreted lipid mediators in OA progression. And targeted RCAN1 inhibition in senescent synovium is a promising approach for restore the joint homeostasis.
SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state
Authors: Sebastian-Perez Ruben , Nakagawa Shoma , Tu Xiaochuan , Aranda Sergi , Pesaresi Martina , Gomez-Garcia Pablo Aurelio , Alcoverro-Bertran Marc , Gomez-Vazquez Jose Luis , Carnevali Davide , Borràs Eva , Sabidó Eduard , Martin Laura , Nissim-Rafinia Malka , Meshorer Eran , Neguembor Maria Victoria , Di Croce Luciano , Cosma Maria Pia
Published: April 2023

Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin establishment, we generated an inducible system to convert embryonic stem cells (ESCs) to 2C-like cells. This conversion is marked by a global reorganization and dispersion of H3K9me3-heterochromatin foci, which are then reversibly formed upon re-entry into pluripotency. By profiling the chromatin-bound proteome (chromatome) through genome capture of ESCs transitioning to 2C-like cells, we uncover chromatin regulators involved inde novoheterochromatin formation. We identified TOPBP1 and investigated its binding partner SMARCAD1. SMARCAD1 and TOPBP1 associate with H3K9me3-heterochromatin in ESCs. Interestingly, the nuclear localization of SMARCAD1 is lost in 2C-like cells. SMARCAD1 or TOPBP1 depletion in mouse embryos leads to developmental arrest, reduction of H3K9me3, and remodeling of heterochromatin foci. Collectively, our findings contribute to comprehending the maintenance of chromocenters during early development.
Building the Next Generation Workforce: Why We Need Science Policy Training at the Undergraduate Level
Authors: Bogard Gwendolyn , Saybolt Erin , Castro-Faix Moraima , Bankston Adriana
Published: April 2023

Diverse pathways into the science policy workforce are necessary for providing opportunities to students at all levels to engage in the field and to bring their talents to the future of policymaking. Both classroom and experiential training opportunities are essential to achieving this goal. In this publication, we assessed the current landscape of science policy training for undergraduate students in the United States by conducting a keyword search for experiential career training opportunities at varying levels of education. We also reviewed existing science policy publications for undergraduate opportunities, an area that has been largely unexplored to date. From these assessments, we found that most experiential training opportunities are geared towards Science, Technology, Engineering and Math (STEM) students in PhDs program or recent PhD graduates, followed by Masters-level students or graduates, and fewer opportunities exist for undergraduate students and Bachelor-degree holders. We then conducted focus group-style interviews with early career scientists involved in science policy, including undergraduate students, to discuss their experiences and ideas for change. Based on our findings, we recommend that universities, organizations, and funding agencies expand upon their existing resources for curriculum, academic advising, training opportunities, and funding, and dedicate resources toward raising awareness and creating additional opportunities in science policy at the undergraduate level. These steps can help create pathways for undergraduate students to enter and contribute to the science policy workforce.
STING activation of IRF3 is tuned by PELI2 to suppress basal activation and reinforce the anti-viral response
Authors: Ritchie Christopher , Li Lingyin
Published: April 2023

The STING pathway is the first line of defense against a variety of threats. STING activation leads to two main signaling branches, IRF3 signaling and NF-κB signaling, that have differential roles in anti-cancer, anti-viral, and anti-bacterial immunity and autoimmunity. However, it is unknown how these two signaling branches are differentially regulated depending on context. Here, we identify PELI2 as a regulator of STING that preferentially inhibits IRF3 signaling while enhancing NF-κB signaling. Mechanistically, we show that PELI2 inhibits IRF3 signaling by binding to phosphorylated Thr354 and Thr356 on the C-terminal tail of STING, leading to ubiquitination and function switching of TBK1. PELI2 is expressed under basal conditions to suppress IRF3 signaling and prevent interferonopathies. During viral infection, however, STING signaling rapidly downregulates PELI2 to unleash production of anti-viral type-I interferons. Normally, PELI2 levels are restored following viral clearance. However, lupus patients have insufficient PELI2 levels and high basal interferon production, suggesting dysregulation of PELI2 may have a causative role in lupus and other interferonopathies.
Atoh1 is required for the formation of lateral line electroreceptors and hair cells, whereas Foxg1 represses an electrosensory fate
Authors: Minařík Martin , Campbell Alexander S. , Franěk Roman , Vazačová Michaela , Havelka Miloš , Gela David , Pšenička Martin , Baker Clare V. H.
Published: April 2023

In electroreceptive jawed fishes and amphibians, individual lateral line placodes form lines of neuromasts on the head containing mechanosensory hair cells, flanked by fields of ampullary organs containing electroreceptors - modified hair cells that respond to weak electric fields. Extensively shared gene expression between neuromasts and ampullary organs suggests that conserved molecular mechanisms are involved in their development, but a few transcription factor genes are restricted either to the developing electrosensory or mechanosensory lateral line. Here, we used CRISPR/Cas9-mediated mutagenesis in F0-injected sterlet embryos (Acipenser ruthenus, a sturgeon) to test the function of three such genes. We found that the ‘hair cell’ transcription factor geneAtoh1is required for both hair cell and electroreceptor differentiation in sterlet, and forPou4f3andGfi1expression in both neuromasts and ampullary organs. These data support the conservation of developmental mechanisms between hair cells and electroreceptors. Targeting ampullary organ-restrictedNeurod4did not yield any phenotype, potentially owing to redundancy with otherNeurodgenes that we found to be expressed in sterlet ampullary organs. After targeting mechanosensory-restrictedFoxg1, ampullary organs formed within neuromast lines, suggesting that Foxg1 normally represses their development. We speculate that electrosensory organs may be the ‘default’ fate of lateral line primordia in electroreceptive vertebrates.
Scalable, flexible carbon fiber electrode thread arrays for three-dimensional spatial profiling of neurochemical activity in deep brain structures of rodents
Authors: Xia Mingyi , Agca Busra Nur , Yoshida Tomoko , Choi Jiwon , Amjad Usamma , Bose Kade , Keren Nikol , Zukerman Shahar , Cima Michael J. , Graybiel Ann M. , Schwerdt Helen N.
Published: April 2023

We developed a flexible “electrode-thread” array for recording dopamine neurochemical activity from a lateral distribution of subcortical targets (up to 16) transverse to the axis of insertion. Ultrathin (∼ 10 µm diameter) carbon fiber (CF) electrode-threads (CFETs) are clustered into a tight bundle to introduce them into the brain from a single entry point. The individual CFETs splay laterally in deep brain tissue during insertion due to their innate flexibility. This spatial redistribution allows navigation of the CFETs towards deep brain targets spreading horizontally from the axis of insertion. Commercial “linear” arrays provide single entry insertion but only allow measurements along the axis of insertion. Horizontally configured neurochemical recording arrays inflict separate penetrations for each individual channel (i.e., electrode). We tested functional performance of our CFET arraysin vivofor recording dopamine neurochemical dynamics and for providing lateral spread to multiple distributed sites in the striatum of rats. Spatial spread was further characterized using agar brain phantoms to measure electrode deflection as a function of insertion depth. We also developed protocols to slice the embedded CFETs within fixed brain tissue using standard histology techniques. This method allowed extraction of the precise spatial coordinates of the implanted CFETs and their recording sites as integrated with immunohistochemical staining for surrounding anatomical, cytological, and protein expression labels. Neurochemical recording operations tested here can be integrated with already widely established capabilities of CF-based electrodes to record single neuron activity and local field potentials, to enable multi-modal recording functions. Our CFET array has the potential to unlock a wide range of applications, from uncovering the role of neuromodulators in synaptic plasticity, to addressing critical safety barriers in clinical translation towards diagnostic and adaptive treatment in Parkinson’s disease and major mood disorders.
Structure and function of a hexameric cyanophycin synthetase 2
Authors: Markus Linda M. D. , Sharon Itai , Munro Kim , Grogg Marcel , Hilvert Donald , Strauss Mike , Schmeing T. Martin
Published: April 2023

Cyanophycin is a natural polymer composed of a poly-aspartate backbone with arginine attached to each of the aspartate sidechains. Produced by a wide range of bacteria, which mainly use it as a store of fixed nitrogen, it has many promising industrial applications. Cyanophycin can be synthesized from the amino acids Asp and Arg by the widespread cyanophycin synthetase 1 (CphA1), or from the dipeptide β-Asp-Arg by the cyanobacterial enzyme cyanophycin synthetase 2 (CphA2). CphA2 enzymes display a range of oligomeric states, from dimers to dodecamers. Recently, the crystal structure of a CphA2 dimer was solved but could not be obtained in complex with substrate. Here, we report cryo-EM structures of the hexameric CphA2 fromStanieriasp. at ~2.8 Å resolution, both with and without ATP and cyanophycin. The structures show a trimer-of-dimers hexameric architecture, and substrate-binding interactions that are similar to those of CphA1. Mutagenesis experiments demonstrate the importance of several conserved substrate-binding residues. We also find that a Q416A/R528G double mutation prevents hexamer formation and use this double mutant to show that hexamerization augments the rate of cyanophycin synthesis. Together, these results increase our mechanistic understanding of how an interesting green polymer is biosynthesized.
Gardnerellavaginolysin potentiates glycan molecular mimicry byNeisseria gonorrhoeae
Authors: Morrill Sydney , Saha Sudeshna , Varki Ajit P , Lewis Warren G. , Ram Sanjay , Lewis Amanda L.
Published: April 2023

Bacterial vaginosis (BV) is a condition of the vaginal microbiome in which there are lower levels of “healthy”Lactobacillusspecies and an outgrowth of diverse anaerobic bacteria. BV is associated with increased risk of infection by the bacteriumNeisseria gonorrhoeae- the causative agent of gonorrhea. Here we test if one known facet of BV - the presence of bacterial cytolysins – leads to the mobilization of specific intracellular contents that aid in gonococcal virulence. We cloned and expressed recombinant vaginolysin (VLY), a cytolysin produced by the BV-associated bacteriumGardnerella, verifying that it liberates the contents of red blood cells and cervical epithelial (HeLa) cells while vector control preparations made in parallel did not. We tested if VLY mediates a well-known virulence mechanism of gonococcus – the molecular mimicry of host glycans. To evade host immunity,N. gonorrhoeaecaps its surface lipooligosaccharide (LOS) with α2-3-linked sialic acid. To do this, gonococci must scavenge an intermediate metabolite made and used inside host cells. Flow-cytometry based lectin-binding assays showed that, compared to controls, gonococci exposed to vaginolysin-liberated contents of HeLa cells displayed greater sialic acid capping of their LOS. This higher level of bacterial sialylation was accompanied by increased binding of the complement regulatory protein Factor H, and greater resistance to complement attack. Together these results suggest that cytolytic activities present during BV may enhance the ability ofN. gonorrhoeaeto capture intracellular metabolites and evade host immunity via glycan molecular mimicry.
High-resolution genome-wide mapping of chromosome-arm-scale truncations induced by CRISPR-Cas9 editing
Authors: Lazar Nathan H. , Celik Safiye , Chen Lu , Fay Marta , Irish Jonathan C. , Jensen James , Tillinghast Conor A. , Urbanik John , Bone William P. , Roberts Genevieve H. L. , Gibson Christopher C. , Haque Imran S.
Published: April 2023

CRISPR-Cas9 editing is a scalable technology for mapping of biological pathways, but it has been reported to cause a variety of undesired large-scale structural changes to the genome. We performed an arrayed CRISPR-Cas9 scan of the genome in primary human cells, targeting 17,065 genes for knockout with 101,029 guides. High-dimensional phenomics reveals a “proximity bias” in which CRISPR knockouts bear unexpected phenotypic similarity to knockouts of biologically-unrelated genes on the same chromosome arm, recapitulating both canonical genome structure and structural variants. Transcriptomics connects proximity bias to chromosome-arm truncations. Analysis of published large-scale knockout and knockdown experiments confirms that this effect is general across cell types, labs, Cas9 delivery mechanisms, and assay modalities, and suggests proximity bias is caused by DNA double-strand-breaks with cell cycle control in a mediating role. Finally, we demonstrate a simple correction for large-scale CRISPR screens to mitigate this pervasive bias while preserving biological relationships.
Intestelligence: A pharmacological neural network using intestine data
Authors: Watanabe Yusuke , Ban Hiroshi , Hagura Nobuhiro , Ikegaya Yuji
Published: April 2023

A neural network is a machine learning algorithm that can learn and make predictions by adjusting the strength of the connections between nodes. The sigmoid function is commonly used as an activation function in these nodes. This study explores the potential applicability of biological materials in the development of alternative activation functions. Inspired by the fact that acetylcholine induces intestinal contractions that follow a sigmoid function, we used pharmacological data obtained from guinea pig ilea in a layered neural network for image classification tasks. We found that the intestinal data-based neural network with the same structure as a conventional three-layer perceptron achieved an impressive classification accuracy of 85.7% ± 0.6% based on the MNIST handwritten digit dataset (chance = 10%). Additionally, the neural network was trained to determine whether objects in photographs collected from the internet were digestible, achieving an accuracy of 88.5% ± 0.9% (chance = 50%). Our approach highlights the potential applicability of intestine data in neural computations based on pharmacological mechanisms.
Neoadjuvant systemic oncolytic vesicular stomatitis virus is safe and may enhance long-term survivorship in dogs with naturally occurring osteosarcoma
Authors: Makielski Kelly M. , Sarver Aaron L. , Henson Michael S. , Stuebner Kathleen M. , Borgatti Antonella , Suksanpaisan Lukkana , Preusser Caitlin , Tabaran Alexandru-Flaviu , Cornax Ingrid , O’Sullivan M. Gerard , Chehadeh Andrea , Groschen Donna , Bergsrud Kelly , Pracht Sara , Winter Amber , Mills Lauren J. , Schwabenlander Marc D. , Wolfe Melissa , Farrar Michael A. , Cutter Gary R. , Koopmeiners Joseph S. , Russell Stephen J. , Modiano Jaime F. , Naik Shruthi
Published: April 2023

Osteosarcoma is a devastating bone cancer that disproportionally afflicts children, adolescents, and young adults. Standard therapy includes surgical tumor resection combined with multiagent chemotherapy, but many patients still suffer from metastatic disease progression. Neoadjuvant systemic oncolytic virus (OV) therapy has the potential to improve clinical outcomes by targeting primary and metastatic tumor sites and inducing durable antitumor immune responses. Here we described the first evaluation of neoadjuvant systemic therapy with a clinical-stage recombinant oncolytic Vesicular stomatitis virus (VSV), VSV-IFNβ-NIS, in naturally occurring cancer, specifically appendicular osteosarcoma in companion dogs. Canine osteosarcoma has a similar natural disease history as its human counterpart. VSV-IFNβ-NIS was administered prior to standard of care surgical resection, permitting microscopic and genomic analysis of tumors. Treatment was well-tolerated and a “tail” of long-term survivors (∼35%) was apparent in the VSV-treated group, a greater proportion than observed in two contemporary control cohorts. An increase in tumor inflammation was observed in VSV-treated tumors and RNAseq analysis showed that all the long-term responders had increased expression of a T-cell anchored immune gene cluster. We conclude that neoadjuvant VSV-IFNβ-NIS is safe and may increase long-term survivorship in dogs with naturally occurring osteosarcoma, particularly those that exhibit pre-existing antitumor immunity.
Neurodevelopmental disorders and cancer networks share pathways; but differ in mechanisms, signaling strength, and outcome
Authors: Yavuz Bengi Ruken , Arici M Kaan , Demirel Habibe Cansu , Tsai Chung-Jung , Jang Hyunbum , Nussinov Ruth , Tuncbag Nurcan
Published: April 2023

Neurodevelopmental disorders (NDDs) and cancer are connected, with immunity as their common factor. Their clinical presentations differ; however, individuals with NDDs are more likely to acquire cancer. Schizophrenia patients have ∼50% increased risk; autistic individuals also face an increased cancer likelihood. NDDs are associated with specific brain cell types at specific locations, emerging at certain developmental time windows during brain evolution. Their related mutations are germline; cancer mutations are sporadic, emerging during life. At the same time, NDDs and cancer share proteins, pathways, and mutations. Here we ask exactly which features they share, and how despite their commonality, they differ in outcomes. Our pioneering bioinformatics exploration of the mutations, reconstructed disease-specific networks, pathways, and transcriptome profiles of autism spectrum disorder (ASD) and cancers, points to elevated signal strength in pathways related to proliferation in cancer, and differentiation in ASD. Signaling strength, not the activating mutation, is the key factor in deciding cancer versus NDDs.
A Machine Learning-optimized system for on demand, pulsatile, photo- and chemo-therapeutic treatment using near-infrared responsive MoS2-based microparticles in a breast cancer model
Authors: Kanelli Maria , Bardhan Neelkanth M. , Sarmadi Morteza , Alsaiari Shahad , Rothwell William T. , Pardeshi Apurva , De Fiesta Dominique C. , Mak Howard , Spanoudaki Virginia , Henning Nicole , Han Jooli , Belcher Angela M. , Langer Robert S. , Jaklenec Ana
Published: April 2023

Cancer therapy research is of high interest because of the persistence and mortality of the disease and the side effects of traditional therapeutic methods, while often multimodal treatments are necessary based on the patient’s needs. The development of less invasive modalities for recurring treatment cycles is thus of critical significance. Herein, a light-activatable microparticle system was developed for localized, pulsatile delivery of anticancer drugs with simultaneous thermal ablation, by applying controlled ON-OFF thermal cycles using near-infrared laser irradiation. The system is composed of poly(caprolactone) microparticles of 200 μm size with incorporated molybdenum disulfide (MoS2) nanosheets as the photothermal agent and hydrophilic doxorubicin or hydrophobic violacein, as model drugs. Upon irradiation the nanosheets heat up to ≥50 °C leading to polymer matrix melting and release of the drug. MoS2nanosheets exhibit high photothermal conversion efficiency and allow for application of low power laser irradiation for the system activation. A Machine Learning algorithm was applied to acquire optimal laser operation conditions; 0.4 W/cm2laser power at 808 nm, 3-cycle irradiation, for 3 cumulative minutes. In a mouse subcutaneous model of 4T1 triple-negative breast cancer, 25 microparticles were intratumorally administered and after 3-cycle laser treatment the system conferred synergistic phototherapeutic and chemotherapeutic effect. Our on-demand, pulsatile synergistic treatment resulted in increased median survival up to 40 days post start of treatment compared to untreated mice, with complete eradication of the tumors at the primary site. Such a system could have potential for patients in need of recurring cycles of treatment on subcutaneous tumors.

GRAPHICAL ABSTRACT
Information storage across a microbial community using universal RNA memory
Authors: Kalvapalle Prashant B. , Staubus August , Dysart Matthew J. , Gambill Lauren , Reyes Gamas Kiara , Chieh Lu Li , Silberg Jonathan J. , Stadler Lauren B. , Chappell James
Published: April 2023

Biological recorders can code information in DNA, but they remain challenging to apply in complex microbial communities. To program microbiome information storage, a synthetic catalytic RNA (cat-RNA) was used to write information in ribosomal RNA (rRNA) about gene transfer host range. By reading out native and modified rRNA using amplicon sequencing, we find that 140 out of 279 wastewater microbial community members from twenty taxonomic orders participate in conjugation and observe differences in information storage across amplicon sequence variants. Twenty of the variants were only observed in modified rRNA amplicons, illustrating information storage sensitivity. This autonomous and reversible RNA-addressable memory (RAM) will enable biosurveillance and microbiome engineering across diverse ecological settings and studies of environmental controls on gene transfer and cellular uptake of extracellular materials.

One-Sentence Summary

Ribosomal RNA sequencing detects cellular events recorded across a wastewater microbial community using synthetic biology.
Multidimensional responses of ecological stability to eutrophication in grasslands
Authors: Chen Qingqing , Wang Shaopeng , Borer Elizabeth T. , Bakker Jonathan D. , Seabloom Eric W. , Harpole W. Stanley , Eisenhauer Nico , Lekberg Ylva , Buckley Yvonne M. , Catford Jane A. , Roscher Christiane , Donohue Ian , Power Sally A. , Daleo Pedro , Ebeling Anne , Knops Johannes M. H. , Martina Jason P. , Eskelinen Anu , Morgan John W. , Risch Anita C. , Caldeira Maria C. , Bugalho Miguel N , Virtanen Risto , Barrio Isabel C , Niu Yujie , Jentsch Anke , Stevens Carly J. , Alberti Juan , Hautier Yann
Published: April 2023

Eutrophication usually impacts biodiversity, species composition, and functioning of grassland communities. Whether such effects propagate to influence the stability of these community aspects is unknown. Using standardized experiments across 55 global grasslands, we quantified the effects of nutrient addition on five stability facets (i.e., temporal invariability and resistance during and recovery after dry and wet growing seasons) for three community aspects (i.e., aboveground biomass, community composition, and species richness). Nutrient addition reduced the temporal invariability and resistance of species richness and community composition, but not biomass, during dry and wet growing seasons. Temporal invariability and resistance during, but not recovery after, dry and wet growing seasons were strongly positively correlated in both ambient and eutrophic conditions. This indicates that maintaining and restoring the stability of plant communities requires increasing resistance rather than recovery. Harnessing the complexity of ecological stability provides new insights for grassland ecosystem sustainability in a changing world.
Proliferative response of ERα-positive breast cancer cells to 10 μM enterolactone, and the associated alteration in the transcriptomic landscape
Authors: Hatwik Juana , Patil Hrishikesh Nitin , Limaye Anil Mukund
Published: April 2023

Enterolactone (EL) is a product of gut-microbial metabolism of dietary plant lignans. Studies linking EL with breast cancer risk have bolstered investigations into its effects on the mammary epithelial cells, and the mechanisms thereof. While it binds to the estrogen receptor α; ERα, its effect on the proliferation of mammary tumor cell lines is reportedly ambivalent; depending on its concentration. The genomic correlates of EL actions also remain unexplored. Here we have elaborately studied the effect of EL on proliferation of ERα-positive, and ERα-negative cell lines. 10 µM EL significantly enhanced the growth of the ERα-positive MCF-7 or T47D breast cancer cells, but not the ERα-negative MDA-MB-231 or MDA-MB-453 cells. In MCF-7 cells, it significantly increased the expression ofTFF1mRNA, an estrogen-induced transcript. The binding of ERα to the estrogen response element within theTFF1locus further demonstrates the pro-estrogenic effect of 10 µM EL. We further explored the genome-wide transcriptomic effect of 10 µM EL. Analysis of RNA-seq data obtained from control- or 10 µM EL treated-MCF-7 cells revealed modulation of expression of diverse sets of functionally related genes, which reflected cell cycle progression, rather than cell cycle arrest or apoptosis. The manner in which 10 µM EL regulated the hallmark G2/M checkpoint, and estrogen-response-late genes correlated with proliferation inducing, and estrogen-like effects of EL on MCF-7 cells.
Multipotent Progenitors Instruct Ontogeny of the Superior Colliculus
Authors: Cheung Giselle , Pauler Florian M. , Koppensteiner Peter , Krausgruber Thomas , Streicher Carmen , Schrammel Martin , Gutmann-Özgen Natalie , Ivec Alexis E. , Bock Christoph , Shigemoto Ryuichi , Hippenmeyer Simon
Published: April 2023

The superior colliculus (SC) in the mammalian midbrain is essential for multisensory integration, attention, and complex behavior (Basso and May, 2017; Cang et al., 2018). The mature SC cytoarchitecture is organized into distinct laminae and composed of a rich variety of neuronal and glial cell types (Ayupe et al., 2023; Edwards et al., 1986; May, 2006; Xie et al., 2021; Zeisel et al., 2018). Precise execution of the developmental programs regulating the generation of SC cell-type diversity is essential, because deficits due to genetic mutations have been associated with neurodevelopmental diseases and SC dysfunction (Jure, 2018; McFadyen et al., 2020). However, the fundamentals directing the ontogeny of the SC are not well understood. Here we pursued systematic lineage tracing at the single progenitor cell level in order to decipher the principles instructing the generation of cell-type diversity in the SC. We combinedin silicolineage reconstruction with a novel genetic MADM (Mosaic Analysis with Double Markers)-CloneSeq approach. MADM-CloneSeq enables the unequivocal delineation of cell lineagesin situ, and cell identity based on global transcriptome, of individual clonally-related cells. Our systematic reconstructions of cell lineages revealed that all neuronal cell types in SC emerge from local progenitors without any extrinsic source. Strikingly, individual SC progenitors are exceptionally multipotent with the capacity to produce all known excitatory and inhibitory neuron types of the prospective mature SC, with individual clonal units showing no pre-defined composition. At the molecular level we identified an essential role for PTEN signaling in establishing appropriate proportions of specific inhibitory and excitatory neuron types. Collectively, our findings demonstrate that individual multipotent progenitors generate the full spectrum of excitatory and inhibitory neuron types in the developing SC, providing a novel framework for the emergence of cell-type diversity and thus the ontogeny of the mammalian SC.
SHARPIN enhances ferroptosis in synovial sarcoma cells via NF-κB- and PRMT5-mediated PGC1α reduction
Authors: Tamiya Hironari , Urushihara Naoko , Shizuma Kazuko , Ogawa Hisataka , Nakai Sho , Wakamatsu Toru , Takenaka Satoshi , Kakunaga Shigeki
Published: April 2023

Sarcoma is a rare type of cancer for which new therapeutic agents are required. Ferroptosis is a nonapoptotic cell death triggered by iron-mediated lipid peroxidation. We found that transferrin receptor 1 (TFRC), an iron uptake protein, was expressed at higher levels in sarcoma cell lines than in noncancer and carcinoma cell lines. Glutathione peroxidase 4 (GPX4) protects cells against ferroptosis, and its inhibition using RAS-selective lethal 3 (RSL3) had an antitumor effect that was more pronounced in sarcoma cell lines, particularly synovial sarcoma cells, than in non-sarcoma cells. Because NF-κB can provoke ferroptosis, we examined the role of SHARPIN, an activator of NF-κB, in sarcoma. We found that SHARPIN expression is significantly associated with reduced survival in cohorts of patients with cancer, including sarcoma. In addition, SHARPIN promotes the sensitivity of sarcoma cells to ferroptosis. Further analyses revealed that the PGC1α/NRF2/SLC7A11 axis and BNIP3L/NIX-mediated mitophagy are regulated through NF-κB and PRMT5 downstream of SHARPIN. Our findings suggest that ferroptosis could have a therapeutic effect in sarcoma, particularly in subpopulations with high TFRC and SHARPIN expression.
A Hidden Proportional Feedback Mechanism Underlies Enhanced Dynamic Performance and Noise Rejection in Sensor-Based Antithetic Integral Control
Authors: Filo Maurice , Hou Mucun , Khammash M.
Published: April 2023

Efficient regulation of cellular processes is essential for both endogenous and synthetic biological processes. The design of biomolecular feedback controllers that achieve robust and timely regulation is the subject of considerable research at the interface between synthetic biology and control theory. Integral feedback controllers, known for their ability to confer the property of Robust Perfect Adaptation (RPA), are increasingly becoming common features in biological control design. Antithetic integral feedback (AIF) controllers, in particular, have enabled effective chemical reaction realizations of integral controllers that deliver RPA in both deterministic and stochastic settings. This paved the way to experimental implementations of integral controllers in bacterial and mammalian cells. While AIF controllers deliver favorable adaptation properties, they do not necessarily lead to good transient performance or noise reduction properties and may in some cases lead to increased overshoot or cell-to-cell variability. These limitations are commonly circumvented by augmenting new circuitry that realize proportional or derivative feedback mechanisms to enhance dynamic and noise rejection features without affecting the AIF controller’s adaptation properties. In this paper, we report that a sensor-based variant of the basic AIF motif exhibits favorable transient dynamic properties and (as reported elsewhere) reduced noise variance. We show that these features are attributed to a “hidden” proportional feedback component that is inherent in the controller structure and that such mechanism is solely responsible for the controller’s underlying enhanced dynamic performance and noise rejection properties. This sensor-based AIF controller hence offers a minimal biomolecular realization of Proportional-Integral (PI) control, whereby both integral and proportional feedback mechanisms are achieved through a single actuation reaction.
Systemic inflammation modulates the levels of EBI2 and 7α,25-OHC synthesizing (CH25H, CYP7B1) and degrading (HSD3B7) enzymes in brain microvascular cells
Authors: Caratis Fionä , Karaszewski Bartosz , Klejbor Ilona , Furihata Tomomi , Rutkowska Aleksandra
Published: April 2023

The endogenous ligand for the EBI2 receptor, oxysterol 7α,25OHC, crucial for immune responses, is finely regulated by CH25H, CYP7B1 and HSD3B7 enzymes. Lymphoid stromal cells and follicular dendritic cells within T cell follicles maintain a gradient of 7α,25OHC, with stromal cells increasing and dendritic cells decreasing its concentration. This gradient is pivotal for proper B cell positioning in lymphoid tissue. In the animal model of multiple sclerosis, the experimental autoimmune encephalomyelitis, the levels of 7α,25OHC rapidly increase in the central nervous system driving the migration of EBI2 expressing immune cells through the blood-brain barrier (BBB). To explore if blood vessel cells in the brain express these enzymes, we examined normal mouse brain microvessels and studied their expression changes during inflammation. EBI2 was abundantly expressed in endothelial cells, pericytes/smooth muscle cells, and astrocytic endfeet. CH25H, CYP7B1, and HSD3B7 were variably detected in each cell type, suggesting their active involvement in oxysterol 7α,25OHC synthesis and gradient maintenance under normal conditions. Under acute inflammatory conditions, EBI2 and synthesizing enzyme modulation occurred in brain vasculature, with variations based on the enzyme and cell type. Significant species-specific differences emerged in EBI2 and enzyme levels between mouse and human BBB-forming cells. Overall, our investigation suggest a direct role of the brain microvascular cells in regulating 7α,25OHC levels, shedding light on potential therapeutic targets for neuroinflammatory disorders.