bluuebunny/crossref_metadata_2025_split huggingface dataset:
CCR2-targeting pepducins reduce T cell-nociceptor interaction driving bone cancer pain
Authors: Midavaine Élora , Brouillette Rebecca L. , Théberge Élizabeth , Mona Christine E. , Kashem Sakeen W. , Côté Jérôme , Zeugin Vera , Besserer-Offroy Élie , Longpré Jean-Michel , Marsault Éric , Sarret Philippe 
Published: September 2023

AbstractInhibition of the CCL2/CCR2 chemokine signaling represents a promising avenue for the development of non-opioid pain treatment, particularly for painful bone metastases. To investigate the involvement of CCR2 in cancer-induced bone pain, we generated and characterized the functional activities of a novel cell-penetrating pepducin, namely PP101, acting as an intracellular negative allosteric modulator of CCR2.In vivo, PP101 was effective in relieving neuropathic and bone cancer pain. By targeting CCR2, PP101 reduced bone cancer pain by preventing infiltration of CD4+and CD8+T cells and by decreasing the neuroimmune communication network within the dorsal root ganglia. Importantly, reduced neuroinflammatory milieu in the dorsal root ganglia induced by PP101 did not result in deleterious tumor progression or behavioral adverse effects. Thus, targeting the neuroimmune crosstalk through allosteric inhibition of CCR2 may represent an effective and safe avenue for the management of bone cancer pain.Graphical AbstractHighlightsBreast cancer bone metastases induce pain by activating CCR2 on sensory neurons.DRG-infiltrating CD4+and CD8+T cells promote the development of bone cancer pain.CCR2 inhibition by PP101 suppresses DRG neuroinflammation and neuronal excitability.PP101 alleviates bone cancer pain without behavioral or physiological side effects.
Sensory neuron population expansion enhances odor tracking without sensitizing projection neurons
Authors: Takagi Suguru , Sancer Gizem , Abuin Liliane , Stupski S. David , Arguello J. Roman , Prieto-Godino Lucia L. , Stern David L. , Cruchet Steeve , Álvarez-Ocaña Raquel , Wienecke Carl F. R. , van Breugel Floris , Jeanne James M. , Auer Thomas O. , Benton Richard 
Published: September 2023

SummaryThe evolutionary expansion of sensory neuron populations detecting important environmental cues is widespread, but functionally enigmatic. We investigated this phenomenon through comparison of homologous neural pathways ofDrosophila melanogasterand its close relativeDrosophila sechellia, an extreme specialist forMorinda citrifolianoni fruit.D. sechelliahas evolved species-specific expansions in select, noni-detecting olfactory sensory neuron (OSN) populations, through multigenic changes. Activation and inhibition of defined proportions of neurons demonstrate that OSN population increases contribute to stronger, more persistent, noni-odor tracking behavior. These sensory neuron expansions result in increased synaptic connections with their projection neuron (PN) partners, which are conserved in number between species. Surprisingly, having more OSNs does not lead to greater odor-evoked PN sensitivity or reliability. Rather, pathways with increased sensory pooling exhibit reduced PN adaptation, likely through weakened lateral inhibition. Our work reveals an unexpected functional impact of sensory neuron expansions to explain ecologically-relevant, species-specific behavior.
NGAL deficiency elicits Hemophilia-like bleeding and clotting disorder
Authors: Xue Min , Wang Shaoying , Li Changjiang , Wang Yuewei , Liu Ming , Xiao Dandan , Yin Qikai , Niu Liyuan , Shen Chuanbin , Wang Jianxun , Tang Xiaopeng 
Published: September 2023

AbstractCoagulation is related to inflammation, but the key pathways, especially innate immunity inflammatory response-coagulation, hemostasis, and thrombosis regulation is poorly understood and need to be further explored. In the current study, we showed that innate immunity inflammatory mediator neutrophil gelatinase-associated apolipoprotein (NGAL) which was upregulated in plasma of deep vein thrombosis patients interacted with and potentiated thrombin, kallikrein, FXIa, and FVIIa and suppressed antithrombin to induce coagulation, hemostasis, and thrombosis. Furthermore, NGAL can augment thrombin-induced platelet aggregation. In multiple mice hemostasis and thrombosis models, NGAL overexpression or intravenous administration promoted coagulation and hemostasis and aggravated thrombus, whereas NGAL knockout or treatment with anti-NGAL monoclonal antibody significantly prolonged bleeding time and alleviated thrombus formation. Notably, NGAL knockout prolonged both mice tail bleeding time and artery occlusion time to over 40 min, resembling uncontrollable bleeding and clotting disorder seen in Hemophilia mice. Furthermore, anti-NGAL monoclonal antibody treatment markedly reduced the formation of blood clots in a mouse-tail thrombosis model induced by carrageenan, which is linked to inflammation. Collectively, these findings suggest NGAL is a crucial coagulation regulator and mediates the crosstalk between innate immunity inflammation and coagulation, hemostasis, and thrombus, and provide new target and strategy for the development of innovative antithrombotic drugs.
Endothelial-fibroblast interactions during Scarb1 accelerate heart failure
Authors: Katsuki Toshiomi , Kusumoto Dai , Akiba Yohei , Kimura Mai , Komuro Jin , Nakamura Takahiro , Hashimoto Hisayuki , Kuoka Thukaa , Suzuki Yutaka , Kubota Yoshiaki , Fukuda Keiichi , Yuasa Shinsuke , Ieda Masaki 
Published: September 2023

SummaryEndothelial cells (ECs) maintain cardiac homeostasis and EC dysfunction causes heart failure progression. Moreover, pathological changes occur via interactions between multiple cells, including ECs. Here, we conducted single-cell RNA-seq analysis of non-cardiomyocytes in mouse hearts during heart failure progression to elucidate the pathological changes in ECs and fibroblasts (FBs) mediated by cell-cell interactions. We show that capillary and arterial ECs exhibit mesenchymal gene expression changes with heart failure progression, indicating that endothelial-to-mesenchymal transition (EndMT) is a major pathological alteration in ECs. We also found that the interaction between ECs and FBs was enriched during heart failure, particularly when involving Scavenger Receptor Class B Member 1 (Scarb1) in ECs. FBs induce mesenchymal gene alterations in ECs in the EC-FB co-culture system, which is inhibited by blocking SCARB1. RNA-seq analysis showed that administration of a SCARB1 inhibitor blocked mesenchymal gene expression, and inflammatory changes, suggesting that the EC-FB interaction via Scarb1 is important for EndMT induction in ECs. Systemic administration of a SCARB1 inhibitor attenuated heart failure progression and cardiac fibrosis. EC-specificScarb1knockout mouse showed improved cardiac function, suggesting a crucial role of Scarb1 in heart failure progression. Our results suggest that Scarb1 is a promising candidate for novel heart failure treatments that target ECs.
The asynchrony in the exit from naive pluripotency cannot be explained by differences in the cell cycle phase
Authors: Jayaram Swathi , Romeike Merrit , Buecker Christa 
Published: September 2023

ABSTRACTDevelopment is characterized by consecutive cell state transitions that build on each other and ultimately lead to the generation of the numerous different cell types found in the organism. During each of these transitions, cells change their gene expression profiles and take on new identities. Cell state transitions have to be tightly coordinated with proliferation to ensure simultaneous growth and differentiation. The exit from naive pluripotency is an ideal model system for studying the temporal coordination of proliferation and differentiation. Individual cells initiate differentiation earlier compared to others, thereby leading to an asynchronous exit from naive pluripotency. One of the major differences among the cells of the starting population of mouse embryonic stem cells (mESCs) is the cell cycle status, and could therefore be an underlying cause of the differences in the onset of the exit from naive pluripotency. However, through comprehensive analysis including single cell RNA sequencing (scRNA-seq), cell cycle synchronization, and perturbation experiments, we demonstrate here that the cell cycle phase at the initiation of differentiation does not influence the timing of the exit from naive pluripotency.
Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype
Authors: Marichannegowda Manukumar Honnayakanahalli , Setua Saini , Bose Meera , Sanders-Buell Eric , King David , Zemil Michelle , Wieczorek Lindsay , Diaz-Mendez Felisa , Chomont Nicolas , Thomas Rasmi , Francisco Leilani , Eller Leigh Anne , Polonis Victoria R. , Tovanabutra Sodsai , Tagaya Yutaka , Michael Nelson L. , Robb Merlin L. , Song Hongshuo 
Published: September 2023

AbstractNearly all transmitted/founder (T/F) HIV-1 are CCR5 (R5)-tropic. While previous evidence suggested that CXCR4 (X4)-tropic HIV-1 are transmissible, detection was not at the earliest stages of acute infection. Here, we identified an X4-tropic T/F HIV-1 in a participant in acute infection cohort. Coreceptor assays demonstrated that this T/F virus is strictly CXCR4 tropic. The participant experienced significantly faster CD4 depletion compared with R5 virus infected participants in the same cohort. Naïve and central memory CD4 subsets declined faster than effector and transitional memory subsets. All CD4 subsets, including naïve, were productively infected. Increased CD4+T cell activation was observed over time. This X4-tropic T/F virus is resistant to broadly neutralizing antibodies (bNAbs) targeting V1/V2 and V3 regions. These findings demonstrate that X4-tropic HIV-1 is transmissible through the mucosal route in people with the wild-type CCR5 genotype and have implications for understanding the transmissibility and immunopathogenesis of X4-tropic HIV-1.
Structural and dynamic changes in P-Rex1 upon activation by PIP3and inhibition by IP4
Authors: Ravala Sandeep K. , Adame-Garcia Sendi Rafael , Li Sheng , Chen Chun-Liang , Cianfrocco Michael A. , Gutkind J. Silvio , Cash Jennifer N. , Tesmer John J. G. 
Published: September 2023

AbstractPIP3-dependent Rac exchanger 1 (P-Rex1) is abundantly expressed in neutrophils and plays central roles in chemotaxis and cancer metastasis by serving as a guanine-nucleotide exchange factor (GEF) for Rac. The enzyme is synergistically activated by PIP3and the heterotrimeric Gβγ subunits, but mechanistic details remain poorly understood. While investigating the regulation of P-Rex1 by PIP3, we discovered that Ins(1,3,4,5)P4(IP4) inhibits P-Rex1 activity and induces large decreases in backbone dynamics in diverse regions of the protein. Cryo-electron microscopy analysis of the P-Rex1·IP4complex revealed a conformation wherein the pleckstrin homology (PH) domain occludes the active site of the Dbl homology (DH) domain. This configuration is stabilized by interactions between the first DEP domain (DEP1) and the DH domain and between the PH domain and a 4-helix bundle (4HB) subdomain that extends from the C-terminal domain of P-Rex1. Disruption of the DH–DEP1 interface in a DH/PH-DEP1 fragment enhanced activity and led to a more extended conformation in solution, whereas mutations that constrain the occluded conformation led to decreased GEF activity. Variants of full-length P-Rex1 in which the DH–DEP1 and PH–4HB interfaces were disturbed exhibited enhanced activity during chemokine-induced cell migration, confirming that the observed structure represents the autoinhibited state in living cells. Interactions with PIP3-containing liposomes led to disruption of these interfaces and increased dynamics protein-wide. Our results further suggest that inositol phosphates such as IP4help to inhibit basal P-Rex1 activity in neutrophils, similar to their inhibitory effects on phosphatidylinositol-3-kinase.
Mechanisms of action and synergies of a novel lipid IVAbiosynthesis inhibitor
Authors: Holden Emma R , Yasir Muhammad , Turner A Keith , Webber Mark A , Charles Ian , Siegwart Ed , Raynham Tony , Mistry Ajay , George John , Gilmour Matthew 
Published: September 2023

AbstractThe development of novel antimicrobials provides additional treatment options for infectious diseases, including antimicrobial resistant infections. There are many hurdles to antimicrobial development and identifying an antimicrobial’s mechanism of action is a crucial step in progressing candidate molecules through the drug discovery pipeline. We used the genome wide screening method TraDIS-Xpressto identify genes in two model Gram-negative bacteria that affected sensitivity to three analogues of a novel antimicrobial compound (OPT-2U1). TraDIS-Xpressidentified that all three analogues targeted the lipid IVAbiosynthetic pathway inE. coliandSalmonellaTyphimurium. Specifically, we determined that the antimicrobial target was likely to be LpxD, and validated this by finding a 5 log2-fold increase in the MIC of the OPT-2U1 analogues inE. coliwhenlpxDwas overexpressed. Synergies were identified between OPT-2U1 analogues combined with rifampicin or colistin, to varying strengths, in bothE. coliandS. Typhimurium. LPS composition was a likely reason for differences betweenE. coliand S.Typhimurium, as perturbation of LPS synthesis affected synergy between antibiotics and OPT-2U1 analogues. Finally, genes involved in ATP synthesis and membrane signalling functions were also found to affect the synergy between colistin and OPT-2U1 analogues. TraDIS-Xpresshas proven a powerful tool to rapidly assay all genes (and notably, essential genes) within a bacterium for roles in dictating antimicrobial sensitivity. This study has confirmed the predicted target pathway of OPT-2U1 and identified synergies which could be investigated for development of novel antimicrobial formulations.Data SummaryNucleotide sequence data supporting the analysis in this study has been deposited in ArrayExpress under the accession number E-MTAB-13250. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Single-molecule FRET and tracking of transfected biomolecules: multi-dimensional protein dynamics in living cells
Authors: Anandamurugan Abhinaya , Eidloth Antonia , Wortmann Philipp , Schrangl Lukas , Aprile-Garcia Fernando , Lan Chenyang , Sawarkar Ritwick , Schütz Gerhard J. , Hugel Thorsten 
Published: September 2023

AbstractProteins in cells exhibit conformational dynamics, equally influenced by dynamic interactions with other biomolecules and their spatial variations, which can be induced by the protein’s compartment. Altogether this multi-dimensional dynamic is difficult to measurein cellula, because of limitations in instrumentation, fluorescence methodologies and the difficulty to track freely diffusing molecules. Here, we present a bottom-up engineering approach, which allows us to track transfected proteinsin cellulaand analyze time-resolved single-molecule FRET efficiencies. This has been achieved by alternating laser excitation (ALEX) based three-channel (donor, acceptor and FRET intensity) tracking with a live-cell HILO microscope. Unexpectedly, we find that the heat shock protein Hsp90 shows different conformational populationsin vitroandin cellula. Moreover, Hsp90’s conformational states depend on the localization within the cell, which is demonstrated by comparing a physical (microinjection) and a biological (SLO) transfection method. FRET-TTB (Tracking of Transfected Biomolecules) opens the path to study protein conformational dynamics of transfected and native biomoleculesin cellula, including time-resolved cellular localization.
Kinematic performance declines as group size increases during escape responses in a schooling coral reef fish
Authors: Bacchus Monica D. , Domenici Paolo , Killen Shaun S. , McCormick Mark I. , Nadler Lauren E. 
Published: September 2023

AbstractEscaping predation is essential for species survival, but prey must effectively match their response to the perceived threat imposed by a predator. For social animals, one mechanism to reduce risk of predation is living in larger group sizes, which dilutes each individual’s risk of capture. When a predator attacks, individuals from a range of taxa (e.g., fishes, sharks, amphibians) perform an escape response, to evade the attack. Here, using the schooling coral reef damselfishChromis viridis, we assess if there is an optimal group size that maximizes both individual escape response performance as well as group cohesion and coordination following a simulated predator attack, comparing schools composed of four, eight, and sixteen fish. We found that fish in various group sizes exhibited no difference in their reaction timing to a simulated predator attack (i.e., escape latency), but larger groups exhibited slower kinematics (i.e., lower average turning rate and shorter distance covered during the escape response), potentially because larger groups perceived the predator attack as less risky due to safety in numbers. Both school cohesion and coordination (as measured through alignment and nearest neighbor distance, respectively) declined in the 100ms after the predator’s attack. While there was no impact of group size on alignment, larger group sizes exhibited closer nearest neighbor distances at all times. This study highlights that larger group sizes may allow individuals to save energy on costly behavioral responses to avoid predators, potentially through a greater threshold of the threat necessary to trigger a rapid escape response.
Characterization of Dr20/22: Molecular Insights and Antibody Response in Naturally Infected Dogs withDirofilaria repens
Authors: Pękacz Mateusz , Basałaj Katarzyna , Młocicki Daniel , Kamaszewski Maciej , Carretón Elena , Morchón Rodrigo , Wiśniewski Marcin , Zawistowska-Deniziak Anna 
Published: September 2023

AbstractSubcutaneous dirofilariasis, caused by the parasitic nematode Dirofilaria repens, is a growing concern in Europe, affecting both dogs and humans. This study focused on D. repens Dr20/22, a protein encoded by an alt (abundant larval transcript) gene family. While well-documented in L3 larvae of other filariae species, this gene family had not been explored in dirofilariasis. The research involved cloning Dr20/22 cDNA, molecular characterization, and evaluating its potential application in the diagnosis of dirofilariasis. Although Real-Time analysis revealed mRNA expression in both adult worms and microfilariae, the native protein remained undetected in lysates from both developmental stages. This suggests the protein’s specificity for L3 larvae and may be related to a process called SLTS (spliced leader trans-splicing), contributing to stage-specific gene expression. The antigen’s apparent specificity for invasive larvae makes it a strong candidate for an early dirofilariasis marker. ELISA tests using sera from infected and healthy dogs detected specific IgG antibody responses in both groups, indicating that specific IgG in healthy dog sera may contribute to dirofilariasis immunity. Although further research is necessary, the molecular and immunological characterization of Dr20/22 can enhance our understanding of host-parasite interactions and provide insights into the mechanisms that facilitate immune system evasion.
LeishmaniaRibosomal Protein (RP) paralogous genes compensate each other’s expression maintaining protein native levels
Authors: Borges Francisca S. , Quilles José C. , Lorenzon Lucas B. , Espada Caroline R. , Freitas-Castro Felipe , Defina Tânia P. A. , Holetz Fabíola B. , Cruz Angela K. 
Published: September 2023

AbstractIn the protozoan parasite Leishmania, most of the genes encoding for ribosomal proteins (RPs) are present as two or more copies in the genome, their untranslated regions (UTRs) are predominantly divergent, and might be associated with a distinct regulation of the paralogous genes’ expression. Here, we investigated the expression profiles of two RPs (S16 and L13a) encoded by duplicated genes in Leishmania major. The genes encoding for S16 protein have identical CDSs and divergent UTRs while the L13a CDSs diverge in two amino acids with divergent UTRs. Using CRISPR/Cas9 genomic editing system, we generated knockout (Δ) and tagged transfectants for each paralog of L13a and S16. Combining tagged and Δ cell lines we show that the expression of both RPS16 and RPL13a isoforms differ throughout the parasite development with one of the isoforms being always more abundant than its respective copy. Additionally, compensatory expression was observed for each paralog when one of the isoforms was deleted, evidencing functional conservation of these proteins. Such phenomenon is related to post-translational processes, since the compensation happened at the protein levels, with no alterations observed at the transcript levels. Ribosomal profiles for RPL13a point out a standard behavior for these paralogues as already reported for other RPs in trypanosomatids, showing its interaction with heavy RNA-protein complexes. The identification of sets of proteins binding specifically to the 3’UTRs of either the high or less abundant transcripts suggests a possible role of these proteins to differently control the levels of expression of these RP genes. In addition, conserved cis-elements were identified in the 3’UTRs of RPS16 or RPL13a; among these, exclusive cis-elements for the more or for the less expressed transcripts were identified.
An enduring role for hippocampal pattern completion in addition to an emergent non-hippocampal contribution to holistic episodic retrieval after a 24-hour delay
Authors: Joensen Bárður H. , Ashton Jennifer E. , Berens Sam C. , Gaskell M. Gareth , Horner Aidan J. 
Published: September 2023

AbstractEpisodic memory retrieval is associated with the holistic neocortical reinstatement of all event information; an effect driven by hippocampal pattern completion. However, whether holistic reinstatement occurs, and whether hippocampal pattern completion continues to drive reinstatement, after a period of consolidation is unclear. Theories of systems consolidation predict either a time-variant or -invariant role of the hippocampus in the holistic retrieval of episodic events. Here, we assessed whether episodic events continue to be reinstated holistically and whether hippocampal pattern completion continues to facilitate holistic reinstatement following a period of consolidation. Female and male human participants learnt ‘events’ that were composed of multiple overlapping pairs of event elements (e.g., person-location, object-location, location-person). Importantly, encoding occurred either immediately before or 24-hours before retrieval. Using fMRI during the retrieval of events, we show evidence for holistic reinstatement, as well as a correlation between reinstatement and hippocampal pattern completion, regardless of whether retrieval occurred immediately or 24-hours after encoding. Thus, hippocampal pattern completion continues to contribute to holistic reinstatement after a delay. However, our results also revealed that some holistic reinstatement can occur without evidence for a corresponding signature of hippocampal pattern completion after a delay (but not immediately after encoding). We therefore show that hippocampal pattern completion, in addition to a non-hippocampal process, has a role in holistic reinstatement following a period of consolidation. Our results point to a consolidation process where the hippocampus and neocortex may work in an additive, rather than compensatory, manner to support episodic memory retrieval.