bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vasoactive Endothelial Growth Factor and Heat Shock Protein Gene Expression Response in Kawasaki Disease
Authors: Rashid Asrar , Alkhzaimi Hoda , Benakatti Govind , Malik Zainab A. , Sharma Varun , Sharma Anuka , Malik Rayaz , Quraishi Nasir , Shaikh Guftar , Al-Dubai Ahmed , Hussain Amir 
Published: September 2022

AbstractKawasaki Disease (KD) is a childhood vasculitis primarily affecting medium-sized arteries, which can lead to severe complications, particularly with respect to coronary artery disease (CAD). The impact of thermal stress on KD coronary artery pathogenesis, in association with prolonged fever and inflammation, remains unclear. In this study, we hypothesized that altered gene expression (GE) of angiogenesis-inducing Heat Shock Proteins (HSPs) is associated with KD-CAD through pro-inflammation. Transcriptomic analysis was performed using the three largest KD peripheral blood studies in the clinical literature (KD1-KD3), and one study direct from coronary artery tissue (KD4). The analysis revealed a significant increase in TNF and NFKB1 GE, indicating the presence of inflammation based on gene expression profiles. Gene set enrichment analysis (GSEA) of KD1-KD3 datasets identified inflammatory pathways, including TNFA signaling via NFKB, IL6 JAK STAT 3 Signalling, and p53 (Heat Shock Protein 90). The study also focused on specific HSPs known to be associated with angiogenesis, namely HSPB1, HSPA1A, and HSP90AB1. The temporal transcript model (TTM) consistently showed up-regulation of pro-inflammatory genes VEGF-A, TNF, and NFKB1, as well as up-regulation of HSPA1A. GSEA revealed gene ontology pathways associated with VEGF production. These findings suggest that the binding of VEGF-A or VEGF-B to their receptors could potentially impact the coronary artery in KD. Additionally, the up-regulation of the gene HSPAB1 in KD has not been described previously. In contrast, KD4 showed no differential GE for the studied genes potentially related to end-stage KD. This study provides valuable insights into VEGF and HSPs in KD-associated inflammation. Future research should focus on developing a VEGF-HSP CAD model to explore implications for KD biomarking as well as developing precision management strategies.
Lysosome repair by ER-mediated cholesterol transfer
Authors: Radulovic Maja , Wenzel Eva Maria , Gilani Sania , Holland Lya K.K. , Lystad Alf Håkon , Phuyal Santosh , Olkkonen Vesa M. , Brech Andreas , Jäättelä Marja , Maeda Kenji , Raiborg Camilla , Stenmark Harald 
Published: September 2022

ABSTRACTLysosome integrity is essential for cell viability, and lesions in lysosome membranes are repaired by the ESCRT machinery. Here we describe an additional mechanism for lysosome repair that is activated independently of ESCRT recruitment. Lipidomic analyses showed increases in lysosomal phosphatidylserine and cholesterol after damage. Electron microscopy demonstrated that lysosomal membrane damage is rapidly followed by formation of contacts with the endoplasmic reticulum (ER), which depend on the ER proteins VAPA/B. The cholesterol-binding protein ORP1L was recruited to damaged lysosomes, accompanied by cholesterol accumulation by a mechanism that required VAP-ORP1L interactions. The PtdIns 4-kinase PI4K2A rapidly produced PtdIns4P on lysosomes upon damage, and knockout of PI4K2A inhibited damage-induced accumulation of ORP1L and cholesterol and led to failure of lysosomal membrane repair. The cholesterol-PtdIns4P transporter OSBP was also recruited upon damage, and its depletion caused lysosomal accumulation of PtdIns4P and resulted in cell death. We conclude that ER contacts are activated on damaged lysosomes in parallel to ESCRTs to provide lipids for membrane repair, and that PtdIns4P generation and removal are central in this response.
Serum amyloid alpha 1-2 are not required for systemic inflammation in the 4T1 murine breast cancer model
Authors: He Chenfeng , Konishi Riyo , Harata Ayano , Nakamura Yuki , Mizuno Rin , Yoda Mayuko , Toi Masakazu , Kawaguchi Kosuke , Kawaoka Shinpei 
Published: September 2022

AbstractCancers induce the production of acute phase proteins such as serum amyloid alpha (SAA) in the liver and cause systemic inflammation. Despite the well-known coincidence of acute phase response and systemic inflammation, the direct roles of SAA proteins in systemic inflammation in the cancer context remains incompletely characterized, particularly in vivo. Here, we investigate the in vivo significance of SAA proteins in systemic inflammation in the 4T1 murine breast cancer model. 4T1 cancers elevate the expression of SAA1 and SAA2, the two major murine acute phase proteins in the liver. The elevation of Saa1-2 correlates with the up-regulation of immune cell-related genes including neutrophil markers. To examine this correlation in detail, we generate mice that lack Saa1-2 and investigate immune-cell phenotypes. RNA-seq experiments reveal that deletion of Saa1-2 does not strongly affect 4T1-induced activation of immune cell-related genes in the liver and bone marrow. Flow cytometry experiments demonstrate the dispensable roles of SAA1-2 in cancer-dependent neutrophil infiltration to the liver. This study clarifies the negligible contribution of SAA1-2 proteins in systemic inflammation in the 4T1 breast cancer model.
Biochemical identification of a nuclear coactivator protein required for AtrR-dependent gene regulation in Aspergillus fumigatus
Authors: Paul Sanjoy , Ror Shivani , McDonald W. Hayes , Moye-Rowley W. Scott 
Published: September 2022

AbstractAzole drugs represent the primary means of treating infections associated with the filamentous fungal pathogen Aspergillus fumigatus. A central player in azole resistance is the Zn2Cys6 zinc cluster-containing transcription factor AtrR. This factor stimulates expression of the both the cyp51A gene encoding the azole drug target enzyme as well as an ATP-binding cassette transporter-encoding gene called abcG1 (aka cdr1B). We have used a fusion protein between AtrR and the tandem affinity purification (TAP) moiety to purify proteins that associate with AtrR from A. fumigatus. Protein fractions associated with AtrR-TAP were subjected to MudPIT mass spectrometry and one of the proteins identified was encoded by the AFUA_6g08010 gene. We have designated this protein NcaA (Nuclear Co-Activator of AtrR). Loss of ncaA caused a reduction in voriconazole resistance and drug-induced abcG1 expression, although did not impact induction of cyp51A transcription. We confirmed association of AtrR and NcaA by co-immunoprecipitation from otherwise wild-type cells. Expression of fusion proteins between AtrR and NcaA with green fluorescent protein allowed determination that these two proteins were localized in the A. fumigatus nucleus. Together, these data support the view that NcaA is required for nuclear gene transcription controlled by AtrR.ImportanceAspergillus fumigatus is the major filamentous fungal pathogen in humans and is susceptible to the azole antifungal class of drugs. However, loss of azole susceptibility has been detected with increasing frequency in the clinic and infections associated with these azole resistant isolates linked to treatment failure and worse outcomes. Many of these azole resistant mutant strains contain mutant alleles of the cyp51A gene encoding the azole drug target. A transcription factor essential for cyp51A gene transcription has been identified and designated AtrR. AtrR is required for azole inducible cyp51A transcription but we know little of the regulation of this transcription factor. Using a biochemical approach, we identify a new protein called NcaA that is involved in regulation of AtrR at certain target gene promoters. Understanding the mechanisms controlling AtrR function is an important goal in preventing or reversing azole resistance in this pathogen.
Influence of high-energy laser therapy to the patellar tendon on its ligamentous microcirculation: a quasi-experiment
Authors: Brandl Andreas , Egner Christoph , Reisser Ursel , Lingenfelder Christian , Schleip Robert 
Published: September 2022

AbstractLaser therapeutic applications, such as the use of high energy lasers (HILT), are widely used in physical therapy, but basic studies on the mechanisms of action of HILT on tendinous/ligamentous tissue are largely lacking. The aim of this study was to investigate microcirculatory changes of the patellar tendon by HILT. 21 healthy volunteers were treated with HILT. Before and after the intervention, as well as 10 minutes later, the microcirculation was measured by noninvasive laser spectroscopy (O2C device). Tissue temperature was recorded at the measurement time points using thermography. Blood flow increased significantly by 86.38 AU (p < 0.001) after the intervention and by 25.76 AU (p < 0.001) at follow-up. Oxygen saturation increased by 20.14% (p < 0.001) and 13.48%, respectively (p < 0.001), whereas relative hemoglobin decreased by 6.67 AU and 7.90 AU, respectively. Tendon temperature increased by 9.45° and 1.94° Celsius, respectively. Acceleration of blood flow by improving the flow properties of erythrocytes and platelets may have caused the results.
Towards optimised extracellular vesicle proteomics from cerebrospinal fluid
Authors: Kangas Petra , Nyman Tuula A. , Metsähonkala Liisa , Burns Cameron , Tempest Robert , Williams Tim , Karttunen Jenni , Jokinen Tarja S. 
Published: September 2022

AbstractThe proteomic profile of extracellular vesicles (EVs) from cerebrospinal fluid (CSF) can reveal novel biomarkers for diseases of the brain. Here, we validate an ultrafiltration combined with size-exclusion chromatography (UF-SEC) method for isolation of EVs from canine CSF and probe the effect of starting volume on the EV proteomics profile. First, we performed a literature review of CSF EV articles to define the current state of art, discovering a need for basic characterisation of CSF EVs. Secondly, we isolated EVs from CSF by UF-SEC and characterised the SEC fractions by protein amount, particle count, transmission electron microscopy, and immunoblotting. Data are presented as mean ± standard deviation. Using proteomics, SEC fractions 3-5 were compared and enrichment of EV markers in fraction 3 was detected, whereas fractions 4-5 contained more apolipoproteins. Lastly, we compared starting volumes of pooled CSF (6ml, 3ml, 1ml, and 0.5ml) to evaluate the effect on the proteomic profile. Even with a 0.5ml starting volume, 743±77 or 345±88 proteins were identified depending on whether ‘matches between runs’ was active in MaxQuant. The results confirm that UF-SEC effectively isolates CSF EVs and that EV proteomic analysis can be performed from 0.5ml of canine CSF.
Highly Sensitive and Specific Amyloid-β Oligomers Detection Using CRISPR-Cas12a Probe System aided by Graphene Oxide for Early Diagnosis of Alzheimer’s Diseases
Authors: Tang Jiaqi , Zhu Zongwei , Yang Chuanxu 
Published: September 2022

AbstractAlzheimer’s disease (AD) is highly age-specific that results in cognitive incapability including dementia. It is proposed that AD is caused by the dysfunctional gene producing excessive amyloid-β protein that eventually results in aggregated form of amyloid-β Oligomers (AβO). We couple the CRISPR-Cas12a system with a specially designed single-stranded DNA (ssDNA) aptamer that specifically forms a hybrid complex with AβO. We exploit the aptamer as the substrate for the crRNA-aptamer duplex due to its high flexibility, sensitivity, and selectivity. We further adopted the graphene oxide (GO) fluorescent system to couple with our CRISPR-Cas12a probe system. Our coupled probe system can effectively detect the presence of AβO by quantitatively returning fluorescent signals with high specificity and accuracy.
Integrative Single Cell Multiomic Profiling Analysis Reveals HOX-PBX Gene Regulatory Network Contributing to the Survival of mTOR Hyperactive Cells
Authors: Olatoke Tasnim F. , Wagner Andrew , Astrinidis Aristotelis A. , Guo Minzhe , Zhang Erik Y. , Zhang Alan G. , Mattam Ushodaya , Chilton Kyla , Kopras Elizabeth J. , Gupta Nishant , Smith Eric P. , Karbowniczek Magdalena , Markiewkski Maciej M. , Wikenheiser-Brokamp Kathryn , Whitsett Jeffrey A. , McCormack Francis X. , Xu Yan , Yu Jane J. 
Published: September 2022

ABSTRACTLymphangioleiomyomatosis (LAM) is a rare, debilitating lung disease that predominantly affects women of reproductive age. LAM is characterized by the infiltration of the lungs by abnormally proliferating smooth muscle-like cells of unknown origin via an estrogen-dependent metastatic mechanism. LAM cells carry deleterious mutations of tuberous sclerosis complex (TSC1/TSC2) genes, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) and ultimately dysregulated cell growth. Sirolimus, an FDA approved mTORC1 inhibitor and current best-choice medication for LAM stabilizes lung function in most LAM patients. However, it requires sustained application and remains inefficacious in some patients. The greatest barriers to finding a cure for LAM include its undetermined origin and unclear underlying pathogenesis. Our study aims to advance knowledge on the origin of LAM, and ultimately serve as a premise for the development of novel therapeutic targets for LAM. Single cell RNA sequencing (scRNA-seq) is a powerful tool in biomedical research that informs gene expression differences at the cellular level and may provide insights into the most fundamental origin of LAM cells. Our scRNA-seq analysis of LAM cells revealed a unique population of cells (LAMCORE), expressing uterine-similar homeobox transcription factors (HOX) and Pre-B-cell leukemia homeobox 1 (PBX1), which are absent in normal lung, suggesting that the uterus is the primary origin of LAM. PBX1 is a transcription factor critical for female reproductive tract development and maintenance, and its overexpression is implicated in some female reproductive cancers. In this study we hypothesize that PBX1 promotes survival and lung colonization of LAM (TSC2-null) cells. Using LAM patient-derived cells, we validated the transcriptional profile, gene expression and protein levels of PBX1. We have the first functional evidence that PBX1 and its downstream targets are upregulated in LAM cells. In a mouse model of LAM, we monitored the effect of suppression of PBX1 by short hairpin RNA-mediated gene silencing on lung colonization and tumor growth. We also found that pharmacological suppression of PBX1 attenuates LAM lung colonization and promotes death of LAM cells in vivo and vitro. Our data collectively suggests that PBX1 is a critical regulator of LAM progression.
Spatially Resolved Single-cell Translatomics at Molecular Resolution
Authors: Zeng Hu , Huang Jiahao , Ren Jingyi , Wang Connie Kangni , Tang Zefang , Zhou Yiming , Aditham Abhishek , Shi Hailing , Sui Xin , Wang Xiao 
Published: September 2022

AbstractThe precise control of mRNA translation is a crucial step in post-transcriptional gene regulation of cellular physiology. However, it remains a major challenge to systematically study mRNA translation at the transcriptomic scale with spatial and single-cell resolutions. Here, we report the development of RIBOmap, a three-dimensional (3D) in situ profiling method to detect mRNA translation for thousands of genes simultaneously in intact cells and tissues. By applying RIBOmap to 981 genes in HeLa cells, we revealed remarkable dependency of translation on cell-cycle stages and subcellular localization. Furthermore, we profiled single-cell translatomes of 5,413 genes in the adult mouse brain tissue with a spatial cell atlas of 62,753 cells. This spatial translatome profiling detected widespread patterns of localized translation in neuronal and glial cells in intact brain tissue networks. Together, RIBOmap presents the first spatially resolved single-cell translatomics technology, accelerating our understanding of protein synthesis in the context of subcellular architecture, cell types, and tissue anatomy.
The Rho GTPase exchange factor Vav2 promotes extensive age-dependent rewiring of the skin stem cell transcriptome
Authors: Lorenzo-Martín L. Francisco , Bustelo Xosé R. 
Published: September 2022

ABSTRACTBoth the number and regenerative activity of skin stem cells (SSCs) are regulated by Vav2, a GDP/GTP exchange factor involved in the catalytic stimulation of the GTPases Rac1 and RhoA. However, whether Vav2 signaling changes in SSCs over the mouse lifespan is not yet known. Using a mouse knock-in mouse model, we now show that the expression of a catalytically-active version of Vav2 (Vav2Onc) promotes an extensive rewiring of the overall transcriptome of SSCs, the generation of new transcription factor hubs, and the synchronization of many transcriptional programs associated with specific SSC states and well-defined signaling pathways. Interestingly, this transcriptome rewiring is not fixed in time, as it involves the induction of 15 gene expression waves with diverse distribution patterns during the life of the animals. These expression waves are consistent with the promotion by Vav2Onc of several functional SSC states that differ from those normally observed in wild-type SSCs. These results further underscore the role of Vav2 in the regulation of the functional state of SSCs. They also indicate that, unlike other Vav2-dependent biological processes, the signaling output of this exchange factor is highly contingent on age-dependent intrinsic and/or extrinsic SSC factors that shape the final biological readouts triggered in this cell type.AUTHOR SUMMARYSkin stem cells (SSCs) are essential for the homeostatic balance of the skin, yet little is known to date about the biological and molecular mechanisms that modulate their abundance, long-term stability, or functional states during ageing. To address this issue, in this work we have used a genetically-engineered gain-of-function mouse model for Vav2, a Rho guanine nucleotide exchange factor (GEF) that has been recently shown to be involved in skin stem cell homeostasis. By performing time-course genome-wide expression analyses combined with a number of computational methods, here we show that: (i) Vav2 plays a critical role in regulating the functional state of SSCs, and (ii) the signaling output of constitutively active Vav2 is highly contingent on age-dependent intrinsic and/or extrinsic SSC factors that shape the final biological readouts triggered in this cell type. We believe that these data represent, to our knowledge, one of the first examples of the time-dependent output of an oncogenic version of a Rho GEF along a wide time interval in mice.
Cannabidiol targets a modulatory system for excitatory-inhibitory synaptic coordination, contributing to its anti-seizure action
Authors: Rosenberg Evan , Chamberland Simon , Bazelot Michael , Nebet Erica R. , Wang Xiaohan , McKenzie Sam , Jain Swati , Greenhill Stuart , Wilson Max , Salah Alejandro , Bailey Shanice , Patra Pabitra Hriday , Rose Rebecca , Chenouard Nicolas , Sun Simon D. , Jones Drew , Buzsáki György , Devinsky Orrin , Woodhall Gavin , Scharfman Helen , Whalley Benjamin , Tsien Richard 
Published: September 2022

AbstractCannabidiol (CBD), a non-euphoric component of cannabis, reduces seizures in multiple forms of pediatric epilepsy, but the mechanism(s) of anti-seizure action remain unclear. In one leading model, CBD acts at glutamatergic axon terminals, blocking pro-excitatory actions of an endogenous membrane phospholipid, lysophosphatidylinositol (LPI), at the G protein-coupled receptor GPR55. However, the impact of LPI-GPR55 signaling at inhibitory synapses and in epileptogenesis remains underexplored. We found that LPI transiently increased hippocampal CA3→CA1 excitatory presynaptic release probability and evoked synaptic strength in WT mice, while attenuating inhibitory postsynaptic strength by decreasing GABAARγ2 and gephyrin puncta. Effects of LPI at both excitatory and inhibitory synapses were eliminated by CBD pretreatment and absent after GPR55 deletion. Acute pentylenetrazole-induced seizures elevated levels of GPR55 and LPI, and chronic lithium pilocarpine-induced epileptogenesis potentiated the pro-excitatory effects of LPI. We propose that CBD exerts potential therapeutic effect both by blocking synaptic effects of LPI and dampening hyperexcitability.
Genetic diversity, paternal origin and pathogen resistance inCataglyphisdesert ants
Authors: Eyer Pierre-André , Guery Pierre-Antoine , Aron Serge 
Published: September 2022

Group diversity is usually associated with a reduced risk of disease outbreak and a slower rate of pathogen transmission. In social insects, multiple mating by queens (polyandry) evolved several times although reducing worker’s inclusive fitness. One major hypothesis suggests that polyandry has been selected for to mitigate the risk of outbreak thanks to increased genetic diversity within colonies. We investigated this hypothesis in the antCataglyphis mauritanica, in which nestmate workers are produced by several clonal, single-mated queens. Using natural colonies, we correlated genetic diversity with worker survival to a fungal entomopathogen. We further tested whether workers from different paternal lineages (but a common maternal genome) show differential resistance in experimentally singleor multiple-patriline groups, and whether an increased number of patrilines in a group improved disease incidence.We show that workers from distinct patrilines vary in their resistance to pathogen in single-patriline colonies, but the difference among patrilines disappears when they are mixed in multiple-patriline colonies. Furthermore, pathogen resistance was affected by the number of patrilines in a group, with twoand three-patriline groups being more resistant than single-patriline groups. However, resistance did not differ between groups made of two and three patrilines; similarly, it was not associated with genetic diversity in natural colonies. Overall, our results suggest that collective disease defenses might homogenize workers’ resistance from different patrilines and, thereby, stabilize colony resistance.
Interactions between insect vectors and plant pathogens span the parasitism-mutualism continuum
Authors: Santiago Ma. Francesca M. , King Kayla C. , Drew Georgia C. 
Published: September 2022

AbstractPlants infected with vector-borne pathogens can suffer severe negative consequences, but the extent to which phytopathogens affect the fitness of their vector hosts remains unclear. Evolutionary theory predicts that selection on vector-borne pathogens should favour low virulence or mutualistic phenotypes in the vector, traits facilitating effective transmission between plant hosts. Here, we use a multivariate meta-analytic approach on 115 effect sizes across 34 unique plant-vector-pathogen systems to quantify the overall effect of phytopathogens on vector host fitness. In support of theoretical models, we report that phytopathogens overall have a neutral fitness effect on vector hosts. However, the range of possible fitness outcomes are diverse and span the parasitism-mutualism continuum. Contrary to previous predictions we found no evidence that transmission strategy, or the direct effects and indirect (plant-mediated) effects, of phytopathogens have divergent fitness outcomes for the vector. We discuss these findings in the context of plant – pathogen – vector ecology.