bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identifying transcriptomic downstream targets of genes commonly mutated in Hereditary Hemorrhagic Telangiectasia
Authors: Ali Md Khadem , Liu Yu , Schimmel Katharina , Juul Nicholas H. , Stockman Courtney A. , Wu Joseph C. , Spiekerkoetter Edda F. 
Published: November 2022

AbstractHereditary Hemorrhagic Telangiectasia (HHT) is an autosomal dominant disease that causes arteriovenous vascular malformations (AVMs) in different organs, including the lung. Three genes, ENG (endoglin), ACVRL1 (ALK1) and SMAD4, all members of the TGF-β/BMPR2 signaling pathway, are responsible for over 85% of all HHT cases. However, how these loss-of-function gene mutations lead to AVMs formation and what common downstream signaling they target is unknown. Here, using a combination of siRNA-mediated gene silencing, whole transcriptomic RNA sequencing, bioinformatic analysis, transcriptomic-based drug discovery, endothelial cells functional assays and VEGF signaling analysis, andex vivoprecision cut lung slice (PCLS) cultures approach, we uncovered common downstream transcriptomic gene signatures of HHT-casing genes and identified promising drug for HHT. We found the commonly used BMPR2-signaling downstream target ID1 is not a common downstream target of all the three HHT genes knockdown in human pulmonary microvascular endothelial cells (PMVECs). We identified novel common downstream targets of all the three HHT-causing genes that were enriched for HHT-related biological process and signaling pathways. Among those downstream genes, LYVE1, GPNMB, and MC5R were strong downstream targets that could serve as a better common downstream target than ID1. Furthermore, using the common downstream upregulated genes (HHT disease signature) following HHT gene knockdown, we identified a small molecule drug, Brivanib, that reversed the HHT disease signature, and inhibited VEGF-induced ERK1/2 phosphorylation, proliferation, and angiogenesis in PMVECs and inhibited some of the upregulated HHT disease genes in PCLS. Our findings suggest that Brivanib could be an emerging new drug for HHT.
H4K20me3 controls Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin
Authors: Möller Mareike , Ridenour John B. , Wright Devin F. , Freitag Michael 
Published: November 2022

AbstractFacultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungusZymoseptoria tritici, a globally important pathogen of wheat. Deletion ofkmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Reversal of silencing in the absence of H4K20me3 not only affected genes but also a large number of novel, previously undetected, non-coding transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation inkmt5deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with a H4K20M mutation in the single histone H4 gene ofZ. triticirecapitulated these chromatin changes, suggesting that H4K20me3 is essential for Ash1-mediated H3K36me3. The Δkmt5mutants we obtained are more sensitive to genotoxic stressors and both, Δkmt5and Δash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into a novel, and unsuspected, mechanism controlling the assembly and maintenance of facultative heterochromatin.SignificanceFacultative heterochromatin contains genes important for specific developmental or life cycle stages. Transcriptional regulation of these genes is influenced by chromatin structure. Here, we report that a little studied histone modification, trimethylation of lysine 20 on histone H4 (H4K20me3), is enriched in facultative heterochromatin and important for transcriptional repression in these regions in an important agricultural pathogen. Furthermore, normal levels of H4K20me3 are essential for deposition of another repressive histone mark, Ash1-mediated H3K36me3, and affect the distribution of other marks including H3K27me3. We conducted the first genome-wide assessment of H4K20 methylation levels in a fungus, and our discoveries reveal that multiple chromatin modifications are required to establish transcriptional silencing, providing the framework to understand epistasis relationships among these histone marks.
The dynamic nature of neurotensin receptor 1 (NTS1) allostery and signaling bias
Authors: Bumbak Fabian , Inoue Asuka , Pons Miquel , Paniagua Juan Carlos , Yan Fei , Wu Hongwei , Robson Scott A. , Bathgate Ross A. D. , Scott Daniel J. , Gooley Paul R. , Ziarek Joshua J. 
Published: November 2022

ABSTRACTThe neurotensin receptor 1 (NTS1) is a G protein-coupled receptor (GPCR) with promise as a drug target for the treatment of pain, schizophrenia, obesity, addiction, and various cancers. A detailed picture of the NTS1structural landscape has been established by X-ray crystallography and cryo-EM and yet, the molecular determinants for why a receptor couples to G protein versus arrestin transducers remain poorly defined. We used13CεH3-methionine NMR spectroscopy to show that phosphatidylinositol-4,5-bisphosphate (PIP2) promotes transducer complexation not by dramatically altering the receptor structure but by strengthening long-range allosteric connections, in the form of correlated conformational kinetics, between the orthosteric pocket and highly-conserved activation motifs. β-arrestin-1 further remodels the receptor ensemble by reducing conformational exchange kinetics for a subset of resonances, whereas G protein coupling has little to no effect on the rate. A β-arrestin biased allosteric modulator transforms the NTS1:G protein complex into a concatenation of substates, without triggering transducer dissociation, suggesting that it may function by stabilizing signaling incompetent G protein conformations such as the non-canonical state. Together, our work demonstrates the importance of kinetic information to a complete picture of the GPCR activation landscape.
Identification of novel natural product inhibitors of BRD4 using high throughput virtual screening and MD simulation
Authors: Barman Soumen , Sahoo Snehasudha Subhadarsini , Padhan Jyotirmayee , Sudhamalla Babu 
Published: November 2022

AbstractBromodomains are evolutionarily conserved structural motifs that recognize acetylated lysine residues on histone tails. They play a crucial role in shaping chromatin architecture and regulating gene expression in various biological processes. Mutations in bromodomains containing proteins leads to multiple human diseases, which makes them attractive target for therapeutic intervention. Extensive studies have been done on BRD4 as a target for several cancers, such as Acute Myeloid Leukemia (AML) and Burkitt Lymphoma. Several potential inhibitors have been identified against the BRD4 bromodomain. However, most of these inhibitors have drawbacks such as nonspecificity and toxicity, decreasing their appeal and necessitating the search for novel non-toxic inhibitors. This study aims to address this need by virtually screening natural compounds from the NPASS database against the Kac binding site of BRD4-BD1 using high throughput molecular docking followed by similarity clustering, pharmacokinetic screening, MD simulation, and MM-PBSA binding free energy calculations. Using this approach, we identified five natural product inhibitors having a similar or better binding affinity to the BRD4 bromodomain compared to JQ1 (previously reported inhibitor of BRD4). Further systematic analysis of these inhibitors resulted in the top three hits: NPC268484 (Palodesangren-B), NPC295021 (Candidine), and NPC313112 (Buxifoliadine-D). Collectively, ourin silicoresults identified some promising natural products that have the potential to act as potent BRD4-BD1 inhibitors and can be considered for further validation through futurein vitroandin vivostudies.
The cytochromebcarboxyl-terminal region is necessary for mitochondrial Complex III assembly
Authors: Flores-Mireles Daniel , Camacho-Villasana Yolanda , Lutikurti Madhurya , García-Guerrero Aldo E. , Lozano-Rosas Guadalupe , Chagoya Victoria , Gutiérrez-Cirlos Emma Berta , Brandt Ulrich , Cabrera-Orefice Alfredo , Pérez-Martínez Xochitl 
Published: November 2022

AbstractMitochondrialbc1complex from yeast has ten subunits, but only Cytochromeb(Cytb) subunit is encoded in the mitochondrial genome. Cytbhas eight transmembrane helices containing two hemesbfor electron transfer. Cbp3 and Cbp6 assist Cytbsynthesis, and together with Cbp4 induce Cytbhemylation. Subunits Qcr7/Qcr8 participate in the first steps of assembly, and lack of Qcr7 reduces Cytbsynthesis through an assembly-feedback mechanism involving Cbp3/Cbp6. Since Qcr7 resides near the Cytbcarboxyl-region, we wondered whether this region is important for Cytbsynthesis/assembly. Although deletion of the CytbC-region did not abrogate Cytbsynthesis, the assembly-feedback regulation was lost, so Cytbsynthesis was normal even if Qcr7 was missing. Mutants lacking the CytbC-terminus were non-respiratory due to absence of fully assembledbc1complex. By performing complexome profiling, we showed the existence of aberrant early-stage subassemblies in the mutant. In this work we demonstrate that the C-terminal region of Cytbis critical for regulation of Cytbsynthesis andbc1complex assembly.
Isolation and characterization of a novel phage ofVibrio parahaemolyticuswith biocontrol potential
Authors: Chen Yubing , Li Wenqing , Shi Keming , Fang Zheng , Yang Yunlan , Zhang Rui 
Published: November 2022

AbstractVibrio parahaemolyticusis a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistantV. parahaemolyticusstrains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. Here, a lytic vibriophage, vB_VpaM_R16F (R16F), was isolated from sewage from a seafood market by infectingV. parahaemolyticus1.1997T. R16F was found to infectV. parahaemolyticus, but not nine otherVibriospp. The phage belongs to the myovirus morphotype and lysed host cells with a short latent period (<10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G+C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. In consideration of its biological and genetic properties, R16F is suggested to be a candidate biocontrol agent for use againstV. parahaemolyticus.
Contrasting genomic consequences of anthropogenic reintroduction and natural recolonisation in high-arctic wild reindeer
Authors: Burnett Hamish A. , Bieker Vanessa C. , Moullec Mathilde Le , Peeters Bart , Rosvold Jørgen , Pedersen Åshild Ønvik , Dalén Love , Loe Leif Egil , Jensen Henrik , Hansen Brage B. , Martin Michael D. 
Published: November 2022

AbstractAnthropogenic reintroduction can supplement natural recolonisation in reestablishing a species’ distribution and abundance. However, both reintroductions and recolonisations can give rise to population bottlenecks that reduce genetic diversity and increase inbreeding, potentially causing accumulation of genetic load and reduced fitness. Most current populations of the endemic high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus) originate from recent reintroductions or recolonisations following regional extirpations due to past overharvesting. We investigated and compared the genomic consequences of these two paths to reestablishment using whole-genome shotgun sequencing of 100 Svalbard reindeer across their range. We found little admixture between reintroduced and natural populations. Two reintroduced populations, each founded by 12 individuals around four decades (i.e. 8 reindeer generations) ago, formed two distinct genetic clusters. Compared to the source population, these populations showed only small decreases in genome-wide heterozygosity and increases in inbreeding and lengths of runs of homozygosity. In contrast, the two naturally recolonised populations without admixture possessed much lower heterozygosity, higher inbreeding, and longer runs of homozygosity, possibly caused by serial population bottlenecks and/or fewer or more genetically related founders than in the reintroduction events. Naturally recolonised populations can thus be more vulnerable to the accumulation of genetic load than reintroduced populations. This suggests that in some organisms even small-scale reintroduction programs based on genetically diverse source populations can be more effective than natural recolonisation in establishing genetically diverse populations. These findings warrant particular attention in the conservation and management of populations and species threatened by habitat fragmentation and loss.
Oxygen levels at the time of activation determine T cell persistence and immunotherapeutic efficacy
Authors: Cunha Pedro P. , Minogue Eleanor , Krause Lena C. M. , Hess Rita M. , Bargiela David , Wadsworth Brennan J. , Barbieri Laura , Brombach Carolin , Foskolou Iosifina P. , Bogeski Ivan , Veliça Pedro , Johnson Randall S. 
Published: November 2022

SummaryOxygenation levels are a determinative factor in T cell function. Here we describe that the oxygen tensions sensed by T cells at the moment of activation act to persistently modulate both differentiation and function. We found that in a protocol of CAR-T cell generation, 24 hours of low oxygen levels during initial CD8+T cell priming is sufficient to enhance antitumour cytotoxicity in a preclinical model. This is the case even when CAR-T cells are subsequently cultured under high oxygen tensions prior to adoptive transfer. Increased hypoxia inducible transcription factor (HIF) expression was able to alter T cell fate in a similar manner to exposure to low oxygen tensions; however, only a controlled or temporary increase in HIF signalling was able to consistently improve cytotoxic function of T cells. These data show that oxygenation levels during and immediately after T cell activation play an essential role in regulating T cell function.
Rapid generation of CD19 CAR-T Cells by minicircle DNA enables anti-tumor activity and prevents fatal CAR-B leukemia
Authors: Ye Xueshuai , Wu Yongqiang , Cai Ziqi , Yuan Qichen , Cai Jianhui 
Published: November 2022

AbstractManufacturing CAR (chimeric antigen receptor)-T cell with viral vector is expensive and time-consuming. Besides, during viral transduction, the genes encoding CARs are randomly integrated into the genome, which could cause oncogenesis or produce devastating CAR-tumor cells. Here, using virus-free and non-transgenic minicircle DNA (mcDNA) vector, we enable rapid generation of CD19 CAR-T cells within two days. Further, we demonstrate in vitro and in xenograft models that the anti-tumor effects of CD19 CAR-T cells produced by mcDNA are as effective as those produced by viral vectors. Finally, we show that our manufacturing process can avoid the production of fatal CAR-tumor cells. Taken together, we provide a fast, effective, and therapeutically safe method to generate CD19 CAR-T cells for treating leukemia.
SlideCNA: Spatial copy number alteration detection from Slide-seq-like spatial transcriptomics data
Authors: Zhang Diane , Segerstolpe Asa , Slyper Michal , Waldman Julia , Murray Evan , Cohen Ofir , Ashenberg Orr , Abravanel Daniel , Jané-Valbuena Judit , Mages Simon , Lako Ana , Helvie Karla , Rozenblatt-Rosen Orit , Rodig Scott , Chen Fei , Wagle Nikhil , Regev Aviv , Klughammer Johanna 
Published: November 2022

AbstractSolid tumors are spatially heterogeneous in their genetic, molecular and cellular composition, and this variation can be meaningful for diagnosis, prognosis and therapy. Recent spatial profiling studies have mostly charted genetic and RNA variation in tumors separately. To leverage the potential of RNA to identify copy number alterations (CNAs), we developed SlideCNA, a computational tool to extract sparse spatial CNA signals from spatial transcriptomics data, using expression-aware spatial binning. We test SlideCNA on simulated and real Slide-seq data of metastatic breast cancer (MBC) and demonstrate its potential for spatial sub-clone detection.
Unique functions of two overlappingPAX6retinal enhancers
Authors: Uttley Kirsty , Papanastasiou Andrew S. , Lahne Manuela , Brisbane Jennifer M. , MacDonald Ryan B. , Bickmore Wendy A. , Bhatia Shipra 
Published: November 2022

AbstractEnhancers play a critical role in development by precisely modulating spatial, temporal, and cell type-specific gene expression. Sequence variants in enhancers have been implicated in disease, however establishing the functional consequences of these variants is challenging due to a lack of understanding of precise cell types and developmental stages where the enhancers are normally active.PAX6is the master regulator of eye development, and has a regulatory landscape containing multiple enhancers driving expression in the eye. Whether these enhancers perform additive, redundant, or distinct functions is unknown. Here we describe the precise cell types and regulatory activity of twoPAX6retinal enhancers, HS5 and NRE. Using a unique combination of live imaging and single-cell RNA sequencing in dual enhancer-reporter zebrafish embryos, we find significant differences in the spatiotemporal activity of these enhancers, and show that HS5 and NRE are active in distinct cell types of the developing retina. Our results show that although overlapping, these enhancers have distinct activities in different cell types and therefore likely non-redundant functions. This work demonstrates that unique cell type-specific functions can be uncovered for apparently similar enhancers when investigated at high resolution in vivo.
Resilient CD8+T cells maintain a high cytotoxic capacity by balancing ROS via ME1 upregulation
Authors: Gicobi Joanina K. , Mao Zhiming , DeFranco Grace , Li Ying , Liu Xin , Hirdler Jacob B. , Vianzon Vianca V. , Dellacecca Emilia R. , Hsu Michelle A. , Barham Whitney , Kim Yohan , Abraha Feven , Harmsen William S. , Yan Yiyi , Dronca Roxana S. , Zhu Mojun , Markovic Svetomir N. , Mansfield Aaron S. , Lin Yi , Wu Xiaosheng , Owen Dawn , Grams Michael P. , Orme Jacob J. , Lucien Fabrice , Zeng Hu , Park Sean S. , Dong Haidong 
Published: November 2022

AbstractCytotoxic T lymphocytes (CTL) are indispensable in anti-tumor immunity. Although CTLs are prone to exhaustion in patients with advanced cancer, T cell resiliency explains the presence of tumor-reactive CTLs that are less exhausted, capable of cytolytic function, expansion, and rebound in response to immunotherapy to reject metastatic malignances. However, the features of resilient T cells have not been clearly defined. In this report, we demonstrate that peripheral CX3CR1+CD8+T cells with low mitochondrial membrane potential rebounded CTL function quickly after radiation therapy in patients with large tumor burden portraying their functional resiliency. Furthermore, CX3CR1+CD8+T cell with low, but not high, mitochondrial membrane potential are highly cytotoxic, accumulate less reactive oxygen species (ROS), and express more Malic enzyme 1 (ME1). ME1 overexpression increases ATP production in a glycolysisindependent manner while concurrently curtailing excessive ROS in activated CD8+T cells; and expands CX3CR1+NKG7+effector CD8+T cells with enhanced cytotoxicity. Importantly, transfection ofME1mRNA promotes tumoricidal activity in CD8+T cells from patients with advanced cancers. Our study reveals a mechanism used by CTLs to balance excessive ROS via ME1 to maintain a metabolic and functional resiliency. Modification of ME1 expression in CTLs may be a novel method to improve the efficacy of cancer immunotherapy by preventing T cell exhaustion.Graphical abstractHighlightsCX3CR1+and low Dy m identify functional resilient CD8+T cells.Resilient CD8+T cells are highly cytotoxic and have less ROS.Resilient CD8+T cells express more ME1 that can balance extra ROS.ME1 overexpression can promote CTL function of CD8+T cells.
Evolution of Secondary Cell Number and Position In the Drosophila Accessory Gland
Authors: Takashima Yoko A. , Majane Alex C. , Begun David J. 
Published: November 2022

AbstractIn animals with internal fertilization, males transfer gametes and seminal fluid during copulation, both of which are required for successful reproduction. InDrosophilaand other insects, seminal fluid is produced in the paired accessory gland (AG), the ejaculatory duct, and the ejaculatory bulb. TheD. melanogasterAG has emerged as an important model system for this component of male reproductive biology. Seminal fluid proteins produced in theDrosophilaAG are required for proper storage and use of sperm by the females, and are also critical for establishing and maintaining a suite of short- and long-term postcopulatory female physiological responses that promote reproductive success. TheDrosophilaAG is composed of two main cell types. The majority of AG cells, which are referred to as main cells, are responsible for production of many seminal fluid proteins. A minority of cells, about 4%, are referred to as secondary cells. These cells, which are restricted to the distal tip of theD. melanogasterAG, may play an especially important role in the maintenance of the long-term female post-mating response. Many studies ofDrosophilaAG evolution have suggested that the proteins produced in the gland evolve quickly, as does the transcriptome. Here, we investigate the evolution of secondary cell number and position in the AG in a collection of eight species spanning the entire history of theDrosophilagenus. We document a heretofore underappreciated rapid evolutionary rate for both number and position of these specialized AG cells, raising many interesting questions about the developmental, functional, and evolutionary significance of this variation.