bluuebunny/crossref_metadata_2025_split huggingface dataset:
Defining the Ligand-dependent Interactome of the Sigma 1 Receptor
Authors: Zhao Jing , Veeranan-Karmegam Rajalakshmi , Baker Frederick C. , Mysona Barbara A. , Bagchi Pritha , Liu Yutao , Smith Sylvia B. , Gonsalvez Graydon B. , Bollinger Kathryn E. 
Published: June 2022

AbstractSigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular systems. It is proposed to function as a ligand-dependent molecular chaperone that modulates multiple intracellular signaling pathways. The purpose of this study was to define the S1R interactome under native conditions and upon binding to well-characterized ligands. This was accomplished by fusing the biotin ligase, Apex2, to the C terminus of S1R. Cells stably expressing S1R-Apex or a GFP-Apex control were used to map specific protein interactions. Biotinylated proteins were labeled under native conditions and in a ligand dependent manner, then purified and identified using quantitative mass spectrometry. Under native conditions, S1R biotinylates over 200 novel proteins, many of which localize within the endomembrane system (ER, Golgi, secretory vesicles) and function within the secretory pathway. Under conditions of cellular exposure to either S1R agonist or antagonist, results show enrichment of proteins integral to secretion, extracellular matrix formation, and cholesterol biosynthesis. Notably, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) displays increased binding to S1R under conditions of treatment with Haloperidol, a well-known S1R antagonist; whereas Low density lipoprotein receptor (LDLR) binds more efficiently to S1R upon treatment with (+)-Pentazocine ((+)-PTZ), a classical S1R agonist. Our results are consistent with the postulated role of S1R as an intracellular chaperone and further suggest important and novel functionalities related to cholesterol metabolism and biosynthesis.
Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system
Authors: Jean-Pierre Fabrice , Hampton Thomas H. , Schultz Daniel , Hogan Deborah A. , Groleau Marie-Christine , Déziel Eric , O’Toole George A. 
Published: June 2022

ABSTRACTInterspecies interactions can drive the emergence of unexpected microbial phenotypes that are not observed when studying monocultures. The cystic fibrosis (CF) lung consists of a complex environment where particular microbes, living as polymicrobial biofilm-like communities, are associated with negative clinical outcomes for persons with CF (pwCF). However, the current lack of in vitro models integrating the microbial diversity observed in the CF airway hampers our understanding of why polymicrobial communities are recalcitrant to therapy in this disease. Here, integrating computational approaches informed by clinical data, we built a mixed community of clinical relevance to the CF lung composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica. We developed and validated this model biofilm community with multiple isolates of these four genera. When challenged with tobramycin, a front-line antimicrobial used to treat pwCF, the microorganisms in the polymicrobial community show altered sensitivity to this antibiotic compared to monospecies biofilms. We observed that wild-type P. aeruginosa is sensitized to tobramycin in a mixed community versus monoculture, and this observation holds across a range of community relative abundances. We also report that LasR loss-of-function, a variant frequently detected in the CF airway, induces tolerance of P. aeruginosa to tobramycin specifically in the mixed community. The molecular basis of this community-specific recalcitrance to tobramycin for the LasR mutant variant is the increased production of redox-active phenazines. Our data support the importance of studying clinically-relevant model polymicrobial biofilms to understand community-specific traits relevant to infections.SIGNIFICANCE STATEMENTThe CF lung is colonized by biofilm-like microbial communities that exhibit both resistance and tolerance (collectively called “recalcitrance”) to antimicrobials used in the clinic. Here, we leveraged clinical data from pwCF to inform our understanding of communities exhibiting recalcitrance. We developed and validated an in vitro model that revealed novel, community-specific phenotypes relevant to the clinic. We used this model to explore the underlying mechanism associated with a community-specific emergent behavior. We posit that in vitro models of polymicrobial communities may help in developing new antimicrobial strategies to improve patient outcomes, and that the approach used here can be applied to other polymicrobial models.
CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side
Authors: van den Berg Cyntha M. , Volkov Vladimir A. , Schnorrenberg Sebastian , Huang Ziqiang , Stecker Kelly E. , Grigoriev Ilya , Patzke Sebastian , Zimmermann Timo , Dogterom Marileen , Akhmanova Anna 
Published: June 2022

AbstractMicrotubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates elongation and stability of ciliary axonemes and other microtubule-based structures.
Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts
Authors: Cardoen Ben , Vandevoorde Kurt , Gao Guang , Alan Parsa , Liu William , Tiliakou Ellie , Vogl A. Wayne , Hamarneh Ghassan , Nabi Ivan R. 
Published: June 2022

AbstractIdentification and morphological analysis of mitochondria-ER contacts (MERCs) by fluorescent microscopy is limited by sub-pixel resolution inter-organelle distances. Application of a Membrane Contact Site (MCS) detection algorithm, MCS-DETECT, to 3D STED super-resolution image volumes reconstructs sub-resolution MERCs. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria-ER linker expression in COS-7 cells. riboMERC expression is reduced in Gp78 knockout HT-1080 cells and induced by Gp78 ubiquitin ligase activity in COS-7 cells. Knockdown of the riboMERC tether RRBP1 eliminates riboMERCs in both wild-type and Gp78 knockout HT-1080 cells. By MCS-DETECT, Gp78-dependent riboMERCs present complex tubular shapes that intercalate between and contact multiple mitochondria, that are lost upon RRBP1 knockdown. MCS-DETECT of 3D whole cell super-resolution image volumes therefore identifies a novel dual regulatory mechanism for tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.eTOC SummaryApplication of the sub-pixel resolution Membrane Contact Site (MCS) detection algorithm, MCS-DETECT, to 3D STED super-resolution image volumes identifies a novel dual regulatory mechanism for tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.
Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle
Authors: Capovilla Giovanna , Braakman Rogier , Fournier Gregory , Hackl Thomas , Schwartzman Julia , Lu Xinda , Yelton Alexis , Longnecker Krista , Soule Melissa Kido , Thomas Elaina , Swarr Gretchen , Mongera Alessandro , Payette Jack , Waldbauer Jacob , Kujawinski Elizabeth B. , Cordero Otto X. , Chisholm Sallie W. 
Published: June 2022

ABSTRACTMarine picocyanobacteria (Prochlorococcus and Synechococcus), the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, we find that genes for breaking down chitin - an abundant source of organic carbon that primarily exists as particles - are widespread in this group. We further show that cells with a chitin degradation pathway display chitin degradation activity, attach to chitin particles and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated form of chitin. Marine chitin is largely derived from arthropods, whose roots lie in the early Phanerozoic, 520-535 million years ago, close to when marine picocyanobacteria began colonizing the ocean. We postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Transitioning to a constitutive planktonic life without chitin associations along a major early branch within the Prochlorococcus tree led to cellular and genomic streamlining. Our work highlights how coevolution across trophic levels creates metabolic opportunities and drives biospheric expansions.
Grk7 but not Grk1 undergoes cAMP-dependent phosphorylation in zebrafish cone photoreceptors in the dark and mediates recovery of the cone photoresponse in response to forskolin
Authors: Chrispell Jared D. , Xiong Yubin , Weiss Ellen R. 
Published: June 2022

AbstractIn the vertebrate retina, phosphorylation of photoactivated visual pigments in rods and cones by G protein-coupled receptor kinases is essential for sustained visual function. In vitro analysis demonstrates that GRK1 and GRK7 are phosphorylated by PKA and that phosphorylation is associated with a decreased capacity to phosphorylate rhodopsin, while in vivo observations show that GRK phosphorylation is cAMP-dependent. In many vertebrates, including humans, GRK1 is expressed in both rods and cones while GRK7 is expressed only in cones. However, mice express only GRK1 in both rods and cones and lack GRK7. We recently reported that a mutation deleting the phosphorylation site, Ser21, in GRK1 is associated with a delay in dark adaptation in mouse rods but not in cones, suggesting that GRK1 may serve a different role depending upon the photoreceptor cell type in which it is expressed. Here, we present immunochemical and electrophysiological studies using zebrafish as a model. Since zebrafish display a retinal GRK expression profile similar to humans, these studies will allow us to further evaluate the role of cAMP-dependent GRK phosphorylation in cone photoreceptor recovery that may be relevant to human physiology. ERG analyses of wildtype and Grk-knockout zebrafish larvae treated with forskolin show that elevated intracellular cAMP significantly decreases recovery of the cone photoresponse, which is mediated by Grk7a rather than Grk1b. Using a cone-specific dominant negative PKA transgenic zebrafish, we show for the first time that PKA is required for Grk7a phosphorylation in vivo. Lastly, immunoblot analyses in rod grk1a and cone grk1b knockout zebrafish, as well as the ‘all cone’ Nrl-/- mouse, show that cone-expressed Grk1 does not undergo cAMP-dependent phosphorylation in vivo. These results provide a better understanding of the function of Grk phosphorylation in the context of cone adaptation and recovery.
Restoration of β-GC trafficking improves the lysosome function in Gaucher’s disease
Authors: Patel Saloni , Radhakrishnan Dhwani , Kumari Darpan , Bhansali Priyanka , Setty Subba Rao Gangi 
Published: June 2022

AbstractLysosomes function as a primary site for catabolism and cellular signaling. These organelles digest a variety of substrates received through endocytosis, secretion and autophagy with the help of resident acid hydrolases. Lysosomal enzymes are folded in the endoplasmic reticulum (ER) and trafficked to lysosomes via Golgi and endocytic route. The inability of hydrolase trafficking due to mutations or mutations in its receptor or cofactor leads to cargo accumulation (storage) in lysosomes, resulting in lysosome storage disorder (LSD). In Gaucher’s disease (GD), the lysosomes accumulate glucosylceramide due to a lack of β-glucocerebrosidase (β-GC) activity that causes lysosome enlargement/dysfunction. We hypothesize that improving the trafficking of mutant β-GC to lysosomes may delay the progression of GD. RNAi screen using high throughput based lysosomal enzyme activity assay followed by reporter trafficking assay utilizing β-GC-mCherry lead to the identification of nine potential phosphatases. Depletion of these phosphatases in HeLa cells enhanced the β-GC activity by increasing the folding and trafficking of Gaucher’s mutants to the lysosomes. Consistently, the lysosomes in primary fibroblasts from GD patients restored their function upon the knockdown of these phosphatases. Thus, these studies provide evidence that altering phosphatome activity possibly delays the GD and forms an alternative therapeutic strategy for this genetic disease.Key pointsPhosphatome RNAi screen identified both activators and inhibitors of cellular glucocerebrosidase activityDepletion of selective phosphatases in HeLa cells improved the folding and trafficking of mutant β-glucocerebrosidase to lysosomesKnockdown of selective phosphatases restored the low basal β-glucocerebrosidase activity to that of wild-type in primary cells derived from Gaucher’s disease patientsDepletion of selective phosphatases displayed variable β-GC activity in neuropathic and non-neuropathic Gaucher’s disease patient cells
Fine-grained deconvolution of cell-type effects from human bulk brain data using a large single-nucleus RNA sequencing based reference panel
Authors: van den Oord Edwin J.C.G. , Aberg Karolina A. 
Published: June 2022

AbstractBrain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology. When studying bulk tissue, cellular diversity may cause many genes that are differentially expressed in cases and controls to remain undetected. Furthermore, identifying the specific cell-types from which association signals originate is key to formulating refined hypotheses of disease etiology, designing proper follow-up experiments and, eventually, developing novel clinical interventions. Cell-type effects can be deconvoluted statistically from bulk expression data using cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we analyzed data from the seven largest single nucleus RNA-seq (snRNA-seq) studies. Seventeen cell-types were robustly detected across all seven studies. To estimate the cell-type proportions, we proposed an empirical Bayes estimator that is suitable for the new panel that involves multiple low abundant cell-types. Furthermore, to avoid the use of a very large reference panel and prevent challenges with public access of nuclei level data, our estimator uses a panel comprising mean expression levels rather than the nuclei level snRNA-seq data. Evaluations show that our empirical Bayes estimator produces highly accurate and unbiased cell-type proportion estimates. Transcriptome-wide association studies performed with permuted bulk RNA-seq data showed that it is possible to perform TWASs for even the rarest cell-types without an increased risk of false positives. Furthermore, we determined that for optimal statistical power the best approach is to analyze all cell-types in the panel as opposed to grouping or omitting (rare) cell-types.
OligoFlow: rapid and sensitive virus quantification using flow cytometry and oligonucleotide hybridization
Authors: Paterson James S. , Dann Lisa M. , Carlson-Jones Jessica , Giles Sarah , McIvor Connor , Speck Peter G. , Mitchell James G. 
Published: June 2022

AbstractFlow cytometry is an established method for the detection and enumeration of viruses. However, the technique is unable to target specific viral species. Here, we present OligoFlow, a novel method for the rapid detection and enumeration of viruses by incorporating flow cytometry with species specific oligonucleotide hybridization. Using Ostried herpesvirus and dengue virus as model organisms, we demonstrate high-level detection and specificity. Our results represent a significant advancement in viral flow cytometry, opening the possibilities for the rapid identification of viruses in time critical settings.
Differentials in clinical severity and other patient activity indicators amongst Black and South Asian cancer patients in England
Authors: Willis Steffan , Aparicio Pedro Figueiredo , Steel Rhoda , Leblay Gaetan 
Published: June 2022

AbstractThe link between ethnicity, deprivation and health inequalities is well-established. The relationship between ethnicity and cancer is more complex and influenced by a variety of socio-economic, cultural and physiological factors. Understanding the relationship between ethnicity and patient care indicators for specific cancer types is vital if NHS England is to meet the UK government’s stated priority to reduce health inequalities as it recovers from COVID-19.This paper explores the impact of ethnicity on clinical severity, treatment costs and a range of patient activity indicators across three cancer types – chronic lymphocytic leukaemia, multiple myeloma and prostate cancer.The paper uses a dataset derived from the Hospital Episodes Statistics (secondary care) database covering 2016/17 to 2020/21,. This enabled the differential impact of the pandemic on ethnic minority patients to be considered. The data was aggregated by ethnicity and deprivation quintile at a national and Integrated Care System (ICS) level. Clinical severity was proxied using co-morbidity and complications (CC) scores. Multivariate linear regression (OLS) models were used to explore the associations with ethnicity.Black and South Asian patients CC scores were 12.2% and 15.8% higher than the population average (4.1). Controlling for socio-economic deprivation, South Asian patients had higher average clinical severity (+0.57, p<0.01). In addition, ICSs with large South Asian populations were associated with higher CC scores (+0.69, p<0.01). Treatment costs were higher for Black prostate cancer patients with interventions (+£842, p<0.001) and South Asian multiple myeloma patients (+£1686, p<0.001). Both Black and South Asian patients tend to have more spells in hospital. COVID-19 saw total inpatient admissions fall by 18.9%. Black and South Asian inpatient admissions fell by 1.9 and 2.9 percentage points more than the national average respectively. Average clinical severity increased by 7.1% with the largest increase amongst South Asian (+11.5%) and Black (+8.1%) patients.The higher clinical severity in South Asian patients and higher treatment costs in Black patients observed in this study are not accompanied by significant variations in patient activity indicators, which may point to drivers associated with delays to diagnosis or barriers to access to primary care.
Insulin receptor turnover in fasting is dependent on β-dystroglycan deglycosylation
Authors: Joseph Sunu , Zbidat Sewar , Volodin Alexandra , Kasiviswanathan Dharanibalan , Fried Adina I. , Armani Andrea , Gilda Jennifer E. , Cohen Shenhav 
Published: June 2022

ABSTRACTFasting exerts various physiological effects, most notably, reduced signaling through the insulin receptor. We showed that insulin receptor activity requires association with Dystrophin Glycoprotein Complex (DGC). Here, we demonstrate that insulin receptor turnover by lysosomes during fasting is dependent on deglycosylation of the principal DGC component, β-dystroglycan. We show that the lysosomal enzymes HexA and Man2b1, which specifically remove N-linked glycans, mediate β-dystroglycan deglycosylation and consequently insulin receptor-DGC loss. Surprisingly, the lysosomal enzyme NAGLU, which cannot process N-linked glycosylation, also facilitated β-dystroglycan deglycosylation and insulin receptor loss. NAGLU enhances the activity of the transcriptional complex PPAR-γ/RXR-α, which in turn promotes Man2b1 and HexA induction and the resulting β-dystroglycan deglycosylation. Accordingly, downregulation of HexA, Man2b1, NAGLU or RXR-α during fasting blocked β-dystroglycan deglycosylation, and caused accumulation of insulin receptor-DGC assemblies on the membrane. Thus, NAGLU mediates physiological adaptation to fasting by promoting indirectly β-dystroglycan deglycosylation.
Distinct roles of Nrf1 and Nrf2 in monitoring the reductive stress response to dithiothreitol (DTT)
Authors: Wufur Reziyamu , Fan Zhuo , Yuan Jianxin , Zheng Ze , Hu Shaofan , Sun Guiyin , Zhang Yiguo 
Published: June 2022

AbstractTranscription factor Nrf2 (nuclear factor, erythroid 2-like 2, encoded by Nfe2l2) has been accepted as a key player in redox regulatory responses to oxidative or reductive stresses. However, it is less or not known about the potential role for Nrf1 (nuclear factor, erythroid 2-like 1, encoded by Nfe2l1) in the redox responses, particularly to reductive stress, albeit this ‘fossil-like’ factor is indispensable for cell homeostasis and organ integrity during life process. Here, we examine distinct roles of Nrf1 and Nrf2 in monitoring the defense response to 1,4–dithiothreitol (DTT, serving as a reductive stressor), concomitantly with unfolded protein response being induced by this chemical (also as an endoplasmic reticulum stressor). The results revealed that intracellular reactive oxygen species (ROS) were modestly increased in DTT-treated wild-type (WT) and Nrf1α–/– cell lines, but almost unaltered in Nrf2–/–ΔTA or caNrf2ΔN cell lines (with a genetic loss of its transactivation or N-terminal Keap1-binding domains, respectively). This chemical treatment also enabled the rate of oxidized to reduced glutathione (i.e., GSSG to GSH) to be amplified in WT and Nrf2–/–ΔTA cells, but diminished in Nrf1α–/– cells, along with no changes in caNrf2ΔN cells. Consequently, Nrf1α–/–, but not Nrf2–/–ΔTA or caNrf2ΔN, cell viability was reinforced by DTT against its cytotoxicity, as accompanied by decreased apoptosis. Further experiments unraveled that Nrf1 and Nrf2 differentially, and also synergistically, regulated DTT-inducible expression of critical genes for defending redox stress and endoplasmic reticulum stress. In addition, we have also identified that Cys342 and Cys640 of Nrf1 (as redox-sensing sites within its N-glycodomain and DNA-binding domain, respectively) are required for its protein stability and transcription activity.