bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mesothelial cells are not a source of adipocytes in mice
Authors: Westcott Gregory P. , Emont Margo P. , Li Jin , Jacobs Christopher , Tsai Linus , Rosen Evan D. 
Published: May 2021

SummaryVisceral adipose tissue (VAT) depots are associated with the adverse metabolic consequences of obesity, such as insulin resistance. The developmental origin of VAT depots and the identity and regulation of adipocyte progenitor cells have been active areas of investigation. In recent years, a paradigm of mesothelial cells as a source of VAT adipocyte progenitor cells has emerged based on lineage-tracing studies using the Wilms’ tumor gene, Wt1, as a marker for cells of mesothelial origin. Here we show that Wt1 expression in adipose tissue is not limited to the mesothelium, but is also expressed by a distinct preadipocyte population in both mice and humans. We identify keratin 19 (Krt19) as a highly-specific marker for the adult mouse mesothelium, and demonstrate that Krt19-expressing mesothelial cells do not differentiate into visceral adipocytes. These results contradict the assertion that the VAT mesothelium can serve as a source of adipocytes.
DeGlyPHER: an ultrasensitive method for analysis of viral spike N-glycoforms
Authors: Baboo Sabyasachi , Diedrich Jolene K , Martínez-Bartolomé Salvador , Wang Xiaoning , Schiffner Torben , Groschel Bettina , Schief William R , Paulson James C , Yates John R 
Published: May 2021

AbstractViruses can evade the host immune system by displaying numerous glycans on their surface “spike-proteins” that cover immune epitopes. We have developed an ultrasensitive “single pot” method to assess glycan occupancy and the extent of glycan processing from high-mannose to complex forms at each N-glycosylation site. Though aimed at characterizing glycosylation of viral spike-proteins as potential vaccines, this method is applicable for analysis of site-specific glycosylation of any glycoprotein.
The EphB2-MYC Axis is a Major Determinant of Barrett’s Pathobiology and a Therapeutic Vulnerability in Esophageal Cancer
Authors: Venkitachalam Srividya , Babu Deepak , Ravillah Durgadevi , Katabathula Ramachandra M. , Joseph Peronne , Singh Salendra , Udhayakumar Bhavatharini , Miao Yanling , Martinez-Uribe Omar , Hogue Joyce A. , Kresak Adam M. , Dawson Dawn , LaFramboise Thomas , Willis Joseph E. , Chak Amitabh , Garman Katherine S. , Blum Andrew E. , Varadan Vinay , Guda Kishore 
Published: May 2021

ABSTRACTEsophageal adenocarcinoma (EAC), a highly aggressive cancer with limited therapeutic options, often arises in the backdrop of a molecularly-complex esophageal metaplasia disorder, Barrett’s Esophagus (BE). Using transcriptomics and systems biology analyses of treatment-naïve malignant/pre-malignant biopsy tissues, we found Eph receptor B2 (EphB2) tyrosine kinase signaling to be frequently hyperactivated during early stages of EAC development, and across the BE-EAC continuum. Functional studies revealed EphB2 to be an upstream post-translational regulator of c-MYC activity and as a key molecular dependency in BE/EAC. Single-cell transcriptomics in a porcine esophageal 3D spheroid model showed enhanced EphB2 and MYC activity to be significantly associated with BE-like cell fate. shRNA-based knockdown of EphB2 or small molecule inhibitors of MEK, that modulate MYC protein stability, proved effective in suppressing EAC tumor growth in vivo. These findings point to EphB2-MYC axis as an early promoter of EAC and a novel therapeutic vulnerability in this increasingly-prevalent esophageal malignancy.STATEMENT OF SIGNIFICANCEWe identify EphB2 signaling as a potential master regulator and early promoter of esophageal adenocarcinoma, and the proto-oncogene MYC as a key downstream effector of EphB2 function. Targeting the EphB2-MYC axis could be a promising therapeutic strategy for these often refractory and lethal EAC tumors.
Molecular diversity and lineage commitment of human interneuron progenitors
Authors: Velmeshev Dmitry , Chavali Manideep , Nowakowski Tomasz J. , Bhade Mohini , Mayer Simone , Goyal Nitasha , Alvarado Beatriz , Mancia Walter , Wang Shaohui , Speir Matthew , Haeussler Maximilian , Rowitch David , Alvarez-Buylla Arturo , Huang Eric J. , Paredes Mercedes , Kriegstein Arnold 
Published: May 2021

AbstractCortical interneurons are indispensable for proper function of neocortical circuits. Changes in interneuron development and function are implicated in human disorders, such as autism spectrum disorder and epilepsy. In order to understand human-specific features of cortical development as well as the origins of neurodevelopmental disorders it is crucial to identify the molecular programs underlying human interneuron development and subtype specification. Recent studies have explored gene expression programs underlying mouse interneuron specification and maturation. We applied single-cell RNA sequencing to samples of second trimester human ganglionic eminence and developing cortex to identify molecularly defined subtypes of human interneuron progenitors and immature interneurons. In addition, we integrated this data from the developing human ganglionic eminences and neocortex with single-nucleus RNA-seq of adult cortical interneurons in order to elucidate dynamic molecular changes associated with commitment of progenitors and immature interneurons to mature interneuron subtypes. By comparing our data with published mouse single-cell genomic data, we discover a number of divergent gene expression programs that distinguish human interneuron progenitors from mouse. Moreover, we find that a number of transcription factors expressed during prenatal development become restricted to adult interneuron subtypes in the human but not the mouse, and these adult interneurons express species- and lineage-specific cell adhesion and synaptic genes. Therefore, our study highlights that despite the similarity of main principles of cortical interneuron development and lineage commitment between mouse and human, human interneuron genesis and subtype specification is guided by species-specific gene programs, contributing to human-specific features of cortical inhibitory interneurons.
The histone chaperone Spt6 is required for normal recruitment of the capping enzyme Abd1 to transcribed regions
Authors: Gopalakrishnan Rajaraman , Winston Fred 
Published: May 2021

AbstractThe histone chaperone Spt6 is involved in promoting elongation of RNA polymerase II (RNAPII), maintaining chromatin structure, regulating co-transcriptional histone modifications, and controlling mRNA processing. These diverse functions of Spt6 are partly mediated through its interactions with RNAPII and other factors in the transcription elongation complex. In this study, we used mass spectrometry to characterize the differences in RNAPII interacting factors between wild-type cells and those depleted for Spt6, leading to the identification of proteins that depend on Spt6 for their interaction with RNAPII. The altered association of some of these factors could be attributed to changes in steady-state protein levels. However, Abd1, the mRNA cap methyltransferase, had decreased association with RNAPII after Spt6 depletion despite unchanged Abd1 protein levels, showing a requirement for Spt6 in mediating the Abd1-RNAPII interaction. Genome-wide studies showed that Spt6 is required for maintaining the level of Abd1 over transcribed regions, as well as the level of Spt5, another protein known to recruit Abd1 to chromatin. Abd1 levels were particularly decreased at the 5’ ends of genes after Spt6 depletion, suggesting a greater need for Spt6 in Abd1 recruitment over these regions. Together, our results show that Spt6 is important in regulating the composition of the transcription elongation complex and reveal a previously unknown function for Spt6 in the recruitment of Abd1.
Influenza A virus defective viral genomes are inefficiently packaged into virions relative to wild-type genomic RNAs
Authors: Alnaji Fadi G. , Reiser William K. , Velthuis Aartjan te , Brooke Christopher B. 
Published: May 2021

AbstractDeletion-containing viral genomes (DelVGs) are commonly produced during influenza A virus infection and have been implicated in influencing clinical infection outcomes. Despite their ubiquity, the specific molecular mechanisms that govern DelVG formation and their packaging into defective interfering particles (DIPs) remain poorly understood. Here, we utilized next-generation sequencing to analyze DelVGs that form de novo early during infection, prior to packaging. Analysis of these early DelVGs revealed that deletion formation occurs in clearly defined hotspots and is significantly associated with both direct sequence repeats and enrichment of adenosine and uridine bases. By comparing intracellular DelVGs with those packaged into extracellular virions, we discovered that DelVGs face a significant bottleneck during genome packaging relative to wild type genomic RNAs. Surprisingly, packaged DelVGs exhibited no signs of enrichment for specific deletion characteristics suggesting that all DelVGs are equally limited in packaging efficiency. Our data provide the first unbiased, high-resolution portrait of the diversity of DelVGs that are generated by the IAV replication machinery and shed light on the mechanisms that underly DelVG formation.ImportanceDefective interfering particles (DIPs) are commonly produced by RNA viruses and have been implicated in modulating clinical infection outcomes, hence, there is increasing interest in the potential of DIPs as antiviral therapeutics. For influenza viruses, DIPs are formed by the packaging of genomic RNAs harboring internal deletions. Despite decades of study, the mechanisms that drive the formation of these deletion-containing viral genomes (DelVGs) remain elusive. Here, we used a specialized sequencing pipeline to characterize the first wave of DelVGs that form during influenza virus infection. This dataset provides an unbiased profile of the deletion-forming preferences of the influenza virus replicase. Additionally, by comparing the early intracellular DelVGs with those that get packaged into extracellular virions, we described a significant segment-specific bottleneck that limits DelVG packaging relative to wild type viral RNAs. Altogether, these findings reveal factors that govern the production of both DelVGs and DIPs during influenza virus infection.
The role of accelerated growth plate fusion in the absence of SOCS2 on osteoarthritis vulnerability
Authors: Samvelyan Hasmik J. , Huesa Carmen , Lin Lucy Cui , Farquharson Colin , Staines Katherine A. 
Published: May 2021

AbstractOsteoarthritis is the most prevalent systemic musculoskeletal disorder characterised by articular cartilage degeneration and subchondral bone (SCB) sclerosis. Here we sought to examine the contribution of accelerated growth to osteoarthritis development using a murine model of excessive longitudinal growth. Suppressor of cytokine signalling 2 (SOCS2) is a negative regulator of growth hormone (GH) signalling, thus mice deficient in SOCS2 (Socs2-/-) display accelerated bone growth. We examined vulnerability ofSocs2-/-mice to osteoarthritis following surgical induction of disease (destabilisation of the medial meniscus (DMM)), and with ageing, by histology and micro-CT. We observed significant increase in number (WT DMM: 532±56; WT sham: 495±45; KO DMM: 169±49; KO sham: 187±56; P<0.01) and density (WT DMM: 2.2±0.9; WT sham: 1.2±0.5; KO DMM: 13.0±0.5; KO sham: 14.4±0.7) of growth plate bridges inSocs2-/-in comparison to wild-type (WT). Histological examination of WT andSocs2-/-knees revealed articular cartilage damage with DMM in comparison to sham (WT DMM: 3.4±0.4; WT sham: 0.3±0.05 (P<0.05); KO DMM: 3.2±0.8; KO sham: 0.8±0.3). Articular cartilage lesion severity scores (mean and maximum) were similar in WT andSocs2-/-mice with either DMM, or with ageing. Micro-CT analysis revealed significant decreases in SCB thickness, epiphyseal trabecular number and thickness in the medial compartment ofSocs2-/-, in comparison to WT (P<0.001). DMM had no effect on the SCB thickness in comparison to sham in either genotype. Together these data suggest that enhanced GH signalling through SOCS2 deletion accelerates growth plate fusion, however this has no effect on osteoarthritis vulnerability in this model.Summary statementDeletion of SOCS2 results in accelerated growth plate fusion, however this has no effect on osteoarthritis vulnerability.
Overdominant mutations restrict adaptive loss of heterozygosity at linked loci
Authors: Fisher Kaitlin J. , Vignogna Ryan C. , Lang Gregory I. 
Published: May 2021

ABSTRACTLoss of heterozygosity is a common mode of adaptation in asexual diploid populations. Because mitotic recombination frequently extends the full length of a chromosome arm, the selective benefit of loss of heterozygosity may be constrained by linked heterozygous mutations. In a previous laboratory evolution experiment with diploid yeast, we frequently observed homozygous mutations in the WHI2 gene on the right arm of Chromosome XV. However, when heterozygous mutations arose in the STE4 gene, another common target on Chromosome XV, loss of heterozygosity at WHI2 was not observed. Here we show that mutations at WHI2 are partially dominant and that mutations at STE4 are overdominant. We test whether beneficial heterozygous mutations at these two loci interfere with one another by measuring loss of heterozygosity at WHI2 over 1,000 generations for ∼300 populations that differed initially only at STE4 and WHI2. We show that the presence of an overdominant mutation in STE4 reduces, but does not eliminate, loss of heterozygosity at WHI2. By sequencing 40 evolved clones, we show that populations with linked overdominant and partially dominant mutations show less parallelism at the gene level, more varied evolutionary outcomes, and increased rates of aneuploidy. Our results show that the degree of dominance and the phasing of heterozygous beneficial mutations can constrain loss of heterozygosity along a chromosome arm, and that conflicts between partially dominant and overdominant mutations can affect evolutionary outcomes.SIGNIFICANCE STATEMENTIn diploid populations, it is beneficial for partially dominant beneficial mutations to lose heterozygosity, but it is deleterious for overdominant beneficial mutations to do so. Because loss-of-heterozygosity tracts often encompass entire chromosome arms, a conflict will arise when a partially dominant beneficial mutation and an overdominant beneficial mutation exist in close proximity. We demonstrate that this conflict occurs, and that it restricts loss of heterozygosity, resulting in more variable evolutionary outcomes.
iSubGen: Integrative Subtype Generation by Pairwise Similarity Assessment
Authors: Fox Natalie S. , Haider Syed , Li Constance H. , Boutros Paul C. 
Published: May 2021

AbstractThere are myriad types of biomedical data– genetics, transcriptomics, clinical, imaging, wearable devices and many more. When a group of patients with the same underlying disease exhibit similarities across multiple types of data, this is called a subtype. Disease subtypes can reflect etiology and sometimes predict clinical behaviour. Existing subtyping approaches struggle to simultaneously handle multiple diverse data types, particularly when there is missing information, as is common in most real-world clinical datasets. To improve subtype discovery, we exploited changes in the correlation-structure between different data types to create iSubGen, an algorithm forintegrativesubtypegeneration. iSubGen can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen recapitulates known subtypes across multiple diseases, even in the face of substantial missing data. It identifies groups of patients with divergent clinical outcomes, and can combine arbitrary data types for subtype discovery, such as merging molecular, mutational signature, pathway and micro-environmental data. iSubGen can accommodate any feature that can be compared with a similarity-metric, and provides a versatile approach for creating subtypes. It is available athttps://CRAN.R-project.org/package=iSubGen.
A platform for deep sequence-activity mapping and engineering antimicrobial peptides
Authors: DeJong Matthew P. , Ritter Seth C. , Fransen Katharina A. , Tresnak Daniel T. , Golinski Alexander W. , Hackel Benjamin J. 
Published: May 2021

SummaryDeveloping potent antimicrobials, and platforms for their study and engineering, is critical as antibiotic resistance grows. A high-throughput method to quantify antimicrobial peptide and protein (AMP) activity across a broad continuum can elucidate sequence-activity landscapes and identify potent mutants. We developed a platform to perform sequence-activity mapping of AMPs via depletion (SAMP-Dep): a bacterial host culture is transformed with an AMP mutant library, induced to express AMPs, grown, and deep sequenced to quantify mutant frequency. The slope of mutant growth rate versus induction level indicates potency. Using SAMP-Dep, we screened 170,000 mutants of oncocin, a proline-rich AMP, for intracellular activity against Escherichia coli. Clonal validation of 36 mutants supported SAMP-Dep sensitivity and accuracy. The efficiency and accuracy of SAMP-Dep enabled mapping the oncocin sequence-activity space with remarkable detail and scale and guided focused, successful synthetic peptide library design, yielding a mutant with two-fold enhancement in both intracellular and extracellular activity.
Differential receptor crosstalk in DRD1-DRD2 heterodimer upon phasic and tonic dopamine signals
Authors: Kim Hyunbin , Nam Min-Ho , Jeong Sohyeon , Lee Hyowon , Oh Soo-Jin , Kim Jeongjin , Choi Nakwon , Seong Jihye 
Published: May 2021

AbstractIn response to phasic and tonic release, dopamine neurotransmission is regulated by its receptor subtypes, mainly dopamine receptor type 1 and 2 (DRD1 and DRD2). These dopamine receptors are known to form a heterodimer, however the receptor crosstalk between DRD1 and DRD2 was only suspected by measuring their downstream signaling products, due to the lack of methodology for selectively detecting individual activity of different dopamine receptors. Here, we develop red DRD1 sensor (R-DRD1) and green DRD2 sensor (G-DRD2) which can specifically monitor the real-time activity of DRD1 and DRD2, and apply these multicolor sensors to directly measure the receptor crosstalk in the DRD1-DRD2 heterodimer. Surprisingly, we discover that DRD1 activation in the heterodimer is inhibited only at micromolar phasic concentration of dopamine, while DRD2 activation is selectively inhibited at nanomolar tonic dopamine level. Differential receptor crosstalk in the DRD1-DRD2 heterodimer further modulates their downstream cAMP level. These data imply a novel function of the DRD1-DRD2 heterodimer at physiological dopamine levels of phasic and tonic release. Our approach utilizing multicolor receptor sensors will be useful to discover novel function of GPCR heterodimers.
Assessing the role of cold-shock protein C: A novel regulator of Acinetobacter baumannii biofilm formation and virulence
Authors: Tomlinson Brooke R. , Denham Grant A. , Brzozowski Robert S. , Allen Jessie L. , Eswara Prahathees J. , Shaw Lindsey N. 
Published: May 2021

AbstractAcinetobacter baumannii is a formidable opportunistic pathogen that is notoriously difficult to eradicate from hospital settings and can spread quickly via healthcare personnel despite preventive measures. This resilience is often attributed to a proclivity for biofilm formation, which grants A. baumannii a higher tolerance towards external stress, desiccation, and antimicrobials. Despite this, little is known regarding the mechanisms orchestrating A. baumannii biofilm formation. Herein, we performed RNA-seq on biofilm and planktonic populations for the multidrug resistant isolate, AB5075, and identified 438 genes with altered expression. To assess the potential role of genes upregulated within biofilms, we tested the biofilm forming capacity of their respective mutants from an A. baumannii transposon library. In so doing, we uncovered 24 genes whose disruption led to reduced biofilm formation. One such element, cold shock protein C (cspC), produced a mucoidal, non-mucoviscous colony phenotype. RNA-sequencing of this mutant revealed the down regulation of pili and fimbriae in the cspC mutant, which would explain the decreased biofilm observed. Using MIC assays, we note that the mutant displayed increased antibiotic tolerance that we hypothesize is mediated by overexpression of multi-drug efflux pumps and altered mRNA stability of their corresponding transcriptional repressor. Finally, we show that CspC is required for survival during oxidative stress and challenge by the human immune system, and plays a pivotal role during systemic infection. Collectively, our work identifies a cadre of new biofilm associated genes within A. baumannii and provides insight into the global regulatory network of this emerging human pathogen.
SAR11 Cells Rely on Enzyme Multifunctionality to Transport and Metabolize a Range of Polyamine Compounds
Authors: Noell Stephen E. , Barrell Gregory E. , Suffridge Christopher , Morré Jeff , Gable Kevin P. , Graff Jason R. , VerWey Brian J. , Hellweger Ferdi L. , Giovannoni Stephen J. 
Published: May 2021

AbstractIn the ocean surface layer and cell culture, the polyamine transport protein PotD of SAR11 bacteria is often one of the most abundant proteins detected. Polyamines are organic cations produced by all living organisms and are thought to be an important component of dissolved organic matter (DOM) produced in planktonic ecosystems. We hypothesized that SAR11 cells transport and metabolize multiple polyamines and use them as sources of carbon and nitrogen. Metabolic footprinting and fingerprinting were used to measure the uptake of five polyamine compounds (putrescine, cadaverine, agmatine, norspermidine, and spermidine) in two SAR11 strains that represent the majority of SAR11 cells in the surface ocean environment, Ca. Pelagibacter st. HTCC7211 and C. P. ubique st. HTCC1062. Both strains transported all five polyamines and concentrated them to micromolar or millimolar intracellular concentrations. Both strains could use most of the polyamines to meet their nitrogen requirements, but we did not find evidence of use as carbon sources. We propose potABCD transports cadaverine, agmatine, and norspermidine, in addition to its usual substrates of spermidine and putrescine, and that spermidine synthase, speE, is reversible, catalyzing the breakdown of spermidine and norspermidine, in addition to its usual biosynthetic role. These findings provide support for the hypothesis that enzyme multifunctionality enables streamlined cells in planktonic ecosystems to increase the range of DOM compounds they oxidize.ImportanceGenome streamlining in SAR11 bacterioplankton has resulted in a small repertoire of genes, yet paradoxically they consume a substantial fraction of primary production in the oceans. Enzyme multifunctionality is hypothesized to be an adaptation that increases the range of organic compounds oxidized by cells in environments where selection favors genome minimization. We provide experimental support for this hypothesis by demonstrating that SAR11 cells use multiple polyamine compounds and propose that a small set of multifunctional genes catalyze this metabolism. We also report polyamine uptake rates can exceed metabolism, resulting in high intracellular concentrations of these nitrogen-rich compounds and an increase in cell size. Increases in cytoplasmic solute concentrations during transient episodes of high nutrient exposure has previously been observed in SAR11 cells and may be a feature of their strategy for maximizing the share of labile DOM acquired when in competition with other cell types.