bluuebunny/crossref_metadata_2025 huggingface dataset:
Big Five Personality Traits Influence Tinnitus Improvement Over Time
Authors: Simões Jorge , Schlee Winfried , Schecklmann Martin , Langguth Berthold , Farahmand Daria , Neff Patrick
Published: June 2019

Previous studies investigating the relation between personality and tinnitus distress showed that high neuroticism and low extraversion scores are related to higher tinnitus distress measured by the Tinnitus Handicap Inventory (THI) and the Tinnitus Questionnaire (TQ). However, little is known about the role of personality on tinnitus distress over time.

We collected the THI, TQ and Big Five Factor Index 2 of 388 patients who visited the Tinnitus Center Regensburg between 2012 and 2017, and filled in a survey with the same questionnaires in 2018. We used personality traits and facets to predict tinnitus distress cross-sectionally and longitudinally. Neuroticism and extraversion were significant predictors of THI and TQ scores in cross-sectional linear regression setups, and could explain up to 40% of the variance. However, the linear regressions could explain only little variance of both THI and TQ longitudinally. We clustered patients in three groups based in the difference THI and TQ between the two assessments: “clinically improved”, “clinically stable” and “clinically worsened”. The patients in the “clinically improved” and “clinically stable” groups scored statistically significantly lower in neuroticism and higher in extraversion than patients in the group “clinically worsened”. We observed a similar trend among patients who tried at least one clinical treatment.

Our results suggest that personality traits, namely neuroticism and extraversion, are relevant markers of tinnitus distress over time and could be used to statistically distinguish patient groups with clinically relevant changes of tinnitus distress. These markers could inform both treatment responses from clinical studies and future choices on more efficient individual tinnitus treatments.
An acute bleomycin inflammatory and fibrotic mouse model of morphea is dependent upon CXCL9 and CXCR3
Authors: Richmond Jillian M. , Patel Dhrumil , Watanabe Tomoya , Garelli Colton J. , Garg Madhuri , Dresser Karen , Deng April , Feghali-Bostwick Carol A. , Harris John E. , Jacobe Heidi
Published: June 2019

Morphea, or localized scleroderma, is characterized by an inflammatory phase followed by cutaneous fibrosis, which may lead to disfigurement and/or disability. Previous work from our group showed that the CXCR3 ligands CXCL9 and CXCL10 are highly upregulated in lesional skin of morphea patients. Here, we used an acute inflammatory and fibrotic bleomycin mouse model of morphea to examine the role of the CXCR3 chemokine axis in pathogenesis. We first characterized which cells produce the CXCR3 ligands in the skin using the Reporter of Expression of CXCR3 ligands mouse (REX3). We found that fibroblasts contribute the bulk of CXCL9 and CXCL10, whereas endothelial cells are key dual chemokine producers. Macrophages, which have high MFI of chemokine expression, upregulated CXCL9 production over time, fibroblasts CXCL10 production, and T cells dual chemokine expression. To determine whether bleomycin treatment could directly induce expression of these chemokines, we treated cultured REX3 mouse dermis monolayers in vitro with bleomycin or IFNγ with TNF and found that bleomycin could induce low amounts of CXCL9 directly in fibroblasts, whereas the cytokines were required for optimal CXCL9 and CXCL10 production. To determine whether these chemokines are mechanistically involved in pathogenesis, we induced fibrosis in CXCL9, CXCL10, or CXCR3 deficient mice and found that fibrosis is dependent on CXCL9 and CXCR3. Addition of recombinant CXCL9, but not CXCL10, to cultured mouse fibroblasts induces collagen 1a1 mRNA expression, indicating the chemokine itself can contribute to fibrosis. Taken together, our studies provide evidence that acute intradermal bleomycin administration in mice can model inflammatory morphea, and that CXCL9 and its receptor CXCR3 are mechanistically involved in pathogenesis.

One Sentence Summary

CXCL9 drives acute morphea pathogenesis in mice.
Current characteristics and outcomes of Cytomegalovirus Reactivation in kidney transplant seropositive recipients in the era of prophylaxis treatment. Lesson from single Moroccan center experience
Authors: Rezzouk Bouchra. , Bouattar Tarik. , Belkadi Bouchra. , Razine Rachid. , Bayahia Rabia. , Ouzeddoun Naima. , Benamar Loubna. , Rhou Hakima. , Bouihat Najat. , Ibrahimi Azeddine , Seffar Myriam. , Kabbaj Hakima.
Published: June 2019

Despite the use of antiviral prophylaxis, the active cytomegalovirus (CMV) replication is still occurred in the seropositive kidney recipients. The aim of this study was to assess the incidence of CMV reactivation and potential risk factors associated with CMV disease. Data of sixty kidney transplant recipients who had received CMV prophylaxis were obtained between 2013 and 2017. Quantitative nucleic acid amplification testing for CMV viraemia was assessed using Abbott RealTimePolymerase Chain Reaction (PCR). Among the seropositive recipients, cumulative incidence for reactivation was 63%. In patients with quantitative viraemia, the time of active replication was significantly lower compared to those with detectable viraemia (141.5 ± 96.9vs294.1 ± 112.6 days,P< 0.001). During prophylactic treatment, 46.7% of patients with quantifiable viraemia had experienced active replication and none among patients with detectable viraemia (P= 0.017). Importantly, symptomatic reactivation was significantly observed in the younger patients with higher peak viraemia compared to those with symptoms free (28.8 ± 5.12 vs. 38.1 ± 12.34 years,P= 0.007) and 3.8 ± 1.59 vs. 2.4 ± 0. 79 log10IU/ml,P= 0.003, respectively). Furthermore, the median duration of viraemia (21.2, vs. 13.4 days,P= 0.028) and period of CMV therapy (24.3 vs 12.3 days,P<0.001) were significantly longer for this group. In addition, intercurrent infections (75% vs. 23%,P= 0.028) and acute rejection (50 % vs 0%,P= 0.003) were significantly more frequent in symptomatic reactivation group. In addition, peak viral load was a potential risk factor for development of symptomatic reactivation with odds ratio 3.39, 95%CI=1.21-9.53,P= 0.02). In conclusion, CMV reactivation remains serious problem for seropositive recipients who were expected to be on antiviral prophylaxis. Patients with high level of viraemia may be at an increased risk of progression to CMV disease and adverse outcomes.
Forecasting the impact of population ageing on tuberculosis incidence
Authors: Ku Chu-Chang , Dodd Peter J
Published: June 2019

Background

Tuberculosis (TB) disease reactivates from distant latent infection or recent (re)infection. Progression risks increase with age. Across the World Health Organisation Western Pacific region, many populations are ageing and have the highest per capita TB incidence rates in older age groups. However, methods for analysing age-specific TB incidence and forecasting epidemic trends while accounting for demographic change remain limited.

Methods

We applied the Lee-Carter models, which were originally developed for mortality modelling, to model the temporal trends in age-specific TB incidence data from 2005 to 2018 in Taiwan. Females and males were modelled separately. We combined our demographic forecasts, and age-specific TB incidence forecasts to project TB incidence until 2035. We compared TB incidence projections with demography fixed in 2018 to projections accounting for demographic change.

Results

Our models quantified increasing incidence rates with age and declining temporal trends. By 2035, the forecast suggests that the TB incidence rate in Taiwan will decrease by 54% (95% Prediction Interval (PI): 45%-59%) compared to 2015, while most age-specific incidence rates will reduce by more than 60%. In 2035, adults aged 65 and above will make up 78% of incident TB cases. Forecast TB incidence in 2035 accounting for demographic change will be 39% (95% PI: 36%-42%) higher than without population ageing.

Conclusions

Age-specific incidence forecasts coupled with demographic forecasts can inform the impact of population ageing on TB epidemics. The TB control programme in Taiwan should develop plans specific to older age groups and their care needs.
RADICL-seq identifies general and cell type-specific principles of genome-wide RNA-chromatin interactions
Authors: Bonetti Alessandro , Agostini Federico , Suzuki Ana Maria , Hashimoto Kosuke , Pascarella Giovanni , Gimenez Juliette , Roos Leonie , Nash Alex J. , Ghilotti Marco , Cameron Christopher JF , Valentine Matthew , Medvedeva Yulia A , Noguchi Shuhei , Agirre Eneritz , Kashi Kaori , Samudyata  , Luginbuehl Joachim , Cazzoli Riccardo , Agrawal Saumya , Luscombe Nicholas M , Blanchette Mathieu , Kasukawa Takeya , De Hoon Michiel , Arner Erik , Lenhard Boris , Plessy Charles , Castelo-Branco Gonçalo , Orlando Valerio , Carninci Piero
Published: June 2019

Mammalian genomes encode tens of thousands of noncoding RNAs. Most noncoding transcripts exhibit nuclear localization and several have been shown to play a role in the regulation of gene expression and chromatin remodelling. To investigate the function of such RNAs, methods to massively map the genomic interacting sites of multiple transcripts have been developed. However, they still present some limitations. Here, we introduce RNA And DNA Interacting Complexes Ligated and sequenced (RADICL-seq), a technology that maps genome-wide RNA-chromatin interactions in intact nuclei. RADICL-seq is a proximity ligation-based methodology that reduces the bias for nascent transcription, while increasing genomic coverage and unique mapping rate efficiency compared to existing methods. RADICL-seq identifies distinct patterns of genome occupancy for different classes of transcripts as well as cell type-specific RNA-chromatin interactions, and emphasizes the role of transcription in the establishment of chromatin structure.
HiChIP-Peaks: A HiChIP peak calling algorithm
Authors: Shi Chenfu , Rattray Magnus , Orozco Gisela
Published: June 2019

Motivation

HiChIP is a powerful tool to interrogate 3D chromatin organization. Current tools to analyse chromatin looping mechanisms using HiChIP data require the identification of loop anchors to work properly. However, current approaches to discover these anchors from HiChIP data are not satisfactory, having either a very high false discovery rate or strong dependence on sequencing depth. Moreover, these tools do not allow quantitative comparison of peaks across different samples, failing to fully exploit the information available from HiChIP datasets.

Results

We develop a new tool based on a representation of HiChIP data centred on the re-ligation sites to identify peaks from HiChIP datasets, which can subsequently be used in other tools for loop discovery. This increases the reliability of these tools and improves recall rate as sequencing depth is reduced. We also provide a method to count reads mapping to peaks across samples, which can be used for differential peak analysis using HiChIP data.

Availability

HiChIP-Peaks is freely available at https://github.com/ChenfuShi/HiChIP_peaks

Contact:chenfu.shi@postgrad.manchester.ac.uk
Fitness costs of parasites explain multiple life history tradeoffs in a wild mammal
Authors: Albery Gregory F , Morris Alison , Morris Sean , Kenyon Fiona , Nussey Daniel H , Pemberton Josephine M
Published: June 2019

Reproduction in wild animals can divert limited resources away from immune defence, resulting in increased parasite burdens. A longstanding prediction of life history theory states that these parasites can harm the reproductive individual, reducing its subsequent fitness and producing reproduction-fitness tradeoffs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent fitness in a wild population of individually identified red deer (Cervus elaphus). Using path analysis, we investigated whether costs of lactation for downstream survival and fecundity were mediated by changes in strongyle nematode count and mucosal antibody levels. Lactating females exhibited increased parasite counts, which were in turn associated with substantially decreased fitness in the following year in terms of overwinter survival, fecundity, subsequent calf weight, and parturition date. This study offers observational evidence for parasite regulation of multiple life history tradeoffs, supporting the role of parasites as an important mediating factor in wild mammal populations.
Common genetic variation indicates separate etiologies for periventricular and deep white matter hyperintensities
Authors: Armstrong Nicola J , Mather Karen A , Sargurupremraj Muralidharan , Knol Maria J , Malik Rainer , Satizabal Claudia L , Yanek Lisa R , Wei Wen , Gudnason Vilmundur , Deuker Nicole D , Elliott Lloyd T , Hofer Edith , Jahanshad Neda , Li Shuo , Logue Mark A , Luciano Michelle , Scholz Markus , Smith Albert , Trompet Stella S , Vojinovic Dina , Xia Rui , Alfaro-Almagro Fidel , Ames David , Amin Najaf , Amouyel Philippe , Beiser Alexa S , Brodaty Henry , Deary Ian J , Fennema-Notestine Christine , Gampwar Piyush G , Gottesman Rebecca , Griffanti Ludovica , Jack Clifford R , Jenkinson Mark , Jain Jiyang , Kral Brian G , Kwok John W , Lampe Leonie , Liewald David CM , Maillard Pauline , Marchini Jonathan , Bastin Mark E , Mazoyer Bernard , Pirpamer Lukas , Romero José Rafael , Roshchupkin Gennady V , Schofield Peter R , Schroeter Matthias L , Stott David J , Thalamuth Anbupalam , Trollor Julian , Tzourio Christophe , van der Grond Jeroen , Vernooij Meike W , Witte Veronica A , Wright Maragret J , Yang Qiong , Zoe Moris , Siggurdsson Siggi , Villringer Arno , Schmidt Helena , Haberg Asta L , Van Duijn Cornelia M , Jukema J Wouter , Dichigans Martin , Sacco Ralph L , Wright Clinton B , Kremen William S , Becker Lewis C , Thompson Paul M , Launer Lenore , Mosley Thomas H , Wardlaw Joanna M , Ikram M Afran , Adams Hieab HH , Schmidt Reinhold , Smith Stephen M , Decarli Charles , Sachdev Perminder S , Fornage Myriam , Debbette Stephanie , Seshadri Sudha , Nyquist Paul A
Published: June 2019

We conducted a genome-wide association meta-analysis of two ischemic white matter disease subtypes in the brain, periventricular and deep white matter hyperintensities (PVWMH and DWMH). In 26,654 participants, we found 10 independent genome-wide significant loci only associated with PVWMH, four of which have not been described previously for total WMH burden (16q24.2, 17q21.31, 10q23.1, 7q36.1). Additionally, in both PVWMH and DWMH we observed the previous association of the 17q25.1 locus with total WMH. We found that both phenotypes have shared but also distinct genetic architectures, consistent with both different underlying and related pathophysiology. PVWMH had more extensive genetic overlap with small vessel ischemic stroke, and unique associations with several loci implicated in ischemic stroke. DWMH were characterized by associations with loci previously implicated in vascular as well as astrocytic and neuronal function. Our study confirms the utility of these phenotypes and identifies new candidate genes associated only with PVWMH.
funMotifs: Tissue-specific transcription factor motifs
Authors: Umer Husen M. , Smolinska-Garbulowska Karolina , Marzouka Nour-al-dain , Khaliq Zeeshan , Wadelius Claes , Komorowski Jan
Published: June 2019

Transcription factors (TF) regulate gene expression by binding to specific sequences known as motifs. A bottleneck in our knowledge of gene regulation is the lack of functional characterization of TF motifs, which is mainly due to the large number of predicted TF motifs, and tissue specificity of TF binding. We built a framework to identify tissue-specific functional motifs (funMotifs) across the genome based on thousands of annotation tracks obtained from large-scale genomics projects including ENCODE, RoadMap Epigenomics and FANTOM. The annotations were weighted using a logistic regression model trained on regulatory elements obtained from massively parallel reporter assays. Overall, genome-wide predicted motifs of 519 TFs were characterized across fifteen tissue types. funMotifs summarizes the weighted annotations into a functional activity score for each of the predicted motifs. funMotifs enabled us to measure tissue specificity of different TFs and to identify candidate functional variants in TF motifs from the 1000 genomes project, the GTEx project, the GWAS catalogue, and in 2,515 cancer samples from the Pan-cancer analysis of whole genome sequences (PCAWG) cohort. To enable researchers annotate genomic variants or regions of interest, we have implemented a command-line pipeline and a web-based interface that can publicly be accessed on: http://bioinf.icm.uu.se/funmotifs.
MAP2 is Differentially Phosphorylated in Schizophrenia, Altering its Function
Authors: Grubisha MJ , Sun X , MacDonald ML , Garver M , Sun Z , Paris KA , Patel DS , DeGiosio RA , Lewis DA , Yates NA , Camacho C , Homanics GE , Ding Y , Sweet RA
Published: June 2019

Schizophrenia (Sz) is a highly polygenic disorder, with common, rare, and structural variants each contributing only a small fraction of overall disease risk. Thus, there is a need to identify downstream points of convergence that can be targeted with therapeutics. Reduction of Microtubule-associated Protein 2 (MAP2) immunoreactivity (MAP2-IR) is present in individuals with Sz, despite no change in MAP2 protein levels. MAP2 is phosphorylated downstream of multiple receptors and kinases identified as Sz risk genes, altering its immunoreactivity and function. Using an unbiased phosphoproteomics approach we quantified 18 MAP2 phosphopeptides, 9 of which were significantly altered in Sz subjects. Network analysis grouped MAP2 phosphopeptides into 3 modules, each with a distinct relationship to dendritic spine loss, synaptic protein levels, and clinical function in Sz subjects. We then investigated the most hyperphosphorylated site in Sz, phosphoserine1782 (pS1782). Computational modeling predicted phosphorylation of S1782 reduces binding of MAP2 to microtubules, which was confirmed experimentally. We generated a transgenic mouse containing a phosphomimetic mutation at S1782 (S1782E) and found reductions in basilar dendritic length and complexity along with reduced spine density. Because only a limited number of MAP2 interacting proteins have been previously identified, we combined co-immunoprecipitation with mass spectrometry to characterize the MAP2 interactome in mouse brain. The MAP2 interactome was enriched for proteins involved in protein translation. These associations were shown to be functional as overexpression of wildtype and phosphomimetic MAP2 reduced protein synthesisin vitro. Finally, we found that Sz subjects with low MAP2-IR had reductions in the levels of synaptic proteins relative to nonpsychiatric control (NPC) subjects and to Sz subjects with normal and MAP2-IR, and this same pattern was recapitulated in S1782E mice. These findings suggest a new conceptual framework for Sz - that a large proportion of individuals have a “MAP2opathy” - in which MAP function is altered by phosphorylation, leading to impairments of neuronal structure, synaptic protein synthesis, and function.
Asymmetric, dynamic adaptation in prefrontal cortex during dichotic listening tasks
Authors: Fisher J. A. N. , Gumenchuk I. , Rogovin O. , Yodh A. G. , Busch D. R.
Published: June 2019

Speech comprehension relies on highly distributed, dynamically interconnected neuroanatomical loci. Accordingly, performance on complex speech processing tasks such as dichotic listening can be used to assess the integrity and health of many functional and structural aspects of the brain. Despite the potential merits as a clinical assessment tool, however, the neural substrates activated during dichotic listening remain relatively opaque at higher processing levels. Ultimately, this knowledge gap limits diagnostic use of the task. At the level of the prefrontal cortex, dichotic listening induces an asymmetric response wherein regions on the right hemisphere exhibit a higher functional activation than on the left. Superficially, this finding is counterintuitive given the left hemisphere’s dominance for speech and language. To obtain a more in-depth perspective on the potentially distinct roles of the right and left prefrontal cortex, we optically monitored cerebral blood flow in the dorsolateral prefrontal cortex (DLPFC) during dichotic listening tasks in human subjects. The method permitted us to avoid systematic experimental confounds that functional magnetic resonance imaging (fMRI) measurements suffer from, namely the influence of scanner noise. In addition to reproducing the documented larger activation amplitude in the right hemisphere, we also found that repeated listening task blocks were associated with altered kinetics of blood flow in the right, but not the left DLPFC. Interestingly, subjects with the most prominent regional blood flow changes in the right hemisphere also displayed large distortion product otoacoustic emissions (DPOAEs) in the left ear, possibly signaling a correlation between prefrontal activity and top-down listening control infrastructure through medial olivocochlear efferent projections to the inner ear. Overall, our results suggest that the right prefrontal cortical regions play an active role in optimizing task performance.
Invariants of Frameshifted Variants
Authors: Bartonek Lukas , Braun Daniel , Zagrovic Bojan
Published: June 2019

Frameshifts in protein coding sequences are widely perceived as resulting in either non-functional or even deleterious protein products. Indeed, frameshifts typically lead to markedly altered protein sequences and premature stop codons. By analyzing complete proteomes from all three domains of life, we demonstrate that, in contrast, several key physicochemical properties of protein sequences exhibit significant robustness against +1 and −1 frameshifts in their mRNA coding sequences. In particular, we show that hydrophobicity profiles of many protein sequences remain largely invariant upon frameshifting. For example, over 2900 human proteins exhibit a Pearson correlation coefficient between the hydrophobicity profiles of the original and the +1-frameshifted variants greater than 0.7, despite a median sequence identity between the two of only 6.5% in this group. We observe a similar effect for protein sequence profiles of affinity for certain nucleobases, their matching with the cognate mRNA nucleobase-density profiles as well as protein sequence profiles of intrinsic disorder. Finally, we show that frameshift invariance is directly embedded in the structure of the universal genetic code and may have contributed to shaping it. Our results suggest that frameshifting may be a powerful evolutionary mechanism for creating new proteins with vastly different sequences, yet similar physicochemical properties to the proteins they originate from.

Significance Statement

Genetic information stored in DNA is transcribed to messenger RNAs and then read in the process of translation to produce proteins. A frameshift in the reading frame at any stage of the process typically results in a significantly different protein sequence being produced and is generally assumed to be a source of detrimental errors that biological systems need to control. Here, we show that several essential properties of many protein sequences, such as their hydrophobicity profiles, remain largely unchanged upon frameshifts. This finding suggests that frameshifting could be an effective evolutionary strategy for generating novel protein sequences, which retain the functionally relevant physicochemical properties of the sequences they derive from.
Dysfunction of ventral tegmental area GABA neurons causes mania-like behavior
Authors: Yu Xiao , Ba Wei , Zhao Guangchao , Ma Ying , Harding Edward C. , Yin Lu , Wang Dan , Shi Youran , Vyssotski Alexei L. , Dong Hailong , Franks Nicholas P. , Wisden William
Published: June 2019

The ventral tegmental area (VTA), an important source of dopamine, regulates goal- and reward-directed and social behaviors, wakefulness and sleep. Hyperactivation of dopamine neurons generates behavioral pathologies. But any roles of non-dopamine VTA neurons in psychiatric illness have been little explored. Lesioning or chemogenetically inhibiting VTA GABAergic (VTAVgat) neurons generated persistent wakefulness with mania-like qualities: locomotor activity was increased; sensitivity to D-amphetamine was heightened; immobility times decreased on the tail suspension and forced swim tests; and sucrose preference increased. Furthermore, after sleep deprivation, mice with lesioned VTAVgat neurons did not catch up on the lost NREM sleep, even though they were starting from an already highly sleep-deprived baseline, suggesting that the sleep homeostasis process was bypassed. The mania-like behaviors, including the sleep loss, were reversed by the mood-stabilizing drug valproate, and re-emerged when valproate treatment was stopped. Lithium salts, however, had no effect. The mania like-behaviors partially depended on dopamine, because giving D1/D2/D3 receptor antagonists partially restored the behaviors, but also on VTAVgat projections to the lateral hypothalamus (LH). Optically or chemogenetically inhibiting VTAVgat terminals in the LH elevated locomotion and decreased immobility time during the tail suspension and forced swimming tests. VTAVgat neurons are centrally positioned to help set an animal’s (and human’s) level of mental and physical activity. Inputs that inhibit VTAVgat neurons intensify wakefulness (increased activity, enhanced alertness and motivation), qualities useful for acute survival. Taken to the extreme, however, decreased or failed inhibition from VTAVgat neurons produces mania-like qualities (hyperactivity, hedonia, decreased sleep).
Uncovering the cell type specificity of blood sample derived gene signatures using RNA expression data
Authors: Pomaznoy Mikhail , Ha Brendan , Peters Bjoern
Published: June 2019

Analysis of transcriptomic data derived from blood samples is complicated by the complex mixture of cell types such samples contain. Transcriptomic signatures derived from such samples are often driven by a particular cell lineage within the mixture. Identifying this most contributing lineage can help to provide a biological interpretation of the signature. We created a web application CellTypeScore which quantifies and visually represents the expression level of signature genes in common blood cell types. This is done by constructing an interactive stacked bar plot with the bars representing expression of genes across blood cell types. Summed scores serve as a measure of how highly the combined signature is expressed in different cell types. An online version of the application can be found at https://tools.dice-database.org/celltypescore/.
A quantitative framework for evaluating single-cell data structure preservation by dimensionality reduction techniques
Authors: Heiser Cody N. , Lau Ken S.
Published: June 2019

High-dimensional data, such as those generated using single-cell RNA sequencing, present challenges in interpretation and visualization. Numerical and computational methods for dimensionality reduction allow for low-dimensional representation of genome-scale expression data for downstream clustering, trajectory reconstruction, and biological interpretation. However, a comprehensive and quantitative evaluation of the performance of these techniques has not been established. We present an unbiased framework that defines metrics of global and local structure preservation in dimensionality reduction transformations. Using discrete and continuous scRNA-seq datasets, we find that input cell distribution and method parameters are largely determinant of global, local, and organizational data structure preservation by eleven published dimensionality reduction methods. Code available atgithub.com/KenLauLab/DR-structure-preservationallows for rapid evaluation of further datasets and methods.
A geographical cline in craniofacial morphology across populations of Mesoamerican lake-dwelling fishes
Authors: Powers Amanda K. , Garita-Alvarado Carlos A. , Rodiles-Hernández Rocío , Berning Daniel J. , Gross Joshua B. , Ornelas-García Claudia Patricia
Published: June 2019

The complex geological history and tropical climate of Mesoamerica create a rich source of biodiversity from which we can study evolutionary processes. Here, we discuss highly divergent forms of lake-dwelling fishes distributed across southern Mexico and Central America, originally recognized as members of different genera (AstyanaxandBramocharax). Recent phylogenetic studies suggest these morphotypes group within the same genus and readily hybridize. Despite genetic similarities,Bramocharaxmorphs exhibit stark differences in cranial shape and dentition. We investigated the evolution of several cranial traits that vary across morphs collected from four lakes in Mexico and Nicaragua and discovered an ecomorphological cline from the northern to southern lakes. Northern populations of sympatric morphs exhibit similar cranial shape and tooth morphology. Southern populations ofBramocharax, however, have more maxillary teeth, larger unicuspid teeth, an elongated snout and a streamlined cranium compared toAstyanax. The divergence of craniofacial morphology in southern lakes likely evolved in response to environmental pressures. We discuss the ecological differences across the four lake systems in terms of geological history and trophic dynamics. In summary, our study suggests thatBramocharaxare likely locally-adapted members derived fromAstyanaxlineages, highlighting the complex evolutionary history of theAstyanaxgenus.
Elucidation of protein-protein interactions necessary for maintenance of the BCR-ABL signaling complex
Authors: Gregor Tomas , Bosakova Michaela Kunova , Nita Alexandru , Abraham Sara P. , Fafilek Bohumil , Cernohorsky Nicole H. , Rynes Jan , Foldynova-Trantirkova Silvie , Mayer Jiri , Trantirek Lukas , Krejci Pavel
Published: June 2019

Approximately 50% of chronic myeloid leukemia (CML) patients in deep remission experience a return of clinical CML after withdrawal of tyrosine kinase inhibitors (TKIs). This suggests signaling of inactive BCR-ABL, which allows for survival of cancer cells, leading to relapse. Understanding the dynamics of BCR-ABL signaling complex holds a key to the mechanism of BCR-ABL signaling. Here, we demonstrate that TKIs inhibit catalytic activity of BCR-ABL, but do not dissolve the BCR-ABL core signaling complex consisting of CrkL, SHC1, Grb2, SOS1, cCbl, and SHIP2. We show that CrkL binds to proline-rich regions located in C-terminal, intrinsically disordered region of BCR-ABL, that deletion of pleckstrin homology domain of BCR-ABL diminishes interaction with SHC1, and that BCR-ABL sequence motif located in disordered region around phosphorylated tyrosine 177 mediates binding of at least three core complex members, the Grb2, SOS1 and cCbl. Introduction of Y177F substitution blocks association with Grb2, SOS1 and cCbl. Further, we identified SHIP2 binding sites within the src-homology and tyrosine kinase domains of BCR-ABL. We found that BCR-ABL is unable to phosphorylate SHC1 in cells lacking SHIP2. Reintroducing SHIP2 into Ship2 knock-out cells restored SHC1 phosphorylation, which depended on inositol phosphatase activity of SHIP2. Our findings provide characterization of protein-protein interactions in the BCR-ABL signaling complex, and support the concept of targeting BCR-ABL signaling in CML by inhibition of its interactions with the members of the core complex.
Estrogen controls mTOR signaling and mitochondrial function via WNT4 in lobular carcinoma cells
Authors: Shackleford Madeleine T. , Rao Deviyani M. , Bordeaux Evelyn K. , Hicks Hannah M. , Oesterreich Steffi , Sikora Matthew J.
Published: June 2019

Invasive lobular carcinoma of the breast (ILC) is strongly estrogen-driven and represents a unique context for estrogen receptor (ER) signaling. In ILC, ER controls the expression of the Wnt ligand WNT4, which is critical for endocrine response and anti-estrogen resistance. However, signaling mediated by WNT4 is poorly understood. We utilized reverse phase protein array (RPPA) to characterize ER and WNT4-driven signaling in ILC cells and identified that WNT4 mediates downstream mTOR signaling via S6K. Additionally, independent of mTOR/S6K, ER and WNT4 control levels of MCL-1, which alters mitochondrial function. In this context, WNT4 knockdown caused decreased ATP production and increased mitochondrial fragmentation. WNT4 regulation of both mTOR signaling and MCL-1 were also observed in antiestrogen resistant models of ILC. Further, we identified that highWNT4expression is associated with similar mTOR pathway activation in serous ovarian cancer tumors, suggesting that WNT4 signaling is important in multiple tumor types. The identified downstream pathways offer insight in to WNT4 signaling and represent potential targets to overcome anti-estrogen resistance for patients with ILC.
Altered frequency of CD24highCD38high transitional B cells in patients with cardiac involvement of chronic Chagas disease
Authors: Girard Magalí C. , Acevedo Gonzalo R. , Ossowski Micaela S. , Alcaráz Paula B. , Fernández Marisa , Hernández Yolanda , Chadi Raul , Gómez Karina A.
Published: June 2019

The cardiomyopathy developed by patients with chronic Chagas disease (CCD), one of the most severe consequences of T. cruzi infection, is mainly associated with an imbalance between an excessive inflammatory reaction and a defective immunomodulatory profile cause by host-parasite interaction. Despite the growing importance of the regulatory function of B-cells in many malignancies, few studies have addressed their immunosuppressive role in chronic Chagas disease. In this work, we tackled this issue by studying the proportion of different B cell subpopulations and their capacity to secrete IL-10 in individuals with distinct clinical forms of CCD. Seven-colour flow cytometry was performed to examine the peripheral blood B cell compartment in chronic Chagas disease (CCD) patients with and without cardiac manifestations (n=10 for each group) and non-infected donors (n=9). Peripheral blood mononuclear cells (PBMC) were incubated for 5h with PMA, ionomicyn and brefeldin A. According to the expression of markers CD19, CD24 and CD38, we showed an expansion of total B cell and transitional CD24highCD38high B cell subsets in CCD patients with cardiac involvement compared to non-infected donors. Furthermore, although no differences were observed in the frequency of total IL-10 producing B cells (B10) among the groups, CCD patients with cardiac involvement showed a statistically significant increased proportion of naïve B10 cells and a tendency to an increased frequency of transitional B10 cells compared to non-infected donors. These findings suggest that immature transitional CD24highCD38high B cells are greatly expanded in patients with the cardiac form of chronic Chagas disease and these cells retain their ability to secrete IL-10 compared to non-infected donors. Furthermore, the distribution of naïve, transitional and memory B cells inside the B10 cells followed the same pattern in chronic patients without cardiac involvement and non-infected individuals. Our work provides insight into the phenotypic distribution of regulatory B cell in CCD, an important step towards new strategies to prevent cardiomiopathy associated with T. cruzi infection.
Prenatal alcohol exposure programs offspring disease: Insulin resistance in adult males in a rat model of acute exposure
Authors: Nguyen Tam M T , Steane Sarah E , Moritz Karen M , Akison Lisa K
Published: June 2019

Alcohol consumption is highly prevalent amongst women of reproductive age. Given that approximately 50% of pregnancies are unplanned, alcohol has the potential to affect fetal development and program chronic disease in offspring. We examined the effect of an acute but moderate prenatal alcohol exposure (PAE) on glucose metabolism, lipid levels and dietary preference in adolescent and/or adult rat offspring. Pregnant Sprague-Dawley rats received an oral gavage of ethanol (1g/kg maternal body weight, n=9 dams) or an equivalent volume of saline (control, n=8 dams) at embryonic days 13.5 and 14.5. PAE resulted in a blood alcohol concentration of 0.05-0.06% 1h post-gavage in dams. Fasting blood glucose concentration was not affected by PAE in offspring at any age, nor were blood glucose levels during a glucose tolerance test (GTT) in 6-month old offspring (P>0.5). However, there was evidence of insulin resistance in PAE male offspring at 6 months of age, with significantly elevated fasting plasma insulin (P= 0.001), a tendency for increased first phase insulin secretion during the GTT and impaired glucose clearance following an insulin challenge (P= 0.007). This was accompanied by modest alterations in protein kinase B (AKT) signalling in adipose tissue. PAE also resulted in reduced calorie consumption by offspring compared to controls (P= 0.04). These data suggest that a relatively low-level, acute PAE programs metabolic dysfunction in offspring in a sex-specific manner. These results highlight that alcohol consumption during pregnancy has the potential to affect the long-term health of offspring.

Key points summary

Prenatal alcohol exposure has the potential to affect fetal development and program chronic disease in offspring.

Previous preclinical models typically use high, chronic doses of alcohol throughout pregnancy to examine effects on offspring, particularly on the brain and behaviour.

In this study we use a rat model of moderate, acute, prenatal alcohol exposure to determine if this can be detrimental to maintenance of glucose homeostasis in adolescent and adult offspring.

Although female offspring were relatively unaffected, there was evidence of insulin resistance in 6-month old male offspring exposed to prenatal alcohol, suggestive of a pre-diabetic state.

This result suggests that even a relatively low-dose, acute exposure to alcohol during pregnancy can still program metabolic dysfunction in a sex-specific manner.
Ran GTPase regulates non-centrosomal microtubule nucleation and is transported by actin waves towards the neurite tip
Authors: Huang Yung-An , Hsu Chih-Hsuan , Chiu Ho-Chieh , Ho Chris T. , Lo Wei-Lun , Hwang Eric
Published: June 2019

Microtubule (MT) is the most abundant cytoskeleton in neurons and controls multiple facets of their development. While the organizing center of MTs in mitotic cells is typically located at the centrosome, MT nucleation in post-mitotic neurons switches to non-centrosomal sites. A handful of proteins and organelle have been shown to promote non-centrosomal MT formation in neurons, yet the regulation mechanism remains unknown. Here we demonstrate that the small GTPase Ran is a key regulator of non-centrosomal MT nucleation in neurons. The GTP-bound Ran (RanGTP) localizes to the neurite tips and around the soma. Using the RanGTP- and RanGDP-mimic mutants, we show that RanGTP promotes MT nucleation at the tip of the neurite. To demonstrate that RanGTP can promote MT nucleation in regions other than the neurite tip, an optogenetic tool called RanTRAP was constructed to enable light-induced local production of RanGTP in the neuronal cytoplasm. An increase of non-centrosomal MT nucleation can be observed by elevating the RanGTP level along the neurite using RanTRAP, establishing a new role for Ran in regulating neuronal MTs. Additionally, the mechanism of RanGTP enrichment at the neurite tip was examined. We discovered that actin waves drive the anterograde transport of RanGTP towards the neurite tip. Pharmacological disruption of actin waves abolishes the enrichment of RanGTP and reduces the non-centrosomal MT nucleation at the neurite tip. These observations provide a novel regulation mechanism of MTs and an indirect connection between the actin and MT cytoskeletons in neurons.
Synergic Interaction between Permethrin and Bt toxins discovered using RNA-seq
Authors: Sakamoto Takuma , Kozaki Toshinori , Ogata Norichika
Published: June 2019

Acting against the development of resistance to antibiotics and insecticides, involving negatively correlated cross-resistance (NCR) is an alternative to use- and-discard approach. It is termed NCR that toxic chemicals interact with each other and resistance of target organisms to one chemical is sometimes associated with increased susceptibility to a second chemical when; an allele confers resistance to one toxic chemical and hyper-susceptibility to another, NCR occurs. However, only 11 toxin pairs have been revealed to cause NCR in insects. Finding novel NCRs is needed for integrated pest management. We analyzed permethrin, an insecticide, induced transcriptomes of cultured fat bodies of the silkworm Bombyx mori, a lepidopteran model insect. Differentially expressed gene analyses suggested Bacillus thuringiensis (Bt) toxin was an NCR toxin of permethrin. NCR to permethrin and Bt toxins in Thysanoplusia intermixta, the agricultural pest moth, was examined; the children of permethrin survivor T. intermixta had increased susceptibility to Bt toxin. A novel NCR toxin pair, permethrin and Bt toxin, was discovered. The screening and developmental method for negatively correlated cross-resistance toxins established in this study was effective, in vitro screening using model organisms and in vivo verification using agricultural pests.
Inhibition of IRF4 in dendritic cells by PRR-independent and -dependent signals inhibit Th2 and promote Th17 responses
Authors: Lee Jihyung , Zhang Junyan , Chung Young-Jun , Kim Jun Hwan , Kook Chae Min , González-Navajas José M. , Herdman David S. , Nürnberg Bernd , Insel Paul A. , Corr Maripat , Tao Ailin , Yasuda Kei , Rifkin Ian R. , Broide David , Sciammas Roger , Webster Nicholas J.G. , Raz Eyal
Published: June 2019

Cyclic AMP (cAMP) is involved in multiple biological processes. However, little is known about its role in shaping immunity. Here we show that cAMP-PKA-CREB signaling (a pattern recognition receptor [PRR]-independent) regulates conventional type-2 Dendritic Cells (cDC2s), but not cDC1s and reprograms their Th17-inducing properties via repression of IRF4 and KLF4, transcription factors (TFs) for Th2 induction. Genetic loss of IRF4 phenocopies the effects of cAMP signaling on Th17-induction, indicating that the cAMP effect is secondary to repression of IRF4. Moreover, signaling in cDC2s by a PRR-dependent microbial product, curdlan, represses IRF4 and KLF4, resulting in a pro-Th17 phenotype. These results define a novel signaling pathway by which cDC2s display plasticity and provide a new molecular basis for the novel cDC2 and cDC17 classification. In addition, the data reveal that cAMP signaling can alter DCs function and fate by repressing IRF4 and KLF4, a pathway that can be harnessed for immuno-regulation.
Computational design of anti-CRISPR proteins with improved inhibition potency and expanded specificity
Authors: Mathony Jan , Harteveld Zander , Schmelas Carolin , Upmeier zu Belzen Julius , Aschenbrenner Sabine , Hoffmann Mareike D. , Stengl Christina , Scheck Andreas , Rosset Stéphane , Grimm Dirk , Eils Roland , Correia Bruno E. , Niopek Dominik
Published: June 2019

Anti-CRISPR (Acr) proteins are bacteriophage-derived antagonists of CRISPR-Cas systems. To date, Acrs were obtained either by mining sequence databanks or experimentally screening phage collections, both of which yield a limited repertoire of naturally occurring variants. Here, we applied structure-based engineering on AcrIIC1, a broad-spectrum inhibitor of type II-C CRISPR systems, to improve its efficacy and expand its specificity. We first show that fusing exogenous protein domains into AcrIIC1 dramatically enhances inhibition of the natural Neisseria meningitidis Cas9 target. Then, using structure-guided design, we converted AcrIIC1 into AcrX, a potent inhibitor of the type II-A CRISPR-Cas9 from Staphylococcus aureus widely applied for in vivo genome editing. Our work introduces designer Acrs as important biotechnological tools and provides an innovative strategy to safeguard the CRISPR technology.
Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development
Authors: Kanton Sabina , Boyle Michael James , He Zhisong , Santel Malgorzata , Weigert Anne , Calleja Fatima Sanchis , Sidow Leila , Fleck Jonas , Guijarro Patricia , Han Dingding , Qian Zhengzong , Heide Michael , Huttner Wieland , Khaitovich Philipp , Pääbo Svante , Treutlein Barbara , Camp J. Gray
Published: June 2019

The human brain has changed dramatically since humans diverged from our closest living relatives, chimpanzees and the other great apes1–5. However, the genetic and developmental programs underlying this divergence are not fully understood6–8. Here, we have analyzed stem cell-derived cerebral organoids using single-cell transcriptomics (scRNA-seq) and accessible chromatin profiling (scATAC-seq) to explore gene regulatory changes that are specific to humans. We first analyze cell composition and reconstruct differentiation trajectories over the entire course of human cerebral organoid development from pluripotency, through neuroectoderm and neuroepithelial stages, followed by divergence into neuronal fates within the dorsal and ventral forebrain, midbrain and hindbrain regions. We find that brain region composition varies in organoids from different iPSC lines, yet regional gene expression patterns are largely reproducible across individuals. We then analyze chimpanzee and macaque cerebral organoids and find that human neuronal development proceeds at a delayed pace relative to the other two primates. Through pseudotemporal alignment of differentiation paths, we identify human-specific gene expression resolved to distinct cell states along progenitor to neuron lineages in the cortex. We find that chromatin accessibility is dynamic during cortex development, and identify instances of accessibility divergence between human and chimpanzee that correlate with human-specific gene expression and genetic change. Finally, we map human-specific expression in adult prefrontal cortex using single-nucleus RNA-seq and find developmental differences that persist into adulthood, as well as cell state-specific changes that occur exclusively in the adult brain. Our data provide a temporal cell atlas of great ape forebrain development, and illuminate dynamic gene regulatory features that are unique to humans.