bluuebunny/crossref_metadata_2025 huggingface dataset:
Genetic Fine-mapping with Dense Linkage Disequilibrium Blocks: genetics of nicotine dependence
Authors: Mo Chen , Ye Zhenyao , Hatch Kathryn , Zhang Yuan , Wu Qiong , Liu Song , Kochunov Peter , Hong L. Elliot , Ma Tianzhou , Chen Shuo
Published: December 2020

Fine-mapping is an analytical step to perform causal prioritization of the polymorphic variants on a trait-associated genomic region observed from genome-wide association studies (GWAS). The prioritization of causal variants can be challenging due to the linkage disequilibrium (LD) patterns among hundreds to thousands of polymorphisms associated with a trait. We propose a novelℓ0graph norm shrinkage algorithm to select causal variants from dense LD blocks consisting of highly correlated SNPs that may not be proximal or contiguous. We extract dense LD blocks and perform regression shrinkage to calculate a prioritization score to select a parsimonious set of causal variants. Our approach is computationally efficient and allows performing fine-mapping on thousands of polymorphisms. We demonstrate its application using a large UK Biobank (UKBB) sample related to nicotine addiction. Our results suggest that polymorphic variances in both neighboring and distant variants can be consolidated into dense blocks of highly correlated loci. Simulations were used to evaluate and compare the performance of our method and existing fine-mapping algorithms. The results demonstrated that our method outperformed comparable fine-mapping methods with increased sensitivity and reduced false-positive error rate regarding causal variant selection. The application of this method to smoking severity trait in UKBB sample replicated previously reported loci and suggested the causal prioritization of genetic effects on nicotine dependency.

Author summary

Disentangling the complex linkage disequilibrium (LD) pattern and selecting the underlying causal variants have been a long-term challenge for genetic fine-mapping. We find that the LD pattern within GWAS loci is intrinsically organized in delicate graph topological structures, which can be effectively learned by our novelℓ0graph norm shrinkage algorithm. The extracted LD graph structure is critical for causal variant selection. Moreover, our method is less constrained by the width of GWAS loci and thus can fine-map a massive number of correlated SNPs.
Integrative genomics identifies lncRNA regulatory networks across 1,044 pediatric leukemias and extra-cranial solid tumors
Authors: Modi Apexa , Lopez Gonzalo , Conkrite Karina L. , Su Chun , Leung Tsz Ching , Ramanan Sathvik , Manduchi Elisabetta , Johnson Matthew E. , Cheung Daphne , Gadd Samantha , Zhang Jinghui , Smith Malcolm A. , Guidry Auvil Jaime M. , Gerhard Daniela S. , Meshinchi Soheil , Perlman Elizabeth J. , Hunger Stephen P. , Maris John M. , Wells Andrew D. , Grant Struan F.A. , Diskin Sharon J.
Published: December 2020

Long non-coding RNAs (lncRNAs) play an important role in gene regulation and contribute to tumorigenesis. While pan-cancer studies of lncRNA expression have been performed for adult malignancies, the lncRNA landscape across pediatric cancers remains largely uncharted. Here, we curate RNA sequencing data for 1,044 pediatric leukemia and solid tumors and integrate paired tumor whole genome sequencing and epigenetic data in relevant cell line models to explore lncRNA expression, regulation, and association with cancer. We report a total of 2,657 robustly expressed lncRNAs across six pediatric cancers, including 1,142 exhibiting histotype-specific expression. DNA copy number alterations contributed to lncRNA dysregulation at a proportion comparable to protein coding genes. Application of a multi-dimensional framework to identify and prioritize lncRNAs impacting gene networks revealed that lncRNAs dysregulated in pediatric cancer are associated with proliferation, metabolism, and DNA damage hallmarks. Analysis of upstream regulation via cell-type specific transcription factors further implicated distinct histotype-specific and developmental lncRNAs. We integrated our analyses to prioritize lncRNAs for experimental validation and showed that silencing ofTBX2-AS1, our top-prioritized neuroblastoma-specific lncRNA, resulted in significant growth inhibition of neuroblastoma cells, confirming our computational predictions. Taken together, these data provide a comprehensive characterization of lncRNA regulation and function in pediatric cancers and pave the way for future mechanistic studies.
Bacterial adaptation by a transposition burst of an invading IS element
Authors: Miller Scott R. , Abresch Heidi E. , Ulrich Nikea J. , Sano Emiko B. , Demaree Andrew H. , Garber Arkadiy I.
Published: December 2020

The impact of transposable elements on host fitness range from highly deleterious to beneficial, but their general importance for adaptive evolution remains debated. Here, we investigated whether IS elements are a major source of beneficial mutations during 400 generations of laboratory evolution of the cyanobacteriumAcaryochloris marinastrain CCMEE 5410, which has experienced a recent or on-going IS element expansion. The dynamics of adaptive evolution were highly repeatable among eight independent experimental populations and included beneficial mutations related to exopolysaccharide production and inorganic carbon concentrating mechanisms for photosynthetic carbon fixation. Most detected mutations were IS transposition events, but, surprisingly, the majority of these involved the copy-and-paste activity of only a single copy of an unclassified element (ISAm1) that has recently invaded the genome ofA. marinastrain CCMEE 5410. Our study reveals that the activity of a single transposase can fuel adaptation for at least several hundred generations.

Impact statement

A single transposable element can fuel adaptation to a novel environment for hundreds of generations without an apparent accumulation of a deleterious mutational load.
ORMDL1 is upregulated and associated with favorable outcome in colorectal cancer
Authors: Wang Qian , Liu Wanjun , Chen Si , Luo Qianxin , Li Yichen , Peng Shaoyong , Wang Huaiming , Liu Xiaoxia , Chen Daici
Published: December 2020

Background

ORMDL1 gene encodes a transmembrane protein for endoplasmic reticulum and is known as crucial negative regulator for sphingolipid biogenesis. However, it has been rarely studied in tumor-related context. Therefore, its prognostic value and functional significance in colorectal cancer (CRC) remain to be explored.

Methods

TCGA CRC cohort analysis, qRT-PCR, and immunohistochemistry (IHC) were used to examine the ORMDL1 expression level. The association between ORMDL1 expression and various clinical characteristics were analyzed by Chi-square tests. CRC patients’ overall survival (OS) was analyzed by Kaplan-Meier analysis.In vitroandin vivocell-based assays were performed to explore the role of ORMDL1 in cell proliferation, invasion and migration. Transcriptional changes of cells either with ORMDL1 knockdowned or overexpressed were compared and analyzed.

Results

ORMDL1 was upregulated in CRC tissues either in TCGA cohort or in our cohort. Interestingly, its expression was significantly lower in patients with metastasis compared to patients without metastasis, and high expression group had longer OS than low expression group. Knockdown of ORMDL1 expression can promote proliferation, colony formation and invasion, while attenuate migration in CRC cell lines. In opposite, forced overexpression of ORMDL1 reduced cell proliferation, colony formation and invasion, while enhanced cell migration. Epithelial-to-mesenchymal transition (EMT) related genes were enriched among differentially expressed genes when ORMDL1 was knockdowned in cells, which was consistent with morphologic change by microscopy observation. Finally, stable knockdown of ORMDL1 can promote cancer cell proliferationin vivoto some extent.

Conclusion

ORMDL1 is upregulated and may serve as biomarker to predict favourable outcome in colorectal cancer.
Oblique transmission, conformity, and preference in the evolution of altruism
Authors: Denton Kaleda K. , Ram Yoav , Feldman Marcus W.
Published: December 2020

The evolution of altruism is frequently studied using models of non-random assortment, including kin selection. In genetic kin selection models, under certain assumptions including additive costs and benefits, the criterion for altruism to invade a population is Hamilton’s rule. Deviations from Hamilton’s rule occur when vertical transmission has cultural and genetic components, or when costs and benefits are combined multiplicatively. Here, we include oblique and vertical cultural transmission and genetic transmission in four models—two forms of parent-to-offspring altruism, sibling-to-sibling altruism, and altruism between offspring that meet assortatively—under additive or multiplicative assumptions. Oblique transmission may be conformist (anti-conformist), where the probability that an individual acquires a more common cultural variant is greater (less) than its frequency. Inclusion of conformist or anti-conformist oblique transmission may reduce or increase the threshold for invasion by altruism relative to Hamilton’s rule. Thresholds for invasion by altruism are lower with anti-conformity than with conformity, and lower or the same with additive rather than multiplicative fitness components. Invasion by an allele that increases the preference for altruism does not depend on oblique phenotypic transmission, and with sibling-to-sibling altruism, this allele’s invasion threshold can be higher with additive rather than multiplicative fitnesses.
First Glimpse of Gut Microbiota of Quarantine Insects in China
Authors: Yu Yanxue , Wang Qi , Zhou Ping , Lv Na , Li Wei , Zhao Fangqing , Zhu Shuifang , Liu Di
Published: December 2020

Quarantine insects are economically important pests that frequently invade new habitats. A rapid and accurate monitoring method to trace the geographical source of invaders is therefore needed for prevention, detection, and eradication. Current methods based on insect genetics are often too slow. We developed a novel tracing method based on insect gut microbiota. The source location of microbiota of insects can be used to rapidly determine the insects’ geographic origin. We analyzed 179 gut microbiota samples belonging to 591 individuals of 22 quarantine insect species collected from 36 regions in China and abroad. The gut microbiotas of these insects mainly included Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, Proteobacteria, and Tenericutes. The diversity of the insect gut microbiota was closely related to geographic and environmental factors. Different insect species could be distinguished at the phylum level of microbiota. Populations of individual insect species from different regions could be distinguished at the genus level of microbiota. A method for determining the geographical origin of invasive insect species was tentatively established, but its practical applicability requires further study.
TiMEG: an integrative approach for partially missing multi-omics data with an application to tuberous sclerosis
Authors: Das Sarmistha , Mukhopadhyay Indranil
Published: December 2020

1

Multi-omics data integration is widely used to understand the genetic architecture of disease. In multi-omics association analysis, data collected on multiple omics for the same set of individuals are immensely important for biomarker identification. But when the sample size of such data is limited, the presence of partially missing individual-level observations poses a major challenge in data integration. More often, genotype data are available for all individuals under study but gene expression and/or methylation information are missing for different subsets of those individuals. Here, we develop a statistical model TiMEG, for the identification of disease-associated biomarkers in a case-control paradigm by integrating the above-mentioned data types, especially, in presence of missing omics data. Based on a likelihood approach, TiMEG exploits the inter-relationship among multiple omics data to capture weaker signals, that remain unidentified in single-omics analyses. Its application on a real tuberous sclerosis dataset identified functionally relevant genes in the disease pathway.
Evaluation of seasonal dynamics of fungal DNA assemblages in a flow-regulated stream in a restored forest using eDNA metabarcoding
Authors: Matsuoka Shunsuke , Sugiyama Yoriko , Shimono Yoshito , Ushio Masayuki , Doi Hideyuki
Published: December 2020

Investigation of seasonal variation in fungal communities is essential for understanding biodiversity and ecosystem functions. However, the conventional sampling method, with substrate removal and high spatial heterogeneity of community composition, makes surveying the seasonality of fungal communities challenging. Recently, water environmental DNA (eDNA) analysis has been explored for its utility in biodiversity surveys. In this study, we assessed whether the seasonality of fungal communities can be detected by monitoring eDNA in a forest stream. We conducted monthly water sampling in a forest stream over two years and used DNA metabarcoding to identify fungal eDNA. The stream water contained DNA from functionally diverse aquatic and terrestrial fungi, such as plant decomposers, parasites, and mutualists. The variation in the fungal assemblage showed a regular annual periodicity, meaning that the assemblages in a given season were similar, irrespective of the year or sampling. Furthermore, the strength of the annual periodicity varied among functional groups. Our results suggest that forest streams may act as a “trap” for terrestrial fungal DNA derived from different habitats, allowing the analysis of fungal DNA in stream water to provide information about the temporal variation in fungal communities in both the aquatic and the surrounding terrestrial ecosystems.
Similarities and differences between IL11 and IL11RA1 knockout mice for lung fibro-inflammation, fertility and craniosynostosis
Authors: Ng Benjamin , Widjaja Anissa A. , Viswanathan Sivakumar , Dong Jinrui , Chothani Sonia P. , Lim Stella , Shekeran Shamini G. , Tan Jessie , Schafer Sebastian , Cook Stuart A.
Published: December 2020

Genetic loss of function (LOF) in IL11RA infers IL11 signaling as important for fertility, fibrosis, inflammation and craniosynostosis. The impact of genetic LOF in IL11 has not been characterized. We generated IL11-knockout (Il11-/-) mice, which are born in normal Mendelian ratios, have normal hematological profiles and are protected from bleomycin-induced lung fibro-inflammation. Noticeably, baseline IL6 levels in the lungs of Il11-/- mice are lower than those of wild-type mice and are not induced by bleomycin damage, placing IL11 upstream of IL6. Lung fibroblasts from Il11-/- mice are resistant to pro-fibrotic stimulation and show evidence of reduced autocrine IL11 activity. Il11-/- female mice are infertile. Unlike Il11ra1-/- mice, Il11-/- mice do not have a craniosynostosis-like phenotype and exhibit mildly reduced body weights. These data highlight similarities and differences between LOF in IL11 or IL11RA while establishing further the role of IL11 signaling in fibrosis and stromal inflammation.
Cell type-specific biogenesis of novel vesicles containing viral products in human cytomegalovirus infection
Authors: Momtaz Samina , Molina Belen , Mlera Luwanika , Goodrum Felicia , Wilson Jean M.
Published: December 2020

Human cytomegalovirus (HCMV), while highly restricted for the human species, infects an unlimited array of cell types in the host. Patterns of infection are dictated by the cell type infected, but cell type-specific factors and how they impact tropism for specific cell types is poorly understood. Previous studies in primary endothelial cells showed that HCMV infection induces large multivesicular-like bodies that incorporate viral products including dense bodies and virions. Here we define the nature of these large vesicles using a recombinant virus where UL32, encoding the pp150 tegument protein, is fused in frame with green fluorescent protein (GFP, TB40/E-UL32-GFP). Cells were fixed and labeled with antibodies against subcellular compartment markers and imaged using confocal and super-resolution microscopy. In fibroblasts, UL32-GFP-positive vesicles were marked with classical markers of MVBs, including CD63 and lysobisphosphatidic acid (LBPA), both classical MVB markers, as well as the clathrin and LAMP1. Unexpectedly, UL32-GFP-positive vesicles in endothelial cells were not labeled by CD63, and LBPA was completely lost from infected cells. We defined these UL32-positive vesicles in endothelial cells using markers for the cis-Golgi (GM130), lysosome (LAMP1), and autophagy (LC3B). These findings suggest that virus-containing MVBs in fibroblasts are derived from the canonical endocytic pathway and takeover classical exosomal release pathway. Virus containing MVBs in HMVECs are derived from the early biosynthetic pathway and exploit a less characterized early Golgi-LAMP1-associated non-canonical secretory autophagy pathway. These results reveal striking cell-type specific membrane trafficking differences in host pathways that are exploited by HCMV.

Importance

Human cytomegalovirus (HCMV) is a herpesvirus that, like all herpesvirus, that establishes a life long infection. HCMV remains a significant cause of morbidity and mortality in the immunocompromised and HCMV seropositivity is associated with increased risk vascular disease. HCMV infects many cells in the human and the biology underlying the different patterns of infection in different cell types is poorly understood. Endothelial cells are important target of infection that contribute to hematogenous spread of the virus to tissues. Here we define striking differences in the biogenesis of large vesicles that incorporate virions in fibroblasts and endothelial cells. In fibroblasts, HCMV is incorporated into canonical MVBs derived from an endocytic pathway, whereas HCMV matures through vesicles derived from the biosynthetic pathway in endothelial cells. This work defines basic biological differences between these cell types that may impact the outcome of infection.
HRWR: Predicting Potential Efficacious Drug Combination Based on Hypergraph Random Walk with Restart
Authors: Wang Qi , Yan Guiying
Published: December 2020

Some studies have shown that efficacious drug combination can increase the therapeutic effect, and decrease drug toxicity and side-effects. Thus, drug combinations have been widely used in the treatment of complex diseases, especially cancer. However, experiment-based methods are extremely costly in time and money. Computational models can greatly reduce the cost, but most of the models do not use the data of more than two drugs and lose a lot of useful information. Here, we used high-order drug combination information and developed a hypergraph random walk with restart model (HRWR) for efficacious drug combination prediction.

As a result, compared with the other methods by leave-one-out cross-validation (LOOCV), the Area Under Receiver Operating Characteristic Curve (AUROC) of the HRWR algorithm were higher than others. Moreover, the case studies of lung cancer, breast cancer, and colorectal cancer showed that HRWR had a powerful ability to predict potential efficacious combinations, which provides new prospects for cancer treatment. The code and dataset of HRWR are freely available athttps://github.com/wangqi27/HRWR.
SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses
Authors: Eagles Nicholas J. , Burke Emily E. , Leonard Jacob , Barry Brianna K. , Stolz Joshua M. , Huuki Louise , Phan BaDoi N. , Serrato Violeta Larios , Gutiérrez-Millán Everardo , Aguilar-Ordoñez Israel , Jaffe Andrew E. , Collado-Torres Leonardo
Published: December 2020

RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps a researcher must perform before raw RNA-seq reads yield directly valuable information, such as differential gene expression data. Existing software tools are typically specialized, only performing one step-- such as alignment of reads to a reference genome-- of a larger workflow. The demand for a more comprehensive and reproducible workflow has led to the production of a number of publicly available RNA-seq pipelines. However, we have found that most require computational expertise to set up or share among several users, are not actively maintained, or lack features we have found to be important in our own analyses. In response to these concerns, we have developed a Scalable Pipeline for Expression Analysis and Quantification (SPEAQeasy), which is easy to install and share, and provides a bridge towards R/Bioconductor downstream analysis solutions. SPEAQeasy is user-friendly and lowers the computational-domain entry barrier for biologists and clinicians to RNA-seq data processing as the main input file is a table with sample names and their corresponding FASTQ files. SPEAQeasy is portable across computational frameworks (SGE, SLURM, local, docker integration) and different configuration files are provided.
The effect of acidic pH on the interaction and lytic activity of MP1 and its H-MP1 analog in anionic lipid membrane: a biophysical study by Molecular Dynamics and Spectroscopy
Authors: Martins Ingrid Bernardes Santana , Viegas Taisa Giordano , de Souza Bibiana Monson , Palma Mário Sérgio , Neto João Ruggiero , de Araujo Alexandre Suman
Published: December 2020

Antimicrobial peptides (AMPs) are part of the innate immune system of many species and are compounds with potential application against the development of resistant bacterial strains promoted by conventional antibiotics. The AMPs are rich in cationic and hydrophobic residues and act directly on the lipidic phase of the cell membranes. The MP1 has a broad-spectrum bactericide activity in both Gram-negative and positive bacteria, not being hemolytic or cytotoxic. H-MP1 is a synthetic analog of MP1 with lysines replaced by histidines so that its net charge could be responsive to changes in solution pH. In the present work, we investigated the effect of the solution pH on the structural properties, in the adsorption and insertion, and on the lytic activity of these peptides in lipid bilayers mimicking the cell membrane of Gram-negative bacteria, using experimental and computational biophysical techniques. The results indicate that the lytic activity of H-MP1 is sensitive to pH, increasing to an acidic environment, matching that of MP1, which is not influenced by solution pH. Molecular Dynamic simulations indicated that the adsorption process of both peptides started by the interaction of the N-terminus with the bilayer, followed by the complete adsorption of the peptide laying parallel to the bilayer plane, inducing an increase in the peptide’s helical content enhancing peptides contact with the bilayer hydrophobic phase.
Genetic variation in aneuploidy prevalence and tolerance across theSaccharomyces cerevisiaephylogeny
Authors: Scopel Eduardo F.C. , Hose James , Bensasson Douda , Gasch Audrey P.
Published: December 2020

Individuals carrying an aberrant number of chromosomes can vary widely in their expression of aneuploidy phenotypes. A major unanswered question is the degree to which an individual’s genetic makeup influences its tolerance of karyotypic imbalance. Here we took a population genetics perspective to investigate the selective forces influencing aneuploidy prevalence inSaccharomyces cerevisiaepopulations as a model for eukaryotic biology. We analyzed genotypic and phenotypic variation recently published for over 1,000S. cerevisiaestrains spanning dozens of genetically defined clades and ecological associations. Our results show that the prevalence of chromosome gain and loss varies by clade and can be better explained by differences in genetic background than ecology. The phylogenetic context of lineages showing high aneuploidy rates suggests that increased aneuploidy frequency arose multiple times inS. cerevisiaeevolution. Separate from aneuploidy frequency, analyzing growth phenotypes reveals that some backgrounds – such as European Wine strains – show fitness costs upon chromosome duplication, whereas other clades with high aneuploidy rates show little evidence of major deleterious effects. Our analysis confirms that chromosome amplification can produce phenotypic benefits that can influence evolutionary trajectories. These results have important implications for understanding genetic variation in aneuploidy prevalence in health, disease, and evolution.

ARTICLE SUMMARY

Aneuploidy, an imbalance in the normal chromosome copy number, is detrimental during human development; yet individuals show substantial variability in their aneuploidy susceptibility, suggesting the influence of genetic background on aneuploidy tolerance. Scopelet al.employed a population genetic approach to address this question, analyzing over 1,000 publishedSaccharomyces cerevisiaegenomes. The results demonstrate that genetic background has a substantial effect on aneuploidy frequency and cellular tolerance of aneuploidy stress, presenting important new information on the forces that contribute to aneuploidy prevalence.
Chronic deep brain stimulation of the human nucleus accumbens region disrupts the stability of inter-temporal preferences
Authors: Wagner Ben J. , Schüller Canan B. , Schüller Thomas , Baldermann Juan C. , Kohl Sina , Visser-Vandewalle Veerle , Huys Daniel , Marx Milena , Kuhn Jens , Peters Jan
Published: December 2020

When choosing between rewards that differ in temporal proximity (inter-temporal choice), human preferences are typically stable, constituting a clinically-relevant transdiagnostic trait. Here we show in patients undergoing deep brain stimulation (DBS) of the anterior limb of the internal capsule / nucleus accumbens region for treatment-resistant obsessivecompulsive disorder (OCD), that long-term chronic (but not phasic) DBS disrupts inter-temporal preferences. Hierarchical Bayesian modeling accounting for temporal discounting behavior across multiple time points allowed us to assess both short-term and long-term reliability of inter-temporal choice. In controls, temporal discounting was highly reliable, both long-term (6 months) and short-term (1 week). In contrast, in patients undergoing DBS, short-term reliability was high, but long-term reliability (6 months) was severely disrupted. Control analyses confirmed that this effect was not due to range restriction, the presence of OCD symptoms or group differences in choice stochasticity. Model-agnostic between- and within-subject analyses confirmed this effect. These findings provide initial evidence for long-term modulation of cognitive function via DBS and highlight a potential contribution of the human nucleus accumbens region to inter-temporal preference stability over time.

Significance Statement

Choosing between rewards that differ in temporal proximity is in part a stable trait with relevance for many mental disorders, and depends on prefrontal regions and regions of the dopamine system. Here we show that chronic deep brain stimulation (DBS) of the human anterior limb of the internal capsule / nucleus accumbens region for treatment-resistant obsessive compulsive disorder disrupts the stability of inter-temporal preferences. These findings show that chronic stimulation of one of the brain’s central motivational hubs can disrupt preferences thought to depend on this circuit.
Functional crosstalk between phosphorylation and disease-causing mutations in the cardiac sodium channel Nav1.5
Authors: Galleano Iacopo , Harms Hendrik , Choudhury Koushik , Khoo Keith , Delemotte Lucie , Pless Stephan Alexander
Published: December 2020

The voltage-gated sodium channel Nav1.5 initiates the cardiac action potential. Alterations of its activation and inactivation properties due to mutations can cause severe, life-threatening arrhythmias. Yet despite intensive research efforts, many functional aspects of this cardiac channel remain poorly understood. For instance, Nav1.5 undergoes extensive post-translational modificationin vivo, but the functional significance of these modifications is largely unexplored, especially under pathological conditions. This is because most conventional approaches are unable to insert metabolically stable post-translational modification mimics, thus preventing a precise elucidation of the contribution by these modifications to channel function. Here, we overcome this limitation by using protein semi-synthesis of Nav1.5 in live cells and carry out complementary molecular dynamics simulations. We introduce metabolically stable phosphorylation mimics on both WT and two pathogenic long-QT mutant channel backgrounds and decipher functional and pharmacological effects with unique precision. We elucidate the mechanism by which phosphorylation of Y1495 impairs steady-state inactivation in WT Nav1.5. Surprisingly, we find that while the Q1476R patient mutation does not affect inactivation on its own, it enhances the impairment of steady-state inactivation caused by phosphorylation of Y1495 through enhanced unbinding of the inactivation particle. We also show that both phosphorylation and patient mutations can impact Nav1.5 sensitivity towards the clinically used anti-arrhythmic drugs quinidine and ranolazine, but not flecainide. The data highlight that functional effects of Nav1.5 phosphorylation can be dramatically amplified by patient mutations. Our work is thus likely to have implications for the interpretation of mutational phenotypes and the design of future drug regimens.

Significance statement

The cardiac sodium channel (Nav1.5) is crucial for generating a regular heartbeat. It is thus not surprising that mutations in its sequence have been linked to life-threatening arrhythmias. Interestingly, Nav1.5 activity can also be altered by posttranslational modifications, such as tyrosine phosphorylation. Our combination of protein engineering and molecular modeling studies has revealed that the detrimental effect of a long QT3 patient mutation is only exposed when a proximal tyrosine is phosphorylated. This suggests a dynamic crosstalk between the genetic mutation and a neighboring phosphorylation, a phenomenon that could be important in other classes of proteins. Additionally, we show that phosphorylation can affect the channel’s sensitivity towards clinically-relevant drugs, a finding that may prove important when devising patient-specific treatment plans.
Phagocytosis by stroma confounds co-culture studies
Authors: Herbst Sophie A. , Stolarczyk Marta , Becirovic Tina , Liu Yi , Kolb Carolin , Herling Marco , Müller-Tidow Carsten , Dietrich Sascha
Published: December 2020

Signals provided by the microenvironment can modify and circumvent pathway activities that are therapeutically targeted by drugs. Bone marrow stromal cell co-culture models are frequently used to study the influence of the bone marrow niche on ex-vivo drug response. Here we show that mesenchymal stromal cells from selected donors and NKTert, a stromal cell line which is commonly used for co-culture studies with primary leukemia cells, extensively phagocytose apoptotic cells. This could lead to misinterpretation of the results, especially if the viability readout of the target cells in such co-culture models is based on the relative proportions of dead and alive cells. Future co-culture studies which aim to investigate the impact of bone marrow stromal cells on drug response should take into account that stromal cells have the capacity to phagocytose apoptotic cells.
Effects of early life adversity on maternal effort and glucocorticoids in wild olive baboons
Authors: Patterson Sam K. , Hinde Katie , Bond Angela B. , Trumble Benjamin C. , Strum Shirley C. , Silk Joan B.
Published: December 2020

Adverse experiences during early life exert important effects on development, health, reproduction, and social bonds, with consequences often persisting across generations. A mother’s early life experiences can impact her offspring’s development through a number of pathways, such as maternal care, physiological signaling through glucocorticoids, or even intergenerational effects like epigenetic inheritance. Early life adversity in female yellow baboons (Papio cynocephalus) predicts elevated glucocorticoids, reduced sociality, shortened lifespan, and higher offspring mortality. If baboon mothers with more early life adversity, experience poorer condition and struggle to provide for their offspring, this could contribute to the persisting transgenerational effects of adversity. Here, we examined the effects of mothers’ early life adversity on their maternal effort, physiology, and offspring survivability in a population of olive baboons,Papio anubis.Mothers who experienced more adversity in their own early development exerted greater maternal effort (i.e., spent more time nursing and carrying) and had higher glucocorticoid metabolites than mothers with less early life adversity. Offspring of mothers with more early life adversity had reduced survivability compared to offspring of mothers with less early life adversity. There was no evidence that high maternal social rank buffered against the effects of early life adversity. Our data suggest early life experiences can have lasting consequences on maternal effort and physiology, which may function as proximate mechanisms for intergenerational effects of maternal experience.
TCRMatch: Predicting T-cell receptor specificity based on sequence similarity to previously characterized receptors
Authors: Chronister William D. , Crinklaw Austin , Mahajan Swapnil , Vita Randi , Kosaloglu-Yalcin Zeynep , Yan Zhen , Greenbaum Jason A. , Jessen Leon E. , Nielsen Morten , Christley Scott , Cowell Lindsay G. , Sette Alessandro , Peters Bjoern
Published: December 2020

The adaptive immune system in vertebrates has evolved to recognize non-self-antigens, such as proteins expressed by infectious agents and mutated cancer cells. T cells play an important role in antigen recognition by expressing a diverse repertoire of antigen-specific receptors, which bind epitopes to mount targeted immune responses. Recent advances in high-throughput sequencing have enabled the routine generation of T-cell receptor (TCR) repertoire data. Identifying the specific epitopes targeted by different TCRs in these data would be valuable. To accomplish that, we took advantage of the ever-increasing number of TCRs with known epitope specificity curated in the Immune Epitope Database (IEDB) since 2004. We compared six metrics of sequence similarity to determine their power to predict if two TCRs have the same epitope specificity. We found that a comprehensivek-mer matching approach produced the best results, which we have implemented into TCRMatch, an openly accessible tool (http://tools.iedb.org/tcrmatch/) that takes TCR β-chain CDR3 sequences as an input, identifies TCRs with a match in the IEDB, and reports the specificity of each match. We anticipate that this tool will provide new insights into T cell responses captured in receptor repertoire and single cell sequencing experiments and will facilitate the development of new strategies for monitoring and treatment of infectious, allergic, and autoimmune diseases, as well as cancer.
Single-cell RNA sequencing reveals distinct tumor microenvironmental patterns in lung adenocarcinoma
Authors: Bischoff Philip , Trinks Alexandra , Obermayer Benedikt , Pett Jan Patrick , Lehmann Annika , Jurmeister Philipp , Elsner Aron , Dziodzio Tomasz , Rückert Jens-Carsten , Neudecker Jens , Falk Christine , Beule Dieter , Sers Christine , Morkel Markus , Horst David , Blüthgen Nils , Klauschen Frederick
Published: December 2020

Recent developments in immuno-oncology demonstrate that not only cancer cells, but also features of the tumor microenvironment guide precision medicine. Still, the relationship between tumor and microenvironment remains poorly understood. To overcome this limitation and identify clinically relevant microenvironmental and cancer features, we applied single-cell RNA sequencing to lung adenocarcinomas. While the highly heterogeneous carcinoma cell transcriptomes reflected histological grade and activity of relevant oncogenic pathways, our analysis revealed two distinct microenvironmental patterns. We identified a prognostically unfavorable group of tumors with a microenvironment composed of cancer-associated myofibroblasts, exhausted CD8+ T cells, proinflammatory monocyte-derived macrophages and plasmacytoid dendritic cells (CEP2pattern) and a prognostically favorable group characterized by myeloid dendritic cells, anti-inflammatory monocyte-derived macrophages, normal-like myofibroblasts, NK cells and conventional T cells (MAN2C pattern). Our results show that single-cell gene expression profiling allows to identify patient subgroups based on the tumor microenvironment beyond cancer cell-centric profiling.
Highly multiplexed imaging of biosensors in live cells
Authors: Yang Jr-Ming , Chi Wei-Yu , Liang Jessica , Iglesias Pablo , Huang Chuan-Hsiang
Published: December 2020

Fluorescent biosensors allow for real-time monitoring of biochemical activities in cells, but their multiplexing capacity is severely limited by the availability of spectral space. We overcome this problem by developing a set of barcoding proteins that are spectrally separable from commonly used FRET (fluorescence resonance energy transfer)-based and single-fluorophore biosensors. Mixed populations of barcoded cells expressing different biosensors can be concurrently imaged and computationally unmixed to achieve highly multiplexed tracking of biochemical activities in live cells.
Hippocampal cells multiplex positive and negative engrams
Authors: Shpokayte Monika , McKissick Olivia , Guan Xiaonan , Yuan Bingbing , Rahsepar Bahar , Fernandez Fernando R. , Ruesch Evan , Grella Stephanie L. , White John A. , Liu X. Shawn , Ramirez Steve
Published: December 2020

The hippocampus is involved in processing a variety of mnemonic computations specifically the spatiotemporal components and emotional dimensions of contextual memory.1–3Recent studies have demonstrated vast structural and functional heterogeneity along the dorsal-ventral axis1, 5of the hippocampus. The ventral hippocampus has been shown to be important in the processing of emotion and valence.6–9Here, we combine transgenic and all-virus based activity-dependent tagging strategies to visualize multiple valence-specific engrams in the vHPC and demonstrate two partially segregated cell populations and projections that respond to appetitive and aversive experiences. Next, using RNA sequencing and DNA methylation sequencing approaches, we find that vHPC appetitive and aversive engram cells display distinct transcriptional programs and DNA methylation landscapes compared to a neutral engram population. Additionally, while optogenetic manipulation of tagged cell bodies in vHPC is not sufficient to drive appetitive or aversive behavior in real-time place preference, stimulation of tagged vHPC terminals projecting to the amygdala and nucleus accumbens (NAc), but not the prefrontal cortex (PFC), had the capacity drive preference and avoidance. These terminals can also undergo a “switch” or “reset” in their capacity to drive either, thereby demonstrating their adaptable contributions to behavior. We conclude that the vHPC contains genetically, cellularly, and behaviorally distinct populations of cells processing appetitive and aversive memory engrams. Together, our findings provide a novel means by which to visualize multiple engrams within the same brain and point to their unique genetic signatures as reference maps for the future development of new therapeutic strategies.

One sentence summary

The hippocampus contains neurons that correspond to positive and negative engrams, which are segregated by their molecular, cellular, and projection-specific features.
Individual variation in tolerance of human activity by urban dark-eyed juncos (Junco hyemalis)
Authors: Stansell Hayley M. , Blumstein Daniel T. , Yeh Pamela J. , Nonacs Peter
Published: December 2020

An important goal of urban ecology is determining what differentiates urban-tolerant populations of birds from their non-urban ancestors and urban-intolerant species. One key to urban success may be reacting appropriately to human activity, and the degree to which birds view humans as threats can be quantified by their escape behavior. Understanding individual-level plasticity, however, requires the tracking of known individuals. We compared flight-initiation distances (FID) and distances fled (DF) from approaches by a human across urban and non-urban populations of individually-marked Dark-eyed Juncos (Junco hyemalis) in southern California. The urban population is more tolerant to people as evidenced by attenuated FIDs and DFs relative to non-urban birds. Although individual urban birds either habituated or sensitized to repeated approaches, there was no significant pattern at the population level. Overall, the behavioral patterns exhibited by urban juncos are more supportive ofin situevolution than either being a biased sample from an ancestral non-urban population or intrinsic behavioral plasticity that produces a uniform adjustment to urban life.
Uncovering complementary sets of variants for predicting quantitative phenotypes
Authors: Yılmaz Serhan , Fakhouri Mohamad , Koyutürk Mehmet , Çiçek A. Ercüment , Taştan Öznur
Published: December 2020

Motivation

Genome-wide association studies show that variants in individual genomic loci alone are not sufficient to explain the heritability of complex, quantitative phenotypes. Many computational methods have been developed to address this issue by considering subsets of loci that can collectively predict the phenotype. This problem can be considered a challenging instance of feature selection in which the number of dimensions (loci that are screened) is much larger than the number of samples. While currently available methods can achieve decent phenotype prediction performance, they either do not scale to large datasets or have parameters that require extensive tuning.

Results

We propose a fast and simple algorithm, Macarons, to select a small, complementary subset of variants by avoiding redundant pairs that are in linkage disequilibrium. Our method features two interpretable parameters that control the time/performance trade-off without requiring parameter tuning. In our computational experiments, we show that Macarons consistently achieves similar or better prediction performance than state-of-the-art selection methods while having a simpler premise and being at least 2 orders of magnitude faster. Overall, Macarons can seamlessly scale to the human genome with ~107variants in a matter of minutes while taking the dependencies between the variants into account.

Conclusion

Macarons can offer a reasonable trade-off between phenotype predictivity, runtime and the complementarity of the selected subsets. The framework we present can be generalized to other high-dimensional feature selection problems within and beyond biomedical applications.

Availability

Macarons is implemented in Matlab and the source code is available at:https://github.com/serhan-yilmaz/macarons
Pioneer activity of an oncogenic fusion transcription factor at inaccessible chromatin
Authors: Sunkel Benjamin , Wang Meng , LaHaye Stephanie , Kelly Benjamin J. , Fitch James R. , Barr Frederic G. , White Peter , Stanton Benjamin Z.
Published: December 2020

Recent characterizations of pioneer transcription factors have led to new insights into their structures and patterns of chromatin recognition that are instructive for understanding their role in cell fate commitment and transformation. Intersecting with these basic science concepts, the identification of pioneer factors (PFs) fused together as driver translocations in childhood cancers raises questions of whether these fusions retain the fundamental ability to invade repressed chromatin, consistent with their monomeric PF constituents. In this study, we define the cellular and chromatin localization of the translocation, PAX3-FOXO1, an oncogenic driver of childhood rhabdomyosarcoma (RMS), derived from a genetic fusion of PFs. To quantitatively define its chromatin-targeting functions and capacity to drive epigenetic reprogramming, we developed a new method for ChIP-seq with per-cell normalization (pc-ChIP-seq). Our quantitative localization studies address structural variation in RMS genomes and reveal novel insights into heterochromatin localization of PAX3-FOXO1. From these studies, we report novel pioneer function for the major driver oncogene in RMS, with repressed chromatin binding and nucleosome-motif targeting in human cells.
Evaluation of established methods for DNA extraction and primer pairs targeting 16S rRNA gene for bacterial microbiome profiling of olive xylem sap
Authors: Haro Carmen , Anguita-Maeso Manuel , Metsis Madis , Navas-Cortés Juan A. , Landa Blanca B.
Published: December 2020

Next Generation Sequencing has revolutionized our ability to investigate the microbiota composition of diverse and complex environments. However, a number of factors can affect the accuracy of microbial community assessment, such as the DNA extraction method, the hypervariable region of 16S rRNA gene targeted or the PCR primers used for amplification. The aim of this study was to assess the influence of commercially available DNA extraction kits and different primer pairs to provide a nonbiased vision of the composition of bacterial communities present in olive xylem sap. For that purpose, branches from ‘Picual’ and ‘Arbequina’ olive cultivars were used for xylem sap extraction using a Scholander chamber device. The DNA extraction protocol significantly affected xylem sap bacterial community assessment. That resulted in significant differences in alpha (Richness) and beta diversity (UNIFRAC distances) metrics among DNA extraction protocols, with the 12 DNA extraction kits evaluated being clustered in four groups behaving differently. Although the core number of taxa detected by all DNA extraction kits included four phyla, seven classes, 12 orders, and 16 or 21 families, and 12 or 14 genera when using the Greengenes or Silva database for taxonomic assignation, respectively, some taxa, particularly those identified at low frequency, were detected by some DNA extraction kits only. The most accurate depiction of a bacterial mock community artificially inoculated on sap samples was generated when using the PowerPlant DNA extraction Kit, the combination of 799F/1193R primers amplifying the hypervariable V5-V7 region and the Silva 132 database for taxonomic assignation. The DESeq2 analysis displayed significant differences among genera abundance between the different PCR primer pairs tested. Thus,Enterobacter, Granulicatella, PrevotellaandBrevibacteriumpresented a significant higher abundance in all PCR protocols when compared with primer pair 799F/1193R, while the opposite was true forPseudomonasandPectobacterium. The methodological approach followed in this study can be useful to optimize plant-associated microbiome analysis, especially when exploring new plant niches. Some of the DNA extraction kits and PCR primers selected in this study will contribute to better characterize bacterial communities inhabiting within the xylem sap of olives or other woody crop species.