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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Characteristic Localization of Neuronatin in Rat Tissues

Neuronatin (Nnat) is expressed in the pituitary, pancreas, and other tissues; however, the function of NNAT is still unclear. Recent studies have demonstrated that NNAT is localized in the sex determining region Y-box 2-positive stem/progenitor cells in the developing rat pituitary primordium and is downregulated during differentiation into mature hormone-producing cells. Moreover, NNAT is widely localized in subcellular organelles, excluding the Golgi. Here, we further evaluated NNAT expression and intracellular localization in embryonic and postnatal rat tissues such as the pancreas, tongue, whisker hair follicle, and testis. Immunohistochemistry showed that NNAT was localized in undifferentiated cells (i.e., epithelial basal cells and basement cells in the papillae of the tongue and round and elongated spermatids of the testis) as well as in differentiated cells (insulin-positive cells and exocrine cells of the pancreas, taste receptor cells of the fungiform papilla, the inner root sheath of whisker hair follicles, and spermatozoa). Additionally, NNAT showed novel intracellular localization in acrosomes in the spermatozoa. Because the endoplasmic reticulum (ER) is excluded from spermatozoa and sarco/ER Ca2+-ATPase isoform 2 (SERCA2) is absent from the inner root sheath, these findings suggested that NNAT localization in the ER and its interaction with SERCA2 were cell-or tissue-specific properties.

developmental biology↗

bioRxiv2018

Postmarketing commitments for novel drugs and biologics approved by the US Food and Drug Administration: a cross-sectional analysis

BackgroundPostmarketing commitments are clinical studies that drug sponsors agree to conduct at the time of FDA approval, but which are not required by statute or regulation. The objective of this study was to determine the characteristics, completion, and dissemination of postmarketing commitments agreed upon by sponsors at first FDA approval.\n\nMethodsWe performed a cross-sectional analysis of postmarketing commitments for new drugs and biologics approved 2009-2012. Using public FDA documents, ClinicalTrials.gov, and Scopus, we determined postmarketing commitments and their characteristics known at the time of FDA approval; number of postmarketing commitments subject to reporting requirements, for which FDA is required to make study status information available to the public (\"506B studies\"), and their statuses; and rates of registration and results reporting on ClinicalTrials.gov and publication in peer-reviewed journals for all clinical trials, with follow-up through July 2018.\n\nResultsAmong 110 novel drugs and biologics approved by the FDA between 2009-2012, 61 (55.5%) had at least one postmarketing commitment at the time of first approval. Of 331 total postmarketing commitments, 271 (81.9%) were non-human subjects research, predominantly chemistry, manufacturing, and controls studies; 49 (14.8%) were clinical trials (33 new and 16 ongoing trials for which follow-up results would be reported). Study descriptions for the new clinical trials often lacked information to establish study design features. Of the 89 (26.9%) 506B studies subject to public reporting requirements, of which 42 were clinical trials, 59 (66.3%) did not have an up-to-date status provided by FDA. Nearly all new clinical trials (28 of 31, 90.3%) were registered on ClinicalTrials.gov; of the 23 registered trials that were completed or terminated, 22 (95.7%) had reported results. Only half (14 of 29, 48.3%) of completed or terminated clinical trials, registered or unregistered, were published in peer-reviewed journals. Conclusions: The majority of postmarketing commitments agreed to by sponsors at the time of FDA approval for novel drugs and biologics approved between 2009-2012 were chemistry, manufacturing, and controls studies. While only 15% were clinical trials, these trials were nearly always registered with reported results on ClinicalTrials.gov. However, despite FDA public reporting requirements, up-to-date study status information was often unavailable for 506B studies.

epidemiology↗

bioRxiv2018

Managing river fish biodiversity generates substantial economic benefits in four European countries

Ecosystems and biodiversity produce benefits to society, but many of them are hard to quantify. For example, it is unclear whether European societies gain benefits from experiencing rivers that host high native biodiversity. Without such knowledge, monetary investments into ecologically oriented river management plans are difficult to justify. The objective of this study was to reveal how the public in four European countries values ecological characteristics of domestic rivers and the outcomes of hypothetical river basin management plans designed to improve river ecosystems, particularly fish biodiversity. We conducted a choice experiment among the populations in Norway, Sweden, Germany and France. We found similar preference structures in all countries with high marginal willingness-to-pay for improvements of abiotic river attributes (increased accessiblity of the river banks, improved bathing water quality, decreased river fragmentation). Citizens also benefited from certain fish species occurring in a river with native salmonid species being more valued than nonnatives, particularly in Norway, and from the degree of a rivers native biodiversity. Welfare measures calculated for selected river basin management plans (policy scenarios) revealed societal benefits that were primarily derived from ecological river management whereas a scenario focusing on hydroelectricity production generated the lowest utility. We conclude that ecological river management may produce high nonmarket economic benefits in all study countries, particularly through the management of abiotic river attributes and the restoration of declining or extinct fish species. Our results help to inform decisions on restoration efforts by showcasing the benefits that these measures have for the public.

ecology↗

bioRxiv2018

Unraveling the polygenic architecture of complex traits using blood eQTL meta-analysis

SummaryWhile many disease-associated variants have been identified through genome-wide association studies, their downstream molecular consequences remain unclear.\n\nTo identify these effects, we performed cis- and trans-expression quantitative trait locus (eQTL) analysis in blood from 31,684 individuals through the eQTLGen Consortium.\n\nWe observed that cis-eQTLs can be detected for 88% of the studied genes, but that they have a different genetic architecture compared to disease-associated variants, limiting our ability to use cis-eQTLs to pinpoint causal genes within susceptibility loci.\n\nIn contrast, trans-eQTLs (detected for 37% of 10,317 studied trait-associated variants) were more informative. Multiple unlinked variants, associated to the same complex trait, often converged on trans-genes that are known to play central roles in disease etiology.\n\nWe observed the same when ascertaining the effect of polygenic scores calculated for 1,263 genome-wide association study (GWAS) traits. Expression levels of 13% of the studied genes correlated with polygenic scores, and many resulting genes are known to drive these traits.

genomics↗

bioRxiv2018

The structural basis of lipid scrambling and inactivation in the endoplasmic reticulum scramblase TMEM16K

Membranes in cells have defined distributions of lipids in each leaflet, controlled by lipid scramblases and flip/floppases. However, for some intracellular membranes such as the endoplasmic reticulum the scramblases have not been identified. Members of the TMEM16 family have either lipid scramblase and ion channel activity, or specific chloride channel activity. Although TMEM16K is widely distributed and associated with the neurological disorder autosomal recessive spinocerebellar ataxia type 10 (SCAR10), its location in cells, function and structure are largely uncharacterised. Here we show that TMEM16K is an ER-resident calcium-regulated lipid scramblase. Our crystal structures of TMEM16K show a scramblase fold, with an open lipid transporting groove. Additional structures solved by cryo-EM reveal extensive conformational changes extending from the cytoplasmic to the ER side of the membrane, giving a state with a closed lipid permeation pathway. Molecular dynamics simulations showed that the open-groove conformation is necessary for scramblase activity. Our results suggest mechanisms by which missense variants of TMEM16K could cause SCAR10 ataxia, providing new hypotheses to explore for therapy.

biochemistry↗

bioRxiv2018

scFTD-seq: freeze-thaw lysis based, portable approach toward high-quality distributed single-cell 3 mRNA profiling

Cellular barcoding of 3 mRNAs enabled massively parallel profiling of single-cell gene expression and has been implemented in droplet and microwell based platforms. The latter further adds the value for compatibility with low input samples, optical imaging, scalability, and portability. However, cell lysis in microwells remains suboptimal despite the recently developed sophisticated solutions. Here, we present scFTD-seq, a microchip platform for performing single-cell freeze-thaw lysis directly toward 3 mRNA sequencing. It offers format flexibility with a simplified, widely adoptable workflow that reduces the number of preparation steps and hands-on time, with the quality of data and the cost per sample matching that of the state-of-the-art scRNA-seq platforms. Freeze-thaw, known as an unfavorable lysis method resulting in possible RNA fragmentation, turns out to be fully compatible with single-cell 3 mRNA sequencing, which detects only ~50 bases at the 3 end. We applied it to the profiling of mixed populations including whole tumors for distinguishing all major cell types and to the profiling of circulating follicular helper T cells implicated in systemic lupus erythematosus pathogenesis. Our results delineate the heterogeneity in the transcriptional programs and effector functions of these rare pathogenic T cells. As scFTD-seq decouples on-chip cell isolation and the following library preparation steps, we envision it to potentially allow the sampling (capture of cells/beads in microwells) at the distributed sites including small clinics or point-of-care settings and downstream processing at a centralized facility, which should enable wide-spread adoption beyond academic laboratories - for any users even with no experience in scRNA-seq library generation.

bioengineering↗

bioRxiv2018

Value representations do not explain movement selectivity in DMS-projecting dopamine neurons

Although midbrain dopamine (DA) neurons have been thought to primarily encode reward prediction error (RPE), recent studies have also found movement-related DAergic signals. For example, we recently reported that DA neurons in mice projecting to dorsomedial striatum are modulated by choices contralateral to the recording side. Here, we introduce, and ultimately reject, a candidate resolution for the puzzling RPE vs movement dichotomy, by showing how seemingly movement-related activity might be explained by an action-specific RPE. By considering both choice and RPE on a trial-by-trial basis, we find that DA signals are modulated by contralateral choice in a manner that is distinct from RPE, implying that choice encoding is better explained by movement direction. This fundamental separation between RPE and movement encoding may help shed light on the diversity of functions and dysfunctions of the DA system.

neuroscience↗

bioRxiv2018

Computational Analysis of Single Nucleotide polymorphisms (SNPs) in Human T-Cell Acute Lymphocytic Leukemia Protein 1 (TAL1) Gene/ Comprehensive Study

BackgroundTAL1 is a proto-oncogene whose distorted modifications in committed T-cell Precursors is related with the development of T-ALL, it also found to be related to many other human hematological diseases such as lymphoblastic lymphoma, immunodeficiency 18, acute myeloid leukemia and diamond-blackfan Anemia.\n\nObjectivesThis study aims to predict the effect of nsSNPs on TAL1 protein structure function\n\nMethodsRetrieved nSNPs in the coding and 3UTR regions were analyzed using different in silico tools. Interactions of TAL1 with functionally similar genes were investigated using Genemania. Post-translational modifications in several sites of the protein were also investigated.\n\nResultsOut of ninety nsSNPs identified, only eight were found damaging to protein function of which one is located in the basis helix-loop-helix domain (bHLH). Two SNPs were anticipated by PolymiRTs to prompt disturbance or creation of miR binding sites.\n\nConclusionThe present study is the first ever computational analysis of TAL1s nsSNPs hence this effort might be of help in the near future for inventing early diagnostic and therapeutic measures for T-ALL

bioinformatics↗

bioRxiv2018

Testing the Regulatory Consequences of 1,049 Schizophrenia Associated Variants With a Massively Parallel Reporter Assay

Recent genome-wide association studies (GWAS) identified numerous schizophrenia (SZ) and Alzheimers disease (AD) associated loci, most outside protein-coding regions and hypothesized to affect gene transcription. We used a massively parallel reporter assay (MPRA) to screen, 1,049 SZ and 30 AD variants in 64 and 9 loci respectively for allele differences in driving reporter gene expression. A library of synthetic oligonucleotides assaying each allele 5 times was transfected into K562 chronic myelogenous leukemia lymphoblasts and SK-SY5Y human neuroblastoma cells. 148 variants showed allelic differences in K562 and 53 in SK-SY5Y cells, on average 2.6 variants per locus. Nine showed significant differences in both lines, a modest overlap reflecting different regulatory landscapes of these lines that also differ significantly in chromatin marks. Eight of nine were in the same direction. We observe no preference for risk alleles to increase or decrease expression. We find a positive correlation between the number of SNPs in Linkage Disequilibrium (LD) and the proportion of functional SNPs supporting combinatorial effects that may lead to haplotype selection. Our results prioritize future functional follow up of disease associated SNPs to determine the driver GWAS variant(s), at each locus and enhance our understanding of gene regulation dynamics.

genetics↗

bioRxiv2018

Causal Association between Birth Weight and Adult Diseases: Evidence from a Mendelian Randomisation Analysis

BackgroundIt has long been hypothesized that birth weight has a profound long-term impact on individual predisposition to various diseases at adulthood: a hypothesis commonly referred to as the fetal origins of adult diseases. However, it is not fully clear to what extent the fetal origins of adult diseases hypothesis holds and it is also not completely known what types of adult diseases are causally affected by birth weight. Determining the causal impact of birth weight on various adult diseases through traditional randomised intervention studies is a challenging task.\n\nMethodsMendelian randomisation was employed and multiple genetic variants associated with birth weight were used as instruments to explore the relationship between 21 adult diseases and 38 other complex traits from 37 large-scale genome-wide association studies up to 340,000 individuals of European ancestry. Causal effects of birth weight were estimated using inverse-variance weighted methods. The identified causal relationships between birth weight and adult diseases were further validated through extensive sensitivity analyses and simulations.\n\nResultsAmong the 21 adult diseases, three were identified to be inversely causally affected by birth weight with a statistical significance level passing the Bonferroni corrected significance threshold. The measurement unit of birth weight was defined as its standard deviation (i.e. 488 grams), and one unit lower birth weight was causally related to an increased risk of coronary artery disease (CAD), myocardial infarction (MI), type 2 diabetes (T2D) and BMI-adjusted T2D, with the estimated odds ratios of 1.34 [95% confidence interval (CI) 1.17 - 1.53, p = 1.54E-5], 1.30 (95% CI 1.13 - 1.51, p = 3.31E-4), 1.41 (95% CI 1.15 - 1.73, p = 1.11E-3) and 1.54 (95% CI 1.25 - 1.89, p = 6.07E-5), respectively. All these identified causal associations were robust across various sensitivity analyses that guard against various confounding due to pleiotropy or maternal effects as well as inverse causation. In addition, analysis on 38 additional complex traits found that the inverse causal association between birth weight and CAD/MI/T2D was not likely to be mediated by other risk factors such as blood-pressure related traits and adult weight.\n\nConclusionsThe results suggest that lower birth weight is causally associated with an increased risk of CAD, MI and T2D in later life, supporting the fetal origins of adult diseases hypothesis.

epidemiology↗

bioRxiv2018

Causal Effects of Blood Lipids on Amyotrophic Lateral Sclerosis: A Mendelian Randomization Study

Amyotrophic lateral sclerosis (ALS) is a late-onset fatal neurodegenerative disorder that is predicted to increase across the globe by ~70% in the following decades. Understanding the disease causal mechanism underlying ALS and identifying modifiable risks factors for ALS hold the key for the development of effective preventative and treatment strategies. Here, we investigate the causal effects of four blood lipid traits that include high density lipoprotein (HDL), low density lipoprotein (LDL), total cholesterol (TC), and triglycerides (TG) on the risk of ALS. By leveraging instrument variables from multiple large-scale genome-wide association studies in both European and East Asian populations, we carry out one of the largest and most comprehensive Mendelian randomization analyses performed to date on the causal relationship between lipids and ALS. Among the four lipids, we found that only LDL is causally associated with ALS and that higher LDL level increases the risk of ALS in both the European and East Asian populations. Specifically, the odds ratio of ALS per one standard deviation (i.e. 39.0 mg/dL) increase of LDL is estimated to be 1.14 (95% CI 1.05 - 1.24, p = 1.38E-3) in the European and population and 1.06 (95% CI 1.00 - 1.12, p = 0.044) in the East Asian population. The identified causal relationship between LDL and ALS is robust with respect to the choice of statistical methods and is validated through extensive sensitivity analyses that guard against various model assumption violations. Our study provides important evidence supporting the causal role of higher LDL on increasing the risk of ALS, paving ways for the development of preventative strategies for reducing the disease burden of ALS across multiple nations.

epidemiology↗

bioRxiv2018

Setting Starting Level for a Trial of an Biofilm-Disrupting Adjuvant

Combination therapy is beneficial treatment modality for multiple diseases. Cinnamon oil may be an advantageous agent in a number of combination therapies as cinnamon oil has antibacterial activity. Cinnamon oil has also been shown to be effective against biofilm cultures of Streptococcus mutans and Lactobacillus plantarum. Cinnamomum osmophloeum inhibits planktonic cultures of many gram-positive and gram-negative bacteria, including MRSA (methicillin-resistant Staphylococcus aureus). Subjecting S. epidermidis to cinnamon oil eliminates planktonic cells or staphylococci in biofilms. Cinnamon oil is an essential oil used throughout the food industry because of its pleasant and distinctive aroma. The purpose of this study is to estimate the amount of exposure to cinnamon through selected foods in the United States in order to propose an initial target level for pharmacokinetic studies of a novel combination drug.

pharmacology and toxicology↗

bioRxiv2018

Multiple loci of small effect confer wide variability in efficiency and resistance rate of CRISPR gene drive

Gene drives could allow for control of vector-borne diseases by directly suppressing vector populations or spreading genetic payloads designed to reduce pathogen transmission. CRISPR homing gene drives work by cleaving wild-type alleles, which are then converted to drive alleles by homology-directed repair, increasing the frequency of the drive in a population. However, resistance alleles can form when end-joining repair takes place in lieu of homology-directed repair. Such alleles cannot be converted to drive alleles, which would halt the spread of a drive through a population. To investigate the effects of natural genetic variation on resistance formation, we developed a CRISPR homing gene drive in Drosophila melanogaster and crossed it into the genetically diverse Drosophila Genetic Reference Panel (DGRP) lines, measuring several performance parameters. Most strikingly, resistance allele formation post-fertilization in the early embryo ranged from 7% to 79% among lines and averaged 42{+/-}18%. We performed a Genome-Wide Association Study (GWAS) using our results in the DGRP lines and found that the resistance and conversion rates were polygenic, with several genetic polymorphisms showing relatively weak association. RNAi knockdown of several of these genes confirmed their effect, but their small effect sizes implies that their manipulation will yield only modest improvements to the efficacy of gene drives.

genetics↗

bioRxiv2018

Phasic arousal optimizes decision computations in mice and humans

Decisions are often made by accumulating ambiguous evidence over time. The brains arousal systems are activated during such decisions. In previous work in humans, we showed that evoked responses of arousal centers during decisions are reported by rapid dilations of the pupil, and predict a suppression of biases in the accumulation of decision-relevant evidence (de Gee et al. 2017). Here, we show that this arousal-related suppression in decision bias acts on both conservative and liberal biases, and generalizes across species (humans / mice), sensory systems (visual / auditory), and domains of decision-making (perceptual / memory-based). In challenging sound-detection tasks, the impact of spontaneous or experimentally induced choice biases was reduced under high arousal. Similar bias suppression occurred when evidence was drawn from memory. All these behavioral effects were explained by reduced evidence accumulation biases. Our results pinpoint a general principle of the interplay between phasic arousal and decision-making.

neuroscience↗

bioRxiv2018

Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth

mRNA localization serves key functions in localized protein production making it critical that the translation machinery itself is present at these locations. Here we show that translation factor mRNAs are localized to distinct granules within yeast cells. In contrast to many mRNP granules, such as P-bodies and stress granules, which contain translationally repressed mRNAs, these granules harbor translated mRNAs under active growth conditions. The granules require Pablp for their integrity and are inherited by developing daughter cells in a She2p/ She3p dependent manner. These results point to a model where roughly half the mRNA for certain translation factors are specifically directed in granules toward the tip of the developing daughter cell where protein synthesis is most heavily required, which has particular implications for filamentous forms of growth. Such a feedforward mechanism would ensure adequate provision of the translation machinery where it is to be needed most over the coming growth cycle. SummaryThis study shows that mRNAs encoding a range of translation factors are localized to granules that get transported into the yeast daughter cell using the She2p/She3p machinery. This likely supports an intensification of protein synthetic activity to facilitate apical polarized growth.

cell biology↗

bioRxiv2018

Jackknife model averaging prediction methods for complex phenotypes with gene expression levels by integrating external pathway information

MotivationIn the past few years many novel prediction approaches have been proposed and widely employed in high dimensional genetic data for disease risk evaluation. However, those approaches typically ignore in model fitting the important group structures or functional classifications that naturally exists in genetic data.\n\nMethodsIn the present study, we applied a novel model averaging approach, called Jackknife Model Averaging Prediction (JMAP), for high dimensional genetic risk prediction while incorporating KEGG pathway information into the model specification. JMAP selects the optimal weights across candidate models by minimizing a cross-validation criterion in a jackknife way. Compared with previous approaches, one of the primary features of JMAP is to allow model weights to vary from 0 to 1 but without the limitation that the summation of weights is equal to one. We evaluated the performance of JMAP using extensive simulation studies and compared it with existing methods. We finally applied JMAP to five real cancer datasets that are publicly available from TCGA.\n\nResultsThe simulations showed that, compared with other existing approaches, JMAP performed best or are among the best methods across a range of scenarios. For example, among 14 out of 16 simulation settings with PVE=0.3, JMAP has an average of 0.075 higher prediction accuracy compared with gsslasso. We further found that in the simulation the model weights for the true candidate models have much smaller chances to be zero compared with those for the null candidate models and are substantially greater in magnitude. In the real data application, JMAP also behaves comparably or better compared with the other methods for both continuous and binary phenotypes. For example, for the COAD, CRC and PAAD data sets, the average gains of predictive accuracy of JMAP are 0.019, 0.064 and 0.052 compared with gsslasso.\n\nConclusionThe proposed method JMAP is a novel method that can provide more accurate phenotypic prediction while incorporating external useful group information.

genomics↗

bioRxiv2018

MEK/mTOR-dependent D1 dopamine receptor activation induces local protein synthesis via eEF2 dephosphorylation in neurons

Neuromodulators in general, and dopamine in particular, define brain and neuronal states in different ways including regulation of global and local mRNA translation. Yet, the signaling pathways underlying the effects of dopamine on mRNA translation are not clear. Here, using genetic, pharmacologic, biochemical, and imaging methods, we tested the hypothesis that dopamine regulates phosphorylation of the eukaryotic elongation factor 2 (eEF2). We found that activation of dopamine receptor D1 but not D2 leads to rapid dephosphorylation of eEF2 at Thr56 in cortical primary neuronal culture and in vivo in a time-dependent manner. Additionally, NMDA receptor, mTOR, and ERK pathways are upstream to the D1 receptor-dependent eEF2 dephosphorylation and essential for it. Furthermore, D1 receptor activation resulted in a major reduction in dendritic eEF2 phosphorylation levels together with a correlative increase in local mRNA translation. These results reveal the role of eEF2 in dopamine regulation of local mRNA translation in neurons.\n\nOne-sentence summaryD1 receptor activation increases protein synthesis in dendrites by inactivating eEF2K in an ERK2/mTOR-dependent manner.

neuroscience↗

bioRxiv2018

DPPA2 and DPPA4 are necessary to establish a totipotent state in mouse embryonic stem cells

After fertilization of the transcriptionally silent oocyte, expression from both parental chromosomes is launched through so-called zygotic genome activation (ZGA), occurring in the mouse at the 2-cell stage. Amongst the first elements to be transcribed are the Dux gene, the product of which secondarily induces a wide array of ZGA genes, and a subset of evolutionary recent LINE-1 retrotransposons, which regulate chromatin accessibility in the early embryo. The maternally-inherited factors that activate Dux and LINE-1 transcription have so far remained unknown. Here we identify the paralog proteins DPPA2 and DPPA4 as responsible for this process.

developmental biology↗