Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 721 records · Page 40Linked to original sources

bioRxiv2020

Multiscale and multimodal reconstruction of cortical structure and function

We present a semi-automated reconstruction of L2/3 mouse primary visual cortex from 3 million cubic microns of electron microscopic images, including pyramidal and inhibitory neurons, astrocytes, microglia, oligodendrocytes and precursors, pericytes, vasculature, mitochondria, and synapses. Visual responses of a subset of pyramidal cells are included. The data are being made publicly available, along with tools for programmatic and 3D interactive access. The density of synaptic inputs onto inhibitory neurons varies across cell classes and compartments. We uncover a compartment-specific correlation between mitochondrial coverage and synapse density. Frequencies of connectivity motifs in the graph of pyramidal cells are predicted quite accurately from node degrees using the configuration model of random graphs. Cells receiving more connections from nearby cells exhibit stronger and more reliable visual responses. These example findings illustrate the resources utility for relating structure and function of cortical circuits as well as for neuronal cell biology.

neuroscience↗

bioRxiv2020

Identification of a peroxidase inhibitor that enhances kanamycin activity

BackgroundThe threat of antimicrobial resistance calls for more efforts in basic science, drug discovery, and clinical development, particularly gram-negative carbapenem-resistant pathogens. Objectives and methodsWhole-cell-based screening was performed to identify novel antibacterial agents against Acinetobacter baumannii ATCC19606. Spontaneously resistant mutant selection, whole-genome sequencing, and surface plasmon resonance were used for target identification and confirmation. Checkerboard titration assay was used for drug combination analysis. ResultsA small molecule named 6D1 with the chemical structure of 6-fluorobenzo[d]isothiazol-3(2H)-one was identified and exhibited activity against A. baumannii ATCC19606 strain (minimal inhibitory concentration, MIC = 1 mg/L). The mutation in the plasmid-derived ohrB gene that encodes a peroxidase was identified in spontaneously resistant mutants. Treatment of the bacteria with 6D1 resulted in increased sensitivity to peroxide such as tert-butyl hydroperoxide. The binding of 6D1 and OhrB was confirmed by surface plasmon resonance. Interestingly, the MIC of kanamycin against spontaneously resistant mutants decreased. Finally, we identified the effect of 6D1 on enhancing the antibacterial activity of kanamycin, including New Delhi metallo-{beta}-lactamase (NDM-1)-producing carbapenem-resistant Klebsiella pneumoniae, but not in strains carrying kanamycin resistance genes. ConclusionsIn this study, we identified a peroxidase inhibitor that suppresses the growth of A. baumannii and enhances the antibacterial activity of kanamycin. We propose that peroxidase may be potentially used as a target for kanamycin adjuvant development.

microbiology↗

bioRxiv2020

Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress

Mammalian cells have to adapt to environmental challenges that range from mild to severe stress. While the cellular response to mild stress has been widely studied, how cells respond to severe stress remains unclear. We show here that under severe stress conditions, cells induce a transient hibernation-like mechanism that anticipates recovery. We demonstrate that this Adaptive Pausing Response (APR) is a coordinated cellular response that limits ATP supply and consumption though mitochondrial fragmentation and widespread pausing of mRNA translation. This pausing is accomplished by ribosome stalling at translation initiation codons, which keeps mRNAs poised to resume translation upon recovery from severe stress. We further show that recovery from severe stress involves adaptive ISR (Integrated Stress Response) signaling that in turn permits cell cycle progression, resumption of growth, and reversal of mitochondria fragmentation. Our findings indicate that cells can respond to severe stress through the APR, a mechanism that preserves vital elements of cellular function under harsh environmental conditions.

molecular biology↗

bioRxiv2020

Momilactone B inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling

In competition for limited resources, many plants release allelochemicals to inhibit the growth of neighboring plants. Momilactone B (MB) is a major allelochemical produced by rice (Oryza sativa), however its mode of action is currently unknown. We used Arabidopsis (Arabidopsis thaliana) as a model system to evaluate potential mechanisms underlying the inhibitory effects of MB on seed germination, seedling establishment and root growth through the use of confocal microscopy and the examination of transcriptional responses in MB-treated seedlings. In response to MB treatment, transcript levels for genes encoding several key ABA biosynthetic enzymes and signaling components, including the transcription factor ABA-INSENSITIVE 4 (ABI4), were dramatically increased. Additionally, ABA insensitive 4 (abi4) mutant seedlings exhibited reduced susceptibility to exogenously-provided MB. Although the transcript levels of DELLA genes, which negatively regulate GA signaling, were significantly increased upon MB exposure, exogenous GA application did not reverse the inhibitory effects of MB on Arabidopsis germination and seedling development. Moreover, a reduction in seedling root meristematic activity, associated with reduced expression of auxin biosynthetic genes and efflux transporters, and apparent lowered auxin content, was observed in MB-treated root tips. Exogenous auxin applications partially rescued the inhibitory effects of MB observed in root growth. Our results indicate that MB suppresses Arabidopsis seed germination and root growth primarily via disruption of ABA and auxin signaling. These findings underscore the crucial roles played by phytohormones in mediating responses to allelochemical exposure. One-sentence summaryMomilactone B, the key allelochemical of rice, inhibits Arabidopsis growth and development via disruption of ABA and auxin signaling, suggesting the crucial roles of phytohormones in plant allelopathy

plant biology↗

bioRxiv2020

S-Trimer, a COVID-19 subunit vaccine candidate, induces protective immunity in nonhuman primates

SARS-CoV-2 is the underlying cause for the COVID-19 pandemic. Like most enveloped RNA viruses, SARS-CoV-2 uses a homotrimeric surface antigen to gain entry into host cells. Here we describe S-Trimer, a native-like trimeric subunit vaccine candidate for COVID-19 based on Trimer-Tag technology. Immunization of S-Trimer with either AS03 (oil-in-water emulsion) or CpG 1018 (TLR9 agonist) plus alum adjuvants induced high-levels of neutralizing antibodies and Th1-biased cellular immune responses in animal models. Moreover, rhesus macaques immunized with adjuvanted S-Trimer were protected from SARS-CoV-2 challenge compared to vehicle controls, based on clinical observations and reduction of viral loads in lungs. Trimer-Tag may be an important new platform technology for scalable production and rapid development of safe and effective subunit vaccines against current and future emerging RNA viruses.

immunology↗

bioRxiv2020

Comparative analysis reveals the species-specific genetic determinants of ACE2 required for SARS-CoV-2 entry

Coronavirus interaction with its viral receptor is a primary genetic determinant of host range and tissue tropism. SARS-CoV-2 utilizes ACE2 as the receptor to enter host cell in a species-specific manner. We and others have previously shown that ACE2 orthologs from New World monkey, koala and mouse cannot interact with SARS-CoV-2 to mediate viral entry, and this defect can be restored by humanization of the restrictive residues in New World monkey ACE2. To better understand the genetic determinants behind the ability of ACE2 orthologs to support viral entry, we compared koala and mouse ACE2 sequences with that of human and identified the key residues in koala and mouse ACE2 that restrict viral receptor activity. Humanization of these critical residues rendered both koala and mouse ACE2 capable of binding the spike protein and facilitating viral entry. The single mutation that allowed for mouse ACE2 to serve as a viral receptor provides a potential avenue for the development of SARS-CoV-2 mouse model.

microbiology↗

bioRxiv2020

Co-editing PINK1 and DJ-1 genes via AAV-delivered CRISPR/Cas9 system in adult monkey brains elicits classic Parkinsonian phenotypes

Whether direct manipulation of Parkinsons disease (PD) risk genes in monkey brain can elicit Parkinsonian phenotypes remains an unsolved issue. Here, we employed an adeno-associated virus (AAV)-delivered CRISPR/Cas9 system to directly co-edit PINK1 and DJ-1 genes in the substantia nigra (SN) region of four adult monkey brains. After the operation, two of the monkeys exhibited all classic PD symptoms, including bradykinesia, tremor, and postural instability, accompanied by severe nigral dopaminergic neuron loss (over 60%) and -synuclein pathology. The aged monkeys were more vulnerable to gene editing by showing faster PD progression, higher final total PD scores, and severer pathologic changes compared with their younger counterparts, suggesting both the genetic and aging factors played important roles in PD development. This gene editing system can be used to develop a large quantity of genetically edited PD monkeys over a short period, thus providing a practical transgenic monkey model for future PD studies.

neuroscience↗

bioRxiv2020

BacAnt: the combination annotation server of antibiotic resistance gene, insertion sequences, integron, transposable elements for bacterial DNA sequences

Whole genome sequencing (WGS) of bacteria has become a routine method in diagnostic laboratories. One of the clinically most useful advantages of WGS is the ability to predict antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) in bacterial sequences. This allows comprehensive investigations of such genetic features but can also be used for epidemiological studies. A plethora of software programs have been developed for the detailed annotation of bacterial DNA sequences, such as RAST (Rapid Annotation using Subsystem Technology), Resfinder, ISfinder, INTEGRALL and The Transposon Registry. Unfortunately, to this day, a reliable annotation tool of the combination of ARGs and MGEs is not available, and the generation of genbank files requires much manual input. Here, we present a new webserver which allows the annotation of ARGs, integrons, and transposable elements at the same time. The pipeline generates genbank files automatically, which are compatible with easyfig for comparative genomic analysis. Our BacAnt code and standalone software package are available at https://github.com/xthua/bacant with an accompanying web application at http://bacant.net. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/284273v2_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@262a07org.highwire.dtl.DTLVardef@1914001org.highwire.dtl.DTLVardef@101089corg.highwire.dtl.DTLVardef@dc5807_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2020

Antibody Upstream Sequences Diversity and Its Biological Implications Revealed by Repertoire Sequencing

The sequence upstream of antibody variable region (Antibody Upstream Sequence, or AUS) consists of 5 untranslated region (5 UTR) and two leader regions, L-PART1 and L-PART2. The sequence variations in AUS affect the efficiency of PCR amplification, mRNA translation, and subsequent PCR-based antibody quantification as well as antibody engineering. Despite their importance, the diversity of AUSs has long been neglected. Utilizing the rapid amplification of cDNA ends (5RACE) and high-throughput antibody repertoire sequencing (Rep-Seq) technique, we acquired full-length AUSs for human, rhesus macaque (RM), cynomolgus macaque (CM), mouse, and rat. We designed a bioinformatics pipeline and discovered 2,957 unique AUSs, corresponding to 2,786 and 1,159 unique sequences for 5 UTR and leader, respectively. Comparing with the leader records in the international ImMunoGeneTics (IMGT), while 529 were identical, 313 were with single nucleotide polymorphisms (SNPs), 280 were totally new, and 37 updated the incomplete records. The diversity of AUSs impact on related antibody biology was also probed. Taken together, our findings would facilitate Rep-Seq primer design for capturing antibodies comprehensively and efficiently as well as provide a valuable resource for antibody engineering and the studies of antibody at the molecular level.

bioinformatics↗

bioRxiv2020

The genetic sequences prone to copy number variation and single nucleotide polymorphism are linked to the repair of the poisoned DNA topoisomerase II

TOP2-poisoning bioflavonoids and pesticides are linked to the copy number variation-related autism and chromosome translocation-related leukemia. On the other hand, the poisoned DNA topoisomerase II (TOP2) can lead to chromosome aberration. However, except a limited number of genes such as the MLL fusion, other poisoned TOP2-targeted genes, as well as their relationships with any specific diseases, are not defined. We applied the {gamma}H2A.X antibodies to genome-widely immunoprecipitate the chromatins that were associated with the repair of the TOP2 poison etoposide-induced DNA double strand breaks. We identified many transcriptable protein- and nonprotein-coding DNA sequences that are the candidates of or associated with many gene copy number variation- and/or single nucleotide polymorphism-associated diseases, including but not limited to microdeletion and microduplication syndromes (which are phenotypically presented as developmental, autistic, neurological, psychiatric, diabetic, autoimmune, and neoplastic diseases among many others) as well as stature, obesity, metabolic syndrome, hypertension, coronary artery disease, ischemic stroke, aortic aneurysm and dissection, leukemia, cancer, osteoporosis, Alzheimer disease, Parkinson disease, and Huntington disease. Our data raise the possibility that the poisoned TOP2 might be linked to the specific genetic alterations contributing to these diseases, additional to the known copy number variation-related autism and chromosome translocation-related leukemia. According to our and others data, we propose a model that may interpret the features, such as mosaicism, polygenic traits and pleiotropy, of these diseases. Author SummaryFor the past several decades, the morbidity rate of many diseases, including autism, mental disorders, cancer, cardiovascular diseases, diabetes, and senile dementia, has world-widely been rising. Analysis of the genome of the patients and their family members has identified the genes, whose alterations, so called copy number variation (CNV) and single nucleotide polymorphism (SNP), contribute to the diseases. Moreover, the CNVs and SNPs are de novo, that is, they have occurred only in the recent generations. Epidemiologically, this indicates that for the past several decades, there have existed some unknown world-wide etiologies to which human beings are exposed. If the etiologies are identified, avoiding humans exposure may reduce the morbidity of the diseases. We have found that the repair of the poisoned topoisomerase II involves many genes that contribute to the aforementioned diseases. As the topoisomerase II is known to be located at the genomic sites where the disease-associated CNVs occur, as the poisoned topoisomerase II is susceptible to chromosome aberration, and as the topoisomerase II poisons, such as dietary bioflavonoids, are widely distributed in the environment, our data raise the yet-to-be-confirmed possibility that the environmental topoisomerase II poisons might etiologically contribute to many CNV-associated diseases.

genetics↗

bioRxiv2020

Neuronal Activity-Induced BRG1 Phosphorylation Regulates Enhancer Activation

Neuronal activity-induced enhancers drive the gene induction in response to stimulation. Here, we demonstrate that BRG1, the core subunit of SWI/SNF-like BAF ATP-dependent chromatin remodeling complexes, regulates neuronal activity-induced enhancers. Upon stimulation, BRG1 is recruited to enhancers in an H3K27Ac-dependent manner. BRG1 regulates enhancer basal activities and inducibility by affecting cohesin binding, enhancer-promoter looping, RNA polymerase II recruitment, and enhancer RNA expression. Furthermore, we identified a serine phosphorylation site in BRG1 that is induced by neuronal activities and is sensitive to CaMKII inhibition. BRG1 phosphorylation affects its interaction with several transcription co-factors, possibly modulating BRG1 mediated transcription outcomes. Using mice with knock-in mutations, we showed that non-phosphorylatable BRG1 fails to efficiently induce activity-dependent genes, whereas phosphomimic BRG1 increases the enhancer activities and inducibility. These mutant mice displayed anxiety-like phenotypes and altered responses to stress. Therefore, our data reveal a mechanism connecting neuronal signaling to enhancer activities through BRG1 phosphorylation.

molecular biology↗

bioRxiv2020

FlyWire: Online community for whole-brain connectomics

Due to advances in automated image acquisition and analysis, new whole-brain connectomes beyond C. elegans are finally on the horizon. Proofreading of whole-brain automated reconstructions will require many person-years of effort, due to the huge volumes of data involved. Here we present FlyWire, an online community for proofreading neural circuits in a fly brain, and explain how its computational and social structures are organized to scale up to whole-brain connectomics. Browser-based 3D interactive segmentation by collaborative editing of a spatially chunked supervoxel graph makes it possible to distribute proofreading to individuals located virtually anywhere in the world. Information in the edit history is programmatically accessible for a variety of uses such as estimating proofreading accuracy or building incentive systems. An open community accelerates proofreading by recruiting more participants, and accelerates scientific discovery by requiring information sharing. We demonstrate how FlyWire enables circuit analysis by reconstructing and analysing the connectome of mechanosensory neurons.

neuroscience↗

bioRxiv2020

Abnormal energy metabolism can alter foraging behavior in termites in different social contexts

Foraging behavior, as an energy-consuming behavior, is very important for collective survival in termites. How energy metabolism related to glucose decomposition and ATP production influences foraging behavior in termites is still unclear. Here, we analyzed the change in energy metabolism in the whole organism and brain after silencing the key metabolic gene isocitrate dehydrogenase (IDH) and then investigated its impact on foraging behavior in the subterranean termite Odontotermes formosanus in different social contexts. The IDH gene exhibited higher expression in the abdomen and head of O. formosanus. The knockdown of IDH resulted in metabolic disorders in the whole organism, including the impairment of the NAD+-IDH reaction and decreased ATP levels and glucose accumulation. The dsIDH-injected workers showed significantly reduced walking activity but increased foraging success. Interestingly, IDH downregulation altered brain energy metabolism, resulting in a decline in ATP levels and an increase in IDH activity. Additionally, the social context obviously affected brain energy metabolism and, thus, altered foraging behavior in O. formosanus. We found that the presence of predator ants increased the negative influence on the foraging behavior of dsIDH-injected workers, including a decrease in foraging success. However, an increase in the number of nestmate soldiers could provide social buffering to relieve the adverse effect of predator ants on worker foraging behavior. Our orthogonal experiments further verified that the role of the IDH gene as an inherent factor was dominant in manipulating termite foraging behavior compared with external social contexts, suggesting that energy metabolism, especially brain energy metabolism, plays a crucial role in regulating termite foraging behavior. Author summaryForaging behavior plays a key role in collective survival in social insects, as found in termites. Worker termites are responsible for foraging duty and exhibit large foraging areas and long foraging distances, so they need to consume much energy during foraging. It is well established that energy can influence insect behaviors. However, how energy metabolism affects foraging behavior in termites remains unknown. Here, we found that the downregulation of the conserved metabolic gene IDH impaired whole-organism and the brain energy metabolism and further altered foraging behavior, resulting in decreased walking activity but increased foraging success in the termite O. formosanus, which is an important insect pest damaging embankments and trees in China. Additionally, the social context affected brain energy metabolism and obviously changed foraging behavior in O. formosanus, causing a decline in foraging success in the absence of nestmate soldiers and the presence of predator ants. However, the increasing number of nestmate soldiers strengthened social buffering to relieve the negative effect of predator ants on worker foraging behavior. Our findings provide new insights into the underlying molecular mechanism involved in modulating the sophisticated foraging strategy of termites in different social contexts from the perspective of energy metabolism.

animal behavior and cognition↗

bioRxiv2020

UFold: Fast and Accurate RNA Secondary Structure Prediction with Deep Learning

MotivationFor many RNA molecules, the secondary structure is essential for the correct function of the RNA. Predicting RNA secondary structure from nucleotide sequences is a long-standing problem in genomics, but the prediction performance has reached a plateau over time. Traditional RNA secondary structure prediction algorithms are primarily based on thermodynamic models through free energy minimization, which imposes strong prior assumptions and is slow to run. ResultsHere we propose a deep learning-based method, called UFold, for RNA secondary structure prediction, trained directly on annotated data without any thermodynamic assumptions. UFold improves substantially upon previous models, with approximately 10~30% improvement over traditional thermodynamic models and 14% improvement over other learning-based methods. It achieves an F1 score of 0.91 on base pair prediction accuracy on an RNA structure prediction benchmark dataset. UFold is also fast with an inference time about 160ms per sequence up to 1600bp length. We provide an online web server that implements UFold for RNA structure prediction and is made freely available. AvailabilityAn online web server running UFold is available at https://ufold.ics.uci.edu. Code is available at https://github.com/uci-cbcl/UFold. Contactxhx@uci.edu

bioinformatics↗

bioRxiv2020

SARS-Cov-2-, HIV-1-, Ebola-neutralizing and anti-PD1 clones are predisposed

Antibody repertoire refers to the totality of the superbly diversified antibodies within an individual to cope with the vast array of possible pathogens. Despite this extreme diversity, antibodies of the same clonotype, namely public clones, have been discovered among individuals. Although some public clones could be explained by antibody convergence, public clones in naive repertoire or virus-neutralizing clones from not infected people were also discovered. All these findings indicated that public clones might not occur by random and they might exert essential functions. However, the frequencies and functions of public clones in a population have never been studied. Here, we integrated 2,449 Rep-seq datasets from 767 donors and discovered 5.07 million public clones - ~10% of the repertoire are public in population. We found 38 therapeutic clones out of 3,390 annotated public clones including anti-PD1 clones in healthy people. Moreover, we also revealed clones neutralizing SARS-CoV-2, Ebola, and HIV-1 viruses in healthy individuals. Our result demonstrated that these clones are predisposed in the human antibody repertoire and may exert critical functions during particular immunological stimuli and consequently benefit the donors. We also implemented RAPID - a Rep-seq Analysis Platform with Integrated Databases, which may serve as a useful tool for others in the field.

immunology↗

bioRxiv2020

Different activation signatures in the primary sensorimotor and higher-level regions for haptic three-dimensional curved surface exploration

Haptic object perception begins with continuous exploratory contacts, and the human brain needs to accumulate sensory information continuously over time. However, it is still unclear how the primary sensorimotor cortex (PSC) interacts with these higher-level regions during haptic exploration across time. This functional magnetic resonance imaging (fMRI) study investigates time-dependent haptic object processing by examining brain activity during haptic 3D curve and roughness estimation. For this experiment, we designed sixteen haptic stimuli (4 kinds of curve x 4 kinds of roughness) for the haptic curve and roughness estimation tasks. Twenty participants were asked to move their right index and middle fingers along with the surface twice and to estimate one of the two features--roughness or curvature--dependent on the task instruction. We found that the brain activity in several higher-level regions (e.g., bilateral posterior parietal cortex) linearly increased with curvature through the haptic exploration phase. Surprisingly, we found that the contralateral PSC was parametrically modulated by the number of curves only during the late exploration phase, but not during the early exploration phase. In contrast, we found no similar parametric modulation activity patterns for haptic roughness estimation in either the contralateral PSC or in the higher-level regions. Together, our findings suggest that haptic 3D object perception is processed across the cortical hierarchy, while the contralateral PSC interacts with other higher-level regions across time in a manner that is dependent upon object features. HighlightsO_LIWe observed the brain activity of haptic object perception using parametric stimuli. C_LIO_LIHaptic curve estimation showed parametric modulation across the cortical hierarchy. C_LIO_LICurve parametric modulation in the sensorimotor cortex showed time dependency. C_LIO_LIRoughness parametric modulation showed very little dependency in any regions of the brain. C_LIO_LIThese findings reflect the nature of time-dependent haptic object processing in the brain. C_LI

neuroscience↗

bioRxiv2020

Structure of human sodium leak channel NALCN in complex with FAM155A

NALCN, a sodium leak channel mainly expressed in the central nervous systems, is responsible for the resting Na+ permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we reported the cryo-EM structure of human NALCN in complex with FAM155A, at an overall resolution of 3.1 angstrom. FAM155A forms extensive interactions with the extracellular loops of NALCN that help stabilize NALCN in the membrane. A Na+ ion-binding site, reminiscent of a Ca2+ binding site in Cav channels, is identified in the unique EEKE selectivity filter. Despite its leaky nature, the intracellular gate is sealed by S6I, II-III linker and III-IV linker. Our study establishes the molecular basis of Na+ permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.

biophysics↗

bioRxiv2020

Power analysis of transcriptome-wide association study

The transcriptome-wide association study (TWAS) has emerged as one of several promising techniques for integrating multi-scale omics data into traditional genome-wide association studies (GWAS). Unlike GWAS, which associates phenotypic variance directly with genetic variants, TWAS uses a reference dataset to train a predictive model for gene expressions, which allows it to associate phenotype with variants through the mediating effect of expressions. Although effective, this core innovation of TWAS is poorly understood, since the predictive accuracy of the genotype-expression model is generally low and further bounded by expression heritability. This raises the question: to what degree does the accuracy of the expression model affect the power of TWAS? Furthermore, would replacing predictions with actual, experimentally determined expressions improve power? To answer these questions, we compared the power of GWAS, TWAS, and a hypothetical protocol utilizing real expression data. We derived non-centrality parameters (NCPs) for linear mixed models (LMMs) to enable closed-form calculations of statistical power that do not rely on specific protocol implementations. We examined two representative scenarios: causality (genotype contributes to phenotype through expression) and pleiotropy (genotype contributes directly to both phenotype and expression), and also tested the effects of various properties including expression heritability. Our analysis reveals two main outcomes: (1) Under pleiotropy, the use of predicted expressions in TWAS is superior to actual expressions. This explains why TWAS can function with weak expression models, and shows that TWAS remains relevant even when real expressions are available. (2) GWAS outperforms TWAS when expression heritability is below a threshold of 0.04 under causality, or 0.06 under pleiotropy. Analysis of existing publications suggests that TWAS has been misapplied in place of GWAS, in situations where expression heritability is low. Author SummaryWe compared the effectiveness of three methods for finding genetic effects on disease in order to quantify their strengths and help researchers choose the best protocol for their data. The genome-wide association study (GWAS) is the standard method for identifying how the genetic differences between individuals relate to disease. Recently, the transcriptome-wide association study (TWAS) has improved GWAS by also estimating the effect of each genetic variant on the activity level (or expression) of genes related to disease. The effectiveness of TWAS is surprising because its estimates of gene expressions are very inaccurate, so we ask if a method using real expression data instead of estimates would perform better. Unlike past studies, which only use simulation to compare these methods, we incorporate novel statistical calculations to make our comparisons more accurate and universally applicable. We discover that depending on the type of relationship between genetics, gene expression, and disease, the estimates used by TWAS could be actually more relevant than real gene expressions. We also find that TWAS is not always better than GWAS when the relationship between genetics and expression is weak and identify specific turning points where past studies have incorrectly used TWAS instead of GWAS.

bioinformatics↗