Biology subjects

Li, B.

Publications and source records attributed to Li, B..

At least 595 records · Page 33Linked to original sources

bioRxiv2019

Epistatic Transcription Factor Networks Differentially Modulate Arabidopsis Growth and Defense

Plants integrate internal and external signals to finely coordinate growth and defense allowing for maximal fitness within a complex environment. One common model for the relationship between growth and defense is a trade-off model in which there is a simple negative interaction between growth and defense theoretically driven by energy costs. However, there is a developing consensus that the coordination of growth and defense likely involves a more conditional and intricate connection. To explore how a transcription factor network may coordinate growth and defense, we used high-throughput phenotyping to measure growth and flowering in a set of single and pairwise mutants previously linked to the aliphatic glucosinolate defense pathway. Showing the link between growth and aliphatic glucosinolate defense, 17 of the 20 tested TFs significantly influence plant growth and/or flowering time. These effects were conditional upon the environment, age of the plant and more critically varied amongst the phenotypes when using the same genotype. The phenotypic effects of the TF mutants on SC GLS accumulation and on growth did not display a simple correlation, supporting the coordination model. We propose that large transcription factor networks create a system to integrate internal and external signals and separately modulate growth and the accumulation of the defensive aliphatic GLS.

plant biology↗

bioRxiv2019

Auxin-sensitive Aux/IAA proteins mediate drought tolerance in Arabidopsis by regulating glucosinolate levels

A detailed understanding of abiotic stress tolerance in plants is essential to provide food security in the face of increasingly harsh climatic conditions. Glucosinolates (GLSs) are secondary metabolites found in the Brassicaceae that protect plants from herbivory and pathogen attack. Here we report that in Arabidopsis, aliphatic GLS levels are regulated by the auxin-sensitive Aux/IAA repressors IAA5, IAA6, and IAA19. These proteins act in a transcriptional cascade that maintains expression of GLS levels when plants are exposed to drought conditions. Loss of IAA5/6/19 results in reduced GLS levels and decreased drought tolerance. Further, we show that this phenotype is associated with a defect in stomatal regulation. Application of GLS to the iaa5,6,19 mutants restores stomatal regulation and normal drought tolerance. GLS action is dependent on the receptor kinase GHR1, suggesting that GLS may signal via reactive oxygen species. These results provide a novel connection between auxin signaling, GLS levels and drought response.\n\nOne Sentence SummaryAux/IAA proteins promote drought tolerance by regulating glucosinolate levels.

plant biology↗

bioRxiv2019

EPIC: MHC-I epitope prediction integrating mass spectrometry derived motifs and tissue-specific expression profiles

BackgroundAccurate prediction of epitopes presented by human leukocyte antigen (HLA) is crucial for personalized cancer immunotherapies targeting T cell epitopes. Mass spectrometry (MS) profiling of eluted HLA ligands, which provides high-throughput measurements of HLA associated peptides in vivo, can be used to faithfully model the presentation of epitopes on the cell surface. In addition, gene expression profiles measured by RNA-seq data in a specific cell/tissue type can significantly improve the performance of epitope presentation prediction. However, although large amount of high-quality MS data of HLA-bound peptides is being generated in recent years, few provide matching RNA-seq data, which makes incorporating gene expression into epitope prediction difficult. MethodsWe collected publicly available HLA peptidome and matching RNA-seq data of 34 cell lines derived from various sources. We built position score specific matrixes (PSSMs) for 21 HLA-I alleles based on these MS data, then used logistic regression (LR) to model the relationship among PSSM score, gene expression and peptide length to predict whether a peptide could be presented in each of the cell line. We further built a universal LR model, termed Epitope Presentation Integrated Prediction (EPIP), based on more than 180,000 unique HLA ligands collected from public sources and ~3,000 HLA ligands generated by ourselves, to predict epitope presentation for 66 common HLA-I alleles. ResultsWhen evaluating EPIP on large, independent HLA eluted ligand datasets, it performed substantially better than other popular methods, including MixMHCpred (v2.0), NetMHCpan (v4.0), and MHCflurry (v1.2.2), with an average 0.1% positive predictive value (PPV) of 52.01%, compared to 37.24%, 36.96%, 24.90% and 23.76% achieved by MixMHCpred, NetMHCpan-4.0 (EL), NetMHCpan-4.0 (BA) and MHCflurry, respectively. It is also comparable to EDGE, a recent deep learning-based model that is not publicly available, on predicting epitope presentation and selecting immunogenic cancer neoantigens. However, the simplicity and flexibility of EPIP makes it easier to be applied in diverse situations, and we demonstrated this by generating MS data for the HCC4006 cell line and adding the support of HLA-A*33:03 to EPIP. EPIP is publicly available as a web tool < http://epip.genomics.cn/>. Conclusionswe have developed an easy to use, publicly available epitope prediction tool, EPIP, that incorporates information from both MS and RNA-seq data, and demonstrated its superior performance over existing public methods.

bioinformatics↗

bioRxiv2019

Species dispersal mediates opposing influences of a branching network on genetic variation in a metapopulation

Aim Fractal networks, represented by branching complexity in rivers, are ubiquitous in nature. In rivers, the number of either distal (e.g., in headwater streams) or confluent (e.g., in mainstems) locations can be increased along with their branching complexity. Distal- or confluent-spatial locations can result in fewer or greater corridor linkages that can alter genetic divergence at the metapopulation scale. These mechanisms underlying the resulting genetic structuring remain poorly understood at the metapopulation scale, particularly in terms of the roles of species-specific dispersal traits. The objective of this study is to mechanistically understand how branching complexity can simultaneously influence genetic divergence in opposite directions.Location Northeastern JapanMethods To evaluate the integrated influences of network complexity and species dispersal on genetic divergence among populations at the catchment scale, we conducted simulation modelling on a mechanistic framework based on Bayesian inference by adapting empirical genetic data from four macroinvertebrate species. Simulations were then done using empirical and virtual species-characteristics on virtual river networks.Results Our novel simulation showed that both greater landscape connectivity (resulting from shorter watercourse distance) and greater isolation of distal locations occurred in the more-branched river networks. These two spatial features have negative and positive influences on genetic divergence, with their relative importance varying among different species and dispersal characteristics. Specifically, genetic divergence at the metapopulation scale increased for species having higher downstream-biased dispersal but decreased for species having higher upstream-biased dispersal. Distal populations (e.g., in headwaters) have higher genetic independence when downstream-biased asymmetry is higher.Main conclusions We found a strong association between species dispersal and evolutionary processes such as gene flow and genetic drift. This association mediates the pervasive influences of branching complexity on genetic-divergence in the metapopulation. It also highlights the importance of considering species dispersal-patterns when developing management strategies in the face of rapid environmental-change scenarios.Competing Interest StatementThe authors have declared no competing interest.View Full Text

ecology↗

bioRxiv2019

The Telomerase Reverse Transcriptase (TERT) and p53 Regulate Mammalian PNS and CNS Axon Regeneration downstream of c-Myc

Although several genes have been identified to promote axon regeneration in the central nervous system, our understanding of the molecular mechanisms by which mammalian axon regeneration is regulated is still limited and fragmented. Here by using sensory axon and optic nerve regeneration as model systems, we revealed an unexpected role of telomerase reverse transcriptase (TERT) in regulation of axon regeneration. We also provided strong evidence that TERT and p53 acted downstream of c-Myc to control sensory axon regeneration. More importantly, overexpression of p53 in sensory neurons and retinal ganglion cells (RGCs) was sufficient to promote sensory axon and optic never regeneration, respectively. The study revealed a novel c-Myc-TERT-p53 signaling pathway, expanding horizons for novel approaches promoting CNS axon regeneration.

neuroscience↗

bioRxiv2019

Ionomycin Ameliorates Hypophosphatasia via Rescuing Alkaline Phosphatase Deficiency-mediated L-type Ca2+ Channel Internalization in Mesenchymal Stem Cells

Loss-of-function mutations in ALPL result in hypophosphatasia (HPP), an inborn error of metabolism that causes skeletal mineralization defect. In adults, main clinical involvement includes early loss of primary or secondary teeth, osteoporosis, bone pain, chondrocalcinosis, and fractures. However, guidelines for the treatment of adults with HPP are not available. Here, we show that ALPL deficiency caused reduction of intracellular Ca2+ influx resulting in osteoporotic phenotype due to downregulated osteogenic differentiation and upregulated adipogenic differentiation in both human and mouse BMSCs. To elevate intracellular level of calcium in bone marrow mesenchymal stem cells (BMSCs) by ionomycin treatment rescues the osteoporotic phenotype in alpl+/- mice and BMSC-specific (Prrx1-alpl-/-) conditional alpl knockout mice. Mechanistically, ALPL is required to maintain intracellular Ca2+ influx by regulating L-type Ca2+ channel trafficking via binding to the 2{delta} subunits, which regulates the internalization of L-type Ca2+ channel. Decreased Ca2+ flux inactivates Akt/GSK3{beta}/{beta}-catenin signaling pathway that regulates lineage differentiation of BMSCs. This study identifies a previous unknown role of ectoenzyme ALPL in maintenance of calcium channel trafficking to keep stem cell lineage differentiation and bone homeostasis. Accelerating Ca2+ flux through L-type Ca2+ channel by ionomycin treatment may be a promising therapeutic approach for adult HPP patients. One Sentence SummaryALP regulates internalization of L-Type Ca2+ Channel of BMSCs in Hypophosphatasia.

cell biology↗

bioRxiv2019

Genotypic frequencies at equilibrium for polysomic inheritance under double-reduction

Polyploids are organisms whose genomes consist of more than two complete sets of chromosomes. Both autopolyploids and allopolyploids may display polysomic inheritance. A peculiarity of polysomic inheritance is multivalent formation during meiosis resulting in double-reduction, which occurs when sister chromatid fragments are segregated into the same gamete. Double-reduction can result in gametes carrying identical-by-descent alleles and slightly increasing homozygosity. This will cause the genotypic frequencies to deviate from expected values and will thus bias the results of standard population genetic analytical methods used in molecular ecology and selective breeding. In this study, we extend existing double-reduction models to account for any even level of ploidy, and derive the symbolic expressions for genotypic frequencies via two methods. Inbreeding coefficients and heterozygosity under double-reduction and inbreeding are also calculated. Numerical solutions obtained by computer simulations are compared with analytical solutions predicted by the model to validate the model.

genetics↗

bioRxiv2019

Calcium/calmodulin-dependent protein kinase II regulates mammalian axon growth by affecting F-actin length in growth cone

While axon regeneration is a key determinant of functional recovery of the nervous system after injury, it is often poor in the mature nervous system. Influx of extracellular calcium (Ca2+) is one of the first phenomena that occur following axonal injury, and calcium/calmodulin-dependent protein kinase (CaMKII), a target protein for calcium ions, regulates the status of cytoskeletal proteins such as F-actin. Herein, we found that peripheral axotomy activates CaMKII in dorsal root ganglion (DRG) sensory neurons, and inhibition of CaMKII impairs axon growth in both the peripheral and central nervous systems (PNS and CNS, respectively). Most importantly, we also found that activation of CaMKII promotes PNS and CNS axon growth, and regulatory effects of CaMKII on axon growth occur via affecting the length of the F-actin. Thus, we believe our findings provide clear evidence that CaMKII is a critical modulator of mammalian axon regeneration.

neuroscience↗

bioRxiv2019

IMCC: Quantitative Analysis of the Inter-module Connectivity for Bio-network

Inter-module connectivity, which tend to connect different communities and maintain network architectural integrity, is contributing to functional coordination and information flow between modules in perturbations. Detecting the strength of inter-module connection is essential to characterize the reactive bio-systematical variation. A quantitative evaluation method for inter-module connections is needed. Here, based on the high-throughput microarray data from mouse, an evaluation approach (named as IMCC) for inter-module connectivity was developed. The IMCC model, which is an integration of direct and indirect inter-module connections, successfully excluded inter-module connections without statistical significance or below the cutoff value, and provided a more comprehensive landscape of inter-module relationships. We showed that the IMCC method reflected a more precise functional coordination between modules according to KEGG database, were validated by topological parameter. Application of IMCC in genome-scale stroke networks deciphered characteristic pathological \"core-periphery\" structure of modular map and functional coordination module pair.\n\nAuthor summeryInter-module connectivity, which tend to connect different communities and maintain network architectural integrity, is contributing to functional coordination and information flow between modules in perturbations. Moreover, modular rearrangements provide more efficient ways for phenotype alteration, inter-module connections have been considered to be evolutionary interaction switches\". Such modular map rewiring can be used as a network biomarker to characterize the dynamics of drug responses. Detecting the strength of inter-module connection is essential to characterize the reactive bio-systematical variation response to disease or drug. We aim to construct a quantitative evaluation method for inter-module connections. Thus, this study has implications in systematical exploration detailed variation of inter-module pharmacological action mode of drugs.

systems biology↗

bioRxiv2018

Bi-clustering based biological and clinical characterization of colorectal cancer in complementary to CMS classification

In light of the marked differences in the intrinsic biological underpinnings and prognostic outcomes among different subtypes, Consensus Molecular Subtype (CMS) classification provides a new taxonomy of colorectal cancer (CRC) solely based on transcriptomics data and has been accepted as a standard rule for CRC stratification. Even though CMS was built on highly cancer relevant features, it suffers from limitations in capturing the promiscuous mechanisms in a clinical setting. There are at least two facts about using transcriptomic data for prognosis prediction: the engagement of genes or pathways that execute the clinical response pathway are highly dynamic and interactive with others; and a predefined patient stratification not only largely decrease the statistical analysis power, but also excludes the fact that clusters of patients that confer similar clinical outcomes may or may not overlap with a pre-defined subgrouping. To enable a flexible and prospective stratified exploration, we here present a novel computational framework based on bi-clustering aiming to identify gene regulatory mechanisms associated with various biological, clinical and drug-resistance features, with full recognition of the transiency of transcriptional regulation and complicacies of patients subgrouping with regards to different biological and clinical settings. Our analysis on multiple large scale CRC transcriptomics data sets using a bi-clustering based formulation suggests that the detected local low rank modules can not only generate new biological understanding coherent to CMS stratification, but also identify predictive markers for prognosis that are general to CRC or CMS dependent, as well as novel alternative drug resistance mechanisms. Our key results include: (1) a comprehensive annotation of the local low rank module landscape of CRC; (2) a mechanistic relationship between different clinical subtypes and outcomes, as well as their characteristic biological underpinnings, visible through a novel consensus map; and (3) a few (novel) resistance mechanisms of Oxaliplatin, 5-Fluorouracil, and the FOLFOX therapy are revealed, some of which are validated on independent datasets.

bioinformatics↗

bioRxiv2018

Effect of KNL1 on the proliferation and apoptosis of colorectal cancer cells

BackgroundTo identify the expression of KNL1 in colorectal tumor tissues and to clarify the function of this gene on the proliferation capability of colorectal cancer cells.\n\nMethodsThirty-six pairs of colorectal tumor and normal tissue were collected and subjected to quantitative PCR analysis. KNL1 was under-expressed using lentiviral transfection, and the function of KNL1 was evaluated by proliferation assay, colony formation and apoptosis assay.\n\nResultsKNL1 was highly expressed in colorectal tumor tissues. KNL1 downregulation inhibited colorectal cancer cell proliferation and promoted apoptosis.\n\nConclusionsKNL1 plays an effective role in decreasing the apoptosis and promoting the proliferation of colorectal cancer cells.

cancer biology↗

bioRxiv2018

Image-based Phenotyping and Disease Screening of Multiple Populations for resistance to Verticillium dahliae in cultivated strawberry Fragaria x ananassa

1.0Verticillium dahliae is a highly detrimental pathogen of soil cultivated strawberry (Fragaria x ananassa). Breeding of Verticillium wilt resistance into commercially viable strawberry cultivars can help mitigate the impact of the disease. In this study we describe novel sources of resistance identified in biparental strawberry populations, creating a wealth of data for breeders to exploit. Pathogen-informed experiments have allowed the differentiation of subclade-specific resistance responses, through studying V. dahliae subclade II-1 specific resistance in the cultivar Redgauntlet and subclade II-2 specific resistance in Fenella and Chandler.\n\nA large-scale low-cost phenotyping platform was developed utilising automated unmanned vehicles and near infrared imaging cameras to assess field-based disease trials. The images were used to calculate disease susceptibility for infected plants through the normalized difference vegetation index score. The automated disease scores showed a strong correlation with the manual scores.\n\nA co-dominant resistant QTL; FaRVd3D, present in both Redgauntlet and Hapil cultivars exhibited a major effect of 18.3 % when the two resistance alleles were combined. Another allele, FaRVd5D, identified in the Emily cultivar was associated with an increase in Verticillium wilt susceptibility of 17.2%, though whether this allele truly represents a susceptibility factor requires further research, due to the nature of the bi-parental cross.\n\nMarkers identified in bi-parental populations were validated across a set of 92 accessions to determine whether they remained closely linked to resistance genes in the wider germplasm. The resistant markers FaRVd2B from Redgauntlet and FaRVd6D from Chandler were associated with resistance across the wider germplasm. Furthermore, comparison of imaging versus manual phenotyping revealed the automated platform could identify three out of four disease resistance markers. As such, this automated wilt disease phenotyping platform is considered to be a good, time saving, substitute for manual assessment.

genetics↗

bioRxiv2018

Reference genes for RT-qPCR normalisation in different tissues, developmental stages and stress conditions of Hypericum perforatum

AbstactHypericum perforatum is a widely known medicinal herb used mostly as a remedy for depression because of its abundant secondary metabolites. Quantitative real-time PCR (qRT-PCR) is an optimized method for the efficient and reliable quantification of gene expression studies. In general, reference genes are used in qRT-PCR analysis because of their known or suspected housekeeping roles. However, their expression level cannot be assumed to remain stable under all possible experimental conditions. Thus, the identification of high quality reference genes is very necessary for the interpretation of qRT-PCR data. In this study, we investigated the expression of fourteen candidate genes, including nine housekeeping genes and five potential candidate genes. Additionally, the HpHYP1 gene, belonging to the PR-10 family associated with stress control, was used for validation of the candidate reference genes. Three programs were applied to evaluate the gene expression stability across four different plant tissues, three developmental stages and a set of abiotic stress and hormonal treatments. The candidate genes showed a wide range of Ct values in all samples, indicating that they are differentially expressed. Integrating all of the algorithms and evaluations, ACT2 and TUB-{beta} were the most stable combination overall and for different developmental stages samples. Moreover, ACT2 and EF1- were considered to be the two most applicable reference genes for different tissues and for stress samples. Majority of the conventional housekeeping genes exhibited better than the potential reference genes. The obtained results will contribute to improving credibility of standardization and quantification of transcription levels in future expression research of H. perforatum.

plant biology↗

bioRxiv2018

cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders

Mutations in gene regulatory elements have been associated with a wide range of complex neurological disorders. However, due to their inherent cell type-specificity and difficulties in characterizing their regulatory targets, our ability to identify causal genetic variants has remained limited. To address these constraints, we perform integrative analysis of chromatin interactions using promoter capture Hi-C (pcHi-C), open chromatin regions using ATAC-seq, and transcriptomes using RNA-seq in four functionally distinct neural cell types: iPSC-induced excitatory neurons and lower motor neurons, iPSC-derived hippocampal dentate gyrus (DG)-like neurons, and primary astrocytes. We identify hundreds of thousands of long-range cis interactions between promoters and distal promoter-interacting regions (PIRs), enabling us to link regulatory elements to their target genes and reveal putative pathways that are dysregulated in disease. We validate several novel PIRs using CRISPR techniques in human excitatory neurons, demonstrating that CDK5RAP3, STRAP, and DRD2 are transcriptionally regulated by physically linked enhancers. Finally, we show that physical chromatin interactions mediate genetic interactions in autism spectrum disorder (ASD). Our study illustrates how characterizing the 3D epigenome elucidates novel regulatory relationships in the central nervous system (CNS), shedding light on previously unknown functions for noncoding variants in complex neurological disorders.

genomics↗

bioRxiv2018

Effect of soybean molasses-adsorbents on in vitro ruminal fermentation characteristics, milk production performance in lactating dairy cows

This study aimed to evaluate the in vitro fermentation characteristics of corncob powder (CRP), wheat bran (WB), rice husk (RH), defatted bran (DB) and soybean hulls (SH) when mixed with soybean molasses at a ratio of 30:100 (dry matter basis), using a batch culture incubation. During in vitro study, SH showed better fermentation characteristics (including greater maximum gas production, shorter time to achieve half of Vf, greater concentrations of acetate, propionate and total VFA, and less initial fractional rate of degradation) than other four substrates, while WB had the greatest values of DM and NDF disappearance, NH3-N and butyrate concentrations among substrates. A randomized complete block designed in vivo experiment was conducted with 24 Holstein cows (534 {+/-} 58 kg BW, 2.8 {+/-} 0.7 parity, 129 {+/-} 23 d in milk) randomly assigned to three experimental diets: Control, WB (WB adsorbed to soybean molasses replaced 150 g of corn meal per 1000 g of diet dry matter [DM]) or SH (SH adsorbed to soybean molasses replaced 100 g of wheat bran and 50 g corn meal per 1000 g of diet DM). The results indicated that cows received WB diet had greater (P<0.01) milk fat and total milk solid content than cows fed control and SH diets, and cows received WB and SH diets tended to have greater (P<0.01) milk protein content and blood glutamic-pyruvic transaminase concentration than cows fed control diet. Furtherly, cows received WB diet had greater (P<0.01) blood amylase and lactate dehydrogenase concentration than that of cows fed control diet during middle lactation.\n\nIn conclusion, dietary supplementation of molasses adsorbed by-products like WB and SH have positive effect on promoting rumen fermentation, milk quality and blood metabolism in early- and middle-lactating dairy cows. The results offered a new products and feeding way in dairy farming

animal behavior and cognition↗

bioRxiv2018

SARM1 deficiency, which prevents Wallerian degeneration, upregulates XAF1 and accelerates prion disease

SARM1 (sterile and HEAT/armadillo motifs containing protein) is a member of the MyD88 (myeloid differentiation primary response gene 88) family which mediates innate immune responses. Because inactivation of SARM1 prevents various forms of axonal degeneration, we tested whether it might protect against prion-induced neurotoxicity. Instead, we found that SARM1 deficiency exacerbates the progression of prion pathogenesis. This deleterious effect was not due to SARM1-dependent modulation of prion-induced neuroinflammation, since microglial activation, astrogliosis and brain cytokine profiles were not altered by SARM1 deficiency. Whole-transcriptome analyses indicated that SARM1 deficiency led to strong, selective overexpression of the pro-apoptotic gene XAF1 (X-linked inhibitor of apoptosis-associated factor 1). Consequently, the activity of proapoptotic caspases and neuronal death were enhanced in prion-infected SARM1-/- mice. These results point to an unexpected function of SARM1 as a regulator of prion-induced neurodegeneration, and suggest that XAF1 might constitute a therapeutic target in prion disease.

neuroscience↗

bioRxiv2018

Seasonal diets overwhelm host species in shaping the gut microbiota of Yak and Tibetan sheep

Host genetics and environmental factors can both shaping composition of gut microbiota, yet which factors are more important is still under debating. Yak (Bos grunniens) and Tibetan sheep (Ovis aries) are very different from the size and genetics. Nomadic Tibetan people keep them as main livestock and feeding them with same grazing systems, which provide a good opportunity to study the effects of diet and host species on gut microbiome. We collected fecal samples from yaks and Tibetan sheeps at different seasons when they were feed with different diets. Illumina data showed that major bacterial phyla of both animals are Bacteroidetes and Firmicutes, which agree with the previous reports. And the season effect had a higher impact on the gut microbiota than that of host species, though the animals are taxonomically distinguished each other at subfamily level. Since that the animal grazing differently at different seasons, this study indicated that diet can trump the host genetics even at higher taxonomic level. This finding provides a cautionary note for the researchers to link host genetics to the composition and function of the gut microbiota.\n\nImportanceYak and Tibetan sheep are very different from the size and genetics (from different sub-family). Nomadic Tibetan people keep them as main livestock and feeding them with same grazing systems, which provide a good opportunity to study the effects of diet and host species on the gut microbiota. Results indicated that diet can trump the host genetics even at higher taxonomic level. This finding provides a cautionary note for the researchers to link host genetics to the composition and function of the gut microbiota.

ecology↗

bioRxiv2018

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Single-nucleus RNA-Seq (snRNA-seq) enables the interrogation of cellular states in complex tissues that are challenging to dissociate, including frozen clinical samples. This opens the way, in principle, to large studies, such as those required for human genetics, clinical trials, or precise cell atlases of large organs. However, such applications are currently limited by batch effects, sequential processing, and costs. To address these challenges, we present an approach for multiplexing snRNA-seq, using sample-barcoded antibodies against the nuclear pore complex to uniquely label nuclei from distinct samples. Comparing human brain cortex samples profiled in multiplex with or without hashing antibodies, we demonstrate that nucleus hashing does not significantly alter the recovered transcriptome profiles. We further developed demuxEM, a novel computational tool that robustly detects inter-sample nucleus multiplets and assigns singlets to their samples of origin by antibody barcodes, and validated its accuracy using gender-specific gene expression, species-mixing and natural genetic variation. Nucleus hashing significantly reduces cost per nucleus, recovering up to about 5 times as many single nuclei per microfluidc channel. Our approach provides a robust technique for diverse studies including tissue atlases of isogenic model organisms or from a single larger human organ, multiple biopsies or longitudinal samples of one donor, and large-scale perturbation screens.

genomics↗