Biology subjects

Jiang, Y.

Publications and source records attributed to Jiang, Y..

At least 541 records · Page 30Linked to original sources

bioRxiv2020

Tracing the origin of a new organ by inferring the genetic basis of rumen evolution

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We used 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen origin and evolution. Comparative analyses reveal that the rumen and the first-chamber stomachs of camels and cetaceans shared a common tissue origin from the esophagus. The rumen recruited genes from other tissues/organs and up-regulated many esophagus genes to aquire functional innovations involving epithelium absorption, improvement of the ketone body metabolism and regulation of microbial community. These innovations involve such genetic changes as ruminant-specific conserved elements, newly evolved genes and positively selected genes. Our in vitro experiements validate the functions of one enhancer, one positively selected gene and two newly evolved antibacterial genes. Our study provides novel insights into the origin and evolution of a complex organ.

evolutionary biology↗

bioRxiv2020

Phylogeny and distribution of Y-chromosomal haplotypes in domestic, ancient and wild goats

The male-specific part of the Y-chromosome is in mammalian and many other species the longest haplotype that is inherited without recombination. By its paternal transmission it has a small effective population size in species with dominant males. In several species, Y-chromosomal haplotypes are sensitive markers of population history and introgression. Previous studies have identified in domestic goats four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic differentiation and several regional variants. In this study we used published whole-genome sequences of 70 male goats from 16 modern breeds, 11 ancient-DNA samples and 29 samples from seven wild goat species. We identified single-copy male-specific SNPs in four scaffolds, containing SRY, ZFY, DBY with SSX3Y and UTY, and USP9Y with UMN2001, respectively. Phylogenetic analyses indicated haplogroups corresponding to the haplotypes Y1B, Y2A and Y2B, respectively, but Y1A was split into Y1AA and Y1AB. All haplogroups were detected in ancient DNA samples from southeast Europe and, with the exception of Y1AB, in the bezoar goat, which is the wild ancestor of the domestic goats. Combining these data with those of previous studies and with genotypes obtained by Sanger sequencing or the KASP assay yielded haplogroup distributions for 132 domestic breeds or populations. The phylogeographic differentiation indicated paternal population bottlenecks on all three continents. This possibly occurred during the Neolithic introductions of domestic goats to those continents with a particularly strong influence in Europe along the Danubian route. This study illustrates the power of the Y-chromosomal haplotype for the reconstructing the history of mammalian species with a wide geographic range.

genetics↗

bioRxiv2020

Tensile Force Induced Cytoskeletal Reorganization: Mechanics Before Chemistry

Understanding cellular remodeling in response to mechanical stimuli is a critical step in elucidating mechano-activation of biochemical signaling pathways. Experimental evidence indicates that external stress-induced subcellular adaptation is accomplished through dynamic cytoskeletal reorganization. To study the interactions between subcellular structures involved in transducing mechanical signals, we combined experimental and computational simulations to evaluate real-time mechanical adaptation of the actin cytoskeletal network. Actin cytoskeleton was imaged at the same time as an external tensile force was applied to live vascular smooth muscle cells using a fibronectin-functionalized atomic force microscope probe. In addition, we performed computational simulations of active cytoskeletal networks under a tensile external force. The experimental data and simulation results suggest that mechanical structural adaptation occurs before chemical adaptation during filament bundle formation: actin filaments first align in the direction of the external force, initializing anisotropic filament orientations, then the chemical evolution of the network follows the anisotropic structures to further develop the bundle-like geometry. This finding presents an alternative, novel explanation for the stress fiber formation and provides new insight into the mechanism of mechanotransduction. Author SummaryRemodeling the cytoskeletal network in response to external force is key to mechanosensing and locomotion. Despite much focus on cytoskeletal remodeling in recent years, a comprehensive understanding of actin remodeling in real-time in cells under mechanical stimuli is still lacking. We integrated stress-induced 3D actin imaging and 3D computational simulations of actin cytoskeleton to study how the actin cytoskeleton form bundles and how these bundles evolve over time upon external tensile stress. We found a rapid actin alignment and a slower bundle evolution leading to denser bundles. Based on these results, we propose a "mechanics before chemistry" model of actin cytoskeleton remodeling under external force.

cell biology↗

bioRxiv2020

The origin of domestication genes in goats

Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here we analyze the genomes of worldwide domestic goats, wild caprid species and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7,200 and 8,100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanism of animal domestication. One Sentence SummaryGoat domestication mainly focused on immune and neural genes, with adaptive leaps driven by introgression and selection.

genomics↗

bioRxiv2020

A general role of zinc binding domain revealed by structures of σ28-dependent transcribing complexes

In bacteria, {sigma}28 is the flagella-specific sigma factor that controls the expression of flagella-related genes involving bacterial motility and chemotaxis. However, its transcriptional mechanism remains largely unclear. Here we report cryo-EM structures of {sigma}28-dependent transcribing complexes on a complete flagella-specific DNA promoter. The structures reveal how {sigma}28-RNA polymerase (RNAP) recognizes promoter DNA through strong interaction with -10 element but weak contact with -35 element to initiate transcription. In addition, we observed a distinct architecture in which the {beta}' zinc binding domain (ZBD) of RNAP stretches out from its canonical position to interact with the upstream non-template strand. Further in vitro and in vivo assays demonstrate that this interaction facilitates the isomerization of RNAP-promoter closed to open complex due to compensating the weak interaction between {sigma}4/-35 element, and suggest that ZBD-relocation is a general mechanism employed by the {sigma}70-family factors to enhance transcription from promoters with weak {sigma}4/-35 element interactions.

molecular biology↗

bioRxiv2019

Advanced Whole Genome Sequencing Using a Complete PCR-free Massively Parallel Sequencing (MPS) Workflow

BackgroundSystematic errors can be introduced from DNA amplification during massively parallel sequencing (MPS) library preparation and sequencing array formation. Polymerase chain reaction (PCR)-free genomic library preparation methods were previously shown to improve whole genome sequencing (WGS) quality on the Illumina platform, especially in calling insertions and deletions (InDels). We hypothesized that substantial InDel errors continue to be introduced by the remaining PCR step of DNA cluster generation. In addition to library preparation and sequencing, data analysis methods are also important for the accuracy of the output data.In recent years, several machine learning variant calling pipelines have emerged, which can correct the systematic errors from MPS and improve the data performance of variant calling. ResultsHere, PCR-free libraries were sequenced on the PCR-free DNBSEQ arrays from MGI Tech Co., Ltd. (referred to as MGI) to accomplish the first true PCR-free WGS which the whole process is truly not only PCR-free during library preparation but also PCR-free during sequencing. We demonstrated that PCR-based WGS libraries have significantly (about 5 times) more InDel errors than PCR-free libraries.Furthermore, PCR-free WGS libraries sequenced on the PCR-free DNBSEQ platform have up to 55% less InDel errors compared to the NovaSeq platform, confirming that DNA clusters contain PCR-generated errors.In addition, low coverage bias and less than 1% read duplication rate was reproducibly obtained in DNBSEQ PCR-free using either ultrasonic or enzymatic DNA fragmentation MGI kits combined with MGISEQ-2000. Meanwhile, variant calling performance (single-nucleotide polymorphisms (SNPs) F-score>99.94%, InDels F-score>99.6%) exceeded widely accepted standards using machine learning (ML) methods (DeepVariant or DNAscope). ConclusionsEnabled by the new PCR-free library preparation kits, ultra high-thoughput PCR-free sequencers and ML-based variant calling, true PCR-free DNBSEQ WGS provides a powerful solution for improving WGS accuracy while reducing cost and analysis time, thus facilitating future precision medicine, cohort studies, and large population genome projects.

genomics↗

bioRxiv2019

Reward produces learning of a consciously inaccessible feature

Reward has significant impacts on behavior and perception. Most past work in associative reward learning has used distinct visual cues to associate with different reward values. Thus, it remains unknown to what extent the learned associations depend on the consciousness. Here we resolved this issue by using an inter-ocular suppression paradigm with the monetary rewarding and non-rewarding cues identical to each other except for the eye-of-origin. Thus, the reward coding system cannot rely on the consciousness to select the reward-associated cue. Surprisingly, the targets in the rewarded eye broke into awareness faster than those in the non-rewarded eye. We further revealed that producing this effect required both attention and inter-ocular suppression. These findings suggest that the humans reward coding system can produce two different types of reward-based learning. One is independent of the consciousness yet fairly consuming attentional resource. The other one results from volitional selections guided by top-down attention.

neuroscience↗

bioRxiv2019

YSL3-mediated copper distribution is required for fertility, grain yield, and size in Brachypodium.

Addressing the looming global food security crisis requires the development of high yielding crops. In this regard, the deficiency for the micronutrient copper in agricultural soils decreases grain yield and significantly impacts a globally important crop, wheat. In cereals, grain yield is determined by inflorescence architecture, flower fertility, grain size and weight. Whether copper is involved in these processes and how it is delivered to the reproductive organs is not well understood. We show that copper deficiency alters not only the grain set but also flower development in both wheat and its recognized model, Brachypodium distachyon, We then show that a brachypodium yellow-stripe-like 3 (YSL3) transporter localizes to the phloem and mediates copper delivery to flag leaves, anthers and pistils. Failure to deliver copper to these structures in the ysl3 CRISPR/Cas9 mutant results in delayed flowering, altered inflorescence architecture, reduced floret fertility, grain number, size, and weight. These defects are rescued by copper supplementation and are complemented by the YSL3 cDNA. This new knowledge will help to devise sustainable approaches for improving grain yield in regions where soil quality is a major obstacle for crop production.

plant biology↗

bioRxiv2019

Visualization of two architectures in class-II CAP-dependent transcription activation

Transcription activation by cyclic AMP receptor protein (CAP) is the classic paradigm of transcription regulation in bacteria. CAP was suggested to activate transcription on class-II promoters via a recruitment and isomerization mechanism. However, whether and how it modifies RNA polymerase (RNAP) to initiate transcription remains unclear. Here we report cryo-EM structures of an intact E. coli class-II CAP-dependent transcription activation complex (TAC) with and without de novo RNA transcript. The structures reveal two distinct architectures of TAC and show that CAP-binding induces substantial conformational changes in all the subunits of RNAP and consequently widens the main cleft of RNAP considerably to facilitate DNA promoter entering and formation of initiation open complex. These structural changes vanish during further RNA transcript synthesis. The observations in this study suggest a unique activation mechanism on class-II promoters that CAP activates transcription by first remodeling RNAP conformation and then stabilizing initiation complex.

molecular biology↗

bioRxiv2019

Physiological and genomic analysis of Candidatus Nitrosocosmicus agrestis, an ammonia tolerant ammonia-oxidizing archaeon from vegetable soil

The presences of ammonia tolerant ammonia-oxidizing archaea (AOA) in environments are always underestimated and their adaption to complex habitats has also rarely been reported. Here we present the physiological and genomic characteristics of an ammonia tolerant soil AOA strain Candidatus Nitrosocosmicus agrestis. This strain was able to form aggregates and adhere on the surface of hydrophobic matrix. Ammonia-oxidizing activities were still observed at 200 mM NH4+ (> 1500 M of free ammonia) and 50 mM NO2-. Urea could be used as sole energy source but exogenous organics had no significant effect on the ammonia oxidation. Besides the genes involving in ammonia oxidation, carbon fixation and urea hydrolysis, the genome also encodes a full set of genes (GTs, GHs, CEs, MOP, LPSE, etc) that responsible for polysaccharide metabolism and secretion, suggesting the potential production of extracellular polymeric substances (EPS). Moreover, a pathway connecting urea cycle, polyamines synthesis and excretion was identified in the genome, which indicates the NH4+ in cytoplasm could potentially be converted into polyamines and excreted out of cell, and then contributes to the high ammonia tolerance. Genes encoding the cytoplasmic carbonic anhydrase and putative polyamine exporter are unique in Ca. Nitrosocosmicus agrestis or the genus Ca. Nitrosocosmicus, suggesting the prevalence of ammonia tolerance in this clade. The proposed mechanism of ammonia tolerance via polyamines synthesis and export was verified by using transcriptional gene regulation and polyamines determination. IMPORTANCEAOA are ubiquitous in different environments and play a major role in nitrification. Though AOA have higher affinities for ammonia, their maximum specific cell activity and ammonia tolerance are usually much lower than AOB, resulting in low contribution to the global ammonia oxidation and N2O production. However, in some agricultural soils, the AOA activity would not be suppressed by the fertilization with high concentration of ammonium nitrogen, suggesting the presence of some ammonia tolerant species. This study provides some physiological and genomic characteristics for an ammonia tolerant soil AOA strain Ca. Nitrosocosmicus agrestis and proposes some mechanisms of this AOA adapting to a variety of environments and tolerating to high ammonia. Ammonia tolerance of AOA was always underestimated in many previous studies, physiological and genomic analyses of this AOA clade are benefit to uncover the role of AOA playing in global environmental patterns.

microbiology↗

bioRxiv2019

Global gene expression profile during low temperature in the brain of grass carp (Ctenopharyngodon idellus)

Grass carp is an important commercial fish widely cultured in China. Large range of temperature, in particular extremely low temperature, has dramatic effects on the aquaculture of this teleost. However, there is relatively little research on the molecular responses in the fish exposed to cold. Given the limited vision of approaches targeting individual genes, we investigated the transcriptome profiles of brain in response to cold in order to comprehensively characterize molecular mechanisms behind it. This study indicated that the estrogen signaling pathway was inhibited in brain when grass carp acclimated to low temperature, while terpenoid backbone biosynthesis pathway and steroid biosynthesis pathway were significantly activated. Such a result implied the crucial role of cholesterol in cold acclimation. Moreover, plenty of differentially expressed genes associated with spliceosomes were enriched during cooling process, which suggested alternative splicing may be involved in the regulation of biological process in acclimation to temperature changes. In researches on extremely low-temperature tolerance, we identified four genes (DUSP1, HSPA6, NR4A1 and GADD45B) associated with MAPK signaling pathway. The four genes, extensively up-regulated at 4{degrees}C and remained relatively low expression at moderate temperature, were closely related with extremely cold condition. Further examination of the candidate genes can provide insights into the mechanisms of grass carp to endure extremely low temperature in the winter.

zoology↗

bioRxiv2019

Insulin signal transduction is impaired in the type 2 diabetic retina

Rates of type 2 diabetes are reaching epidemic levels. Yet, the tissue specific alterations due to insulin resistance are only recently being investigated. The goal of the present study was to evaluate retinal insulin signal transduction in a common mouse model of type 2 diabetes, the db/db mouse. Retinal lysates from five month old male db/db and db/+ (control) mice were collected and processed for Western blotting or ELISA analyses for insulin receptor, insulin receptor substrate-1 (IRS-1), Akt, tumor necrosis factor alpha (TNF) and caspase 3 levels. Data demonstrate increased TNF and IRS-1 phosphorylation on serine 307. This led to decreased Akt phosphorylation on serine 473 and increased cleavage of caspase 3. Taken together, the data suggest dysfunctional insulin signaling in the retina of the db/db mouse.

cell biology↗

bioRxiv2019

Fluorescence correlation spectroscopy and photon count histograms in small domains. Part I: General theory

Analysis of fluctuations arising as fluorescent particles pass through a focused laser beam has enabled quantitative characterization of molecular kinetic processes. The mathematical frameworks of both fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analysis, which can measure these fluctuations, assume an infinite Gaussian beam, which prevents their application to particles within domains bounded at the nanoscale. We therefore derived general forms of FCS and PCH for bounded systems. The finite domain form of FCS differs from the classical form in its boundary and initial conditions and requires development of a new Fourier space solution for fitting data. Our finite-domain FCS predicts simulated data accurately and reduces to a previous model for the special case of molecules confined by two boundaries under Gaussian beams. Our approach enables estimation of the concentration of diffusing fluorophores within a finite domain for the first time. The method opens the possibility of quantification of kinetics in several systems for which this has never been possible, including in the one-dimensional lipid tubules discussed in Part 2 of this paper. Statement of SignificanceMethods based on fluorescence measurements of molecular concentration fluctuations, including Fluorescence Correlation Spectroscopy and Photon Count Histogram analysis, are widely used to determine rates of diffusion, chemical reaction and sizes of molecular aggregates. Typically, the range over which the molecules can diffuse is large compared to the size of the focused laser beam that excites the fluorescence. This work extends these measurements to systems that are comparable in size to the excitation laser beam. This extends the application of these methods to very small samples such as the interior of bacterial cells or the diffusion of molecules along individual macromolecules such as DNA.

biophysics↗

bioRxiv2019

Germline and somatic genetic variants in the p53 pathway interact to affect cancer risk, progression and drug response

Insights into oncogenesis derived from cancer susceptibility loci could facilitate better cancer management and treatment through precision oncology. However, therapeutic applications have thus far been limited by our current lack of understanding regarding both their interactions with somatic cancer driver mutations and their influence on tumorigenesis. Here, by integrating germline datasets relating to cancer susceptibility with tumour data capturing somatically-acquired genetic variation, we provide evidence that single nucleotide polymorphism (SNPs) and somatic mutations in the p53 tumor suppressor pathway can interact to influence cancer development, progression and treatment response. We go on to provide human genetic evidence of a tumor-promoting role for the pro-survival activities of p53, which supports the development of more effective therapy combinations through their inhibition in cancers retaining wild-type p53. SignificanceWe describe significant interactions between heritable and somatic genetic variants in the p53 pathway that affect cancer susceptibility, progression and treatment response. Our results offer evidence of how cancer susceptibility SNPs can interact with cancer driver genes to affect cancer progression and identify novel therapeutic targets.

cancer biology↗

bioRxiv2019

TP63, SOX2 and KLF5 Establish Core Regulatory Circuitry and Construct Cancer Specific Epigenome in Esophageal Squamous Cell Carcinoma

Transcriptional network is controlled by master transcription factors (TFs) and cis-regulatory elements through interacting with target sequences and recruiting epigenetic regulators. By integration of enhancer profiling and chromatin accessibility, we establish super-enhancer (SE) mediated core regulatory circuitry (CRC) for esophageal squamous cell carcinoma (ESCC) and identify tumor cells-dependent CRC TFs-TP63, SOX2 and KLF5. They preferentially co-occupy SE loci and form a positive interconnected auto-regulatory loop through SEs to orchestrate chromatin and transcriptional programming. SE-associated oncogene-ALDH3A1 is identified as a novel CRC target contributing to ESCC viability. Using circular chromosome conformation capture sequencing (4C-seq) and CRISPR/Cas9 genome editing, the direct interaction between TP63 promoter and functional enhancers which is mediated by CRC TFs is identified. Deletion of each enhancer decreases expression of CRC TFs and impairs cell viability, phenocopying the knockdown of each CRC TF. Targeting epigenetic regulation by inhibition of either the BET bromodomain or HDAC disrupts the CRC program and its dependent global epigenetic modification, consequently suppressing ESCC tumor growth. Importantly, combination of both compounds result in synergistic anti-tumor effect.\n\nGraphical Abstract\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC=\"FIGDIR/small/825372v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (58K):\norg.highwire.dtl.DTLVardef@1a9f923org.highwire.dtl.DTLVardef@238c90org.highwire.dtl.DTLVardef@1e14f58org.highwire.dtl.DTLVardef@120249a_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LISuper-enhancers mediated transcriptional regulatory circuitry is established for ESCC\nC_LIO_LITP63, SOX2 and KLF5 as CRC TFs co-localize super-enhancer loci to orchestrate chromatin accessibility and transcriptional dysregulation\nC_LIO_LIComplex interaction between functional enhancers and TP63 promoter is mediated by CRC TFs\nC_LIO_LIALDH3A1 is a key downstream target of ESCC CRC and is essential for ESCC cell survival\nC_LIO_LIBET degrader-ARV-771 and HDAC inhibitor-Romidepsin synergistically inhibit ESCC tumor growth\nC_LI

cancer biology↗

bioRxiv2019

DRAMS: A Tool to Detect and Re-Align Mixed-up Samples for Integrative Studies of Multi-omics Data

Studies of complex disorders benefit from integrative analyses of multiple omics data. Yet, sample mix-ups frequently occur in multi-omics studies, weakening statistical power and risking false findings. Accurately aligning sample information, genotype, and corresponding omics data is critical for integrative analyses. We developed DRAMS (https://github.com/Yi-Jiang/DRAMS) to Detect and Re-Align Mixed-up Samples to address the sample mix-up problem. It uses a logistic regression model followed by a modified topological sorting algorithm to identify the potential true IDs based on data relationships of multi-omics. According to tests using simulated data, the more types of omics data used or the smaller the proportion of mix-ups, the better that DRAMS performs. Applying DRAMS to real data from the PsychENCODE BrainGVEX project, we detected and corrected 201 (12.5% of total data generated) mix-ups. Of the 21 mix-ups involving errors of racial identity, DRAMS re-assigned all samples to the correct racial cluster in the 1000 Genomes project. In doing so, quantitative trait loci (QTL) (FDR<0.01) increased by an average of 1.62-fold. The use of DRAMS in multi-omics studies will strengthen statistical power of the study and improve quality of the results. Even though very limited studies have multi-omics data in place, we expect such data will increase quickly with the needs of DRAMS.\n\nAuthor summarySample mix-up happens inevitably during sample collection, processing, and data management. It leads to reduced statistical power and sometimes false findings. It is of great importance to correct mixed-up samples before conducting any downstream analyses. We developed DRAMS to detect and re-align mixed-up samples in multi-omics studies. The basic idea of DRAMS is to align the data and labels for each sample leveraging the genetic information of multi-omics data. DRAMS corrects sample IDs following a two-step strategy. At first, it estimates pairwise genetic relatedness among all the data generated from all the individuals. Because the different data generated from the same individual should share the same genetics, we can cluster all the highly related data and consider that the data from one cluster have only one potential ID. Then, we used a \"majority vote\" strategy to infer the potential ID for individuals in each cluster. Other information, such as match of genetics-based and reported sexes, omics priorority, etc., were also used to direct identifying the potential IDs. It has been proved that DRAMS performs very well in both simulation and PsychENCODE BrainGVEX multi-omics data.

bioinformatics↗

bioRxiv2019

α-ketoglutaric acid stimulates muscle hypertrophy and fat loss through OXGR1-dependent adrenal activation

Beneficial effects of resistance exercise on metabolic health and particularly muscle hypertrophy and fat loss are well established, but the underlying chemical and physiological mechanisms are not fully understood. Here we identified a myometabolite-mediated metabolic pathway that is essential for the beneficial metabolic effects of resistance exercise in vivo. We showed that substantial accumulation of the tricarboxylic acid cycle intermediate -ketoglutaric acid (AKG) is a metabolic signature of resistance exercise performance. Interestingly, human plasma AKG level is also negatively correlated with BMI. Pharmacological elevation of circulating AKG induces muscle hypertrophy, brown adipose tissue (BAT) thermogenesis, and white adipose tissue (WAT) lipolysis in vivo. We further found that AKG stimulates the adrenal release of adrenaline through 2-oxoglutarate receptor 1 (OXGR1) expressed in adrenal glands. Finally, by using both loss-of-function and gain-of-function mouse models, we showed that OXGR1 is essential for AKG-mediated exercise-induced beneficial metabolic effects. These findings reveal an unappreciated mechanism for the salutary effects of resistance exercise, using AKG as a systemically-derived molecule for adrenal stimulation of muscle hypertrophy and fat loss.

molecular biology↗

bioRxiv2019

Sample demultiplexing, multiplet detection, experiment planning and novel cell type verification in single cell sequencing

Identifying and removing multiplets from downstream analysis is essential to improve the scalability and reliability of single cell RNA sequencing (scRNA-seq). High multiplet rates create artificial cell types in the dataset. Sample barcoding, including the cell hashing technology and the MULTI-seq technology, enables analytical identification of a fraction of multiplets in a scRNA-seq dataset.\n\nWe propose a Gaussian-mixture-model-based multiplet identification method, GMM-Demux. GMM-Demux accurately identifies and removes the sample-barcoding-detectable multiplets and estimates the percentage of sample-barcoding-undetectable multiplets in the remaining dataset. GMM-Demux describes the droplet formation process with an augmented binomial probabilistic model, and uses the model to authenticate cell types discovered from a scRNA-seq dataset.\n\nWe conducted two cell-hashing experiments, collected a public cell-hashing dataset, and generated a simulated cellhashing dataset. We compared the classification result of GMM-Demux against a state-of-the-art heuristic-based classifier. We show that GMM-Demux is more accurate, more stable, reduces the error rate by up to 69x, and is capable of reliably recognizing 9 multiplet-induced fake cell types and 8 real cell types in a PBMC scRNA-seq dataset.

bioinformatics↗