Biology subjects

Li, D.

Publications and source records attributed to Li, D..

At least 343 records · Page 19Linked to original sources

bioRxiv2023

A genome-wide CRISPR screen in human prostate cancer cells reveals drivers of macrophage-mediated cell killing and positions AR as a tumor-intrinsic immunomodulator

The crosstalk between prostate cancer (PCa) cells and the tumor microenvironment plays a pivotal role in disease progression and metastasis and could provide novel opportunities for patient treatment. Macrophages are the most abundant immune cells in the prostate tumor microenvironment (TME) and are capable of killing tumor cells. To identify genes in the tumor cells that are critical for macrophage-mediated killing, we performed a genome-wide co-culture CRISPR screen and identified AR, PRKCD, and multiple components of the NF-{kappa}B pathway as hits, whose expression in the tumor cell are essential for being targeted and killed by macrophages. These data position AR signaling as an immunomodulator, and confirmed by androgen-deprivation experiments, that rendered hormone-deprived tumor cells resistant to macrophage-mediated killing. Proteomic analyses showed a downregulation of oxidative phosphorylation in the PRKCD- and IKBKG-KO cells compared to the control, suggesting impaired mitochondrial function, which was confirmed by electron microscopy analyses. Furthermore, phosphoproteomic analyses revealed that all hits impaired ferroptosis signaling, which was validated transcriptionally using samples from a neoadjuvant clinical trial with the AR-inhibitor enzalutamide. Collectively, our data demonstrate that AR functions together with the PRKCD and the NF-{kappa}B pathway to evade macrophage-mediated killing. As hormonal intervention represents the mainstay therapy for treatment of prostate cancer patients, our findings may have direct implications and provide a plausible explanation for the clinically observed persistence of tumor cells despite androgen deprivation therapy.

cancer biology↗

bioRxiv2023

HDAC4-mediated deacetylation of GSDMD prevents pyroptosis by inhibiting GSDMD ubiquitination

Gasdermin D (GSDMD) functions as a key pyroptotic executor and induces cytokine secretion after cleavage by inflammatory caspases. However, less is known about the role of posttranslational modifications (PTMs) in GSDMD-mediated pyroptosis. Here, we report that GSDMD can be acetylated at Lysine 248 residue and the acetylation of GSDMD promotes pyroptosis. We identified histone deacetylase 4 (HDAC4) as the specific deacetylase that mediates GSDMD deacetylation and subsequent pyroptosis inhibition in vitro and in vivo. GSDMD deacetylation impairs the ubiquitination of GSDMD, for which pyroptosis is inhibited. Interestingly, the phosphorylation of HDAC4 is important for its ability of deacetylating GSDMD and suppressing GSDMD-mediated pyroptosis. The Protein phosphatase 1 (PP1) catalytic subunits (PP1 and PP1{gamma}) mediate the dephosphorylation of HDAC4, thereby abrogating its deacetylase activity on GSDMD. Therefore, our work unravels a complex regulatory mechanism involving HDAC4, PP1 and GSDMD, and provides novel insights into the crosstalk among acetylation, ubiquitination and phosphorylation.

cell biology↗

bioRxiv2023

Phage anti-CBASS protein simultaneously sequesters cyclic trinucleotides and dinucleotides

CBASS is a common anti-phage immune system that uses cyclic oligonucleotide signals to activate effectors and limit phage replication. In turn, phages encode anti-CBASS (Acb) proteins. We recently uncovered a widespread phage anti-CBASS protein Acb2 that acts as a "sponge" by forming a hexamer complex with three cGAMP molecules. Here, we identified that Acb2 binds and sequesters many CBASS and cGAS-produced cyclic dinucleotides in vitro and inhibits cGAMP-mediated STING activity in human cells. Surprisingly, Acb2 also binds CBASS cyclic trinucleotides 333-cyclic AMP-AMP-AMP (cA3) and 333-cAAG with high affinity. Structural characterization identified a distinct binding pocket within the Acb2 hexamer that binds two cyclic trinucleotide molecules and another binding pocket that binds to cyclic dinucleotides. Binding in one pocket does not allosterically alter the other, such that one Acb2 hexamer can simultaneously bind two cyclic trinucleotides and three cyclic dinucleotides. Phage-encoded Acb2 provides protection from Type III-C CBASS that uses cA3 signaling molecules in vivo and blocks cA3-mediated activation of the endonuclease effector in vitro. Altogether, Acb2 sequesters nearly all known CBASS signaling molecules through two distinct binding pockets and therefore serves as a broad-spectrum inhibitor of cGAS-based immunity.

microbiology↗

bioRxiv2023

Individualized network analysis reveals a link between the gut microbiome, diet intervention and Gestational Diabetes Mellitus

Gestational Diabetes Mellitus (GDM), a serious complication during pregnancy which is defined by abnormal glucose regulation, is commonly treated by diabetic diet and lifestyle changes. While recent findings place the microbiome as a natural mediator between diet interventions and diverse disease states, its role in GDM is still unknown. Here, based on observation data from healthy pregnant control group and GDM patients, we developed a new network approach using patterns of co-abundance of microorganism to construct microbial networks that represent human-specific information about gut microbiota in different groups. By calculating network similarity in different groups, we analyze the gut microbiome from 27 GDM subjects collected before and after two weeks of diet therapy compared with 30 control subjects to identify the health condition of microbial community balance in GDM subjects. Although the microbial communities remain similar after the diet phase, we find that the structure of their inter-species co-abundance network is significantly altered, which is reflected in that the ecological balance of GDM patients was not "healthier" after the diet intervention. In addition, we devised a method for individualized network analysis of the microbiome, thereby a pattern is found that individuals with large deviations in microbial networks are usually accompanied by their abnormal glucose regulation. This approach may help the development of individualized diagnosis strategies and microbiome-based therapies in the future. Author SummaryIn this study, we aimed to investigate the role of the gut microbiome in gestational diabetes mellitus (GDM), a condition that affects pregnant women and is characterized by abnormal glucose regulation. Specifically, we asked whether and how the gut microbiome is affected by diabetic diet which is commonly used to treat GDM patients. We developed a new network approach to analyze patterns of co-abundance of microorganisms in the gut microbiota of GDM patients and healthy pregnant women. Our findings show that although the microbial communities remained similar after the diet phase, the structure of their inter-species co-abundance network was significantly altered, indicating that the ecological balance of GDM patients was not "healthier" after the diet intervention. Furthermore, we suggest that abnormal glucose regulation is associated with large network deviations, which could lead to the development of individualized microbiome-based therapies in the future. Our work highlights the importance of studying the microbiome from a network perspective to better understand the dynamic interactions among microorganisms in the community balance of the microbiome.

systems biology↗

bioRxiv2023

Phase-encoded fMRI tracks down brainstorms of natural language processing with sub-second precision

The human language system interacts with cognitive and sensorimotor regions during natural language processing. However, where, when, and how these processes occur remain unclear. Existing noninvasive subtraction-based neuroimaging techniques cannot simultaneously achieve the spatial and temporal resolutions required to visualize ongoing information flows across the whole brain. Here we have developed phase-encoded designs to fully exploit the temporal information latent in functional magnetic resonance imaging (fMRI) data, as well as overcoming scanner noise and head-motion challenges during overt language tasks. We captured neural information flows as coherent waves traveling over the cortical surface during listening, reciting, and oral cross-language interpreting. The timing, location, direction, and surge of traveling waves, visualized as brainstorms on brain weather maps, reveal the functional and effective connectivity of the brain in action. These maps uncover the functional neuroanatomy of language perception and production and motivate the construction of finer-grained models of human information processing.

neuroscience↗

bioRxiv2023

All-optical interrogation of brain-wide activity in freely swimming larval zebrafish

We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in freely swimming larval zebrafish. The system consists of three main components: a 3D tracking module, a dual color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior. HighlightsO_LIWe develop an all-optical technique that enables simultaneous whole brain imaging and optogenetic manipulation of selective brain regions in freely behaving larval zebrafish. C_LIO_LIA combination of a genetically encoded calcium indicator and a long Stokes-shift red fluorescence protein, together with the adaptive filter algorithm, enables us to reliably distinguish calcium activity from motion-induced signal contamination. C_LIO_LIRapid 3D image reconstruction and registration enables real-time targeted optogenetic stimulation of distinct brain regions in a freely swimming larval zebrafish. C_LI

neuroscience↗

bioRxiv2023

Genomic and transcriptomic analysis revealed new insights into the influence of key T6SS genes hcp and vgrG on drug resistance and interbacterial competition in Klebsiella pneumoniae

Type VI secretion systems (T6SSs) act as a molecular weapon in interbacterial competition and play an important role in cell-cell interactions. Different species of bacteria use their T6SSs to perform a variety of functions according to ecological niche. Therefore, it is necessary to better understand the T6SS potential of Klebsiella pneumoniae (K. pneumoniae), a common clinical opportunistic pathogen. Here, we conducted a genomic analysis on the evolution, T6SS, virulence and antimicrobial resistance of 65 K. pneumoniae in patients with different infections. And we combined transcriptome analysis after knockout of key gene in T6SS of this species. Results showed that genes encoding a T6SS were present in all K. pneumoniae in this study, and there was no correlation was found between T6SS cluster and carbapenem resistance and virulence genes. Differentially expressed genes (DEGs) including 1298 co-upregulated and 1714 co-downregulated were identified after hcp or vgrG deletion. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis have demonstrated common changes in quorum sensing, propionate metabolism and other pathways. And we found that the deletion of hcp or vgrG genes up-regulated of beta-lactam (blaKPC-2) and other resistance genes. Interbacterial competition experiments showed that hcp and vgrG are essential genes for competitive ability of ST11 K. pneumoniae. Taken together, the entire study provides further insight into the investigation of T6SS in K. pneumoniae through genomic and transcriptomic analysis. ImportanceGram-negative bacteria use T6SS to deliver toxin effectors to interact with neighboring cells for niche advantage. K. pneumoniae is an opportunistic nosocomial pathogen that often carriers multiple cope T6SSs, but the function of its T6SS has not yet elucidated. Here, we performed a genomic analysis of 65 clinical K. pneumoniae strains, in order to explore the relationship between T6SS and virulence and resistance genes. We also study the repertoire after knockout of key gene in T6SS of this species by transcriptomics. It was suggested that T6SS is associated with drug resistance, and its key genes hcp and vgrG are critical for the interspecies competition of K. pneumoniae.

microbiology↗

bioRxiv2023

Background matching can reduce responsiveness of jumping spiders to stimuli in motion

Motion and camouflage were previously considered to be mutually exclusive, as sudden movements can be easily detected. Background matching, for instance, is a well-known, effective camouflage strategy where the color and pattern of a stationary animal match its surrounding background. However, background matching may lose its efficacy when the animal moves, as the boundaries of the animal become more defined against its background. Recent evidence shows otherwise, as camouflaged objects can be less detectable than uncamouflaged objects even while in motion. Here, we explored if the detectability of computer-generated stimuli varies with the speed of motion, background (matching and unmatching) and size of stimuli in six species of jumping spiders (Araneae: Salticidae). Our results showed that in general, the responsiveness of all six salticid species tested decreased with increasing stimulus speed regardless of whether the stimuli were conspicuousness or camouflaged. Importantly, salticid responses to camouflaged stimuli were significantly lower compared to conspicuous stimuli. There were significant differences in motion detectability across species when the stimuli were conspicuous, suggesting differences in visual acuity in closely related species of jumping spiders. Furthermore, small stimuli elicited significantly lower responses than large stimuli across species and speeds. Our results thus suggest that background matching is effective even when stimuli are in motion, reducing the detectability of moving stimuli. Summary StatementContrary to belief, stimuli in motion can remain camouflaged against their backgrounds. Using computer-generated stimuli, we show that smaller and faster stimuli against camouflaged background elicit lower responses from jumping spiders.

animal behavior and cognition↗

bioRxiv2023

Loss of IRF5 increases ribosome biogenesis leading to alterations in mammary gland architecture and metastasis

Despite the progress made in identifying cellular factors and mechanisms that predict progression and metastasis, breast cancer remains the second leading cause of death for women in the US. Using The Cancer Genome Atlas and mouse models of spontaneous and invasive mammary tumorigenesis, we identified that loss of function of interferon regulatory factor 5 (IRF5) is a predictor of metastasis and survival. Histologic analysis of Irf5-/- mammary glands revealed expansion of luminal and myoepithelial cells, loss of organized glandular structure, and altered terminal end budding and migration. RNA-seq and ChIP-seq analyses of primary mammary epithelial cells from Irf5+/+ and Irf5-/-littermate mice revealed IRF5-mediated transcriptional regulation of proteins involved in ribosomal biogenesis. Using an invasive model of breast cancer lacking Irf5, we demonstrate that IRF5 re-expression inhibits tumor growth and metastasis via increased trafficking of tumor infiltrating lymphocytes and altered tumor cell protein synthesis. These findings uncover a new function for IRF5 in the regulation of mammary tumorigenesis and metastasis. HighlightsLoss of IRF5 is a predictor of metastasis and survival in breast cancer. IRF5 contributes to the regulation of ribosome biogenesis in mammary epithelial cells. Loss of IRF5 function in mammary epithelial cells leads to increased protein translation.

cancer biology↗

bioRxiv2023

ZBP1-mediated macrophage necroptosis inhibits ASFV replication

African swine fever (ASF) is an infectious disease characterized by hemorrhagic fever, highly pathogenic, and severe mortality in domestic pigs caused by the African swine fever virus (ASFV). ASFV is a large DNA virus and primarily infects porcine monocyte macrophages. The interaction between ASFV and host macrophages is the major reason for gross pathological lesions caused by ASFV. Necroptosis is an inflammatory programmed cell death and plays an important immune role during virus infection. However, whether and how ASFV induces macrophage necroptosis and what effect of necroptosis signaling on host immunity and ASFV infection remains unknown. This study uncovered that ASFV activates the necroptosis signaling in the spleen, lung, liver, and kidney from ASFV-infected pigs. And macrophage necroptosis also was induced by ASFV infection in vitro. Further evidence showed that the macrophage necroptosis is independent of TNF--RIPK1 or TLR-TRIF pathway but depends on Z-DNA binding protein 1 (ZBP1). ASFV infection upregulates the expression of ZBP1 and RIPK3 to consist of the ZBP1-RIPK3-MLKL necrosome and further activates macrophage necroptosis. Subsequently, multiple Z-DNA sequences were predicted to be present in the ASFV genome. And the Z-DNA signals were further confirmed to be present and colocalized with ZBP1 in the cytoplasm and nucleus of ASFV-infected cells. Moreover, ZBP1-mediated macrophage necroptosis caused the extracellular release of proinflammatory cytokines TNF- and IL-1{beta} induced by ASFV infection. Finally, we demonstrated that ZBP1-mediated necroptosis signaling significantly inhibits ASFV replication in host macrophages. Our findings uncovered a novel mechanism by which ASFV induces macrophage necroptosis by facilitating Z-DNA accumulation and ZBP1 necrosome assembly, providing significant insights into the pathogenesis of ASFV infection. ImportanceASFV infection causes an acute, febrile, hemorrhagic, and severely lethal disease in swine, which seriously threatens the global porcine industry. Understanding the interaction mechanism between ASFV and host macrophages during infection is essential for elucidating the pathogenesis of ASFV. To our knowledge, this study revealed the interaction mechanism between ASFV infection and host macrophage necroptosis. The results showed that ASFV infection induces macrophage necroptosis through ZBP1 activation instead of the TNF--RIPK1 or TLR-TRIF pathway. ASFV infection promotes Z-DNA accumulation, which causes ZBP1-RIPK3-MLKL necrosome assembly and macrophage necroptosis. The ZBP1-mediated necroptosis signaling facilitates the extracellular release of proinflammatory cytokines, inhibiting ASFV replication in host macrophages. This study found a new interaction mechanism between ASFV and host macrophages, which may help understand the pathogenesis caused by ASFV infection.

microbiology↗

bioRxiv2023

Endocardial HDAC3 is required for myocardial trabeculation

Failure of proper ventricular trabeculation is often associated with congenital heart disease (CHD). Support from endocardial cells, including the secretion of extracellular matrix (ECM) and growth factors is critical for trabeculation. However, it is poorly understood how the secretion of ECM and growth factors is initiated and regulated by endocardial cells. We found that genetic knockout (KO) of histone deacetylase 3 (Hdac3) in the endocardium in mice resulted in early embryo lethality and ventricular hypotrabeculation. Single cell RNA sequencing identified significant downregulation of ECM components in Hdac3 KO endocardial cells. Secretome from cultured Hdac3 KO mouse cardiac endothelial cells lacked transforming growth factor {beta}3 (TGF{beta}3) and showed significantly reduced capacity in stimulating cultured cardiomyocyte proliferation, which was remarkably rescued by TGF{beta}3 supplementation. Mechanistically, we identified that HDAC3 induced Tgf{beta}3 expression through repressing microRNA (miR)-129-5p. Our findings provide novel insights into the pathogenesis of CHD and conceptual strategies to promote myocardial regeneration.

developmental biology↗

bioRxiv2023

Amoeboid cells undergo durotaxis with soft end polarized NMIIA

Cell migration towards stiff substrates has been coined as durotaxis and implicated in development, wound healing and cancer, where complex interplays between immune and non-immune cells are present. Compared to the emerging mechanisms underlying the strongly adhesive mesenchymal durotaxis, little is known about whether immune cells - migrating in amoeboid mode - could follow mechanical cues. Here we develop an imaging-based confined migration device with stiffness gradient. By tracking live cell trajectory and analyzing the directionality of T cells and neutrophils, we observe that amoeboid cells can durotax. We further delineate the underlying mechanism to involve non-muscle myosin IIA (NMIIA) polarization towards the soft-matrix-side but may not require differential actin flow up- or down-stiffness gradient. Using the protista Dictyostelium, we demonstrate the evolutionary conservation of amoeboid durotaxis. Finally, these experimental phenomena are theoretically captured by an active gel model capable of mechanosensing. Collectively, these results may shed new lights on immune surveillance and recently identified confined migration of cancer cells, within the mechanically inhomogeneous tumor microenvironment or the inflamed fibrotic tissues.

cell biology↗

bioRxiv2023

Comparative single cell epigenomic analysis of gene regulatory programs in the rodent and primate neocortex

Sequence divergence of cis-regulatory elements drives species-specific traits, but how this manifests in the evolution of the neocortex at the molecular and cellular level remains to be elucidated. We investigated the gene regulatory programs in the primary motor cortex of human, macaque, marmoset, and mouse with single-cell multiomics assays, generating gene expression, chromatin accessibility, DNA methylome, and chromosomal conformation profiles from a total of over 180,000 cells. For each modality, we determined species-specific, divergent, and conserved gene expression and epigenetic features at multiple levels. We find that cell type-specific gene expression evolves more rapidly than broadly expressed genes and that epigenetic status at distal candidate cis-regulatory elements (cCREs) evolves faster than promoters. Strikingly, transposable elements (TEs) contribute to nearly 80% of the human-specific cCREs in cortical cells. Through machine learning, we develop sequence-based predictors of cCREs in different species and demonstrate that the genomic regulatory syntax is highly preserved from rodents to primates. Lastly, we show that epigenetic conservation combined with sequence similarity helps uncover functional cis-regulatory elements and enhances our ability to interpret genetic variants contributing to neurological disease and traits.

genomics↗

bioRxiv2023

Deep Learning Enhanced Fast Fluorescence Lifetime Imaging with A Few Photons

We present a deep learning (DL) framework, which we term FPFLI (Few-Photon Fluorescence Lifetime Imaging), for fast analyzing fluorescence lifetime imaging (FLIM) data under highly low-light conditions with only a few photon-per-pixels (PPPs). FPFLI breaks the conventional pixel-wise lifetime analysis paradigm and fully exploits the spatial correlation and intensity information of fluorescence lifetime images to estimate lifetime images, pushing the photon budget to an unprecedented low level. The DL framework can be trained by synthetic FLIM data and easily adapted to various FLIM systems. FPFLI can effectively and robustly estimate FLIM images within seconds using synthetic and experimental data. The fast analysis of low-light FLIM images made possible by FPFLI will promise a broad range of potential applications.

bioengineering↗

bioRxiv2023

Self-supervised denoising for structured illumination microscopy enables long-term super-resolution live-cell imaging

Detection noise significantly degrades the quality of structured illumination microscopy (SIM) images, especially under low-light conditions. Although supervised learning based denoising methods have shown prominent advances in eliminating the noise-induced artifacts, the requirement of a large amount of high-quality training data severely limits their applications. Here we developed a pixel-realignment-based self-supervised denoising framework for SIM (PRS-SIM) that trains an SIM image denoiser with only noisy data and substantially removes the reconstruction artifacts. We demonstrated that PRS-SIM generates artifact-free images with 10-fold less fluorescence than ordinary imaging conditions while achieving comparable super-resolution capability to the ground truth (GT). Moreover, the proposed method is compatible with multiple SIM modalities such as total internal reflective fluorescence SIM (TIRF-SIM), three-dimensional SIM (3D-SIM), lattice light-sheet SIM (LLS-SIM), and non-linear SIM (NL-SIM). With PRS-SIM, we achieved long-term super-resolution live-cell imaging of various bioprocesses, revealing the clustered distribution of clathrin coated pits and detailed interaction dynamics of multiple organelles and the cytoskeleton.

cell biology↗

bioRxiv2023

The novel roles of bovine milk-derived exosomes on skin anti-aging

Exosomes are small vesicles released from cells and present in various mammal biological fluids, such as bovine milk, which worked for skin care for many years besides dairy. In addition, Exosomes were regarded as a vehicle for intercellular communication. Therefore, we aimed to investigate the novel roles of bovine milk-derived exosomes (MK-Exo) on human skin anti-aging. Purified MK-Exo can be directly uptake by the keratinocytes and fibroblast in vitro and upregulate the expression of the natural factors related to skin moisturizing, including Filaggrin (FLG), Aquaporin 3 (AQP3), CD44 in the keratinocytes and hyaluronidase (HAS2) in the fibroblast, and MK-Exo promoted the cell migration of the fibroblast, while rescue its expression of type I collagen (Col I), type III collagen (Col III) after ultraviolet radiation. Furthermore, the phototoxicity test, photoallergy test, repeated skin irritation test, skin allergy test, and patch test confirm the safety of MK-Exo on the skin. Finally, the roles of MK-Exo in preserving moisture and anti-wrinkle were also identified in humans. Then, MK-Exo was smeared on the facial skin of 31 female volunteers twice a day for 28 days, and the functions were evaluated following the safety assessment in vivo. These studies reveal the novel roles of bovine milk-derived exosomes in human skin aging, which opens a new way of skin care.

cell biology↗

bioRxiv2023

Tools and methods for high-throughput single-cell imaging with the mother machine

Despite much progress, image processing remains a significant bottleneck for high-throughput analysis of microscopy data. One popular platform for single-cell time-lapse imaging is the mother machine, which enables long-term tracking of microbial cells under precisely controlled growth conditions. While several mother machine image analysis pipelines have been developed in the past several years, adoption by a non-expert audience remains a challenge. To fill this gap, we implemented our own software, MM3, as a plugin for the multidimensional image viewer napari. napari-MM3 is a complete and modular image analysis pipeline for mother machine data, which takes advantage of the high-level interactivity of napari. Here, we give an overview of napari-MM3 and test it against several well-designed and widely-used image analysis pipelines, including BACMMAN and DeLTA. Researchers often analyze mother machine data with custom scripts using varied image analysis methods, but a quantitative comparison of the output of different pipelines has been lacking. To this end, we show that key single-cell physiological parameter correlations and distributions are robust to the choice of analysis method. However, we also find that small changes in thresholding parameters can systematically alter parameters extracted from single-cell imaging experiments. Moreover, we explicitly show that in deep learning based segmentation, "what you put is what you get" (WYPIWYG) - i.e., pixel-level variation in training data for cell segmentation can propagate to the model output and bias spatial and temporal measurements. Finally, while the primary purpose of this work is to introduce the image analysis software that we have developed over the last decade in our lab, we also provide information for those who want to implement mother-machine-based high-throughput imaging and analysis methods in their research.

systems biology↗

bioRxiv2023

Clustering scRNA-seq data via qualitative and quantitative analysis

Single-cell RNA sequencing (scRNA-seq) technologies have been driving the development of algorithms of clustering heterogeneous cells. We introduce a novel clustering algorithm scQA, which can effectively and efficiently recognize different cell types via qualitative and quantitative analysis. It iteratively extracts quasi-trend-preserved genes to conform a consensus by representing expression patterns with dropouts qualitatively and quantitatively, and, then automatically clusters cells using a new label propagation strategy without specifying the number of cell types in advance. Validated on 20 public scRNA-seq datasets, scQA consistently outperformed 9 salient tools in both accuracy and efficiency across 16 out of 20 datasets tested, and ranked top 2 or 3 across the other 4 datasets. Furthermore, we demonstrate scQA can extract informative genes in both perspectives of biology and data wise by performing consensus, allowing genes used for landmark construction multiple characteristics, which is essential for clustering cells accurately. Overall, scQA could be a useful tool for discovery of cell types that can be integrated into general scRNA-seq analyses.

bioinformatics↗