Biology subjects

Lin, W.

Publications and source records attributed to Lin, W..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Eyes on nature: Embedded vision cameras for multidisciplinary biodiversity monitoring

Global environmental challenges require comprehensive data to manage and protect biodiversity. Currently, vision-based biodiversity monitoring efforts are mixed, incomplete, human-dependent, and passive. To tackle these issues, we present a portable, modular, low-power device with embedded vision for biodiversity monitoring. Our camera uses interchangeable lenses to resolve barely visible and remote subjects, as well as customisable algorithms for blob detection, region-of-interest classification, and object detection to identify targets. We showcase our system in six case studies from the ethology, landscape ecology, agronomy, pollination ecology, conservation biology, and phenology disciplines. Using the same devices, we discovered bats feeding on durian tree flowers, monitored flying bats and their insect prey, identified nocturnal insect pests in paddy fields, detected bees visiting rapeseed crop flowers, triggered real-time alerts for waterbirds, and tracked flower phenology over months. We measured classification accuracies between 55% and 96% in our field surveys and used them to standardise observations over highly-resolved time scales. The cameras are amenable to situations where automated vision-based monitoring is required off the grid, in natural and agricultural ecosystems, and in particular for quantifying species interactions. Embedded vision devices such as this will help addressing global biodiversity challenges and facilitate a technology-aided global food systems transformation.

ecology↗

bioRxiv2023

Co-opted cytosolic host proteins form unique condensate substructures within the membranous tombusviral replication organelles

Positive-strand RNA viruses co-opt intracellular organellar membranes for the biogenesis of viral replication organelles (VROs). The membranous VROs are the sites of viral replication. Tombusviruses co-opt numerous host proteins, many of them cytosolic, not membrane-bound, such as the glycolytic and fermentation enzymes. It is currently not known what type of molecular organization keeps these enzymes enriched and sequestered within the membranous VROs. Here, we show evidence that the tomato bushy stunt virus (TBSV) p33 and the closely-related carnation Italian ringspot virus (CIRV) p36 replication proteins sequester several co-opted cytosolic proteins in unique condensate substructures associated with the membranous VROs. We find that TBSV p33 and CIRV p36 replication proteins form droplets in vitro organized by their intrinsically disordered region (IDR). The replication proteins also organize the partitioning of several co-opted host proteins to p33/p36 droplets. We also show that the VRO-associated condensates containing co-opted glycolytic and fermentation enzymes are critical for local ATP production within the VRO to support the energy need of virus replication. A short segment with charged amino acids in p33/p36 IDR plays a critical role in droplet formation in vitro, in organizing the VRO-associated condensates and affects both ATP production in VROs and viral replication. We find that the co-opted ER membranes and actin filaments form meshworks within and around the condensate, likely contributing to the unique composition and structure of VROs. We propose that the p33/p36 replication proteins organize liquid-liquid phase separation of co-opted highly concentrated host proteins in condensate substructures within VROs to allow for the dynamic regulation of viral replication. Overall, we demonstrate that distinct substructures co-exist in tombusvirus VROs. These are the subverted membranes and condensate substructures, both of which are critical for VRO functions. The p33/p36 replication proteins induce and connect the two substructures within the VROs. Interfering with condensate formation in VROs might open up new antiviral approaches.

microbiology↗

bioRxiv2023

Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition

Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-seq comparing osteoblasts differentiated from Ezh2R684C/+and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases Kdm6a/6b substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state, and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.

genetics↗

bioRxiv2023

Reciprocal polarization imaging of complex media.

The vectorial evolution of polarized light interaction with a medium can reveal its microstructure and anisotropy beyond what can be obtained from scalar light interaction. Anisotropic properties (diattenuation, retardance, and depolarization) of a complex medium can be quantified by polarization imaging by measuring the Mueller matrix. However, polarization imaging in the reflection geometry, ubiquitous and often preferred in diverse applications, has suffered a poor recovery of the mediums anisotropic properties due to the lack of suitable decomposition of the Mueller matrices measured inside a backward geometry. Here, we present reciprocal polarization imaging of complex media after introducing reciprocal polar decomposition for backscattering Mueller matrices. Based on the reciprocity of the optical wave in its forward and backward scattering paths, the anisotropic diattenuation, retardance, and depolarization of a complex medium are determined by measuring the backscattering Mueller matrix. We demonstrate reciprocal polarization imaging in various applications for quantifying complex non-chiral and chiral media, uncovering their anisotropic microstructures with remarkable clarity and accuracy. Reciprocal polarization imaging will be instrumental in imaging complex media from remote sensing to biomedicine and will open up new applications of polarization optics in reflection geometry.

biophysics↗

bioRxiv2023

Arabidopsis NF-YCs interact with CRY2 and PIF4/5 to repress blue light-mediated hypocotyl growth

Plants can not move automatically, thus they have to perceive the changing environment (light, temperate and so on) by developing the adapted phenotypes. Light-induced hypocotyl length is an ideal phenotype for studying how plants response to light. So far, many signaling components in light-induced hypocotyl growth have been reported. Here, we focused on identifying transcription factors (TFs) involved in blue light-induced hypocotyl growth by constructing Arabidopsis TFs overexpressing lines and screening blue light-induced hypocotyl length. Finally, we found that three NF-YC proteins, NF-YC7, NF-YC5 and NF-YC8 (NF-YCs as short name), develop longer hypocotyls than the wild type under blue light. While deficient mutants, nf-yc5nf-yc7 and nf-yc7nf-yc8, fail to promote the hypocotyl elongation under blue light. NF-YCs physically interacted with CRY2 and PIF4/5, while the NF-YCs-PIF4/5 interactions were repressed by CRY2. Moreover, overexpression of CRY2 or deficiency of PIF4/5 repressed the hypocotyl elongation induced by NF-YC7 under blue light. Further investigation revealed that NF-YC7 increased the blue light-induced CRY2 degradation and regulated the activities of PIF4/5. Taking together, this study provided a new insight into that NF-YCs function as CRY2-and PIF4/5-interacting proteins and modulate their stabilization to repress the blue light-mediated hypocotyl growth. Author SummaryLight is an essential environmental factor for plants growth and development. Plants response to light signaling by displaying short hypocotyls, green leaves, and so on. The mechanisms of light responding to light have aroused extensive attention. In this study, we clarified that NF-YC family members NF-YC5/7/8 interact with CRY2, PIF4/5 and modulate their stabilization to repress the blue light-mediated hypocotyl growth. It was the first time for reporting NF-Y family members function as CRY2-and PIF4/5-interacting proteins. Therefore, this study provides a novel understanding how plants adapt to light.

genetics↗

bioRxiv2023

VariPred: Enhancing Pathogenicity Prediction of Missense Variants Using Protein Language Models

Computational approaches for predicting the pathogenicity of genetic variants have advanced in recent years. These methods enable researchers to determine the possible clinical impact of rare and novel variants. Historically these prediction methods used hand-crafted features based on structural, evolutionary, or physiochemical properties of the variant. In this study we propose a novel framework that leverages the power of pre-trained protein language models to predict variant pathogenicity. We show that our approach VariPred (Variant impact Predictor) outperforms current state-of-the-art methods by using an end-to-end model that only requires the protein sequence as input. By exploiting one of the best performing protein language models (ESM-1b), we established a robust classifier, VariPred, requiring no pre-calculation of structural features or multiple sequence alignments. We compared the performance of VariPred with other representative models including 3Cnet, EVE and ESM variant. VariPred outperformed all these methods on the ClinVar dataset achieving an MCC of 0.751 vs. an MCC of 0.690 for the next closest predictor.

bioinformatics↗

bioRxiv2023

NDC80 status pinpoints mitotic kinase inhibitors as emerging therapeutic options in clear cell renal cell carcinoma

[~]30% of clear cell renal cell carcinoma (ccRCC) patients present with metastatic disease at the time of diagnosis, causing a dire 5-year survival rate of 13%. Whereas anti-PD-1 immunotherapy has improved survival, a strong need remains for new therapeutic options. Using integrated network analysis, we identified the mitotic regulator NDC80 as a predictor of ccRCC progression. Overexpression of NDC80 fosters the malignant phenotype by promoting cell cycle progression through S phase as well as boosting glycolysis and mitochondrial respiration. Despite high levels of immune infiltration, particularly derived from tumor resident CD8+ T cells with an exhausted phenotype, NDC80 defines a class of ccRCCs that poorly respond to immune checkpoint blockade. Instead, bioinformatics identified NDC80-high ccRCCs as sensitive to inhibitors of mitotic kinases, PLK1 and AURK, therapeutic approaches we validated in cell lines and mouse xenograft studies. Thus, NDC80 status pinpoints mitotic kinase inhibitors as promising therapeutic options in difficult-to-treat ccRCCs.

cancer biology↗

bioRxiv2023

Light sheet autofluorescence lifetime imaging with a single photon avalanche diode array

Single photon avalanche diode (SPAD) array sensors can increase the imaging speed for fluorescence lifetime imaging microscopy (FLIM) by transitioning from laser scanning to widefield geometries. While a SPAD camera in epi-fluorescence geometry enables widefield FLIM of fluorescently labeled samples, label-free imaging of single-cell autofluorescence is not feasible in an epi-fluorescence geometry because background fluorescence from out-of-focus features masks weak cell autofluorescence and biases lifetime measurements. Here, we address this problem by integrating the SPAD camera in a light sheet illumination geometry to achieve optical sectioning and limit out-of-focus contributions, enabling fast label-free FLIM of single-cell NAD(P)H autofluorescence. The feasibility of this NAD(P)H light sheet FLIM system was confirmed with time-course imaging of metabolic perturbations in pancreas cancer cells with 10 s integration times, and in vivo NAD(P)H light sheet FLIM was demonstrated with live neutrophil imaging in a zebrafish tail wound, also with 10 s integration times. Finally, the theoretical and practical imaging speeds for NAD(P)H FLIM were compared across laser scanning and light sheet geometries, indicating a 30X to 6X frame rate advantage for the light sheet compared to the laser scanning geometry. This light sheet system provides faster frame rates for 3D NAD(P)H FLIM for live cell imaging applications such as monitoring single cell metabolism and immune cell migration throughout an entire living organism.

bioengineering↗

bioRxiv2023

Epigenetically silenced DACT3 promotes tumor growth via affecting Wnt/beta-catenin signaling and supports chidamide plus azacitidine therapy in acute myeloid leukemia

BackgroundDACT gene is a potential Wnt antagonist and tumor suppressor gene. However, the expression of DACT gene in acute myeloid leukemia (AML) and its role are still unknown. MethodsIn this study, we first multidimensionally analyzed the expression of DACT gene in AML through RNA seq, qRT-PCR and Western blotting analysis as well as TCGA database analysis. Then DACT3 was identified as playing a critical role in AML, and its clinical significance was further explored. The molecular mechanism of DACT3 down-regulation in AML from aspects of DNA methylation and histone acetylation were inquired. Finally, the biological functions of DACT3 in AML were investigated by cell models in vitro and animal experiments in vivo. ResultsCompared with DACT1 and DACT2, DACT3 was the most differentially expressed DACT family member in AML, suggesting that DACT3 plays the major role. The mRNA and protein expression levels of DACT3 were significantly decreased and positively correlated in AML. Moreover, low expression of DACT3 is associated with no remission disease status and poor prognosis in AML patients. In addition, down-regulation of DACT3 in AML was not completely dependent on promoter methylation, but also affected by histone deacetylation. We found that loss of DACT3 in AML is related to activation of Wnt signaling pathway. Furthermore, DACT3 inhibits the growth of AML cells in vitro and in severe immunodeficiency (SCID) mice. Importantly, DACT3 improved the sensitivity of adriamycin in treating AML cells. Further research showed that co-treatment of chidamide and azacytidine up-regulates DACT3 expression and promotes cell apoptosis via inhibiting Wnt/{beta}-catenin signaling in AML, suggesting a promising therapeutic prospects in FLT3-mutant AML. ConclusionThis is the first study revealing the epigenetic regulatory molecular mechanism of the down regulated expression of DACT3 in AML. Our data also shows that DACT3 is a candidate gene for therapeutic target and targeting DACT3 has the potential to validate the combination therapy of DNMT inhibitors and HDAC inhibitors.

molecular biology↗

bioRxiv2023

Structural insights into transcription activation mechanism of the global regulator GlnR from actinobacteria

GlnR, an OmpR/PhoB subfamily protein, is an orphan response regulator that globally coordinates the expression of genes responsible for nitrogen, carbon and phosphate metabolism in actinobacteria. Although much efforts at biochemical and genetic analyses have been made on the mechanism of GlnR-dependent transcription activation, it still remains unclear owing to lacking the structure of GlnR-dependent transcription activation complex (GlnR-TAC). Here, we report a crystal structure of a binary complex including a C terminal DNA binding domain of GlnR (GlnR_DBD) and its regulatory cis-element DNA, and a cryo-EM structure of GlnR-TAC comprising of Mycobacterium tuberculosis RNA polymerase, GlnR, and a promoter containing four well-characterized conserved GlnR binding sites. These structures show four GlnR protomers coordinately engage promoter DNA in a head-to-tail manner, with two N-terminal receiver domains of GlnR (GlnR-RECs) jointly act as a bridge to connect RNAP NTD with the upstream GlnR_DBD. GlnR-TAC is stabilized by complex protein-protein interactions between GlnR and the conserved {beta} flap, {sigma}AR4, CTD, NTD domains of RNAP. These are in good agreement with our mutational and kinetic single-molecule fluorescence assays. Altogether, our results reveal a general transcription activation mechanism for the global regulator GlnR and other OmpR/PhoB subfamily proteins, and present a unique mode of bacterial transcription regulation. Significance statementIn low-GC gram-negative bacteria, the typical two component system NtrB/NtrC accounts for the expression of genes related to nitrogen metabolism. In high-GC gram-positive actinobacteria, GlnR, an atypical and orphan response regulator (RR) of the OmpR/PhoB subfamily proteins, globally coordinates transcription of genes involved in nitrogen, carbon and phosphate metabolism. Here, using crystallography, cryo-electron microscopy, and single-molecule fluorescence assays, we show that GlnR activates transcription by contacting DNA between the -10 and -35 elements and further upstream through contacting {sigma} region 4 and RNAP {beta} flap subunit. We also identify a previously unobserved cooperative engagement of four GlnR protomers to the promoter DNA, which not only makes the transcription initiation complex (RPo) more stable, but also provides better transcription activities.

biochemistry↗

bioRxiv2022

Spatial-temporal evolution characteristics of land use and its driving factor analysis during the period of 2000-2020 in Putian City, Fujian Province

Exploring the spatial and temporal evolution characteristics of land use and its driving force can provide scientific basis for the construction of regional ecological civilization. Based on the remote sensing cloud computing platform of Google Earth Engine (GEE), the study took the remote sensing images of the three periods of 2000, 2010 and 2020 as the basic data and interpreted them to obtain the basic land use data of Putian city and its five districts and counties. The land-use change characteristics of Putian city in those periods were systematically analyzed by using the methods of single land-use dynamics and Geo-informatic Tupu, so as to reveal the Tupu characteristics of land-use transfer and the spatial-temporal evolution pattern in the past 20 years. Then social and economic development indicators were selected to further explore the key driving force of land-use evolution in the study area by canonical correspondence analysis. The results showed that: 1) the land use structure of Putian city was mainly composed of cultivated land and forest land, and the other land types were embedded in them and the built-up land continued to expand outward. 2) The spatial distribution of Tupu units of land use transfer in Putian city was significantly different, change types of land use were diversified and the areas of cultivated land and grassland transferred out were the most obvious. Different degrees of cultivated land abandonment had occurred in various regions. Putian city was facing great challenges in ensuring food security and curbing the non-agricultural and non grain of cultivated land. 3) The macro-economic development in a specific period, especially the urban expansion and the development of the secondary industry caused by the merger of cities and counties, were the key factors driving the spatial and temporal evolution of land use and the differential distribution pattern in Putian city. The author suggested that land resources should be used efficiently in addition to optimizing the layout of land use and carrying out the renovation of abandoned land. Therefore, the study proposed to strengthen the scientific planning and effective regulation of land use, combine spatial and temporal resources of cultivated land with agriculture, culture and tourism, and build ecological barriers and ecological corridors to ensure the coordinated and sustainable development of regional ecology and economy.

ecology↗

bioRxiv2022

A GFP splicing reporter in a coilin mutant background reveals links between alternative splicing, siRNAs and coilin function in Arabidopsis thaliana

Coilin is a scaffold protein essential for the structure of Cajal bodies, which are nucleolar-associated, nonmembranous organelles that coordinate the assembly of nuclear ribonucleoproteins (RNPs) including spliceosomal snRNPs. To learn more about coilin functions and pathways in plants, we conducted a genetic suppressor screen using a coilin (coi1) mutant in Arabidopsis thaliana and performed an immunoprecipitation-mass spectrometry analysis on coilin protein. The coi1 mutations modify alternative splicing of a GFP reporter gene, resulting in a hyper-GFP phenotype in young coi1 seedlings relative to the intermediate wild-type level. As shown here, this hyper-GFP phenotype is extinguished in older coi1 seedlings by posttranscriptional gene silencing triggered by siRNAs derived from aberrant splice variants of GFP pre-mRNA. In the coi1 suppressor screen, we identified suppressor mutations in WRAP53, a putative coilin-interacting protein; SMU2, a predicted splicing factor; and ZC3HC1, an incompletely characterized zinc finger protein. These suppressor mutations return the hyper-GFP fluorescence of young coi1 seedlings to the intermediate wild-type level. Additionally, zc3hc1 coi1 mutants display more extensive GFP silencing and elevated levels of GFP siRNAs, suggesting the involvement of wild-type ZC3HC1 in siRNA biogenesis or stability. The immunoprecipitation-mass spectrometry analysis reinforced coilins roles in pre-mRNA splicing, nucleolar chromatin structure, and rRNA processing. Coilins participation in these processes, at least some of which incorporate small RNAs, supports the hypothesis that coilin acts as a chaperone for small noncoding RNAs. Our study demonstrates the usefulness of the GFP splicing reporter for investigating alternative splicing, ribosome biogenesis, and siRNA-mediated silencing in the context of coilin function.

plant biology↗

bioRxiv2022

ABLs and TMKs are co-receptors for extracellular auxin

Extracellular perception of auxin, an essential phytohormone in plants, has been debated for decades. Auxin binding protein 1 (ABP1) physically interacts with quintessential transmembrane kinases (TMKs) and was proposed to act as an extracellular auxin receptor, but its role was disputed because abp1 knockout mutants lack obvious morphological phenotypes. Here we identified two new auxin-binding proteins, ABL1 and ABL2, that are localized to the apoplast and directly interact with the extracellular domain of TMKs in an auxin-dependent manner. Furthermore, functionally redundant ABL1 and ABL2 genetically interact with TMKs and exhibit functions that are overlapping with those of ABP1 as well as independent of ABP1. Importantly, the extracellular domain of TMK1 itself binds auxin and synergizes with either ABP1 or ABL1 in auxin binding. Thus, our findings discovered new auxin receptors ABL1 and ABL2 having functions overlapping with but distinct from ABP1 and acting together with TMKs as co-receptors for extracellular auxin.

plant biology↗

bioRxiv2022

ExposomeX: Integrative Exposomic Platform Expediates Discovery of "Exposure-Biology-Disease" Nexus

Exposome has become the hotspot of next-generation health studies. To date, there is no available effective platform to standardize the analysis of exposomic data. In this study, we aim to propose one new framework of exposomic analysis and build up one novel integrated platform "ExposomeX" to expediate the discovery of the "Exposure-Biology-Disease" nexus. We have developed 13 standardized modules to accomplish six major functions including statistical learning (E-STAT), exposome database search (E-DB), mass spectrometry data processing (E-MS), meta-analysis (E-META), biological link via pathway integration and protein-protein interaction (E-BIO) and data visualization (E-VIZ). Using ExposomeX, we can effectively analyze the multiple-dimensional exposomics data and investigate the "Exposure-Biology-Disease" nexus by exploring mediation and interaction effects, understanding statistical and biological mechanisms, strengthening prediction performance, and automatically conducting meta-analysis based on well-established literature databases. The performance of ExposomeX has been well validated by re-analyzing two previous multi-omics studies. Additionally, ExposomeX can efficiently help discover new associations, as well as relevant in-depth biological pathways via protein-protein interaction and gene ontology network analysis. In sum, we have proposed a novel framework for standardized exposomic analysis, which can be accessed using both R and online interactive platform (http://www.exposomex.cn/).

bioinformatics↗

bioRxiv2022

Identification of plant-derived microRNAs in human kidney

Plant-derived microRNAs (miRNAs) have been implicated as functional regulators in human diseases, although conclusive evidence of this effect remains to be reported. To examine their potential functional role, we profiled the plant-derived miRNAs in 139 blood exosome samples from renal transplantation patients and were able to identify 331 plant-derived miRNAs representing 149 families. According to their miRBase annotation, these miRNAs can be traced back to 76 plant species, most of which are foods common to the human diet (e.g., tomato, soybean, potato and rice). We also profiled 41 blood exosome samples from 22 patients with acute immune rejection (AR) of renal transplants and compared them to 21 samples from 11 patients with stable allograft function to explore possible roles of the functional plant miRNAs. We identified three plant-derived miRNAs (miR4995, miR2118/2218 and miR167) associated with allograft AR whose regulatory targets are mRNAs controlling immune response, T cell activation, and other cellular functions. miR4995 mimics were generated, transfected into HEK293T cells, and their function verified. Our findings not only demonstrate the presence of functional plant-derived miRNAs in human cells, but also provide initial evidence that these miRNAs may be involved in malfunction of renal transplantation.

genetics↗

bioRxiv2022

A megaprotein-based molecular bridge critical for lipid trafficking and cold resilience

Cells adapt to cold by increasing levels of unsaturated phospholipids and membrane fluidity through homeostatic mechanisms conserved in nearly all forms of life. As most eukaryotic enzymes for lipid synthesis and desaturation localize on endoplasmic reticulum (ER) membranes, it remains unknown how ER-resident lipids rapidly distribute to plasma membranes (PM). Here we report an exceptionally large and evolutionarily conserved protein LPD-3 in C. elegans that plays critical roles in lipid trafficking and cold resilience. We identified lpd-3 mutants in a mutagenesis screen for genetic suppressors of the lipid desaturase FAT-7, and found that the 452 kDa megaprotein LPD-3 bridges ER and PM, consisting of a structurally predicted hydrophobic tunnel for lipid trafficking. Loss of LPD-3 caused abnormal cellular distribution of phospholipids, diminished FAT-7 abundance, and organismic vulnerability to cold. These phenotypic defects of lpd-3 mutants were rescued by Lecithin comprising unsaturated phospholipids. Importantly, we found that deficient lpd-3 homologues in Zebrafish and mammalian cells led to defects similar to those observed in C. elegans. As mutations in KIAA1109/BLTP1, the human orthologue of lpd-3, cause Alkuraya-Kucinskas syndrome, we propose that the LPD-3 family proteins may serve as evolutionarily conserved "highway bridges" critical for ER-associated non-vesicular trafficking of lipids and resilience to cold stress in eukaryotic cells.

cell biology↗

bioRxiv2022

Detecting boolean asymmetric relationships with a loop counting technique and its implications for analyzing heterogeneity within gene expression datasets

Many traditional methods for analyzing gene-gene relationships focus on positive and negative correlations, both of which are a kind of symmetric relationship. Biclustering is one such technique that typically searches for subsets of genes exhibiting correlated expression among a subset of samples. However, genes can also exhibit asymmetric relationships, such as if-then relationships used in boolean circuits. In this paper we develop a very general method that can be used to detect biclusters within gene-expression data that involve subsets of genes which are enriched for these boolean-asymmetric relationships (BARs). These BAR-biclusters can correspond to heterogeneity that is driven by asymmetric gene-gene interactions, e.g., reflecting regulatory effects of one gene on another, rather than more standard symmetric interactions. Unlike typical approaches that search for BARs across the entire population, BAR-biclusters can detect asymmetric interactions that only occur among a subset of samples. We apply our method to a single-cell RNA-sequencing data-set, demonstrating that the statistically-significant BAR-biclusters indeed contain additional information not present within the more traditional boolean-symmetric-biclusters. For example, the BAR-biclusters involve different subsets of cells, and highlight different gene-pathways within the data-set. Moreover, by combining the boolean-asymmetric- and boolean-symmetric-signals, one can build linear classifiers which outperform those built using only traditional boolean-symmetric signals.

bioinformatics↗

bioRxiv2022

Integrated single-cell sequencing analysis reveals peripheral immune landscape across the human lifespan

Systematic understanding of immune dynamics across the entire human lifespan at single-cell resolution is currently lacking. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell T cell receptor (TCR)/B cell receptor (BCR) sequencing (scTCR/BCR-seq) on over 380,000 peripheral blood mononuclear cells collected from 45 healthy participants aged 0 to over 90 years. We revealed that the functions of T cell subsets were most susceptible to senescence among all PBMCs, featured by increased NF-{kappa}B signaling and IFN-{gamma} responses pathways, while reduced telomere maintenance and energy metabolism. We subsequently explored the rewiring of cell-cell interactions among different immune cells across the lifespan and revealed the major alteration of immune checkpoints in T cells within the cellular interaction networks. By combined analysis of scRNA-seq and scTCR-seq, we revealed that 1) GNLY+ CD8 Effector T cells exhibited a high clonal expansion with distinct functional signatures in children and the elderly; 2) Naive CD4+ T and naive CD8+ T cells displayed different aging patterns in both transcriptomes and immune repertoires; and 3) CD8+ MAIT cells showed a higher cell abundance and clonal diversity in adolescents. Furthermore, we identified a unique cytotoxic B cell subset enriched in children by scRNA-seq and scBCR-seq analysis and experimental validations. In summary, our work provided valuable insights and rich resources for understanding the development and aging of the human immune system across the lifespan.

immunology↗