Biology subjects

Zhao, Z.

Publications and source records attributed to Zhao, Z..

At least 343 records · Page 19Linked to original sources

bioRxiv2022

Optimizing and benchmarking polygenic risk scores with GWAS summary statistics

BackgroundPolygenic risk score (PRS) is a major research topic in human genetics. However, a significant gap exists between PRS methodology and applications in practice due to often unavailable individual-level data for various PRS tasks including model fine-tuning, benchmarking, and ensemble learning. ResultsWe introduce an innovative statistical framework to optimize and benchmark PRS models using summary statistics of genome-wide association studies. This framework builds upon our previous work and can fine-tune virtually all existing PRS models while accounting for linkage disequilibrium. In addition, we provide an ensemble learning strategy named PUMAS-ensemble to combine multiple PRS models into an ensemble score without requiring external data for model fitting. Through extensive simulations and analysis of many complex traits in the UK Biobank, we demonstrate that this approach closely approximates gold-standard analytical strategies based on external validation, and substantially outperforms state-of-the-art PRS methods. ConclusionsOur method is a powerful and general modeling technique that can continue to combine the best-performing PRS methods out there through ensemble learning and could become an integral component for all future PRS applications.

genetics↗

bioRxiv2022

Extracellular matrix stiffness regulates fibroblast differentiation by influencing DNA methyltransferase 1 expression through microtubule polymerization

Cells sense physical cues, such as changes in extracellular matrix (ECM) stiffness, and translate these stimuli into biochemical signals that control various aspects of cellular behavior, thereby facilitating physiological and pathological processes in various organs. Evidence from multiple studies suggests that the anterior vaginal wall stiffness is higher in POP patients than in non-POP patients. Our experiments found that the expression of -smooth muscle actin (-SMA) in the anterior vaginal wall of patients with POP was increased, and the expression of DNMT1 was decreased. We used polyacrylamide gel to simulate matrix stiffening in vitro, and substrate stiffening induced the high expression of myofibroblast markers -SMA and CTGF in L929 cells. Inhibition of DNMT1 promotes fibroblast differentiation into myofibroblasts in vitro. The results of bioinformatics analysis showed that the expression of DNMT1 was significantly correlated with microtubule polymerization-related proteins. The experiment showed that the microtubule polymerization inhibitor nocodazole could eliminate the decrease of DNMT1 expression in fibroblasts induced by high stiffness. We conclude that fibroblasts sense an increase in the stiffness of the surrounding matrix and regulate fibroblast differentiation by regulating the expression of DNA methyltransferase 1 (DNMT1) through the regulation of microtubule polymerization. This study may help to elucidate the complex crosstalk between vaginal fibroblasts and their surrounding matrix in both healthy and pathological conditions, and provide new insights into the implications of potentially targeted phenotypic regulation mechanisms in material-related therapeutic applications.

cell biology↗

bioRxiv2022

Electro-acupuncture alleviates ACE-increased anxiety-like behaviors in mice of adulthood by targeting claustrum D1R CaMKII

Adolescent cocaine exposure (ACE) increases risk of developing psychiatric problems such as anxiety, which may drive relapse in later life, however, its underlying molecular mechanism remains poorly understood. Methods: ACE male mice model were established by exposing to cocaine during adolescent period. Elevated plus maze (EPM) were used to assess anxiety-like behaviors in mice. Within claustrum, local injection of SCH-23390, a specific antagonist for dopamine receptor 1 (D1R), or D1R knocking-down virus were used to regulate D1R function or expression on CaMKII-positive neurons (D1RCaMKII) in vivo. Electro-acupuncture (EA) treatment was performed at acupoints of Baihui and Yintang during withdrawal period. Results: We found that ACE mice exhibited anxiety-like behaviors, along with more activated CaMKII-positive neurons and increased D1RCaMKII levels in claustrum during adulthood. Inhibiting D1R function or knocking-down D1RCaMKII levels in claustrum efficiently reduced claustrum activation, and ultimately suppressed anxiety-like behaviors in ACE mice during adulthood. EA treatment alleviated ACE-evoked claustrum activation and anxiety-like behaviors by suppressing claustrum D1RCaMKII. Conclusion: Our findings identified a novel role of claustrum in ACE-induced anxiety-like behaviors, and put new insight into the D1RCaMKII in the claustrum. The claustrum D1RCaMKII might be a promising pharmacological target, such as EA treatment, to treat drugs-induced anxiety-like behaviors. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/512685v5_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1b22744org.highwire.dtl.DTLVardef@12fed83org.highwire.dtl.DTLVardef@1924caforg.highwire.dtl.DTLVardef@1e896ca_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2022

Deduplication Improves Cost-Efficiency and Yields of De novo Assembly and Binning of Shot-Gun Metagenomes in Microbiome Research

Metagenomics has in the last decade greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads mainly raised from the preparation of metagenomic DNA sequencing library and their impacts on metagenomic assembly and binning have never brought to the attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assembly and binning, based on analyses of four groups of representative metagenomes with distinct microbiome complexity. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic datasets examined thanks to improved contig length and coverage profiling of metagenome-assembled contigs. Specifically, 411 versus 397, 331 versus 317, 104 versus 88 and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication reduced the computational costs of metagenomic assembly including elapsed time (by 9.0% to 29.9%) and maximum memory requirement (by 4.3% to 37.1%). Collectively, it is recommended to remove duplicate reads in metagenomic data before assembly and binning analyses, particularly for complex environmental samples, such as forest soils examined in this study. ImportanceDuplicated reads are usually considered as technical artefacts. Their presence in metagenomes would theoretically not only introduce bias in the quantitative analysis, but also result in mistakes in coverage profile, leading to negative effects or even failures on metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldomly noticed and its impacts on the downstream key bioinformatic procedures (e.g., assembly and binning) still remained unclear. In this study, we comprehensively evaluated for the first time the impacts of duplicate reads on de novo assembly and binning of real metagenomic datasets by comparing assembly quality, binning yields and the requirements of computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields and significantly reduced the computational costs including elapsed time and maximum memory requirement. The results provide empirical reference for more cost-efficient metagenomic analyses in microbiome research.

bioinformatics↗

bioRxiv2022

The Ycf48 accessory factor occupies the site of the oxygen-evolving manganese cluster during photosystem II biogenesis

Robust oxygenic photosynthesis requires a suite of accessory factors to ensure efficient assembly and repair of the oxygen-evolving photosystem two (PSII) complex. The highly conserved Ycf48 assembly factor binds to the newly synthesized D1 reaction center polypeptide and promotes the initial steps of PSII assembly, but its binding site is unclear. Here we have used cryo-electron microscopy to determine the structure of a cyanobacterial PSII D1/D2 reaction center assembly complex with Ycf48 attached. Ycf48, a 7-bladed beta propeller, binds to the amino-acid residues of D1 that ultimately ligate the Mn4CaO5 cluster that catalyzes water oxidation, thereby preventing the premature binding of Mn2+ and Ca2+ ions and protecting the site from damage. Interactions with D2 help explain how Ycf48 promotes assembly of the D1/D2 complex. Overall, our work provides new insights into the early stages of PSII assembly and the structural changes that create the binding site for the Mn4CaO5 cluster.

biochemistry↗

bioRxiv2022

Characterizing biofilm interactions between Ralstonia insidiosa and Chryseobacterium gleum

Ralstonia insidiosa and Chryseobacterium gleum are bacterial species commonly found in potable water systems and these two species contribute to the robustness of biofilm formation in a model six-species community from the International Space Station (ISS) potable water system. Here, we set about characterizing the interaction between these two ISS-derived strains and examining the extent to which this interaction extends to other strains and species in these two genera. The enhanced biofilm formation between the ISS strains of R. insidiosa and C. gleum is robust to starting inoculum and temperature, occurs in some but not all tested growth media, and evidence does not support a soluble mediator or co-aggregation mechanism. These findings shed light on the ISS R. insidiosa and C. gleum interaction, though such enhancement is not common between these species based on our examination of other R. insidiosa and C. gleum strains, as well as other species of Ralstonia and Chryseobacterium. Thus, while the findings presented here increase our understanding of the ISS potable water model system, not all our findings are broadly extrapolatable to strains found outside of the ISS. ImportanceBiofilms present in drinking water systems and terminal fixtures are important for human health, pipe corrosion, and water taste. Here we examine the enhanced biofilm of cu-cultures for two very common bacteria from potable water systems, Ralstonia insidiosa and Chryseobacterium gleum. While strains originally isolated on the International Space Station show enhanced dual-species biofilm formation, terrestrial strains do not show the same interaction properties. This study contributes to our understanding of these two species in both dual and mono-culture biofilm formation.

microbiology↗

bioRxiv2022

Structures and membrane interactions of native serotonin transporter in complexes with psychostimulants

The serotonin transporter (SERT) is a member of the SLC6 neurotransmitter transporter family that mediates serotonin reuptake at presynaptic nerve terminals. SERT is the target of both therapeutic antidepressant drugs and illicit psychostimulant substances such as cocaine and methamphetamines, which are small molecules that perturb normal serotonergic transmission by interfering with serotonin transport. Despite decades of studies, important functional aspects of SERT such as the oligomerization state of native SERT and its interactions with potential proteins remain unresolved. Here we develop methods to isolate SERT from porcine brain (pSERT) using a mild, non-ionic detergent, utilize fluorescence- detection size-exclusion chromatography to investigate its oligomerization state and interactions with other proteins, and employ single-particle cryo-electron microscopy to elucidate the structures of pSERT in complexes with methamphetamine or cocaine, providing structural insights into psychostimulant recognition and accompanying pSERT conformations. Methamphetamine and cocaine both bind to SERT central site, stabilizing the transporter in an outward open conformation. We also identify densities attributable to multiple cholesterol or cholesteryl hemisuccinate (CHS) molecules, as well as to a detergent molecule bound to SERT allosteric site. Under our conditions of isolation, we find that pSERT is best described as a monomeric entity, isolated without interacting proteins, and is ensconced by multiple cholesterol or CHS molecules. SignificanceThe serotonin transporter (SERT) is the target of antidepressants and illicit psychostimulants. Despite its importance in the nervous, cardiovascular and gastrointestinal systems, there is no direct knowledge of SERTs oligomerization state(s) and interactions with other proteins. Here, we develop methods to isolate porcine SERT (pSERT) from native brain tissue in the presence of a mild, non-ionic detergent, and investigated its properties by biochemical, structural and computational methods. We show how cocaine and methamphetamine exert their pharmacological effect on SERT, binding to a site halfway across the membrane-spanning region of the transporter, stabilizing pSERT in an outward open conformation. pSERT is best described as a monomeric entity, requiring neither oligomerization or additional proteins for its structure or function.

biophysics↗

bioRxiv2022

Reducing the Complexity of Fc Glycan Enables the Construction of Antibody Conjugates with Unexpected High Efficiency and Payload Capacity via Glycoengineering

Glycoengineering has been demonstrated to be a powerful tool to construct site-specific antibody conjugates. However, with most glycoengineering strategies, several hours to days are needed to complete the reaction, and the payloads are limited to small molecules. Herein, we show that reducing the complexity of Fc glycan could dramatically boost the enzymatic glycoengineering of IgG molecules to achieve unexpectedly high efficiency and payload capacity. Notably, antibodies with the modified Fc glycan were successfully conjugated with biomacromolecules, e.g., oligonucleotides and nanobodies, in one step by an engineered fucosyltransferase. Moreover, the conversion of this chemoenzymatic engineering could be finished in minutes, or up to hours, affording homogeneous products. The trisaccharide linker of these antibody conjugates exhibits excellent hydrophilicity and stability and reduced ADCC activity. Using this platform, we successfully synthesized an antibody-conjugate-based HER2/CD3 bispecific antibody and applied it to selectively destroy patient-derived cancer organoids by reactivating endogenous T cells inside the organoid. These results suggest that this bispecific antibody format has a high translational value.

biochemistry↗

bioRxiv2022

Chemoenzymatic Measurement of Cell-surface Glycan in Single-cell Multiomics: LacNAc as an Example

Despite the rich information of a cells physiological state encoded in the dynamic changes of cell-surface glycans, methods of capturing glycosylation states at the single-cell level are quite limited. Here we report a chemoenzymatic single-cell N-acetyllactosamine (LacNAc) detection method via tagging the LacNAc with a specific DNA barcode. Compared to the lectin-based glycan detection, the chemoenzymatic labeling does not change the transcriptional status of immune cells and is more compatible with scRNA-seq. Integrated analysis of LacNAc and transcriptome of T cells at a single-cell level reveals that the quantity of cell-surface LacNAc is significantly upregulated in activated CD8+ T cells but maintained at the basal level in quiescent CD8+ T cells (i.e., naive and central memory T cells). Further analysis confirms that the LacNAc level is positively correlated to the glycolytic activity of CD8+ T cells at all statues. Taken together, our study demonstrates the feasibility of chemoenzymatic detection of cell-surface glycan in single-cell RNA sequencing-based multiomics with information of TCR sequence and cell-surface epitopes (i.e., scTCR and CITE-seq) and offers a new way to characterize the biological role of glycan in diversified physiological states.

immunology↗

bioRxiv2022

Establishment Strategy and Temporal Dynamics of Tetrasphaera-Enriched Microbiome for Enhanced Biological Phosphorus Removal and Recovery

Tetrasphaera were recently identified based on the 16S rRNA gene as among the most abundant polyphosphate-accumulating organisms (PAOs) in global full-scale wastewater treatment plants (WWTPs) with enhanced biological phosphorus removal (EBPR). However, it is unclear how Tetrasphaera PAOs are selectively enriched in the context of the EBPR microbiome. In this study, an EBPR microbiome enriched with Tetrasphaera (accounting for 40% of 16S sequences on day 113) was built using a top-down design approach featuring multicarbon sources and a low dosage of allylthiourea. The microbiome showed enhanced nutrient removal (P removal ~85% and N removal ~80%) and increased P recovery (up to 23.2 times) compared with the seeding activated sludge from a local full-scale WWTP. The supply of 1 mg/L allylthiourea promoted the coselection of Tetrasphaera PAOs and Microlunatus PAOs and sharply reduced the relative abundance of both ammonia oxidizer Nitrosomonas and putative competitors Brevundimonas and Paracoccus, facilitating the establishment of the EBPR microbiome. Based on 16S rRNA gene analysis, a putative novel PAO species, EBPR-ASV0001, was identified with Tetrasphaera japonica as its closest relative. This study provides new knowledge on the establishment of a Tetrasphaera-enriched microbiome facilitated by allylthiourea, which can be further exploited to guide future process upgrading and optimization to achieve and/or enhance simultaneous biological phosphorus and nitrogen removal from high-concentration wastewater.

bioengineering↗

bioRxiv2022

β1-adrenergic receptor on pyramidal neurons of mPFC regulates METH-preferred behaviors in METH-sired male mice

Paternal abuse of drugs, such as methamphetamine (METH), elevates the risk of developing addiction in subsequent generations, however, its underlying molecular mechanism remains poorly understood. Male adult mice (F0) were exposed to METH for 30 days, followed by mating with naive female mice to create the first-generation mice (F1). When growing to adulthood, F1 were subjected to conditioned place preference (CPP) test. Subthreshold dose of METH, insufficient to induce CPP normally, were used in F1 (METHF1). Selective antagonist (betaxolol) for {beta}1-adrenergic receptor (ADRB1) or its knocking-down virus were administrated into mPFC to regulate ADRB1 function and expression on CaMKII-positive neurons. METH-sired male F1 acquired METHF1-induced CPP, indicating that paternal METH exposure induce higher sensitivity to METH in male F1. Compared with saline (SAL)-sired male F1, CaMKII-positive neuronal activity was normal without METHF1, but strongly evoked after METHF1 treatment in METH-sired male F1 during adulthood. METH-sired male F1 had higher ADRB1 levels without METHF1, which was kept at higher levels after METHF1 treatment in mPFC. Either inhibiting ADRB1 function with betaxolol, or knocking-down ADRB1 level on CaMKII-positive neurons (ADRB1CaMKII) with virus transfection efficiently suppressed METHF1-evoked mPFC acyivation, and ultimately blocked METHF1-induced CPP in METH-sired male F1. In the process, the p-ERK1/2 and {Delta}FosB may be potential subsequent signals of mPFC ADRB1CaMKII. The mPFC ADRB1CaMKII mediates paternal METH exposure-induced higher sensitivity to drug addiction in male offspring, raising a promising pharmacological target for predicting or treating transgenerational addiction. HIGHLIGHTSO_LIPaternal methamphetamine (METH) exposure induces higher sensitivity to METH in male F1 during adulthood, accompanied with higher ADRB1 level in mPFC. C_LIO_LIMETH use in F1 (METHF1) evokes more CaMKII-positive neurons in mPFC of METH-sired than saline-sired male F1. C_LIO_LIInhibiting ADRB1 function or knocking-down ADRB1 level on CaMKII-positive neurons (ADRB1CaMKII) efficiently suppresses METHF1-evoked mPFC activation, and ultimately rescues transgenerational susceptibility to addiction in male F1. C_LI

neuroscience↗

bioRxiv2022

High-resolution eye-tracking via digital imaging of Purkinje reflections

Reliably measuring eye movements and determining where the observer looks are fundamental needs in vision science. A classical approach to achieve high-resolution oculomotor measurements is the so-called Dual-Purkinje-Image (DPI) method, a technique that relies on the relative motion of the reflections generated by two distinct surfaces in the eye, the cornea and the back of the lens. This technique has been traditionally implemented in fragile and difficult to operate analog devices, which have remained exclusive use of specialized oculomotor laboratories. Here we describe progress on the development of a digital DPI, a system that builds on recent advances in digital imaging to enable fast, highly precise eye-tracking without the complications of previous analog devices. This system integrates an optical setup with no moving components with a digital imaging module and dedicated software on a fast processing unit. Data from both artificial and human eyes demonstrate sub-arcminute resolution at 1 Khz. Furthermore, when coupled with previously developed gaze-contingent calibration methods, this system enables localization of the line of sight within a few arcminutes.

neuroscience↗

bioRxiv2022

Combinatorial perturbation sequencing on single cells using microwell-based droplet random pairing

Combinatorial drug therapy reduces drug resistance and disease relapse, but informed drug combinations are lacking due to the high scale of possible combinations and the relatively simple phenotyping strategies. Here we report combinatorial perturbation sequencing (CP-seq) on single cells using microwell-base droplet random pairing. CP-seq uses oligonucleotides to barcode drugs, encapsulates drugs and cells in separate droplets, and pairs cell droplets with two drug droplets randomly on a microwell array chip to complete combinatorial drug treatment and barcode-tagging on cells. The subsequent single-cell RNA sequencing simultaneously detects the single-cell transcriptomes and drug barcodes to demultiplex the corresponding drug treatment. The microfluidic droplet operations had robust performance, with overall success rate among the microwells being up to 83%. We then progressively validated the CP-seq by performing single drug treatment and then combinatorial drug treatment. Leveraging the advantage of droplet microfluidics in massive multiplexing, the CP-seq can test thousands of drug combinations in a single experiment and represents a great technology for combinatorial perturbation screening with high throughput and comprehensive profiling.

bioengineering↗

bioRxiv2022

Epigenetic plasticity cooperates with emergent cell-cell interactions to drive neoplastic tissue remodeling in the pancreas

The response to tumor-initiating inflammatory and genetic insults can vary amongst morphologically indistinguishable cells, suggesting yet uncharacterized roles for epigenetic plasticity during early neoplasia. To investigate the origins and impact of such plasticity, we perform single-cell analyses on normal, inflamed, pre-malignant and malignant tissues in autochthonous models of pancreatic cancer. We reproducibly identify heterogeneous cell-states that are primed for diverse late-emerging neoplastic fates and link these to chromatin remodeling at cell-cell communication loci. Using a new inference approach, we reveal signaling gene modules and tissue-level crosstalk, including a neoplasia-driving feedback loop between discrete epithelial and immune cell populations that we validate by genetic perturbation in mice. Our results uncover a neoplasia-specific tissue remodeling program that may be exploited for pancreas cancer interception. One-Sentence SummarySingle-cell analysis reveals that enhanced epigenetic plasticity drives pro-neoplastic crosstalk in early pancreatic cancer.

cancer biology↗

bioRxiv2022

Cellular contributions to ictal population signals

ObjectiveThe amplitude of ictal activity is a defining feature of epileptic seizures, but the determinants of this amplitude have not been identified. Clinically, ictal amplitudes are measured electrographically (using e.g. EEG, ECoG, and depth electrodes), but these methods do not enable the assessment of the activity of individual neurons. To identify the cellular determinants of the ictal signal, we measured single cell and population electrical activity and neuronal calcium levels via optical imaging of the genetically encoded calcium indicator (GECI) GCaMP. MethodsSpontaneous seizure activity was assessed in an awake, behaving mouse model of focal cortical injury and in organotypic hippocampal slice cultures (OHSC), an in vitro preparation from which recurrent seizures can be readily captured. Single cell calcium signals were linked to a range of electrical activities by performing simultaneous GECI-based calcium imaging and whole-cell patch-clamp recordings in spontaneously seizing OHSCs. Neuronal resolution calcium imaging was then performed during spontaneous seizures in vivo and in vitro to quantify the cellular contributions to the population-level calcium signal. ResultsPopulation signal may increase from three potential sources: 1) increased synchrony, i.e. more co-active neurons, 2) altered active state, from bursts of action potentials and/or paroxysmal depolarizing shifts in membrane potential, and 3) altered subthreshold state, which includes all lower levels of activity. The largest contributor to the signal recorded at seizure onset was increased subthreshold activity, consistent with either barrages of excitatory postsynaptic potentials or sustained membrane depolarization. The relative contribution of synchrony increased as seizures progressed, but cell intrinsic alterations in both the subthreshold and active states remained the largest driver of the ictal signal. SignificanceWe introduce here a novel method for the quantification of the relative contributions of inter-versus intra-cellular changes to provide a critical link between single neuron activity and population measures of seizure activity. Key PointsO_LINeuronal calcium as measured by GCaMP reports a range of membrane depolarizations, from EPSPs to action potential firing and paroxysmal depolarizing shifts C_LIO_LIThe mean population calcium signal is highly correlated with the electrographic local field potential C_LIO_LIIncreased calcium signal during seizure onset is largely driven by increased subthreshold calcium within individual neurons C_LIO_LIRecruitment of newly active neurons is a minor contributor to the increasing population-level signal during the transition to frank seizure C_LI

neuroscience↗

bioRxiv2022

Cardiac performance and heat shock response variation related to shell colour morphs in the mudflat snail Batillaria attramentaria

Physiological and transcriptomic response to thermal stress were investigated in the mudflat snail Batillaria attramentaria of different shell colour morphs. Despite no difference in upper lethal temperatures among shell colour morphs, their Arrhenius breakpoint temperatures (ABT) for cardiac thermal performance differed significantly, and the ABT of snails with D type morph was higher than snails with UL type morph. The transcriptomic analysis showed that D type snails exhibit higher levels of four HSPs than UL type snails at control temperature. Unfolded protein response was activated in UL type snails but not in D type snails under moderate thermal stress. And there were 11 HSPs increased in UL type snails in contrast to 1 HSP in D type snails, suggesting a "preparative defense" strategy of heat shock response in D type snails under moderate thermal stress. When exposed to sublethal temperature, eight molecular chaperones were uniquely upregulated in D type snails, suggesting these genes may allow for D type snails improved their cardiac thermal tolerance. The "preparative defense" strategies and higher ABT of cardiac thermal performance may adapt the dark shell snails to the rapid and stronger thermal stress in the field. Our results suggested that physiological selection imposed by moderate and sublethal thermal stress, instead of upper lethal limits, may be a driving force shaping shell colour frequency in the mudflat snail B. attramentaria.

physiology↗

bioRxiv2022

Intratumoral mregDC and CXCL13 T helper niches enable local differentiation of CD8 T cells following PD-1 blockade

Here, we leveraged a large neoadjuvant PD-1 blockade trial in patients with hepatocellular carcinoma (HCC) to search for correlates of response to immune checkpoint blockade (ICB) within T cell-rich tumors. We show that ICB response correlated with the clonal expansion of intratumoral CXCL13+ CH25H+ IL-21+ PD-1+ CD4 T helper cells (CXCL13+ Th) and Granzyme K+ PD-1+ effector-like CD8 T cells, whereas terminally exhausted CD39hi TOXhi PD-1hi CD8 T cells dominated in non-responders. Strikingly, most T cell receptor (TCR) clones that expanded post-treatment were found in pre-treatment biopsies. Notably, PD-1+ TCF-1+ progenitor-like CD8 T cells were present in tumors of responders and non-responders and shared clones mainly with effector-like cells in responders or terminally differentiated cells in non-responders, suggesting that local CD8 T cell differentiation occurs upon ICB. We found that these progenitor CD8 T cells interact with CXCL13+ Th cells within cellular triads around dendritic cells enriched in maturation and regulatory molecules, or "mregDC". Receptor-ligand analysis revealed unique interactions within these triads that may promote the differentiation of progenitor CD8 T cells into effector-like cells upon ICB. These results suggest that discrete intratumoral niches that include mregDC and CXCL13+ Th cells control the differentiation of tumor-specific progenitor CD8 T cell clones in patients treated with ICB.

immunology↗

bioRxiv2022

A single-cell atlas of the human brain in Alzheimer's disease and its implications for personalized drug repositioning

Alzheimers disease (AD) is a neurodegenerative disease with complex pathophysiology, and AD-dysregulated pathways are inconsistent across different brain regions and patients. Although single-cell RNA sequencing (scRNA-seq) has been performed in different regions of postmortem AD brains, the common and distinct molecular features among different regions remains largely unclear. This hinders the discovery of repurposable and personalized drugs for AD. We combined four scRNA-seq datasets and systematically investigated the common and distinct cellular responses, cell subpopulations, and transcription factors involved in AD. Moreover, we explored the transcriptional heterogeneity of different AD subtypes at the single-cell level. Finally, we conducted individual-based drug repurposing analysis to explore repurposable and personalized drugs. Six major brain cell types were detected after scRNA-seq batch-effect removal and noise cells filtering. Integration with genome-wide association studies (GWAS) summary statistics demonstrated that AD-susceptible genes were mainly enriched with differentially expressed genes (DEGs) in glial cells rather than neuronal cells. While most of DEGs were regulated in opposite directions among different cell types, cell-cell communication analysis revealed several common cellular interaction events involved in neurogenesis, as well as increased cell-cell adhesion. Our comprehensive drug repositioning analysis identified new candidates for AD treatment, including trichostatin, which was predicted to be broadly applicable to different identified AD subtypes, and vorinostat, which was specific for one subtype of AD. In summary, we delineated a cell-specific atlas of the AD transcriptome. Our work illustrated strong cellular heterogeneity in AD for defining AD subtypes. The cell-specific features are important for understanding AD etiology, progression, and drug discovery.

bioinformatics↗