Biology subjects

Qin, X.

Publications and source records attributed to Qin, X..

At least 55 records · Page 3Linked to original sources

bioRxiv2023

A comprehensive alignment-filtering methodology improves phylogeny particularly by filtering overly divergent segments

O_LIAlignment problems may be complicated and diverse and the performance of the existing alignment-filtering tools, particularly their potential effect on phylogenetic reconstruction, have remained debated or limitedly explored. C_LIO_LIIn the present study, we developed a new R package named alignmentFilter to treat the diverse alignment problems, especially masking ambiguously-aligned or overly divergent segments using a newly devised grouping-regrouping algorithms acting on sequence divergence in each of sliding windows throughout alignment. Then we tested and compared the power and accuracy of the prevalent alignment-filtering tools, particularly the effect on phylogeny based on Angiospermae genome-scale data and simulated data. C_LIO_LIThe results indicate the alignment-filtering methods alone may affect the phylogeny decisively, producing (strongly-supported) phylogenetic conflicts. In most cases, alignmentFilter most efficiently improves phylogeny, yielding more congruent phylogeny regardless of phylogeny-reconstruction methods, producing phylogeny more concordant to the priori tree regarding to both topology and branch length in simulation, and most efficiently decreasing the root-to-tip length heterogeneity that is implied to be negatively correlated with topological accuracy. C_LIO_LIThe concepts and algorithms of alignmentFilter are quite distinct from existing alignment-filtering methods. It is not susceptible to specific types of alignment errors that usually baffle other methods and can reach the optimal solution frequently with lowest computation complexity. The biological or statistical sense of the key optional stringency-controlling parameter is more straightforward and the setting and outcome may be more adjustable or predictable. A better and more comprehensive solution of alignment problems in this study will benefit tremendous downstream analyses sourced from alignment and phylogeny. C_LI

bioinformatics↗

bioRxiv2023

Oncogenic PIK3CA corrupts growth factor signaling specificity

Pathological activation of the PI3K/AKT pathway is among the most frequent defects in human cancer and is also the cause of rare overgrowth disorders. Yet, there is currently no systematic understanding of the quantitative flow of information within PI3K/AKT signaling and how it is perturbed by disease-causing mutations. Here, we develop scalable, single-cell approaches for systematic analyses of signal processing within the PI3K pathway, enabling precise calculations of its information transfer for different growth factors. Using genetically-engineered human cell models with allele dose-dependent expression of PIK3CAH1047R, we show that this oncogene is not a simple, constitutive pathway activator but a context-dependent modulator of extracellular signal transfer. PIK3CAH1047Rreduces information transmission downstream of IGF1 while selectively enhancing EGF-induced signaling and transcriptional responses. This leads to a gross reduction in signaling specificity, akin to "blurred" signal perception. The associated increase in signaling heterogeneity promotes phenotypic diversity in a human cervical cancer cell line model and in human induced pluripotent stem cells. Collectively, these findings and the accompanying methodological advances lay the foundations for a systematic mapping of the quantitative mechanisms of PI3K/AKT-dependent signal processing and phenotypic control in health and disease. One-sentence summarySingle-cell signaling and information theoretic analyses reveal that oncogenic PI3K/AKT activation leads to a gross reduction in signaling specificity, context-dependent EGF response amplification as well as increased phenotypic heterogeneity.

systems biology↗

bioRxiv2023

Dehydrozaluzanin C- derivative protects septic mice by alleviating over-activated inflammatory response and promotes the phagocytosis of macrophages

Host-directed therapy (HDT) is a new adjuvant strategy that interfere with host cell factors that are required by a pathogen for replication or persistence. In this study, we assessed the effect of dehydrozaluzanin C-derivative (DHZD), a modified compound from dehydrozaluzanin C (DHZC), as a potential HDT agent for severe infection. LPS-induced septic mouse model and Carbapenem resistant Klebsiella pneumoniae (CRKP) infection mouse model was used for testing in vivo. RAW264.7 cells, mouse primary macrophages, and DCs were used for in vitro experiments. Dexamethasone (DXM) was used as a positive control agent. DHZD ameliorated tissue damage (lung, kidney, and liver) and excessive inflammatory response induced by LPS or CRKP infection in mice. Also, DHZD improved the hypothermic symptoms of acute peritonitis induced by CRKP, inhibited heat-killed CRKP (HK-CRKP)-induced inflammatory response in macrophages, and upregulated the proportions of phagocytic cell types in lungs. In vitro data suggested that DHZD decreases LPS-stimulated expression of IL-6, TNF- and MCP-1 via PI3K/Akt/p70S6K signaling pathway in macrophages. Interestingly, the combined treatment group of DXM and DHZD had a higher survival rate and lower level of IL-6 than those of the DXM-treated group; the combination of DHZD and DXM played a synergistic role in decreasing IL-6 secretion in sera. Moreover, the phagocytic receptor CD36 was increased by DHZD in macrophages, which was accompanied by increased bacterial phagocytosis in a clathrin- and actin-dependent manner. This data suggests that DHZD may be a potential drug candidate for treating bacterial infections.

pathology↗

bioRxiv2023

The role of alternative polyadenylation in Epithelial-mesenchymal transition of non-small cell lung cancer

The metastatic non-small cell lung cancer (NSCLC) is one of the cancers with high incidence, poor survival, and limited treatment. Epithelial-mesenchymal transition (EMT) is the first step by which an early tumor converts to an invasive one. Studying the underlying mechanisms of EMT can help the understanding of cancer metastasis and improve the treatment. In this study, 1,013 NSCLC patients and 123 NSCLC cell lines are deeply analyzed for the potential roles of alternative polyadenylation (APA) in the EMT process. A trend of shorter 3-UTRs is discovered in the mesenchymal samples. The identification of EMT-related APA events highlights the proximal poly(A) selection of CARM1. It is a pathological biomarker of mesenchymal tumor and cancer metastasis through losing miRNA binding to upregulate the EMT inducer of CARM1 and releasing miRNAs to downregulate the EMT inhibitor of RBM47. The crucial role of this APA event in EMT also guides its effect on drug responses. The patients with shorter 3-UTR of CARM1 are more benefit from chemotherapy drugs, especially cisplatin. A stratification of NSCLC patients based on this APA event is useful for chemotherapy design in future clinics.

cancer biology↗

bioRxiv2023

Single Cell Expression Analysis of Ductal Carcinoma in Situ Identifies Alterations in Epithelial Integrity

To identify mechanisms underlying the growth of ductal carcinoma in situ (DCIS) and properties that lead to progression to invasive cancer, we performed single-cell RNA-sequencing (scRNA-seq) on DCIS lesions and matched synchronous normal breast tissue. Using inferred copy number variations (CNV), we identified neoplastic epithelial cells from the clinical specimens which contained a mixture of DCIS and normal ducts. Phylogenetic analysis based on the CNVs demonstrated intratumoral clonal heterogeneity was associated with significant gene expression differences. We also classified epithelial cells into mammary cell states and found that individual genetic clones contained a mixture of cell states suggesting an ongoing pattern of differentiation after neoplastic transformation. Cell state proportions were significantly different based on estrogen receptor (ER) expression with ER-DCIS more closely resembling the distribution in the normal breast, particularly with respect to cells with basal characteristics. Using deconvolution from bulk RNA-seq in archival DCIS specimens, we show that specific alterations in cell state proportions are associated with progression to invasive cancer. Loss of an intact basement membrane (BM) is the functional definition of invasive breast cancer (IBC) and scRNA-seq data demonstrated that ongoing transcription of key BM genes occurs in specific subsets of epithelial cell states. Examining BM in archival microinvasive breast cancers and an in vitro model of invasion, we found that passive loss of BM gene expression due to cell state proportion alterations is associated with loss of the structural integrity of the duct leading to an invasive phenotype. Our analyses provide detailed insight into DCIS biology. SIGNIFICANCESingle cell analysis reveals that preinvasive breast cancer is comprised of multiple genetic clones and there is substantial phenotypic diversity both within and between these clones. Ductal carcinoma in situ (DCIS) of the breast is a non-invasive condition commonly identified through mammographic screening. A primary diagnosis of DCIS carries little mortality risk on its own, but its presence is a risk factor for subsequent clonally related invasive breast cancer (IBC) (1-5).

cancer biology↗

bioRxiv2023

CellPolaris: Decoding Cell Fate through Generalization Transfer Learning of Gene Regulatory Networks

Cell fate changes are determined by gene regulatory network (GRN), a sophisticated system regulating gene expression in precise spatial and temporal patterns. However, existing methods for reconstructing GRNs suffer from inherent limitations, leading to compromised accuracy and application generalizability. In this study, we introduce CellPolaris, a computational system that leverages transfer learning algorithms to generate high-quality, cell-type-specific GRNs. Diverging from conventional GRN inference models, which heavily rely on integrating epigenomic data with transcriptomic information or adopt causal strategies through gene co-expression networks, CellPolaris employs high-confidence GRN sources for model training, relying exclusively on transcriptomic data to generate previously unknown cell-type-specific GRNs. Applications of CellPolaris demonstrate remarkable efficacy in predicting master regulatory factors and simulating in-silico perturbations of transcription factors during cell fate transition, attaining state-of-the-art performance in accurately predicting candidate key factors and outcomes in cell reprogramming and spermatogenesis with validated datasets. It is worth noting that, with a transfer learning framework, CellPolaris can perform GRN based predictions in all cell types even across species. Together, CellPolaris represents a significant advancement in deciphering the mechanisms of cell fate regulation, thereby enhancing the precision and efficiency of cell fate manipulation at high resolution.

bioinformatics↗

bioRxiv2023

eMIND: Enabling automatic collection of protein variation impacts in Alzheimer's disease from the literature

Alzheimers disease and related dementias (AD/ADRDs) are among the most common forms of dementia, and yet no effective treatments have been developed. To gain insight into the disease mechanism, capturing the connection of genetic variations to their impacts, at the disease and molecular levels, is essential. The scientific literature continues to be a main source for reporting experimental information about the impact of variants. Thus, development of automatic methods to identify publications and extract the information from the unstructured text would facilitate collecting and organizing information for reuse. We developed eMIND, a deep learning-based text mining system that supports the automatic extraction of annotations of variants and their impacts in AD/ADRDs. In particular, we use this method to capture the impacts of protein-coding variants affecting a selected set of protein properties, such as protein activity/function, structure and post-translational modifications. We conducted an evaluation on the efficacy of eMIND to extract variant impact relations and obtained a recall of 0.84 and a precision of 0.94. The publications and extracted information are integrated into the UniProtKB computationally mapped bibliography to expand annotations on protein entries. eMINDs text-mined output are presented using controlled vocabularies and ontologies for variant, disease and impact along with the evidence sentences. A sample of annotated abstracts can be accessed at URL: https://research.bioinformatics.udel.edu/itextmine/emind.

bioinformatics↗

bioRxiv2023

New machine learning method identifies subtle fine-scale genetic stratification in diverse populations

Fine-scale genetic structure impacts genetic risk predictions and furthers the understanding of the demography of populations. Current approaches (e.g., PCA, DAPC, t-SNE, and UMAP) either produce coarse and ambiguous cluster divisions or fail to preserve the correct genetic distance between populations. We proposed a new machine learning algorithm named ALFDA. ALFDA considers both local and global genetic affinity between individuals and also preserves the multimodal structure within populations. ALFDA outperformed the existing approaches in identifying fine-scale genetic structure and in retaining population geogenetic distance, providing a valuable tool for geographic ancestry inference as well as correction for spatial stratification in population health studies.

genomics↗

bioRxiv2023

The roles of RNA editing in cancer immunity through interacting with interferon

The interferon-activated tumor innate immunity can be primed by specific double-stranded RNA (dsRNA) sensors upon stimulation. A-to-I RNA editing in the dsRNA regions can have a potential function to regulate interferon-related cancer immunity. A systematical analysis of both the editing enzyme and specific enriched editing region in patients, tissues, and cell lines is performed to reveal the underlying mechanisms. We then validate the preferred editing of dsRNA regions, identify the hyper-editing in severe tumors, and discover the negative effect of editing on cancer immunity. Specifically, RNA editing acts as an inhibitor of PKR- and MDA5-related interferon pathways through the regulations of miRNAs and RNA-binding proteins and the deactivation of dsRNA sensors. With the alteration of interferons, subsequently, RNA editing represses the infiltration of CD8 and CD4 T cells and reduces the sensitivities of cancer drugs, such as cisplatin. These analyses on A-to-I RNA editing can improve the knowledge of tumorigenesis, immunology, and cancer-targeted immunotherapy. HighlightsO_LIThe preferred dsRNA region for RNA editing is validated. C_LIO_LIUpregulation of RNA editing in severe tumors is discovered. C_LIO_LIRNA editing inhibits PKR- and MDA5-related cancer immunity. C_LIO_LIRNA editing represses the infiltration of CD8 and CD4 T cells. C_LIO_LIRNA editing reduces the sensitivities of cancer drugs. C_LI

bioinformatics↗

bioRxiv2023

Tumors cells with mismatch repair deficiency induce hyperactivation of Pyroptosis resistant to cell membrane damage but are more sensitive to Co-treatment of IFN-γ and TNF-α to PANoptosis

Hypermutated neoantigens in cancers with DNA mismatch repair deficiency (dMMR) are prerequisite for favorable clinical responses to immune-checkpoint blockade (ICB) therapy. However, TMB is not significantly associated with favorable prognosis from Preclinical and clinical studies. It implys that except for TMB, other mechanisms should be needed to contribute to successful cancer immunotherapy. We found that the hyperactivation of PANoptotic effective molecules in dMMR tumor cells caused cell membrane damage, and induced ESCRT mediated membrane repair, and protectd tumor cells from the damage caused by Triton X100, while DNA mismatch repair proficient (pMMR) tumor cells were sensitive to Triton X100 mediating cell membrane damage due to the lack of ESCRT mediated membrane repair. There were hyperactivation of GSDMD, GSDME and p-MLKL in dMMR tumor cells. Co-treatment of IFN-{gamma} and TNF- induced rapid death of dMMR tumor cells by inducing PANoptosis including pyroptosis, apoptosis not necrosis. pMMR tumor cells had defects in PANoptosis pathway and were resistant to co-treatment of IFN-{gamma} and TNF-. In conclusion, we can activate immune cells to release IFN-{gamma} and TNF- to overcome resistance to ICB treatment.

cancer biology↗

bioRxiv2023

Functional Genomics of Gastrointestinal Escherichia coli Isolated from Patients with Cancer and Diarrhea

We describe the epidemiology and clinical characteristics of 29 patients with cancer and diarrhea in whom Enteroaggregative Escherichia coli (EAEC) was initially identified by GI BioFire panel multiplex. E. coli strains were successfully isolated from fecal cultures in 14 of 29 patients. Six of the 14 strains were identified as EAEC and 8 belonged to other diverse E. coli groups of unknown pathogenesis. We investigated these strains by their adherence to human intestinal organoids, cytotoxic responses, antibiotic resistance profile, full sequencing of their genomes, and annotation of their functional virulome. Interestingly, we discovered novel and enhanced adherence and aggregative patterns for several diarrheagenic pathotypes that were not previously seen when co-cultured with immortalized cell lines. EAEC isolates displayed exceptional adherence and aggregation to human colonoids compared not only to diverse GI E. coli, but also compared to prototype strains of other diarrheagenic E. coli. Some of the diverse E. coli strains that could not be classified as a conventional pathotype also showed an enhanced aggregative and cytotoxic response. Notably, we found a high carriage rate of antibiotic resistance genes in both EAEC strains and diverse GI E. coli isolates and observed a positive correlation between adherence to colonoids and the number of metal acquisition genes carried in both EAEC and the diverse E. coli strains. This work indicates that E. coli from cancer patients constitute strains of remarkable pathotypic and genomic divergence, including strains of unknown disease etiology with unique virulomes. Future studies will allow for the opportunity to re-define E. coli pathotypes with greater diagnostic accuracy and into more clinically relevant groupings.

microbiology↗

bioRxiv2023

Dynamics of the epigenetic landscape during development and in response to drought stress in sorghum

Sorghum bicolor is a C4 plant with the characteristics of high stress tolerance, which may be conferred partly by the underlying epigenetic mechanism unique to sorghum. In this study, we revealed some epigenomic features in sorghum that have never been reported before. The long H3K27me3 regions clustered in four areas, which we defined as H3K27me3 islands, were identified in sorghum. H3K36me3 plays some role in inhibiting the deposition of both H3K27me3 and H2A.Z, which may serve as partial motivation for the removal of H3K27me3 and H2A.Z in leaf and root. All the 7 histone marks are involved in the regulation of tissue-specific genes, especially the specific expression of C4 genes in leaf and peroxidase (POD) encoding genes in root, which are involved in the photosynthesis in leaf and lignin synthesis in root, respectively. These marks except H3K36me3 and H3K27me3 also engage in the regulation of stress genes in response to PEG treatment. However, we found that differential enrichment of histone marks on many tissue-specific genes was observed only between leaf and root but hardly in response to PEG treatment, although expression of these genes changed after PEG treatment.

plant 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

A Single-cell Perturbation Landscape of Colonic Stem Cell Polarisation

Cancer cells are regulated by oncogenic mutations and microenvironmental signals, yet these processes are often studied separately. To functionally map how cell-intrinsic and cell-extrinsic cues co-regulate cell-fate in colorectal cancer (CRC), we performed a systematic single-cell analysis of 1,071 colonic organoid cultures regulated by 1) CRC oncogenic mutations, 2) microenvironmental fibroblasts and macrophages, 3) stromal ligands, and 4) signalling inhibitors. Multiplexed single-cell analysis revealed a stepwise epithelial differentiation landscape dictated by combinations of oncogenes and stromal ligands, spanning from fibroblast-induced Clusterin (CLU)+ revival colonic stem cells (revCSC) to oncogene-driven LRIG1+ hyper-proliferative CSC (proCSC). The transition from revCSC to proCSC is regulated by decreasing WNT3A and TGF-{beta}-driven YAP signalling and increasing KRASG12D or stromal EGF/Epiregulin-activated MAPK/PI3K flux. We find APC-loss and KRASG12D collaboratively limit access to revCSC and disrupt stromal-epithelial communication - trapping epithelia in the proCSC fate. These results reveal that oncogenic mutations dominate homeostatic differentiation by obstructing cell-extrinsic regulation of cell-fate plasticity. HighlightsO_LI1,071-condition single-cell transition map of colonic stem cell polarisation regulated by oncogenic and mircoenvironmental cues. C_LIO_LIFibroblasts polarise WT colonic epithelia towards Clu+ revCSC via TGF-{beta}1 and YAP signalling. C_LIO_LIAPC-loss and KRASG12D drive a Birc5+, Lrig1+, and Ephb2+ proCSC fate via MAPK and PI3K. C_LIO_LIOncogenic mutations disrupt stromal regulation of epithelial plasticity, trapping cells in the proCSC fate. C_LI

cancer biology↗

bioRxiv2023

In situ architecture of Opa1-dependent mitochondrial cristae remodeling

Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling. HighlightsO_LIIn situ ultrastructural characterization of mitochondrial cristae with different forms of Opa1. C_LIO_LIMitochondria with predominantly l-Opa1 show crista stacking, longer cristae, reduced globular cristae and an absence of tubular cristae. C_LIO_LIMitochondria with mostly s-Opa1 showed irregular cristae packing with wider cristae junctions and narrower cristae. C_LIO_LIl-Opa1 expressing cells with WT-like cristae junction properties, show wild-type apoptotic response and calcium handling. C_LIO_LIImbalance in Opa1 processing show compromised respiratory function and an increase in amorphous cristae. C_LI

biophysics↗

bioRxiv2023

iTie controls intestinal tolerance through suppressing the NLRP6 inflammasome

Intestines are full of commensal bacteria that possess numerous pathogen-associated molecular patterns. How the intestinal epithelial cells are tolerant to these stimuli under normal conditions is still elusive. Here we show that iTie is expressed in small intestinal enterocytes and its deficiency leads to body weight loss in mice, accompanied by length reduce of small intestines and intestinal villi. The activation of NLRP6 inflammasome is exacerbated upon iTie deletion. iTie has a higher binding affinity for NLRP6 than NLRP6s physiological ligand LTA does. iTie deficiency gives rise to uncontrolled GSDMD activation and pyroptosis of small intestinal enterocytes. Inhibition of GSDMD permeabilization on cell membrane ameliorates the damage caused by iTie deficiency. iTes expression is diminished in small intestines of patients with Crohns disease. Our results uncover a self-control system for mouse intestine to tolerate commensal bacteria which might shed new light on the treatment of bowel diseases.

immunology↗

bioRxiv2022

Cancer-Associated Fibroblasts Regulate Patient-Derived Organoid Drug Responses

Patient-derived organoids (PDOs) can model personalized therapy responses, however current screening technologies cannot reveal drug response mechanisms or study how tumor microenvironment cells alter therapeutic performance. To address this, we developed a highly-multiplexed mass cytometry platform to measure post translational modification (PTM) signaling in >2,500 colorectal cancer (CRC) PDOs and cancer-associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment-specific drug responses in thousands of single-cell datasets, we developed Trellis -- a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is patient-specific. We found drug-induced apoptosis does not correlate with genotype or clinical staging but does align with cell-intrinsic PTM signaling in PDOs. CAFs protect chemosensitive PDOs by shifting cancer cells into a slow-cycling cell-state and CAF chemoprotection can be reversed by inhibiting YAP. HighlightsO_LI>2,500 single-cell PTM signaling, DNA-damage, cell-cycle, and apoptosis responses from drug-treated PDOs and CAFs. C_LIO_LITrellis: hierarchical tree-based treatment effect method for single-cell screening analysis. C_LIO_LIPDOs have patient-specific drug responses that align with cell-intrinsic PTM signaling states. C_LIO_LICAFs chemoprotect PDOs by altering PDO cell-state via YAP signaling. C_LI

cancer biology↗

bioRxiv2022

Single-cell Landscape Analysis of the Circulating Human B Cell Pool under Selective Pressure of Allogeneic Stem Cell Transplantation

Alloreactivity can drive autoimmune syndromes. After allogeneic hematopoietic stem cell transplantation (allo-HCT) chronic graft-versus-host disease (cGVHD), a B cell-mediated autoimmune-like syndrome, commonly occurs. Because donor-derived B cells continually develop under selective pressure from host alloantigens, aberrant B Cell Receptor (BCR)-activation and IgG production can emerge and contribute to cGVHD pathobiology. To better understand molecular programing of B cells under selective pressure of alloantigens, we performed scRNA-Seq analysis on high numbers of purified B cells from allo-HCT patients. An unsupervised analysis revealed 10 clusters, distinguishable by signature genes for maturation, activation and memory. We found striking transcriptional differences in the memory B cell compartment after allo-HCT compared to healthy or infected individuals. To identify intrinsic properties when B-cell tolerance is lost after allo-HCT, we then assessed clusters for differentially expressed genes (DEGs) between patients with vs. without autoimmune-like manifestations (Active cGVHD vs. No cGVHD, respectively). DEGs were found in Active cGVHD in both naive and BCR-activated clusters, suggesting functional diversity. Some DEGs were also differentially expressed across most clusters, suggesting common molecular programs that may promote B cell plasticity. Our study of human allo-HCT and cGVHD provides new understanding of B-cell memory in the face of chronic alloantigen stimulation. One Sentence SummaryOur scRNA-Seq study of purified B cells after allo-HCT clarifies molecular differences in human B cell subsets when immune tolerance is lost or maintained. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/512162v4_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@5c452eorg.highwire.dtl.DTLVardef@1c1d34borg.highwire.dtl.DTLVardef@171310org.highwire.dtl.DTLVardef@e4bf15_HPS_FORMAT_FIGEXP M_FIG C_FIG The circulating human B cell compartment under the selective pressure of allogeneic hematopoietic stem cell transplantation (Allo-HCT) has an intrinsically altered memory B cell pool. In allo-HCT, genetically disparate donor stem and progenitor cells engraft, regenerating a new peripheral B cell compartment in the host. During ongoing B lymphopoiesis and diversification, selective pressure from alloantigens and other extrinsic factors, including B Cell Activating Factor (BAFF), result in either B cell maturation and immune tolerance (No Chronic GVHD) or altered B cell homeostasis and autoimmune manifestations (Active Chronic GVHD). B cells within defined subsets in patients with Active GVHD have distinct intrinsic programs delineated by differentially expressed genes (DEGs). Some DEGs occur across nearly all B cell subsets ( Differentially Expressed Broadly), while other DEGs are more restricted within only one or a few B cell subsets ( Naive, BCR-activated, or Memory). We affirm altered trajectories for diversification (blue arrow) and enrichment of an atypical memory B cell (ABC) pool, with intrinsic differences when chronic GVHD occurs.

immunology↗