Biology subjects

Xie, J.

Publications and source records attributed to Xie, J..

At least 163 records · Page 9Linked to original sources

bioRxiv2023

Predicting Disease-gene Associations through Self-supervised Mutual Infomax Graph Convolution Network

Illuminating associations between diseases and genes can help reveal the pathogenesis of syndromes and contributes to treatments, but a large number of associations still remained unexplored. To identify novel disease-gene association, many computational methods have been developed using disease and gene related prior knowledge. However, these methods remain of relatively inferior performance due to the limited external data sources and the inevitable noise among the prior knowledge. In this study, we have developed a new method, Self-Supervised Mutual Infomax Graph Convolution Network (MiGCN), to predict disease-gene associations under the guidance of external disease-disease and gene-gene collaborative graphs. The noises within the collaborative graphs were eliminated by maximizing the mutual information between nodes and neighbors through a graphical mutual infomax layer. In parallel, the node interactions were strengthened by a novel informative message passing layer to improve the learning ability of graph neural network. The extensive experiments showed that our model achieves performance improvement over the state-of-art method by more than 8% on AUC. The datasets, source codes and trained models of MiGCN are available at https://github.com/biomed-AI/MiGCN.

bioinformatics↗

bioRxiv2023

Mechanically stimulated osteocytes maintain tumor dormancy in bone metastasis of non-small cell lung cancer by releasing small extracellular vesicles

Although preclinical and clinical studies have shown that exercise can inhibit bone metastasis progression, the mechanism remains poorly understood. Here, we found that non-small cell lung cancer (NSCLC) cells adjacent to bone tissue had a much lower proliferative capacity than the surrounding tumor cells. Subsequently, it was demonstrated that osteocytes, sensing mechanical stimulation generated by exercise, inhibit NSCLC cell proliferation and sustain the dormancy thereof by releasing small extracellular vesicles with tumor suppressor microRNAs, such as miR-99b-3p. Furthermore, mechanical loading of the tibia inhibited the bone metastasis progression of NSCLC. Notably, bone metastasis progression of NSCLC was inhibited by moderate exercise, and combinations with zoledronic acid had additive effects. Moreover, exercise preconditioning effectively suppressed bone metastasis progression. This study significantly advances the understanding of the mechanism underlying exercise-afforded protection against bone metastasis progression.

cancer biology↗

bioRxiv2023

Building a genetic and epigenetic predictive model of breast cancer intrinsic subtypes using large-scale data and hierarchical structure learning

Breast cancer subtyping is a difficult clinical and scientific challenge. The prevalent Prediction Analysis of Microarray of 50 genes (PAM50) system and its Immunohistochemistry (IHC) surrogate showed significant inconsistencies. This is because of the limited training samples, highly variable molecular features and in-efficient strategies used in these classifiers. The rapid development of early screening technologies, especially in the field of circulating tumor DNA, has also challenged the subtyping of breast cancer at the DNA level. By integrating large-scale DNA-level data and using a hierarchical structure learning algorithm, we developed Unified Genetic and Epigenetic Subtyping (UGES), a new intrinsic subtype classifier. The benchmarks showed that the use of all classes of DNA alterations worked much better than single classes, and that the multi-step hierarchical learning is crucial, which improves the overall AUC score by 0.074 compared to the one-step multi-classification method. Based on these insights, the ultimate UGES was trained as a three-step classifier on 50831 DNA features of 2065 samples, including mutations, copy number aberrations, and methylations. UGES achieved overall AUC score 0.963, and greatly improved the clinical stratification of patients, as each stratas survival difference became statistically more significant p-value=9.7e-55 (UGES) vs 2.2e-47 (PAM50). Finally, UGES identified 52 subtype-level DNA biomarkers that can be targeted in early screening technology to significantly expand the time window for precision care. The analysis code is freely available at https://github.com/labxscut/UGES.

bioinformatics↗

bioRxiv2023

Identifying gastric cancer molecular subtypes by integrating DNA-based hierarchical classification strategy and clinical stratification

BackgroundMolecular subtyping has been introduced to better understand the genetic landscape of gastric cancer (GC), but current subtyping methods only had limited success because of the mixed use of molecular features, a lack of strategy optimization, and the limited availability of GC samples. The community urgently calls for a precise, and easily adoptable subtyping method to enable DNA-based early screening and treatment. MethodsBased on TCGA subtypes, we developed a novel classifier, termed Hierarchical DNA-based Classifier for Gastric Cancer Molecular Subtyping (HCG), leveraging all DNA-level alterations as predictors, including gene mutations, copy number aberrations and methylations. By adding the closely related esophageal adenocarcinomas (EA) dataset, we expanded the TCGA GC dataset for training and testing HCG (n=453). We optimized HCG with three hierarchical strategies evaluated by their overall accuracy using Lasso-Logistic regression, and by their clinical stratification capacity using multivariate survival analysis. We used difference tests to identify subtype-specific DNA alteration biomarkers based on HCG defined subtypes. ResultsOur HCG classifier achieved an overall AUC score of 0.95 and significantly improved the clinical stratification of patients (overall p-value=0.032). 25 subtype-specific DNA alterations were identified by difference tests, including high level of mutations in SYNE1, ITGB4 and COL22A1 genes for the MSI subtype, high level of methylations of ALS2CL, KIAA0406 and RPRD1B genes for the EBV subtype. ConclusionsHCG is an accurate and robust classifier for DNA-based GC molecular subtyping with high-performing clinical stratification capacity. The training and test datasets and analysis programs of HCG are available at https://github.com/labxscut/HCG.

bioinformatics↗

bioRxiv2023

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

SifiNet is a robust and accurate computational pipeline for identifying distinct gene sets, extracting and annotating cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Uniquely, SifiNet bypasses the cell clustering stage, commonly integrated into other cellular annotation pipelines, thereby circumventing potential inaccuracies in clustering that may compromise subsequent analyses. Consequently, SifiNet has demonstrated superior performance in multiple experimental datasets compared with other state-of-the-art methods. SifiNet can analyze both single-cell RNA and ATAC sequencing data, thereby rendering comprehensive multiomic cellular profiles. It is conveniently available as an open-source R package.

bioinformatics↗

bioRxiv2023

Parallel genetic excisions of the cardiac troponin I N-terminal extension in tachycardic mammals

Mammalian cardiac troponin I (cTnI) contains a highly conserved N-terminal extension harboring protein kinase A targets (Ser23/24) which are phosphorylated during {beta}-adrenergic stimulation to increase cardiomyocyte relaxation rate. Here, we show that the Ser23/24 encoding exon 3 of TNNI3 was pseudoexonized multiple times in shrews and moles to mimic Ser23/24 phosphorylation without adrenergic stimulation, facilitating the evolution of exceptionally high resting heart rates ([~]1000 beats min-1). We further reveal alternative exon 3 splicing in distantly related bat families and that both exon 3- and exon 3+ cTnI isoforms are incorporated into cardiac myofibrils. Finally, exon 3 of human TNNI3 is shown to exhibit a relatively low splice strength score, offering an evolutionarily informed strategy to excise this exon to improve diastolic function during heart failure.

evolutionary biology↗

bioRxiv2023

Syndecan-4 is the Key Proteoglycan Mediating LPS-induced Sepsis-associated Lung Injury

The occurrence of acute sepsis-associated lung injury (ALI) is closely related to vascular endothelial cell dysfunction, but the exact isoform of the functional syndecans (SDCs) located in the inner endothelial membrane of blood vessels and involved in regulating inflammation is not clear. The present study aimed to clarify whether SDC2 and/or 4 is involved in the inflammation process.Using the Gene Expression Omnibus (GEO) database, differentially expressed genes (DEGs) were extracted and analyzed. A bioinformatic analysis was conducted using R language, gene ontology (GO), and the Kyoto Encyclopedia of Genes and Genomes (KEGG) with the aim of predicting SDC2 and 4 expression levels. Subsequently, the expression profiles of these two proteins were examined after construction of a sepsis-associated ALI mmodel was constructed in both human lung vascular endothelial cells (HLVEC) and animal models under inflammatory conditions. Eventually, the transcription factors (TF) of SDC2/4 were predicted based on the available dataset, and their involvement in septic inflammation was indirectly assessed. The GSE 5883 microarray gene-chip data profile was found to be suitable for analyzing lipopolysaccharide (LPS)-induced endothelial inflammatory injury. After analyzing the DEGs, 224 and 102 genes were found to be up- and down-regulated, respectively. All DEGs were involved in modulating receptor ligand and signaling receptor activator activities, cytokine receptor binding in biological processes, such as responses to lipopolysaccharide (LPS) and molecules from bacterial origins, positive regulation of cell adhesion, and other functions. In the case of localization of cellular components, most DEGs were enriched in cytoplasmic ribonucleoprotein granules, transcription regulator complex, and membrane rafts and were involved in the tumor necrosis factor (TNF) signaling and cytokine receptor interaction pathways. When compared with the control group, SDC4 gene expression in the LPS group increased by 4.5-fold, and comparable results were found in terms of SDC2 gene expression. From an experimental aspect, SDC4 was found to be markedly up-regulated with respect to mRNA and protein expression levels in response to inflammatory injury; moreover, down-regulation of SDC4 could severely exacerbate inflammatory responses either in in vivo or in vitro models. Altogether, SDC4, rather than SDC2, was found to be involved in LPS-induced sepsis-associated ALI.

bioinformatics↗

bioRxiv2023

Multimodal engineering of extracellular vesicles for efficient intracellular protein delivery

Extracellular vesicles (EVs) are promising tools to transfer macromolecular therapeutic molecules to recipient cells, however, efficient functional intracellular protein delivery by EVs remains challenging. Here, we have developed novel and versatile systems that leverage selected molecular tools to engineer EVs for robust cytosolic protein delivery both in vitro and in vivo. These systems, termed VSV-G plus EV-sorting Domain-Intein-Cargo (VEDIC) and VSV-G-Foldon-Intein-Cargo (VFIC), exploit an engineered mini-intein (intein) protein with self-cleavage activity to link cargo to an EV-sorting domain and release it from the EV membrane inside the EV lumen. In addition, we utilize the fusogenic protein VSV-G to facilitate endosomal escape and cargo release from the endosomal system to the cytosol of recipient cells. Importantly, we demonstrate that the combination of the self-cleavage intein, fusogenic protein and EV-sorting domain are indispensable for efficient functional intracellular delivery of cargo proteins by engineered EVs. As such, nearly 100% recombination and close to 80% genome editing efficiency in reporter cells were observed by EV-transferred Cre recombinase and Cas9/sgRNA RNPs, respectively. Moreover, EV-mediated Cre delivery by VEDIC or VFIC engineered EVs resulted in significant in vivo recombination in Cre-LoxP R26-LSL-tdTomato reporter mice following both local and systemic injections. Finally, we applied these systems for improved treatment of LPS-induced systemic inflammation by delivering a super-repressor of NF-B activity. Altogether, this study describes a platform by which EVs can be utilized as a vehicle for the efficient intracellular delivery of macromolecular therapeutics for treatments of disease. Graphic summary: Development of VEDIC and VFIC systems for high-efficiency intracellular protein delivery in vitro and in vivo.Intein in tripartite fusion protein (EV-sorting Domain-Intein-Cargo) performs C-terminal cleavage during the process of EV-biogenesis, resulting in enriched free cargo proteins inside of vesicles. Together with fusogenic protein, VSV-G, these engineered EVs achieve high-efficiency intracellular delivery of cargo protein (Cre and super repressor of NF-B) or protein complex (Cas9/sgRNA RNPs) both in reporter cells and in mice models. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/535834v4_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@d0da37org.highwire.dtl.DTLVardef@1a6514corg.highwire.dtl.DTLVardef@235c9aorg.highwire.dtl.DTLVardef@194bbfa_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

WNK1 enforces macrophage lineage fidelity

The appropriate development of macrophages, the bodys professional phagocyte, is essential for organismal development, especially in mammals. This dependence is exemplified by the observation that loss-of-function mutations in colony stimulating factor 1 receptor (CSF1R) results in multiple tissue abnormalities owing to an absence of macrophages. Despite this importance, little is known about the molecular and cell biological regulation of macrophage development. Here, we report the surprising finding that the chloride-sensing kinase With-no-lysine 1 (WNK1) is required for development of tissue-resident macrophages (TRMs). Myeloid-specific deletion of Wnk1 resulted in a dramatic loss of TRMs, disrupted organ development, systemic neutrophilia, and mortality between 3 and 4 weeks of age. Strikingly, we found that myeloid progenitors or precursors lacking WNK1 not only failed to differentiate into macrophages, but instead differentiated into neutrophils. Mechanistically, the cognate CSF1R cytokine macrophage-colony stimulating factor (M-CSF) stimulates macropinocytosis by both mouse and human myeloid progenitors and precursor cells. Macropinocytosis, in turn, induces chloride flux and WNK1 phosphorylation. Importantly, blocking macropinocytosis, perturbing chloride flux during macropinocytosis, and inhibiting WNK1 chloride-sensing activity each skewed myeloid progenitor differentiation from macrophages into neutrophils. Thus, we have elucidated a role for WNK1 during macropinocytosis and discovered a novel function of macropinocytosis in myeloid progenitors and precursor cells to ensure macrophage lineage fidelity. Highlights- Myeloid-specific WNK1 loss causes failed macrophage development and premature death - M-CSF-stimulated myeloid progenitors and precursors become neutrophils instead of macrophages - M-CSF induces macropinocytosis by myeloid progenitors, which depends on WNK1 - Macropinocytosis enforces macrophage lineage commitment

immunology↗

bioRxiv2023

Engineering Nme2Cas9 Adenine Base Editors with Improved Activity and Targeting Scope

Nme2Cas9 has been established as a genome editing platform with compact size, high accuracy, and broad targeting range, including single-AAV-deliverable adenine base editors. Here, we have engineered Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors. We first used domain insertion to position the deaminase domain nearer the displaced DNA strand in the target-bound complex. These domain-inlaid Nme2Cas9 variants exhibited shifted editing windows and increased activity in comparison to the N-terminally fused Nme2-ABE. We next expanded the editing scope by swapping the Nme2Cas9 PAM-interacting domain with that of SmuCas9, which we had previously defined as recognizing a single-cytidine PAM. We used these enhancements to correct two common MECP2 mutations associated with Rett syndrome with little or no bystander editing. Finally, we validated domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.

molecular biology↗

bioRxiv2023

Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing in vivo

Guide RNAs offer programmability for CRISPR-Cas9 genome editing but also add challenges for delivery. Chemical modification, which has been key to the success of oligonucleotide therapeutics, can enhance the stability, distribution, cellular uptake, and safety of nucleic acids. Previously, we engineered heavily and fully modified SpyCas9 crRNA and tracrRNA, which showed enhanced stability and retained activity when delivered to cultured cells in the form of the ribonucleoprotein complex. In this study, we report that a short, fully stabilized oligonucleotide (a "protecting oligo"), which can be displaced by tracrRNA annealing, can significantly enhance the potency and stability of a heavily modified crRNA. Furthermore, protecting oligos allow various bioconjugates to be appended, thereby improving cellular uptake and biodistribution of crRNA in vivo. Finally, we achieved in vivo genome editing in adult mouse liver and central nervous system via co-delivery of unformulated, chemically modified crRNAs with protecting oligos and AAV vectors that express tracrRNA and either SpyCas9 or a base editor derivative. Our proof-of-concept establishment of AAV/crRNA co-delivery offers a route towards transient editing activity, target multiplexing, guide redosing, and vector inactivation.

molecular biology↗

bioRxiv2023

Redefinition of archetypal phytoplankton-associated bacteria taxa based on globally distributed dinoflagellates and diatoms

Bacteria colonizing in the phycosphere formed by phytoplankton exudates play important roles in marine ecosystems, yet their taxonomy is poorly defined. Here, we customized the analytical approaches for the microalga-attached microbiotas from 110 diatom and 86 dinoflagellate samples to reveal key bacterial players and their ecological significance in the phycosphere. The results demonstrated a co-occurrence of host-specificity and conservation of phytoplankton-associated bacterial communities, defined 8 diatom- and 23 dinoflagellate-affiliated characteristic genera, as well as identifying 14 core genera prevalent with phytoplankton populations. Further classification of these 14 core genera into three tiers showed their distinct ecological features regarding occupancy, connectivity and community-stabilizing, whilst also matching their inherent metabolic properties. Our study redefines the archetypal phytoplankton-associated bacteria taxa more specifically up to the genus level, highlighting the significance of rarely noticed bacteria in the phycosphere, which is invaluable when selecting target bacteria for studying phytoplankton-bacteria interactions.

microbiology↗

bioRxiv2022

STING-dependent cytosolic DNA sensing pathway drives the progression to leukemia in TET2-mutated HSPCs

Somatic loss-of-function mutations of the dioxygenase Ten-eleven translocation-2 (TET2) occur frequently in individuals with clonal hematopoiesis (CH) and acute myeloid leukemia (AML). These common hematopoietic disorders can be recapitulated in mouse models. However, the underlying mechanisms by which the deficiency in TET2 promotes these disorders remain largely unknown. Here we show that the cyclic guanosine monophosphate-adenosine monophosphate synthase (cGAS)-stimulator of interferon genes (STING) pathway is activated to mediate the effect of TET2 deficiency in leukemogenesis in mouse models. DNA damage arising in Tet2-deficient hematopoietic stem/progenitor cells (HSPCs) leads to activation of the cGAS-STING pathway which in turn induces the development of CH and myeloid transformation. Notably, both pharmacological inhibition and genetic deletion of STING suppresses Tet2 mutation-induced aberrant myelopoiesis. In patient-derived xenograft (PDX) models, STING inhibition specifically attenuates the proliferation of leukemia cells from TET2-mutated individuals. These observations suggest that the hematopoietic transformation associated with TET2 mutations is powered through sterile inflammation dependent on the activated cGAS-STING pathway, and that STING may represent a potential target for intervention of relevant hematopoietic malignancies. Key pointsO_LITet2 deficiency leads to DNA damage which in turn activates the cGAS-STING pathway to induce an inflammatory response C_LIO_LIBlocking STING in TET2-mutated hematopoietic stem/progenitor cells suppresses clonal hematopoiesis in mice and leukemogenesis in patient-derived xenograft models C_LI

cancer biology↗

bioRxiv2022

Fast and accurate protein function prediction from sequence through pretrained language model and homology-based label diffusion

Protein function prediction is an essential task in bioinformatics which benefits disease mechanism elucidation and drug target discovery. Due to the explosive growth of proteins in sequence databases and the diversity of their functions, it remains challenging to fast and accurately predict protein functions from sequences alone. Although many methods have integrated protein structures, biological networks or literature information to improve performance, these extra features are often unavailable for most proteins. Here, we propose SPROF-GO, a Sequence-based alignment-free PROtein Function predictor which leverages a pretrained language model to efficiently extract informative sequence embeddings and employs self-attention pooling to focus on important residues. The prediction is further advanced by exploiting the homology information and accounting for the overlapping communities of proteins with related functions through the label diffusion algorithm. SPROF-GO was shown to surpass state-of-the-art sequence-based and even network-based approaches by more than 14.5%, 27.3% and 10.1% in AUPR on the three sub-ontology test sets, respectively. Our method was also demonstrated to generalize well on non-homologous proteins and unseen species. Finally, visualization based on the attention mechanism indicated that SPROF-GO is able to capture sequence domains useful for function prediction. Key pointsO_LISPROF-GO is a sequence-based protein function predictor which leverages a pretrained language model to efficiently extract informative sequence embeddings, thus bypassing expensive database searches. C_LIO_LISPROF-GO employs self-attention pooling to capture sequence domains useful for function prediction and provide interpretability. C_LIO_LISPROF-GO applies hierarchical learning strategy to produce consistent predictions and label diffusion to exploit the homology information. C_LIO_LISPROF-GO is accurate and robust, with better performance than state-of-the-art sequence-based and even network-based approaches, and great generalization ability on non-homologous proteins and unseen species C_LI

bioinformatics↗

bioRxiv2022

Localizing Rare-Variant Association Regions via Multiple Testing Embedded in an Aggregation Tree

Rare variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNATE (DYNamic Aggregation TEsting). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with controlled weighted false discovery rate. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared to existing methods. Importantly, DYNATE-identified regions have higher enrichment levels of disease-associated RVs. We applied DYNATE to an amyotrophic lateral sclerosis (ALS) study and identified a new gene, EPG5, harboringpossibly pathogenic mutations.

genetics↗

bioRxiv2022

The protist ubiquitin ligase effector PbE3-2 targets RD21A to impede plant immunity

Clubroot caused by the soil-borne protist pathogen Plasmodiophora brassicae is one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, the molecular mechanism by which this pathogen promotes infection remains largely unknown. Here, we identified a P. brassicae-secreted effector PbE3-2 that impedes plant immunity by ubiquitinating the immune regulator RD21A for degradation. Overexpression of PbE3-2 in Arabidopsis thaliana resulted in higher susceptibility to P. brassicae and decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated RD21A in vitro and in vivo. Mutant plants deficient in RD21A exhibited similar susceptibility and compromsied immune responses as in PbE3-2 overexpression plants. These results suggest that P. brassicae promotes clubroot disease through RD21A degradation mediated by the effector PbE3-2. As PbE3-2 is widely conserved across different P. brassicae pathotypes, the degradation of RD21A by PbE3-2 might be a prevalent infection strategy in this pathogen.

microbiology↗

bioRxiv2022

DRAM1 promotes antibacterial autophagy and lysosomal delivery of Mycobacterium marinum in macrophages

Damage-Regulated Autophagy Modulator 1 (DRAM1) is an infection-inducible membrane protein, whose function in the immune response is incompletely understood. Based on previous results in a zebrafish infection model, we have proposed that DRAM1 is a host resistance factor against intracellular mycobacterial infection. To gain insight into the cellular processes underlying DRAM1-mediated host defence, here we studied the interaction of DRAM1 with Mycobacterium marinum in murine RAW264.7 macrophages. We found that shortly after phagocytosis, DRAM1 localised in a punctate pattern to mycobacteria, which gradually progressed to full DRAM1 envelopment of the bacteria. Within the same time frame, DRAM1-positive mycobacteria colocalised with the LC3 marker for autophagosomes and LysoTracker and LAMP1 markers for (endo)lysosomes. Knockdown analysis revealed that DRAM1 is required for recruitment of LC3 and for acidification of mycobacteria-containing vesicles. A reduction in the presence of LAMP1 further suggested reduced fusion of lysosomes with mycobacteria-containing vesicles. Finally, we show that DRAM1 knockdown impairs the ability of macrophages to control mycobacterial infection. Together, these results support that DRAM1 promotes the trafficking of mycobacteria through the degradative (auto)phagolysosomal pathway. Considering its prominent effect on host resistance to intracellular infection, DRAM1 is a promising target for therapeutic modulation of the microbicidal capacity of macrophages.

immunology↗

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↗