Biology subjects

Fei, L.

Publications and source records attributed to Fei, L..

14 recordsLinked to original sources

bioRxiv2026

A Community-Driven Single-Cell PBMC Reference Integrating Landmark Datasets Spanning Health and Disease

Blood provides an accessible window into human health, yet the absence of a peripheral blood mononuclear cells (PBMCs) reference with standardized immune cell annotations has constrained comparisons between single-cell RNA sequencing (scRNAseq) studies. Here, we present HARP (Human Cell Atlas Reference for PBMCs), an integrated atlas of ~9 million PBMCs from >2,600 donors across 15 studies spanning four continents, encompassing diverse populations, neonates to 97 years, across health and diverse immune-related diseases. We developed optimized integration workflows, including novel label-free metrics to assess integration quality, and generated community-driven consensus annotations for 192 immune cell subsets, identifying rare populations representing as few as 0.004% of PBMCs. HARP reveals coordinated cellular modules associated with age, sex, and disease, identifies female-biased interferon and inflammatory gene programs and their perturbation by COVID-19, and uncovers a novel sexual dimorphism in prostaglandin signaling. Finally, we introduce scTiger, a hierarchical label-transfer framework that accurately projects these 192 cell annotations onto ~18 million additional PBMCs, providing a robust and transferable reference for harmonizing future PBMC studies. HARP provides a high-resolution community-driven reference atlas for PBMC annotation and analysis, as a basis for emerging clinical applications of single-cell genomics.

immunology↗

bioRxiv2026

An integrated multimodal pan-organ atlas of the female reproductive system across the lifespan contextualises gynaecological pathologies

Single cell transcriptomics has transformed our knowledge of reproductive tissues, yet studies remain largely organ-specific and temporally limited, leaving an incomplete picture of how cell types are distributed across the reproductive system over a lifetime. Gynaecological conditions affect more than one in four females and frequently span multiple organs and life stages. To advance our understanding and treatment of these conditions, an integrated cellular reference is essential. Here we present the Human Female Reproductive System Cell Atlas v1: a single-cell transcriptomic resource integrating more than 2M cells across the ovary, fallopian tube, uterus, cervix and vagina over the lifespan and menstrual cycle, further integrated with spatial transcriptomics and chromatin accessibility profiling to define 210 cell types through community-based annotation. Cross-organ integration resolves shared and organ-specific cellular states, identifying uterine-specific perivascular populations lining uterine spiral arteries, hypoxia-sensing type 3 innate lymphoid cells (ILC3s) enriched in the uterus, and lipid-associated macrophages with distinct subsets in each reproductive organ, including a previously undescribed population shared between the uterus and fallopian tube. Cross-organ integration enables detection of ectopic epithelial populations in otherwise healthy donors, including endometrial-like cells within a paediatric ovary consistent with early endometriosis. Integration with genome-wide association studies (GWAS) reveals that risk variants for major gynecological conditions act in mesenchymal cell states defined by specific transcriptional programmes and spatial or temporal context - for instance, heavy menstrual bleeding risk is enriched in basal fibroblasts (SFRP5) of the regenerative endometrial compartment. An integrated chromatin accessibility atlas provides peak-to-gene maps across reproductive cell types, enabling nomination of disease effector genes and providing the first regulatory evidence linking a Polyendocrine Metabolic Ovarian Syndrome (PMOS) risk locus to INHBB in granulosa cells. Together, this resource establishes a cellular and molecular framework for reproductive biology and the pathogenesis of neglected gynaecological conditions.

Cell Biology↗

bioRxiv2026

NFATC2 in pancreatic cancer-associated fibroblasts predicts treatment response and facilitates ERBB-targeted therapies

Pancreatic ductal adenocarcinoma (PDAC) remains a lethal malignancy, with therapeutic resistance influenced by a dense desmoplastic stroma dominated by cancer-associated fibroblasts (CAF). Using single-cell RNA-sequencing and gene regulatory network modeling of 42 PDAC tumors, we identified a CAF subpopulation characterized by elevated NFATC2 expression that is enriched in patients with improved therapeutic response and survival. NFATC2+ CAFs exhibited tumor-suppressive features, including enhanced apoptotic signaling and suppression of ERBB pathway activity. Co-culture experiments demonstrated that NFATC2+ CAFs restrain pancreatic cancer cell growth and enhance chemotherapy-induced apoptosis, increasing sensitivity to standard-of-care chemotherapy regimens and synergizing with ERBB-targeted therapies. The favorable effect of NFATC2+ CAFs on chemotherapy response was validated in two other PDAC cohorts and in rectal cancer. Together, these findings identify NFATC2+ CAFs as a therapy-conditioned stromal state linked to improved treatment response and uncover a context-dependent vulnerability within the tumor microenvironment that may be exploited to rationally optimize combination therapies.

cancer biology↗

bioRxiv2026

Classical enhancers couple cis-regulatory logic with transcriptional condensates and 3D genome architecture

Deciphering the regulatory logic of enhancers remains a central question in understanding cell- and tissue-specific gene expression in multicellular organisms. This is particularly pertinent at multipartite enhancer clusters such as super-enhancers, where multiple enhancers contribute to the expression of a single gene. Gene expression has been studied largely through sequence-dependent recruitment of transcription factors (TF) and co-activators, whereas 3D chromatin structure has been attributed to architectural proteins such as cohesion and CTCF1-3. However, the contribution of DNA sequence encoded in enhancers to shaping higher-order genome organization remains poorly understood. Here we show that classical enhancers, embedded within multipartite super-enhancer structures, act as determinant regulatory elements that initiate the gene regulatory cascade by linking DNA sequence recognition to 3D chromatin architecture. Classical enhancers are more evolutionarily conserved and display stronger regulatory activity than facilitator elements, which lack intrinsic enhancer activity but potentiate classical enhancer function. We show that classical enhancers are selectively bound by specific TFs with strong intrinsically disordered regions, such as NFE2L2 in liver cancer cells, capable of driving transcriptional condensate formation through phase separation. NFE2L2 depletion reduced enhancer activity and induced widespread chromatin reorganization, characterized by increased cohesin and CTCF occupancy at super-enhancer boundaries and beyond. This "cohesin clogging" impaired DNA loop extrusion, led to formation of smaller topologically associated domains, and weakened enhancer-promoter contacts. These findings highlight that sequence-specific TFs have multifaceted roles beyond transcriptional control, establishing a direct mechanistic link between enhancer sequence, TF binding, condensate formation, and 3D genome organization, with the regulatory logic being encoded in the DNA sequence itself.

genomics↗

bioRxiv2025

barbieQ: An R software package for analysing barcode count data from clonal tracking experiments

MotivationA "clone" encompasses a progenitor cell and its progeny cells. Tracking clonal composition as cells differentiate or evolve is useful in many fields. Various single-cell lineage tracing (clonal tracking) technologies use unique DNA barcodes that are passed from progenitor cells to their offspring. The barcode count for each sample indicates cell number in clones. However, analysis of barcode count data is often bespoke and relies on visualisations and heuristics. A generalized workflow for preprocessing and robust statistical analysis of barcode count data across protocols is needed. ResultsWe introduce barbieQ, a Bioconductor R package for analysing barcode count data across groups of samples. It provides data-driven quality control and filtering, extensive visualisations, and two statistical tests: 1) Differential barcode proportion (differences in proportions between sample groups), and 2) Differential barcode occurrence (differences in presence/absence odds between groups). Both tests handle complex experimental designs using regression models and rigorously account for sample-to-sample variability. We validated both tests on semi-simulated, real data and a case study, demonstrating that they hold their size, are sufficiently powered to detect true differences, and outperform existing approaches. ContactAlicia.oshlack@petermac.org

bioinformatics↗

bioRxiv2025

Construction of recombinant Bacillus subtilis spores surface-displaying PRRSV ORF1b, GP5, M, and N proteins in tandem and evaluation of their immunogenicity in mice

Porcine reproductive and respiratory syndrome virus (PRRSV), a single-stranded RNA virus, is a highly contagious pathogen that causes severe reproductive and respiratory disorders in pigs, leading to significant economic losses in the swine industry worldwide. However, current commercial vaccines provide only limited protection against circulating PRRSV strains, highlighting the urgent need for novel vaccine strategies. B. Bacillus subtilis, a well-characterized probiotic, has emerged as a promising platform for mucosal vaccine delivery due to its safety profile and ability to induce robust immune responses. In this study, we screened B cell and T cell linear epitopes from PRRSV-ORF1b, GP5, M, and N proteins to construct a recombinant tandem antigen (ER), which was displayed on the surface of B. subtilis 168 spores. The resulting recombinant strain, designated B. subtilis BE, was evaluated for immunogenicity in mice via oral administration. The results showed that Oral immunization with B. subtilis BE significantly elevated antigen-specific secretory IgA levels in intestinal contents and IgG levels in serum, indicating potent mucosal and systemic humoral responses. Moreover, B. subtilis BE induced measurable neutralizing antibody titers and enhanced cellular immunity, as evidenced by increased frequencies of CD3+ and CD8+ T cells in mesenteric lymph nodes and upregulation of IFN-, TNF-, and IFN-{gamma} expression in intestinal tissues. Collectively, these findings demonstrate that B. subtilis BE elicits both humoral and cellular immune responses and may serve as a novel oral vaccine candidate against PRRSV, offering a promising alternative for controlling the ongoing epidemic.

immunology↗

bioRxiv2024

A multiomic atlas of human early skeletal development

Bone and joint formation in the developing skeleton rely on co-ordinated differentiation of progenitors in the nascent developing limbs and joints. The cell states, epigenetic processes and key regulatory factors underlying their lineage commitment to osteogenic and other mesenchymal populations during ossification and joint formation remain poorly understood and are largely unexplored in human studies. Here, we apply paired single-nuclei transcriptional and epigenetic profiling of 336,000 droplets, in addition to spatial transcriptomics, to construct a comprehensive atlas of human bone, cartilage and joint development in the shoulder, hip, knee and cranium from 5 to 11 post-conception weeks. Spatial mapping of cell clusters to our highly multiplexed in situ sequencing (ISS) data using our newly developed tool ISS-Patcher revealed new cellular mechanisms of zonation during bone and joint formation. Combined modelling of chromatin accessibility and RNA expression allowed the identification of the transcriptional and epigenetic regulatory landscapes that drive differentiation of mesenchymal lineages including osteogenic and chondrogenic lineages, and novel chondrocyte cell states. In particular, we define regionally distinct limb and cranial osteoprogenitor populations and trajectories across the fetal skeleton and characterise differential regulatory networks that govern intramembranous and endochondral ossification. We also introduce SNP2Cell, a tool to link cell-type specific regulatory networks to numerous polygenic traits such as osteoarthritis. We also conduct in silico perturbations of genes that cause monogenic craniosynostosis and implicate potential pathogenic cell states and disease mechanisms involved. This work forms a detailed and dynamic regulatory atlas of human fetal skeletal maturation and advances our fundamental understanding of cell fate determination in human skeletal development.

developmental biology↗

bioRxiv2023

A spatial human thymus cell atlas mapped to a continuous tissue axis

T cells develop from circulating precursors, which enter the thymus and migrate throughout specialised sub-compartments to support maturation and selection. This process starts already in early fetal development and is highly active until the involution of the thymus in adolescence. To map the micro-anatomical underpinnings of this process in pre- vs. post-natal states, we undertook a spatially resolved analysis and established a new quantitative morphological framework for the thymus, the Cortico-Medullary Axis. Using this axis in conjunction with the curation of a multimodal single-cell, spatial transcriptomics and high-resolution multiplex imaging atlas, we show that canonical thymocyte trajectories and thymic epithelial cells are highly organised and fully established by post-conception week 12, pinpoint TEC progenitor states, find that TEC subsets and peripheral tissue genes are associated with Hassalls Corpuscles and uncover divergence in the pace and drivers of medullary entry between CD4 vs. CD8 T cell lineages. These findings are complemented with a holistic toolkit for spatial analysis and annotation, providing a basis for a detailed understanding of T lymphocyte development.

immunology↗

bioRxiv2023

Co-engagement of TIGIT+ immune cells to PD-L1+ tumours by a bispecific antibody potentiates T-cell response and tumour control

Co-targeting PD-1/PD-L1 and TIGIT/CD226 is being pursued to broaden the efficacy of current immunotherapy. Here we demonstrate that a bispecific antibody (BsAb) targeting PD-L1 and TIGIT, HB0036, shows major advantages over the combination of the two parental monoclonal Abs (mAbs). We demonstrated that HB0036 co-engages PD-L1+ tumour cells and TIGIT+ T cells, and thereby upregulates CD226 on T cells and induces a greater T-cell proliferative response compared to the combination of the parental antibodies in vitro. In vivo, HB0036 recruits greater amounts of TIGIT antibody in PD-L1+ tumours but not in PD-L1- tumours, compared with therapy using the two parental antibodies. We also observed improved tumour control and favourable immunological signatures with HB0036 in syngeneic and xenograft tumour models. Collectively, these findings demonstrate that bispecific antibodies targeting PD-L1 and TIGIT offer superior benefits in cancer immunotherapy compared with therapy using the two parental antibodies. Based on these studies, a phase I clinical trial with HB0036 has been initiated in patients with solid tumours (NCT05417321).

immunology↗

bioRxiv2022

Transposable elements as tissue-specific enhancers in cancers of endodermal lineage

Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we have utilized unbiased massively parallel reporter assay data using whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identified distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

genomics↗

bioRxiv2022

The Hereditary and Epigenetic Fusion Gene Signatures of Multiple Myeloma

Fusion transcripts are thought to be somatic and associated with cancer. However, they have been observed in healthy tissues at high recurrent frequencies. We have used SCIF (SplicingCodes Identify Fusion Transcripts) to analyze RNA-Seq data from 727 multiple myeloma (MM) patients of the MMRF CoMMpass Study. MTG1-SCART1, SCART1-CYP2E1, and TPM4-KLF2 have been detected in 96.1%, 95.7%, and 92.2% of 727 MM patients and formed fusion gene signatures. MTG1-SCART1 and SCART1-CYP2E1 are read-through from the same locus and the two most recurrent epigenetic fusion genes (EFGs) out of 187 EFGs detected in [≥]10% of 727 MM patients. TPM4-KLF2 fusion gene, which was initially thought to be somatic, has been shown by a monozygotic twin genetic model to be a hereditary fusion gene (HFG) and the dominant genetic factor associated with MM. This work provides the first line of evidence that HFGs are the genetic factors and EFGs reflect the consequences between genetics and environments during development.

cancer biology↗

bioRxiv2022

Direct conversion of human fibroblasts to pancreatic epithelial cells through transient progenitor states is controlled by temporal activation of defined factors

Cell fate can be reprogrammed by ectopic expression of lineage-specific transcription factors (TF). For example, few specialized cell types like neurons, hepatocytes and cardiomyocytes have been generated from fibroblasts by defined factors (Wang et al, 2021). However, the exact cell state transitions and their control mechanisms during cell fate conversion are still poorly understood. Moreover, the defined TFs for generating vast majority of the human cell types are still elusive. Here, we report a novel protocol for reprogramming human fibroblasts to pancreatic exocrine cells with phenotypic and functional characteristics of ductal epithelial cells using a minimal set of six TFs. We mapped the molecular determinants of lineage dynamics at single-cell resolution using a novel factor-indexing method based on single-nuclei multiome sequencing (FI-snMultiome-seq) that enables dissecting the role of each individual TF and pool of TFs in cell fate conversion. We show that transdifferentiation - although being considered a direct cell fate conversion method - occurs through transient progenitor states orchestrated by stepwise activation of distinct TFs. Specifically, transition from mesenchymal fibroblast identity to epithelial pancreatic exocrine fate involves two deterministic steps: first, an endodermal progenitor state defined by activation of HHEX concurrently with FOXA2 and SOX17, and second, temporal GATA4 activation essential for maintenance of pancreatic cell fate program. Collectively, our data provide a high-resolution temporal map of the epigenome and transcriptome remodeling events that facilitate cell fate conversion, suggesting that direct transdifferentiation process occurs through transient dedifferentiation to progenitor cell states controlled by defined TFs.

cell biology↗

bioRxiv2022

Top-down modulation and cortical-AMG/HPC interaction in familiar face processing

Humans can accurately recognize familiar faces in only a few hundred milliseconds, but the underlying neural mechanism remains unclear. Here we recorded intracranial electrophysiological signals from ventral temporal cortex (VTC), superior/middle temporal cortex (STC/MTC), medial parietal cortex (MPC) and amygdala/hippocampus (AMG/HPC) in 20 epilepsy patients while they viewed faces of famous people and strangers as well as common objects. In posterior VTC and MPC, familiarity-sensitive responses emerged significantly later than initial face-selective responses, suggesting that familiarity enhances face representations after they are first being extracted. Moreover, viewing famous faces increased the coupling between cortical areas and AMG/HPC in multiple frequency bands. These findings imply that the top-down modulation in local face-selective response and interactions between cortical face areas and AMG/HPC contribute to the superior recognition of familiar faces. TeaserTop-down modulation and cortical-AMG/HPC interactions contribute to the superior processing of familiar faces.

neuroscience↗

bioRxiv2018

Revealing the critical regulators of cell identity in the mouse cell atlas

Recent progress in single-cell technologies has enabled the identification of all major cell types in mouse. However, for most cell types, the regulatory mechanism underlying their identity remains poorly understood. By computational analysis of the recently published mouse cell atlas data, we have identified 202 gene regulatory networks whose activities are highly variable across different cell types, and more importantly, predicted a small set of essential regulators for each of over 800 cell types in mouse for the first time. Systematic validation by automated literature- and data-mining provides strong additional support for our predictions. Thus, these predictions serve as a valuable resource that would be useful for the broad biological community. Finally, we have built a user-friendly, interactive, web-portal to enable users to navigate this mouse cell network atlas.

bioinformatics↗