Biology subjects

Xiao, C.

Publications and source records attributed to Xiao, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Glial betaPix is essential for blood vessel integrity in the zebrafish brain

The formation of blood-brain barrier and vascular integrity depends on the coordinative development of different cell types in the brain. Previous studies have shown that zebrafish bubblehead (bbh) mutant, which has mutation in the betaPix locus, develops spontaneous intracerebral hemorrhage during early development. However, it remains unclear in which brain cells betaPix may function. Here, we established a highly efficient conditional knockout method in zebrafish by using homology-directed repair (HDR)-mediated knockin and knockout technology, and generated betaPix conditional trap (betaPixct) allele in zebrafish. We found that betaPix in glia, but neither neurons, endothelial cells, nor pericytes, was critical for glial and vascular development and integrity, thus contributing to the formation of blood-brain barrier. Single-cell transcriptome profiling revealed that microtubule aggregation signaling stathmins and pro-angiogenic transcription factors Zfhx3/4 were down-regulated in glial and neuronal progenitors, and further genetic analysis suggested that betaPix may act upstream on the PAK1-Stathmin and Zfhx3/4-Vegfaa signaling to regulate glia migration and angiogenesis. Therefore, this work reveals that glial betaPix plays an important role in brain vascular development in zebrafish embryos and possibly human cells.

developmental biology↗

bioRxiv2025

Lack of Bcl6 promotes anti-tumor immunity by activating glycolysis to rescue CD8 T cell function

T cells are one of the most powerful weapons to fight cancer; however, T cell exhaustion and dysfunction restrict their long-lasting function in anti-tumor immunity. B-cell lymphoma 6 (BCL6) has many functions in CD8 T cells but it is unclear how it regulates the effector function and exhaustion of CD8 cells. Overall, a low level of BCL6 mRNA in human cancer samples is associated with better outcomes. We found that BCL6 deficiency in activated CD8 T cells enhanced tumor repression in multiple mouse models. More IL-2-expressing CD8 T cells and reduced proportions of exhausted or dysfunctional CD8 T cells were detected within tumors when Bcl6 was knocked out upon T cell activation. Glycolysis was promoted in BCL6-deficient CD8 T cells owing to derepression of glucose transporter GLUT3 (encoded by Slc2a3). The BCL6 inhibitor Fx1 promoted anti-tumor immunity in a T cell-dependent manner. These findings suggest a novel pathway to restore effector function of CD8 T cells by changing their energy utilization pathways to facilitate long-term tumor resistance. Summary BlurbBCL6 limits CD8 T cell responses to tumors by inhibiting Glut3 expression. Conditional deletion of Bcl6 in activated CD8 T cells or pharmacological inhibition of BCL6 in mice represses tumor growth.

immunology↗

bioRxiv2025

Cloche/Npas4l is a pro-regenerative platelet factor during zebrafish heart regeneration

Zebrafish has full capacity of heart regeneration, but little is known about how blood cells, especially platelets, are involved in this regenerative process. Here we report that cloche/npas4l is a pro-regenerative platelet factor for heart regeneration. We found that haploinsufficiency of npas4l disrupted cardiomyocyte (CM) and endothelial cell (EC) proliferation and heart regeneration after injury. A single-cell transcriptomic atlas revealed that npas4l was dynamically expressed in platelets after heart injury and regulated robust interactions between platelets-CMs or -ECs. Decreasing platelets by either nitroreductase-mediated platelet depletion or platelet-deficient mutant mpl impaired CM and EC proliferation, and over-expression of npas4l in platelets sufficiently induced CM and EC proliferation in uninjured hearts, as well as rescued CM and EC proliferation defects in cloche mutants. Mechanistically, Npas4l positively regulated a panel of ligands expression including bmp6 in platelets to fine-tune CM proliferation and heart regeneration. Therefore, this work unveils a novel platelet Npas4l signaling and presents mechanisms on how platelets modulate CM/EC proliferation via ligand-receptor network during zebrafish heart regeneration.

cell biology↗

bioRxiv2025

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

bioRxiv2025

JRSeek: Artificial Intelligence Meets Jelly Roll Fold Classification in Viruses

The jelly roll (JR) fold is the most common structural motif found in the capsid and nucleocapsid of viruses. Its pervasiveness across many different viral families motives developing a tool to predict its presence from a sequence. In the current work, logistic regression (LR) models trained on six different large language model (LLM) embeddings exhibited over 95% accuracy in differentiating JR from non-JR sequences. The dataset used for training and testing included sequences from single JR viruses, non-JR viruses, and non-virus immunoglobulin-like {beta}-sandwich (IGLBS) proteins which closely resemble the JR fold in structure. The high accuracy is particularly remarkable given the low sequence similarity across viral families and the balanced nature of the dataset. Also, the accuracy of the models was independent of LLM embeddings, suggesting that peak accuracy for predicting viral JR folds hinges more on the data quality and quantity rather than on the specific mathematical models used. Given that many viral capsid and nucleocapsid structures have yet to be resolved, using sequence-based LLMs is a promising strategy that can readily be applied to available data. Principal Component Analysis of the Bert-U100 embeddings demonstrates that most IGLBS sequences and a subset of JR and non-JR sequences are distinguishable even before the application of the LR model, but the LR model is necessary to differentiate a subset of more ambiguous sequences. When applied to double JR folds, the Bert-U100 model was able to assign the JR motif for some viral families, providing evidence for the models generalizability. However, for other families, this generalizability was not observed, motivating a future need to develop other models informed by double JR folds. Lastly, the Bert-U100 model was also able to predict whether sequences from a dataset of unclassified viruses produce the JR fold. Two examples are given and the JR predictions are corroborated by AlphaFold3. Altogether, this work demonstrates that JR folds can, in principle, be predicted from their sequences.

bioinformatics↗

bioRxiv2025

Local Microenvironments of capsomer variants in the PBCV-1

PBCV-1, a giant virus classified among the Nucleocytoviricota virus (NCV) whose structure has been determined to near atomic resolution. The majority capsomers forming the capsid of PBCV-1 are Type I capsomers while five other type of variants have been found in recent high resolution structure. Interestingly, some variants, such as Type V capsomers, are found at particular capsid locations whose roles are unclear. To reveal the roles of a Type V capsomer, we replaced the Type V capsomer by a Type I capsomer to compare the interaction among the two types of capsomer variant, especially the interactions between each of the Type V/Type I capsomer and its local capsid microenvironment. Our results revealed significant differences between Type V and Type I capsomers. Notably, the Type V capsomer demonstrated a stronger binding force to the surrounding capsomers than the Type I capsomer. Moreover, the identified salt bridges between Type V/I capsomers and their surrounding capsomers corroborate the results of electrostatic calculations, further highlighting the important residues involved in these interactions. Understanding these local capsid microenvironments will be essential to elucidate the mechanisms governing viral capsid assembly.

biophysics↗

bioRxiv2025

Regulation of B cell tolerance and autoimmunity by miR-130b

Breakdown of B cell tolerance is a central feature of autoimmune diseases, yet the molecular mechanisms underlying the female predominance of these diseases remain unclear. Here, we identified miR-130b as an essential component of a miRNA network, defined by the GUGCA seed motif, that regulates central B cell tolerance. Elevated miR-130b levels impaired tolerance by promoting the survival of immature B cells upon B cell antigen receptor engagement. This network converged on the estrogen receptor pathway through downregulation of Esr1 and Pten. Genetic ablation of Esr1 in immature B cells was sufficient to compromise central B cell tolerance in females, but not in males, revealing an unrecognized role for ER in this process. In males, Esr1 deficiency reduced bone marrow B cell numbers, whereas in females, B cell numbers were preserved, with a greater proportion of cells displaying lower surface CD19 levels. Transcriptomic analysis revealed sex-specific genetic programs characterized by defective B cell development and skewed immunoglobulin gene usage in males, and increased PI3K-AKT signaling in females. In females, this molecular rewiring compensated for developmental defects, but also attenuated central tolerance mechanisms, allowing the escape of autoreactive B cells to the periphery. In patients with multiple sclerosis, elevated levels of miR-130b in circulating vesicles correlated with more severe disease, including increased formation of new demyelinating lesions, cognitive decline, and neurodegeneration. Together, our findings identify a sex-specific ER-dependent checkpoint in B cell tolerance controlled by a seed-driven miRNA network, providing a mechanistic framework for female predisposition to autoimmunity.

immunology↗

bioRxiv2024

Bipolar and schizophrenia risk gene AKAP11 encodes an autophagy receptor coupling the regulation of PKA kinase network homeostasis to synaptic transmission

Human genomic studies have identified protein-truncating variants in AKAP11 associated with both bipolar disorder (BD) and schizophrenia (SCZ), implicating a shared disease mechanism driven by loss-of-function. AKAP11, a protein kinase A (PKA) adaptor, plays a key role in degrading the PKA-RI complex through selective autophagy. However, the neuronal functions of AKAP11 and the impact of its loss-of-function remains largely uncharacterized. Through multi-omics approaches, cell biology, and electrophysiology analysis in mouse models and human induced neurons, we delineated a central role of AKAP11 in coupling PKA kinase network regulation to synaptic transmission. Loss of AKAP11 distorted compartment-specific PKA and GSK3/{beta} activities and impaired cellular functions that significantly overlap with pathways associated with BD and SCZ. Moreover, we identified interactions between AKAP11, the PKA-RI adaptor SPHKAP, and the ER-resident autophagy-related proteins VAPA/B, which co-adapt and mediate PKA-RI complex degradation in neurons. Notably, AKAP11 deficiency impaired neurotransmission, providing key insights into the mechanism underlying AKAP11-associated psychiatric diseases.

neuroscience↗

bioRxiv2024

MORC-1 is a key component of the C. elegans CSR-1 germline gene licensing mechanism

The Argonaute CSR-1 is essential for germline development in C. elegans. Mutation of csr-1 downregulates thousands of germline-expressed genes, leading to the model that the CSR-1-mediated small RNA pathway promotes, or "licenses," gene expression by an unknown mechanism. CSR-1 also silences a limited number of genes through its canonical endonucleolytic "slicer" activity. We show that the GHKL-type ATPase MORC-1, a CSR-1 slicing target, over-accumulates at CSR-1 "licensed" target genes in csr-1(-), which correlates with ectopic gain of H3K9me3, H3K36me3 loss, and gene downregulation. Loss of morc-1 rescues csr-1(-) defects, while overexpressing MORC-1 in the germline of wild-type worms is sufficient to cause sterility and downregulate CSR-1 targets. These results show that MORC-1 overexpression in csr-1(-) is a primary driver of the CSR-1-mediated gene licensing mechanism. One-Sentence SummaryMORC-1 acts downstream of CSR-1 to regulate germline chromatin states and is a key component of the gene licensing mechanism.

molecular biology↗

bioRxiv2024

A benchmarking study of copy number variation inference methods using single-cell RNA-sequencing data

Single-cell RNA-sequencing (scRNA-seq) has emerged as a powerful tool for cancer research, enabling in-depth characterization of tumor heterogeneity at the single-cell level. Recently, scRNA-seq copy number variation (scCNV) inference methods have been developed, expanding the application of scRNA-seq to study genetic heterogeneity in cancer using transcriptomic data. However, the fidelity of these methods has not been investigated systematically. In this study, we benchmarked five commonly used scCNV inference methods, HoneyBADGER, CopyKAT, CaSpER, inferCNV, and sciCNV. We evaluated their performance across four different scRNA-seq platforms derived data from a multicenter study. We further evaluated the scCNV performance using scRNA-seq datasets derived from mixed samples consisting of five human lung adenocarcinoma cell lines and generated a clinical scRNA-seq dataset from a human small cell lung cancer patient to validate our findings. Our evaluation criteria included sensitivity and specificity of CNV detection, and subclone identification from mixed cancer samples. We found that the sensitivity and specificity of the five scCNV inference methods varied, depending on the selection of reference data, sequencing depths, and read lengths. Overall, CopyKAT and CaSpER exhibited superior performance to other methods, while inferCNV, sciCNV, and CopyKAT outperformed other methods in subclone identification accuracy. Remarkably, inferCNV achieved high accuracy in subclone identification when using data from a "single scRNA-seq protocol", however, when applying these methods to a dataset derived from multiple scRNA-seq platforms from the mixed samples, we found that batch effects significantly affected the performance of subclone identification for most methods, except for HoneyBADGER. Our benchmarking study revealed the strengths and weaknesses of each of the five scCNV inference methods and provided guidance for selecting the optimal CNV inference method using scRNA-seq data.

bioinformatics↗

bioRxiv2024

Epigenomic, transcriptomic and proteomic characterizations of reference samples

A variety of newly developed next-generation sequencing technologies are making their way rapidly into the research and clinical applications, for which accuracy and cross-lab reproducibility are critical, and reference standards are much needed. Our previous multicenter studies under the SEQC-2 umbrella using a breast cancer cell line with paired B-cell line have produced a large amount of different genomic data including whole genome sequencing (Illumina, PacBio, Nanopore), HiC, and scRNA-seq with detailed analyses on somatic mutations, single-nucleotide variations (SNVs), and structural variations (SVs). However, there is still a lack of well-characterized reference materials which include epigenomic and proteomic data. Here we further performed ATAC-seq, Methyl-seq, RNA-seq, and proteomic analyses and provided a comprehensive catalog of the epigenomic landscape, which overlapped with the transcriptomes and proteomes for the two cell lines. We identified >7,700 peptide isoforms, where the majority (95%) of the genes had a single peptide isoform. Protein expression of the transcripts overlapping CGIs were much higher than the protein expression of the non-CGI transcripts in both cell lines. We further demonstrated the evidence that certain SNVs were incorporated into mutated peptides. We observed that open chromatin regions had low methylation which were largely regulated by CG density, where CG-rich regions had more accessible chromatin, low methylation, and higher gene and protein expression. The CG-poor regions had higher repressive epigenetic regulations (higher DNA methylation) and less open chromatin, resulting in a cell line specific methylation and gene expression patterns. Our studies provide well-defined reference materials consisting of two cell lines with genomic, epigenomic, transcriptomic, scRNA-seq and proteomic characterizations which can serve as standards for validating and benchmarking not only on various omics assays, but also on bioinformatics methods. It will be a valuable resource for both research and clinical communities.

genomics↗

bioRxiv2024

Pipeline for Assessing Tumor Immune Status Using Superplex Immunostaining and Spatial Immune Interaction Analysis

The characteristics of the tumor microenvironment (TME) are closely linked to tumor progression and treatment response. The TME comprises various cell types, their spatial distribution, cell-cell interactions, and their organization into cellular niches or neighborhoods. To capture this complexity, several spatial profiling technologies have been developed. However, challenges such as low throughput, high costs, and complicated data analysis have limited their widespread use in immune research. In this study, we introduce the Cyclic-multiplex TSA (CmTSA) staining platform, a high-throughput superplex staining technology based on tyramide signal amplification (TSA) immunostaining combined with an efficient fluorophore recycling method. The CmTSA platform allows for the labeling of 30-60 antigens across multiple parallel formalin-fixed paraffin-embedded (FFPE) slides. Furthermore, the automated CmTSA workflow requires only standard histological equipment and conventional immunohistochemistry (IHC) primary antibodies (Abs), significantly reducing costs. While the superplex images produced contain extensive multidimensional information, extracting the spatial features of the TME from raw pixel data can be challenging. To address this, we present a computer vision-based analysis pipeline, which begins with deep learning-based algorithms to segment individual cells and identify cell types based on defined annotation rules. It then evaluates the spatial distribution tendencies of each cell type, the interaction intensity between paired cells, and the multicellular functional niches. This comprehensive approach enables researchers to visualize and quantify the types, states, and levels of immune activities within the TME effectively, advancing tumor immunology research and precision immune medicine.

cancer biology↗

bioRxiv2024

The effect of norepinephrine on ovarian dysfunction by mediating ferroptosis in mice model

Studies shows that stress is associated with ovarian dysfunction. Norepinephrine (NE), a classic stress hormone in the stress response, is less recognized for its role in ovarian function. A NE-treated mouse model is induced by intraperitoneal injection of NE for 4 weeks. Compared with the normal control, we find that NE-treated mice show disturbances in the estrous cycle, decreased levels of anti-Mullerian hormone (AMH) and estradiol (E2), and increased levels of follicle-stimulating hormone (FSH). Additionally, the number of primordial follicles, primary follicles, secondary follicles, and antral follicles decreased, while the number of atretic follicles increased in NE-treated mice, indicating NE-induced ovarian dysfunction. RNA sequencing further reveals that genes associated with ferroptosis are significantly enriched in NE-treated ovarian tissues. Concurrently, the content of reactive oxygen species (ROS), ferrous ion, and malondialdehyde (MDA) increased, while the expression level of glutathione peroxidase 4 (GPX4) decreased. To elucidate the mechanism of NE-induced ferroptosis in ovaries and the potential reversal by Coenzyme Q10 (CoQ10), an antioxidant, we conduct both in vitro and in vivo experiments. In vitro, we observe that the granulosa cell line KGN, when treated with NE, shows decreased cell viability, reduced expression of GPX4, elevated ferrous ion and ROS content, and increased MDA levels. However, these NE-induced changes are rescued by the addition of CoQ10. In the mouse model, we find that NE-treated mice supplemented with CoQ10 increased GPX4 levels and decreased the contents of iron, ROS, and MDA compared with the NE group. Moreover, the differential expression of genes associated with ferroptosis induced by NE is ameliorated by CoQ10 in NE-treated mice. Additionally, CoQ10 improved ovarian function, as evidenced by increased ovarian weight, more regular estrous cycles, and an increase in follicles at various stages of growth in NE-treated mice. In conclusion, NE induces ovarian dysfunction by triggering ferroptosis in ovarian tissues, and CoQ10 represents a promising approach for protecting reproductive function by inhibiting ferroptosis.

molecular biology↗

bioRxiv2024

Deletion of Setd7 protects against cardiac hypertrophy via inhibiting lipid oxidation

Setd7, a catalytic enzyme responsible for histone H3K4 methylation, is implicated in various cardiac diseases. However, the role of Setd7 in pathological cardiac hypertrophy remains unclear. In this study, we observed that Setd7 is significantly elevated in pathological hypertrophy stimuli cardiomyocytes and mouse failing hearts. Subsequently, we found that mice lacking Setd7 remarkably preserved cardiac function after transverse aortic constriction, as demonstrated by improving myocardial hypertrophy and fibrosis, whereas Setd7 overexpression in cardiomyocytes deteriorated hypertrophy phenotype. Further in vitro analyses revealed that Setd7 mediated-E2F1 activation induces E3 ubiquitin protein ligases WWP2 expression to catalyze the lipid-peroxide-reducing enzyme GPx4 ubiquitination degradation, ultimately causing widespread lipid peroxidation and boosting pathological cardiac hypertrophy. Remarkably, loss of activity of GPx4 blunted the Setd7 knockdown exerts antihypertrophic effect in pathological cardiomyocytes hypertrophy, further confirming an important role of lipid peroxidation in Setd7-mediated failing hearts. In summary, the role of Setd7 in pressure overload-induced cardiac hypertrophy is regulated by the Setd7-E2F1-WWP2-GPx4 signaling pathway, suggesting that targeting Setd7 is a promising therapeutic strategy to attenuate pathological cardiac hypertrophy and heart failure.

molecular biology↗

bioRxiv2024

A Hypothalamic Circuit that Modulates Feeding and Parenting Behaviors

Across mammalian species, new mothers undergo considerable behavioral changes to nurture their offspring and meet the caloric demands of milk production1-5. While many neural circuits underlying feeding and parenting behaviors are well characterized6-9, it is unclear how these different circuits interact and adapt during lactation. Here, we characterized the transcriptomic changes in the arcuate nucleus (ARC) and the medial preoptic area (MPOA) of the mouse hypothalamus in response to lactation and hunger. Furthermore, we showed that heightened appetite in lactating mice was accompanied by increased activity of hunger-promoting agouti-related peptide (AgRP) neurons in the ARC. To assess the strength of hunger versus maternal drives, we designed a conflict assay where female mice chose between a food source or a chamber containing pups and nesting material. Although food-deprived lactating mothers prioritized parenting over feeding, hunger reduced the duration and disrupted the sequences of parenting behaviors in both lactating and virgin females. We discovered that ARCAgRP neurons directly inhibit bombesin receptor subtype-3 (BRS3) neurons in the MPOA, a population that governs both parenting and satiety. Selective activation of this ARCAgRP to MPOABRS3 circuit shifted behaviors from parenting to food-seeking. Thus, hypothalamic networks are modulated by physiological states and work antagonistically during the prioritization of competing motivated behaviors.

neuroscience↗

bioRxiv2024

AARS2 ameliorates myocardial ischemia via fine-tuning PKM2-mediated metabolism

AARS2, an alanyl-tRNA synthase, is essential for protein translation, but its function in mouse hearts is not fully addressed. Here, we found that cardiomyocyte-specific deletion of mouse AARS2 exhibited evident cardiomyopathy with impaired cardiac function, notable cardiac fibrosis and cardiomyocyte apoptosis. Cardiomyocyte-specific AARS2 overexpression in mice improved cardiac function and reduced cardiac fibrosis after myocardial infarction (MI), without affecting cardiomyocyte proliferation and coronary angiogenesis. Mechanistically, AARS2 overexpression suppressed cardiomyocyte apoptosis and mitochondrial reactive oxide species production, and changed cellular metabolism from oxidative phosphorylation toward glycolysis in cardiomyocytes, thus leading to cardiomyocyte survival from ischemia and hypoxia stress. Ribo-Seq revealed that AARS2 overexpression increased pyruvate kinase M2 (PKM2) protein translation and the ratio of PKM2 dimers to tetramers that promote glycolysis. Additionally, PKM2 activator TEPP-46 reversed cardiomyocyte apoptosis and cardiac fibrosis caused by AARS2 deficiency. Thus, this study demonstrates that AARS2 plays an essential role in protecting cardiomyocytes from ischemic pressure via fine-tuning PKM2-mediated energy metabolism, and presents a novel cardiac protective AARS2-PKM2 signaling during the pathogenesis of MI.

cell biology↗

bioRxiv2024

Grifola frondosa polysaccharide Ameliorates Inflammation and Insulin Resistance by Regulating Macrophage Polarization of liver in Type 2 Diabetes Mellitus Rats

Type 2 diabetes mellitus (T2DM) is a common metabolic disease characterized by a lack of insulin secretion, insulin resistance (IR), and hyperglycemia. Given its high prevalence and multifarious complications, diabetes is globally ranked as the third leading cause of mortality. It is critical to discover efficient medication substitutes in order to lessen the drawbacks and adverse effects of traditional diabetes medication therapy. Previous studies have shown that Grifola frondosa polysaccharide (GFP) have the positive effects in regulating blood glucose and insulin resistance, but the understanding of its regulatory mechanism is still limited. Therefore, this study aimed to investigate the effects of GFP on liver inflammation induced by a high-fat diet (HFD) combined with streptozotocin (STZ) in type 2 diabetic rats and to explore its possible mechanisms. The results showed that GFP intervention reduced weight loss and hyperglycemia symptoms, as well as lowered FINS, HOMA-IR, IPGTT-AUC, and IPITT-AUC to different degrees in T2DM rats. At the same time, after GFP intervention, the secretion level of inflammatory factors (TNF-, IL-1{beta}, MCP-1) was down-regulated and the secretion level of anti-inflammatory factor (IL-10) was up-regulated in the liver tissue of T2DM rats. Furthermore, GFP reduced macrophage infiltration in liver tissue, inhibited macrophage M1-type polarization, and promoted M2-type polarization. These results suggest that GFP intervention could attenuate the hepatic inflammatory response in T2DM rats; possible mechanisms for this effect include hepatic macrophage infiltration and M1/M2 polarization. Summary statementThis study revealed the improvement effect of GFP on hepatic inflammation and insulin resistance in T2DM rats and to explore the possible key roles of hepatic macrophages and their potential mechanisms.

immunology↗

bioRxiv2024

Pooled genetic screens identify breast cancer risk genes involved in evasion from T cell-mediated killing

Genome-wide association studies have identified more than 220 loci associated with breast cancer susceptibility. A major challenge is now to identify the effector genes with plausible functions in the context of breast cancer risk. We have previously performed pooled CRISPR screens to identify target genes at risk loci that drive cancer hallmarks including proliferation or modulating DNA damage response. We now extend these screens to identify genes involved in response to cytotoxic T lymphocyte (CTL) killing. We performed knockout and inhibition screens to identify genes that affect the response of the MCF7 human breast cancer cell line to CTL killing in an in vitro co-culture system. We identified 33 candidate risk genes associated with resistance or sensitisation to T cell-mediated killing. Using single gene perturbation, we showed that deletion of candidate risk genes IRF1, ATF7IP, CCDC170 and CASP8 induced resistance, while ablation of CFLAR, CREBBP, and PRMT7 sensitized cells to CTL killing. We used reporter assays to show that the risk-associated alleles at rs736801 and rs3769821 reduced transactivation of the IRF1 and CASP8 promoters, respectively. We showed that pharmacological inhibition of PRMT7 rendered breast cells sensitive to CTL killing and PRMT7 levels were negatively correlated with CD8+ infiltration and patient survival in luminal A breast cancer patient cohorts. Our results demonstrate that phenotypic pooled CRISPR screens are a useful approach for high throughput functional follow-up of GWAS findings, identifying genes which alter immune responses to breast cancer which offer opportunities to enhance immunotherapy.

genetics↗