Biology subjects

Li, S.

Publications and source records attributed to Li, S..

At least 613 records · Page 34Linked to original sources

bioRxiv2024

LncRNA GAS6-AS1 contributes to 5-fluorouracil resistance in colorectal cancer

5-Fluorouracil (5-FU) resistance has always been a formidable obstacle in the adjuvant treatment of advanced colorectal cancer (CRC). In recent years, long non-coding RNAs have emerged as key regulators in various pathophysiological processes including 5-FU resistance. Here, RNA-seq combined with weighted gene correlation network analysis confirmed the close association of GAS6-AS1 with TRG grades. GAS6-AS1 expression was positively correlated with advanced clinicopathological features and poor prognosis in CRC. GAS6-AS1 increased the 50% inhibiting concentration of 5-FU, enhanced cell proliferation, and accelerated G1/S transition in CRC cells, both with and without 5-FU, both in vitro and in vivo. Mechanistically, GAS6-AS1 enhanced the stability of MCM3 mRNA by recruiting PCBP1, consequently increasing MCM3 expression. Furthermore, PCBP1 and MCM3 counteracted the effects of GAS6-AS1 on 5-FU resistance. Notably, the PDX model indicated that combining chemotherapeutic drugs with GAS6-AS1 knockdown yielded superior outcomes in vivo. Together, our findings elucidate that GAS6-AS1 directly binds to PCBP1, enhancing MCM3 expression and thereby promoting 5-FU resistance. GAS6-AS1 may serve as a robust biomarker and potential therapeutic target for combination therapy in CRC.

molecular biology↗

bioRxiv2024

Modulation of circadian rhythms in articular cartilage by heat pulses

ObjectivePrior studies have shown that disruption of the circadian clock leads to cartilage degeneration in mice while shift work is associated with higher risk of osteoarthritis (OA) in humans. In this study we investigated the potential of heat pulses to restore dampened circadian rhythms in articular cartilage. MethodsFemoral head cartilage explants and primary chondrocytes were isolated from PER2::LUC mice. Human femoral condyle cartilage was obtained from osteoarthritic patients undergoing total knee replacement. Tissues and cells were exposed to heat shock at various temperatures (37-43 {degrees}C) and incubation lengths. Bioluminescence from explants and cells was recorded in real-time. RNA sequencing and qPCR were used to assess gene expression changes in response to heat. ResultsWe established that a 60-min pulse at 43 {degrees}C was sufficient to restore dampened PER2::LUC rhythms in mouse cartilage explants or in primary chondrocytes. Transcriptome analysis in mouse articular cartilage showed an up-regulation of genes encoding heat shock proteins and collagens, and a transient down-regulation of Sox9, Runx2, Per1, Clock and Cry2. Heat induced the expression of circadian clock genes in human osteoarthritic knee cartilage. Mechanistically, inhibition of HSP90 activity or perturbation of F-actin polymerisation blocked the heat-induced resynchronisation of circadian rhythms. ConclusionTogether, these data have contributed to a greater understanding of the multifaceted nature of the connections between circadian timekeeping, heat stress responses and homeostasis in articular cartilage. These findings also suggest that time-prescribed temperature increases could be developed into a non-invasive intervention to slow down tissue ageing and restore homeostasis in osteoarthritic joints by improving circadian oscillations of cartilage rhythmic pathways.

cell biology↗

bioRxiv2024

Integrative Omics Uncovers Low Tumorous Magnesium Content as A Driver Factor of Colorectal Cancer

Magnesium (Mg) deficiency is associated with increased risk and malignancy of colorectal cancer (CRC), yet the underlying mechanisms remain elusive. Here we used genomic, proteomic, and phosphoproteomic data to elucidate the impact of Mg deficiency on CRC. Genomic analysis identified 160 genes with higher mutation frequencies in Low-Mg tumors, including key driver genes such as KMT2C and ERBB3. Unexpectedly, initiation driver genes of CRC, such as TP53 and APC, displayed higher mutation frequencies in High-Mg tumors. Additionally, proteomics and phosphoproteomics indicated that low tumorous Mg content may activate epithelial-mesenchymal transition (EMT) by modulating inflammation or remodeling the phosphoproteome of cancer cells. Notably, we observed a negative correlation between the phosphorylation of DBN1 at S142 (DBN1S142p) and Mg content. A mutation in S142 to D (DBN1S142D) mimicking DBN1S142p upregulated MMP2 and enhanced cell migration, while treatment with MgCl2 reduced DBN1S142p, thereby reversing this phenotype. Mechanistically, Mg2+ attenuated the DBN1-ACTN4 interaction by decreasing DBN1S142p, which, in turn, enhanced the binding of ACTN4 to F-actin and promoted F-actin polymerization, ultimately reducing MMP2 expression. These findings shed new light on the crucial role of Mg deficiency in CRC progression and suggest that Mg supplementation may offer a promising preventive and therapeutic strategy for CRC.

cancer biology↗

bioRxiv2024

Stepwise neofunctionalization of the NF-κB family member c-Rel during vertebrate evolution

Adaptive immunity and the five vertebrate NF-{kappa}B/Rel family members first appeared in cartilaginous fish, suggesting that divergence and specialization within the NF-{kappa}B family helped facilitate the evolution of adaptive immunity. One specialized function of the NF-{kappa}B c-Rel protein in macrophages is the activation of Il12b, which encodes a key regulator of T-cell development. We found that c-Rel is a far more potent regulator of Il12b than of any other inducible genes in macrophages, with c-Rel regulation of Il12b dependent on its heightened intrinsic DNA-binding affinity. c-Rel homodimers regulate Il12b transcription in part via motifs with little resemblance to canonical NF-{kappa}B motifs. ChIP-seq experiments further defined distinct c-Rel DNA-binding preferences genome-wide, and X-ray crystallography of a c-Rel/RelA chimeric protein identified key amino acid changes that support the unique c-Rel properties. Unexpectedly, these changes, along with the c-Rel/RelA binding affinity differences, were largely restricted to mammalian species. Together, our findings reveal how a transcription factor family member can undergo a structural transition at a late stage of vertebrate evolution, resulting in an increased intrinsic DNA binding affinity and with clear functional consequences, presumably to support the increasing complexity of immune regulation.

immunology↗

bioRxiv2024

Quantifying Interpretation Reproducibility in Vision Transformer Models with TAVAC

The use of deep learning algorithms to extract meaningful diagnostic features from biomedical images holds the promise to improve patient care given the expansion of digital pathology. Among these deep learning models, Vision Transformer (ViT) models have been demonstrated to capture long-range spatial relationships with more robust prediction power for image classification tasks than regular convolutional neural network (CNN) models, and also better model interpretability. Model interpretation is important for understanding and elucidating how a deep learning model makes predictions, especially for developing transparent models for digital pathology. However, like other deep learning algorithms, with limited annotated biomedical imaging datasets, ViT models are prone to poor performance due to overfitting, which can lead to false predictions due to random noise. Overfitting affects model interpretation when predictions are made out of random noise. To address this issue, we introduce a novel metric - Training Attention and Validation Attention Consistency (TAVAC) - for evaluating ViT model degree of overfitting on imaging datasets and quantifying the reproducibility of interpretation. Specifically, the model interpretation is performed by comparing the high-attention regions in the image between training and testing. We test the method on four publicly available image classification datasets and two independent breast cancer histological image datasets. All overfitted models exhibited significantly lower TAVAC scores than the good-fit models. The TAVAC score quantitatively measures the level of generalization of model interpretation on a fine-grained level for small groups of cells in each H&E image, which cannot be provided by traditional performance evaluation metrics like prediction accuracy. Furthermore, the application of TAVAC extends beyond medical diagnostic AI models; it enhances the monitoring of model interpretative reproducibility at pixel-resolution in basic research, to reveal critical spatial patterns and cellular structures essential to understanding biological processes and disease mechanisms. TAVAC sets a new standard for evaluating the performance of deep learning model interpretation and provides a method for determining the significance of high-attention regions detected from the attention map of the biomedical images.

bioinformatics↗

bioRxiv2024

Architecture of genome-wide transcriptional regulatory network reveals dynamic functions and evolutionary trajectories in Pseudomonas syringae

The model Gram-negative plant pathogen Pseudomonas syringae utilises hundreds of transcription factors (TFs) to regulate its functional processes, including virulence and metabolic pathways that control its ability to infect host plants. Although the molecular mechanisms of regulators have been studied for decades, a comprehensive understanding of genome-wide TFs in Psph 1448A remains limited. Here, we investigated the binding characteristics of 170 of 301 annotated TFs through ChIP-seq. Fifty-four TFs, 62 TFs and 147 TFs were identified in top-level, middle-level and bottom-level, reflecting multiple higher-order network structures and direction of information-flow. More than forty thousand TF-pairs were classified into 13 three-node submodules which revealed the regulatory diversity of TFs in Psph 1448A regulatory network. We found that bottom-level TFs performed high co-associated scores to their target genes. Functional categories of TFs at three levels encompassed various regulatory pathways. Three and 25 master TFs were identified to involve in virulence and metabolic regulation, respectively. Evolutionary analysis and topological modularity network revealed functional variability and various conservation of TFs in P. syringae (Psph 1448A, Pst DC3000, Pss B728a and Psa C48). Overall, our findings demonstrated the global transcriptional regulatory network of genome-wide TFs in Psph 1448A. This knowledge can advance the development of effective treatment and prevention strategies for related infectious diseases.

microbiology↗

bioRxiv2024

Antibiotics affect the pharmacokinetics of n-butylphthalide in vivo by altering the intestinal microbiota

ObjectiveN-butylphthalide (NBP) is a monomeric compound extracted from natural plant celery seeds, whether intestinal microbiota alteration can modify its pharmacokinetics is still unclear. The purpose of this study is to investigate the effect of intestinal microbiota alteration on the pharmacokinetics of NBP and its related mechanisms. MethodsAfter treatment with antibiotics and probiotics, plasma NBP concentrations in SD rats were determined by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The effect of intestinal microbiota changes on NBP pharmacokinetics was compared. Intestinal microbiota changes after NBP treatment were analyzed by 16S rRNA sequencing. Expressions of CYP3A1 mRNA and protein in the liver and small intestine tissues under different intestinal flora conditions were determined by qRT-PCR and Western Blot. KEGG analysis was used to analyze the effect of intestinal microbiota changes on metabolic pathways. ResultsCompared to the control group, the values of Cmax, AUC0-8, AUC0-{infty}, t1/2 in the antibiotic group increased by 56.1% (P<0.001), 56.4% (P<0.001), 53.2% (P<0.001), and 24.4% (P<0.05), respectively. In contrast, the CL and Tmax values decreased by 57.1% (P<0.001) and 28.6% (P<0.05), respectively. Treatment with antibiotics could reduce the richness and diversity of the intestinal microbiota. CYP3A1 mRNA and protein expressions in the small intestine of the antibiotic group were 61.2% and 66.1% of those of the control group, respectively. CYP3A1 mRNA and protein expressions in the liver were 44.6% and 63.9% of those in the control group, respectively. There was no significant change in the probiotic group. KEGG analysis showed that multiple metabolic pathways were significantly down-regulated in the antibiotic group. Among them, the pathways of drug metabolism, bile acid biosynthesis and decomposition, and fatty acid synthesis and decomposition were related to NBP biological metabolism. ConclusionAntibiotic treatment could affect the intestinal microbiota, decrease CYP3A1 mRNA and protein expressions and increase NBP exposure in vivo by inhibiting pathways related to NBP metabolism.

pharmacology and toxicology↗

bioRxiv2024

Inhibition of Alpha Interferon-Induced miR-873 Negatively Affects the Hepatitis B Virus Expression

BackgroundAlpha interferon (IFN-)-based therapy can effectively treat chronic hepatitis B virus (HBV) infection, which remains a serious public health problem. This study aims to identify the potential biomarker of IFN treatment and investigate the effects of miR-873 on chronic hepatitis B (CHB). MethodsWe utilized the random forest to screen core differentially expressed miRNAs (DEmiRNAs) based on the miRNA (GSE29911) dataset. DEmiRNAs expressions were determined in clinical samples from CHB patients and normal controls. HBV-transfected hepatoma cell lines were constructed for vitro study. Quantitative real-time reverse transcription PCR (RT-qPCR) was used to determine miRNA mRNA expressions. ELISA assays were used to detect the secretion levels of HBsAg and HBeAg. ResultsBoruta feature selection revealed miR-873 hinting at a predictive marker for IFN response. MiR-873 was significantly up-regulated in the CHB patients, as compared with normal controls (P<0.001). Increased expression of miR-873 was also found in HBV-infected cells (P<0.001). With IFN- treatment, miR-873 was significantly down-regulated in HBV-infected Huh-7 and HepG-NTCP cells (P<0.05). IFN- treatment and miR-873 inhibitor significantly reduced HBsAg and HBeAg level (P<0.05). The inhibitory effect was enhanced by blocking the IFN--induced miR-873 downregulation by inhibitor transfection (P<0.05). In miR-873 mimic-treated cells, the inhibitory effect was greatly supressed by blocking the IFN--induced miR-873 downregulation by mimic transfection (P< 0.01). ConclusionWe provide evidence that inhibition of miR-873 by IFN- enhances the antiviral effects of IFN-. Our study provides a potential strategy to enhance the anti-HBV effect of IFN- by inhibiting miR-873 expression.

molecular biology↗

bioRxiv2024

Rim4 is a Meiotic Thermal Sensor and Drives Biogenesis of Stress Granules

Rim4 is a meiosis-specific RNA-binding protein (RBP) that sequesters mRNAs to suppress their translation. Previous work has defined the Rim4 C-terminal low-complexity domain (LCD) as sequences that form self-propagating amyloid-like aggregates. Here, we uncovered a dynamic and reversible form of Rim4 self-assembly primarily triggered by heat during meiosis, proportionally from 30{degrees}C to 42{degrees}C. The formed thermal Rim4 condensates in cell promptly stimulates stress granule (SG) assembly, recruiting SG-resident proteins, such as Pab1 and Pbp1, and strikingly, decreases the required temperature for meiotic SG formation ([~]33{degrees}C) by [~]9{degrees}C as compared to mitosis ([~]42{degrees}C). This sensitization of meiotic SG formation to heat effectively prevents meiosis progression and sporulation under harmful thermal turbulence. Meanwhile, the Rim4-positive meiotic SGs protect Rim4 and Rim4-sequestered mRNAs from autophagy to allow a rapid recovery from stalled meiosis upon the stress relief. Mechanistically, we found that the yeast 14-3-3 proteins (Bmh1 and Bmh2) and nucleic acids brake initiation of heat-induced Rim4 self-assembly, and Hsp104 facilitates the restoration of intracellular Rim4 distribution during the recovery.

cell biology↗

bioRxiv2024

PTEN inhibition promotes robust growth of bulbospinal respiratory axons and partial recovery of diaphragm function in a chronic model of cervical contusion spinal cord injury

High spinal cord injury (SCI) leads to persistent and debilitating compromise in respiratory function. Cervical SCI not only causes the death of phrenic motor neurons (PhMNs) that innervate the diaphragm, but also damages descending respiratory pathways originating in the rostral ventral respiratory group (rVRG) located in the brainstem, resulting in denervation and consequent silencing of spared PhMNs located caudal to injury. It is imperative to determine whether interventions targeting rVRG axon growth and respiratory neural circuit reconnection are efficacious in chronic cervical contusion SCI, given that the vast majority of individuals are chronically-injured and most cases of SCI involve contusion-type damage to the cervical region. We therefore employed a clinically-relevant rat model of chronic cervical hemicontusion to test therapeutic manipulations aimed at reconstructing damaged rVRG-PhMN-diaphragm circuitry to achieve recovery of respiratory function. At a chronic time point post-injury, we systemically administered: an antagonist peptide directed against phosphatase and tensin homolog (PTEN), a central inhibitor of neuron-intrinsic axon growth potential; an antagonist peptide directed against receptor-type protein tyrosine phosphatase sigma (PTP{sigma}), another important negative regulator of axon growth capacity; or a combination of these two peptides. PTEN antagonist peptide (PAP4) promoted partial recovery of diaphragm motor activity out to nine months post-injury, while PTP{sigma} peptide did not impact diaphragm function after cervical SCI. Furthermore, PAP4 promoted robust growth of descending bulbospinal rVRG axons caudal to the injury within the denervated portion of the PhMN pool, while PTP{sigma} peptide did not affect rVRG axon growth at this location that is critical to control of diaphragmatic respiratory function. In conclusion, we find that, when PTEN inhibition is targeted at a chronic time point following cervical contusion that is most relevant to the SCI clinical population, our non-invasive PAP4 strategy can successfully promote significant regrowth of damaged respiratory neural circuitry and also partial recovery of diaphragm motor function. HIGHLIGHTSO_LIPTEN antagonist peptide promotes partial diaphragm function recovery in chronic cervical contusion SCI. C_LIO_LIPTP{sigma} inhibitory peptide does not impact diaphragm function recovery in chronic cervical contusion SCI. C_LIO_LIPTEN antagonist peptide promotes growth of bulbospinal rVRG axons in chronic cervical contusion SCI. C_LIO_LIPTP{sigma} peptide does not affect rVRG axon growth in chronic cervical contusion SCI. C_LI

neuroscience↗

bioRxiv2024

Long-read sequencing reveals novel structural variation markers for key agronomic and quality traits of soybean

In plant genomic research, long read sequencing has been widely used to detect structure variations that are not captured by short read sequencing. In this letter, we described an analysis of whole genome re-sequencing of 29 soybean varieties using nanopore long-read sequencing. The compiled germplasm reflects diverse applications, including livestock feeding, soy milk and tofu production, as well as consumption of natto, sprouts, and vegetable soybeans (edamame). We have identified 365,497 structural variations in these newly re-sequenced genomes and found that the newly identified structural variations are associated with important agronomic traits. These traits include seed weight, flowering time, plant height, oleic acid content, methionine content, and trypsin inhibitor content, all of which significantly impact soybean production and quality. Experimental validation supports the roles of predicted candidate genes and structural variant in these biological processes. Our research provides a new source for rapid marker discovery in crop genomes using structural variation and whole genome sequencing.

genomics↗

bioRxiv2024

MAIT cells protect against sterile lung injury

Mucosal-associated invariant T (MAIT) cells, the most abundant unconventional T cells in the lung, have been recently linked to tissue protection and repair. Their role, especially in sterile lung injury, is unknown. Using single cell RNA sequencing (scRNA-seq), spectral analysis and adoptive transfer in a bleomycin-induced sterile lung injury, we found that bleomycin activates murine pulmonary MAIT cells and induces an accompanying tissue repair programme, associated with a protective role against bleomycin-induced lung injury. MAIT cells drive the accumulation of type 1 conventional dendritic cells (cDC1), limiting tissue damage in a DNGR-1 dependent manner. Human scRNA-seq data revealed that MAIT cells were activated, with increased cDC populations in idiopathic pulmonary fibrosis patients. Thus, MAIT cells enhance defence against sterile lung injury by fostering cDC1-driven anti-fibrotic pathways.

immunology↗

bioRxiv2024

Capsaicin acts as a novel NRF2 agonist to suppress ethanol induced gastric mucosa oxidative damage by directly disrupting the KEAP1-NRF2 interaction

Excessive alcohol consumption poses significant health risks and is closely associated with oxidative damage. The KEAP1-NRF2-ARE signaling pathway serves as the primary antioxidant system. However, current small molecule inhibitors are all covalently bound to KEAP1, meaning that once bound, they are not easily dissociated, while continuous inhibition of KEAP1 exhibits severe side effects. In this study, BLI, CETSA, Pull-down, Co-IP and HDX-MS assay analysis were conducted to detect the KEAP1 binding behavior of natural product, capsaicin (CAP), both in vitro and in cells. The ethanol-induced acute gastric mucosal damage rat model was also established to evaluate the therapeutic effect of CAP. Our findings demonstrated that CAP mitigated mitochondrial damage, facilitated the nuclear translocation of NRF2, leading to the up-regulation of downstream antioxidant response elements, HMOX1, TXN, GSS and NQO1 in GES-1 cells. Furthermore, CAP directly bind to KEAP1 and inhibit the interaction between KEAP1 and NRF2. In the KEAP1-knockout 293T cells, CAP failed to activate NRF2 expression. We identified that CAP non-covalently bound to Kelch domain and allosterically regulated three specific regions of KEAP1 : L342-L355, D394-G423 and N482-N495. To improve drug solubility and delivery efficiency, we developed IR-Dye800 modified albumin coated CAP nanoparticles. The nanoparticles significantly reduced the gastric mucosal inflammation and activated NRF2 downstream genes in vivo. Our hypothesis was further verified our hypothesis in Nfe2l2-knockout mice. This study provides new insights that CAP is a safe and novel NRF2 agonist by allosterically regulating KEAP1, which may contribute to the development of lead drugs for oxidative stress-related illness, e.g. aging, cancer, neurodegenerative and cardiovascular diseases.

cell biology↗

bioRxiv2024

Tractography-based automated identification of the retinogeniculate visual pathway with novel microstructure-informed supervised contrastive learning

The retinogeniculate visual pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and is affected by inter-observer variability. In this paper, we present a novel deep learning framework, DeepRGVP, to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP. In addition, we demonstrate a good generalizability of DeepRGVP to dMRI tractography data from neurosurgical patients with pituitary tumors and we show DeepRGVP can successfully identify RGVPs despite the effect of lesions affecting the RGVPs. Overall, our study shows the high potential of using deep learning to automatically identify the RGVP.

neuroscience↗

bioRxiv2024

Multi-omic characterization of allele-specific regulatory variation in hybrid pigs

Genetic variation in the regulation of gene expression contributes substantially to phenotypic variation. Understanding how variation in DNA sequences and epigentic modifications leads to gene expression variation remains a challenging task. In hybrid animals where cellular environments are homogeneous, differences between the expression of paternal and maternal alleles must be due to cis sequence or epigenic differences. Therefore, hybrid mapping is a powerful approach to efficiently identify and characterize genes under regulation through mechanisms in cis. In this study, using reciprocal crosses of the phenotypically divergent Duroc and Lulai pig breeds, we performed a comprehensive multi-omic characterization of regulatory variation across brain, liver, muscle, and placenta in four developmental stages. We produced one of the largest multi-omic datasets to date in pigs, including 16 whole genome sequenced genomes, 48 whole genome bisulfite sequencing, 168 ATAC-Seq and 168 RNA-Seq samples. We developed a novel read count-based method to reliably assess allele-specific methylation, chromatin accessibility, and RNA expression. We showed that tissue specificity was much stronger than developmental stage specificity in all of DNA methylation, chromatin accessibility, and gene expression. We identified 573 genes showing allele specific expression, including those influenced by parent-of-origin as well as allele genotype effects. By integrating methylation, chromatin accessibility, and gene expression data, many of these allele specific expression can be explained by allele specific methylation and/or chromatin accessibility. This study provides one of the most comprehensive characterizations of regulatory variation across multiple tissues and developmental stages in pigs and offers new opportunity of genetic improvement for this important food animal species.

developmental biology↗

bioRxiv2024

CDC5L surveils cellular stress responses and stress granule formation through transcriptional repression

Cells have evolved a variety of mechanisms to respond to stress, such as activating the PERK- eIF2 pathway and forming stress granules (SGs). It is important that these mechanisms are inducted only when necessary and exerted at appropriate levels, to prevent spontaneous or excessive activation of stress responses. However, the mechanisms by which cells keep the stress response programs in check are elusive. In this study, we discovered that downregulation of Cell Division Cycle 5 Like (CDC5L) causes spontaneous SG formation in the absence of any stress, which is independent of its known functions in the cell cycle or the PRP19 complex. Instead, we found that CDC5L binds to the PERK promoter through its DNA-binding domains and represses PERK mRNA transcription. As a result, it negatively regulates the abundance of PERK protein and the phosphorylation levels of eIF2, thereby suppressing the PERK-eIF2 signaling pathway and preventing undesirable SG assembly. Further RNA-sequencing (seq) and chromatin immunoprecipitation (ChIP)-seq analyses reveal a dual function of CDC5L in gene transcription: it acts as a transcriptional activator in cell cycle control but as a repressor in cellular stress responses. Finally, we show that the loss of CDC5L decreases cell viability and fly survival under mild stress conditions. Together, our findings demonstrate a previously unknown role and mechanism of CDC5L in the surveillance of cellular stress through transcriptional repression, which serves as a gatekeeper for the stress response programs such as the PERK-eIF2 pathway and SG formation. Significance statementCells need to respond to stress promptly for survival. Meanwhile, it is equally important to prevent spontaneous or excessive activation of stress response programs when no stress or only minor stress is present. Here, we reveal that the DNA/RNA-binding protein CDC5L represses the transcription of a cluster of stress response genes including PERK. In doing so, CDC5L suppresses the PERK-eIF2 pathway and prevents spontaneous SG assembly. Downregulation of CDC5L releases the restraint on these genes, resulting in an exaggerated response to stress and decreased viability in both cell and fly models. Taken together, this study demonstrates the existence of a gatekeeper mechanism that surveils the stress response programs and highlights the crucial role of CDC5L-mediated transcriptional repression in this regulation.

cell biology↗

bioRxiv2024

EI24-RTRAF interaction represses Nox4 translation, vital for redox balance and insulin production

As a double-edged sword, the content of reactive oxygen species (ROS) is precisely controlled. Disordered actions of ROS contribute to deleterious effects, such as cancer and metabolic dysregulation associated with aging and obesity. Although it is well established that cells have developed evolutionarily conserved programs to sense and adapt to redox fluctuations, it remains unclear how to control the expression of key ROS-producing enzymes to regulate continued ROS production at healthy levels for cells such as neurons and pancreatic beta cells. These cells have weaker antioxidant defense systems but strong secretion ability. Here, we found that the endoplasmic reticulum membrane-localized protein, EI24, controls the translation of nicotinamide adenine dinucleotide phosphate oxidase 4 (NOX4), which constitutively produces hydrogen peroxide (H2O2), by recruiting an RNA transcription, translation, and transport factor (RTRAF) to the 3-UTRs of Nox4. Depletion of EI24 causes RTRAF to relocate into the nucleus, releasing the brake on Nox4 mRNA translation, and thus, the uncontrolled translation of Nox4 leads to a substantial generation of intracellular H2O2. This suppresses the translation of V-maf musculoaponeurotic fibrosarcoma oncogene homolog A (MafA), inhibits its binding to the Ins2 gene promoter, and ultimately hinders insulin transcription. Treatment with a specific NOX4 inhibitor or the antioxidant N-acetyl-cysteine (NAC) restored MafA translation and downstream insulin synthesis while alleviating the diabetic symptoms in pancreatic beta-cell specific Ei24-KO mice. In summary, our study revealed a molecular mechanism that controls the expression of NOX4, a key enzyme responsible for continuous ROS generation. This mechanism ensures low levels of H2O2 and normal biological functions under physiological conditions.

cell biology↗

bioRxiv2024

Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age

The immune system comprises multiple cell lineages and heterogeneous subsets found in blood and tissues throughout the body. While human immune responses differ between sites and over age, the underlying sources of variation remain unclear as most studies are limited to peripheral blood. Here, we took a systems approach to comprehensively profile RNA and surface protein expression of over 1.25 million immune cells isolated from blood, lymphoid organs, and mucosal tissues of 24 organ donors aged 20-75 years. We applied a multimodal classifier to annotate the major immune cell lineages (T cells, B cells, innate lymphoid cells, and myeloid cells) and their corresponding subsets across the body, leveraging probabilistic modeling to define bases for immune variations across donors, tissue, and age. We identified dominant tissue-specific effects on immune cell composition and function across lineages for lymphoid sites, intestines, and blood-rich tissues. Age-associated effects were intrinsic to both lineage and site as manifested by macrophages in mucosal sites, B cells in lymphoid organs, and T and NK cells in blood-rich sites. Our results reveal tissue-specific signatures of immune homeostasis throughout the body and across different ages. This information provides a basis for defining the transcriptional underpinnings of immune variation and potential associations with disease-associated immune pathologies across the human lifespan.

immunology↗