Biology subjects

Guo, M.

Publications and source records attributed to Guo, M..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Reproductive sexual dimorphisms in two willow species, Salix exigua Nutt. and S. nigra Marshall.

Premise of the ResearchThe prevalence of sexual dimorphisms, which evolve due to contrasting strategies to maximize reproductive success in males and females, is variable among dioecious plant species. In the Salicaceae, many traits have been assessed across many studies, but direct or indirect associations between these traits and reproductive allocation are often neglected. Given the dynamic evolution of sex determination systems and the strong interest in wood production in the family, we wondered whether sexual dimorphisms related to reproduction may have gone unreported. Here, we assess sexual dimorphism in reproductive traits in two species of Salix. Recognition of reproductive sexually dimorphic traits will contribute to understanding the evolution of sex determination systems in the Salicaceae. MethodologyWe conducted observational studies in natural populations to assess the presence of sexual dimorphisms in early spring bud density, catkin number, and flower number per catkin across four sampling periods in Salix exigua. We also analyzed flower number and catkin number per flower in Salix nigra. Pivotal ResultsWe observed no sexual dimorphism in pre-season buds per branch in S. exigua but did find that males produced more flowers per catkin and more catkins per branch than females in both S. exigua and S. nigra. ConclusionsHigher flower numbers in males compared to females is consistent with expectations from intra-sexual selection among males. The presence of reproductive sexual dimorphisms in Salix suggests that sexual selection may affect the evolution of mating strategies in Salix species, and the evolution of the sex determination system within this genus.

plant biology↗

bioRxiv2023

APOE-NOTCH Axis Governs Elastogenesis During Human Cardiac Valve Remodeling

BackgroundValve remodeling is a complex process involving extracellular matrix organization, development of trilaminar structures, and physical elongation of valve leaflets. However, the cellular and molecular mechanisms regulating valve remodeling and their roles in congenital valve disorders remain poorly understood. MethodsSemilunar valves and atrioventricular valves from healthy and age-matched human fetal hearts with pulmonary stenosis (PS) were collected. Single-Cell RNA-sequencing (scRNA-seq) was performed to determine the transcriptomic landscape of multiple valvular cell subtypes in valve remodeling and disease. Spatial localization of newly-identified cell subtypes was determined via immunofluorescence and RNA in situ hybridization. The molecular mechanisms mediating valve development was investigated utilizing primary human fetal heart valve interstitial cells (VICs) and endothelial cells (VECs). ResultsscRNA-seq analysis of healthy human fetal valves identified a novel APOE+ elastin-producing VIC subtype (Elastin-VICs) spatially located underneath VECs sensing the unidirectional flow. Knockdown of APOE in fetal VICs resulted in significant elastogenesis defects. In pulmonary valve with PS, we observed decreased expression of APOE and other genes regulating elastogenesis such as EMILIN1 and LOXL1, as well as elastin fragmentation. These findings suggested the crucial role of APOE in regulating elastogenesis during valve remodeling. Furthermore, cell-cell interaction analysis revealed that JAG1 from unidirectional VECs activates NOTCH signaling in Elastin-VICs through NOTCH3. In vitro Jag1 treatment in VICs increased elastogenesis, while similar observations were found in VICs co-cultured with VECs in the presence of unidirectional flow. Notably, we found that the JAG1-NOTCH3 signaling pair was drastically reduced in the PS valves. Lastly, we demonstrated that APOE is indispensable for JAG1-induced NOTCH activation in VICs, reinforcing the presence of a synergistic intrinsic and external regulatory network involving APOE and NOTCH signaling that is responsible for regulating elastogenesis during human valve remodeling. ConclusionscRNA-seq analysis of human fetal valves identified a novel Elastin-VIC subpopulation, and revealed mechanism of intrinsic APOE and external NOTCH signaling in regulating elastogenesis during cardiac valve remodeling. These mechanisms may contribute to deciphering the pathogenesis of elastin malformation in congenital valve diseases. Clinical Perspective What Is New?O_LIHigh-resolution single-cell transcriptome atlas generated from healthy human fetal heart valves and valves affected by pulmonary stenosis during the early phase of valve remodeling prior to birth. C_LIO_LIA unique subset of valve interstitial cells (VICs) that produce elastin (Elastin-VICs) was identified. C_LIO_LIElastin-VICs specifically located underneath the valve endothelial cells (VECs) sensing unidirectional flow, and played a crucial role in elastin maturation via the expression of APOE. C_LIO_LIElastin-VICs communicated with adjacent VECs via the JAG1-NOTCH signaling, facilitating elastin formation and valve remodeling. C_LI What Are the Clinical Implications?O_LIElastin-VICs from patient valvular tissues with Pulmonary Stenosis exhibit decreased APOE-NOTCH signaling and elastin fragmentation. C_LIO_LIDirect targeting of APOE and NOTCH signaling could be a novel approach to promote elastin fiber formation and valve remodeling in patients with valvular defects. C_LI

bioinformatics↗

bioRxiv2023

Molecular, metabolic and functional CD4 T cell paralysis impedes tumor control

CD4 T cells are important effectors of anti-tumor immunity, yet the regulation of CD4 tumor-specific T (TTS) cells during cancer development is still unclear. We demonstrate that CD4 TTS cells are initially primed in the tumor draining lymph node and begin to divide following tumor initiation. Distinct from CD8 TTS cells and previously defined exhaustion programs, CD4 TTS cell proliferation is rapidly frozen in place and differentiation stunted by a functional interplay of T regulatory cells and both intrinsic and extrinsic CTLA4 signaling. Together these mechanisms paralyze CD4 TTS cell differentiation, redirecting metabolic and cytokine production circuits, and reducing CD4 TTS cell accumulation in the tumor. Paralysis is actively maintained throughout cancer progression and CD4 TTS cells rapidly resume proliferation and functional differentiation when both suppressive reactions are alleviated. Strikingly, Treg depletion alone reciprocally induced CD4 TTS cells to themselves become tumor-specific Tregs, whereas CTLA4 blockade alone failed to promote T helper differentiation. Overcoming their paralysis established long-term tumor control, demonstrating a novel immune evasion mechanism that specifically cripples CD4 TTS cells to favor tumor progression.

cancer biology↗

bioRxiv2023

Polymerization force-regulated Arp2/3 complex-actin filament interaction dominates self-adaptive cell migrations

Cells migrate by adapting their leading-edge behaviours to heterogeneous extracellular microenvironments (ECMs) during cancer invasions and immune responses. Yet it remains poorly understood how such complicated dynamic behaviours emerge from millisecond-scale assembling activities of protein molecules, which are hard to probe experimentally. To address this gap, we established a spatiotemporal "resistance-adaptive propulsion" theory based on the protein interactions between Arp2/3 complexes and polymerizing actin filaments, and a multiscale dynamic modelling system spanning from molecular proteins to the cell. Combining spatiotemporal simulations with experiments, we quantitatively find that cells can accurately self-adapt propulsive forces to overcome heterogeneous ECMs via a resistance-triggered positive feedback mechanism, dominated by polymerization-induced actin filament bending and the bending-regulated actin-Arp2/3 binding. However, for high resistance regions, resistance triggered a negative feedback, hindering branched filament assembly, which adapts cellular morphologies to circumnavigate the obstacles. Strikingly, the synergy of the two opposite feedbacks not only empowers cells with both powerful and flexible migratory capabilities to deal with complex ECMs, but also endows cells to use their intracellular proteins efficiently. In addition, we identify that the nature of cell migration velocity depending on ECM history stems from the inherent temporal hysteresis of cytoskeleton remodelling. We also quantitatively show that directional cell migration is dictated by the competition between the local stiffness of ECMs and the local polymerizing rate of actin network caused by chemotactic cues. Our results reveal that it is the polymerization force-regulated actin filament-Arp2/3 complex binding interaction that dominates self-adaptive cell migrations in complex ECMs, and we provide a predictive theory and a spatiotemporal multiscale modelling system at the protein level.

biophysics↗

bioRxiv2023

ANKRD49 promotes the metastasis of NCI-H1299 and NCI-H1703 cells via activating JNK-ATF2/c-Jun-MMP-2/9 axis

Ankyrin repeat domain 49 (ANKRD49) has been found to highly expressed in multiple cancer including lung adenocarcinoma (LUAD) and lung squamous carcinoma (LUSC). However, the function of ANKRD49 in the pathogenesis of NSCLC still remains elusive. Previously, ANKRD49 has been demonstrated to promote the invasion and metastasis of A549 cells, a LUAD cell line, via activating the p38-ATF-2-MMP2/MMP9 pathways. Considering the heterogeneity of tumor cells, the function and mechanism of ANKRD49 in NSCLC need more NSCLC-originated cells to clarify. We found that ANKRD49 promoted the migration and invasion of NCI-H1299 and NCI-H1703 cells via enhancing the levels of MMP-2 and MMP-9. Furthermore, ANKRD49 elevated phosphorylation of JNK and then activated c-Jun and ATF2 which interact in nucleus to promote the binding of ATF2:c-Jun with the promoter MMP-2 or MMP-9. In vivo assay showed that ANKRD49 promoted lung metastasis of injected- NSCLC cells and the high metastatic rate was positively correlated with the high expression of ANKRD49, MMP-2, MMP-9, p-JNK, p-c-Jun and p-ATF2. In conclusion, the present study indicated that ANKRD49 accelerated the invasion and metastasis of NSCLC cells via JNK-mediated transcription activation of c-Jun and ATF2 which regulated the expression of MMP-2/MMP-9.

cancer biology↗

bioRxiv2023

Gastrodin ameliorates synaptic impairment, reestablishes mitochondrial membrane potential and reduces oxidative stress in N2a/APP cells through the ERK1/2 and GSK-3beta pathways

Alzheimers disease (AD) is featured by abnormal {beta}-amyloid (A{beta}) deposition, neurofibrillary tangle formation, downstream mitochondrial dysfunction, oxidative stress, and synaptic loss. Gastrodin, a phenolic glycoside, has shown neuroprotective effect and used in the treatment of a range of brain diseases. Here we aim to assess the mechanisms and signaling pathways involved in the neuroprotective effect of gastrodin in murine neuroblastoma N2a cells expressing human Swedish mutant amyloid precursor protein (N2a/APP). The levels of pre- and postsynaptic proteins, amyloid precursor protein C-terminal fragments (APP-CTFs), levels of tau, glycogen synthase kinase-3 {beta} (GSK-3{beta}), extracellular regulated kinase (ERK), and c-Jun N-terminal Kinase (JNK) were assessed by Western blotting. Flow cytometry assays for mitochondrial membrane potential (JC1) and reactive oxidative stress, as well as immunofluorescence staining for lipid peroxidation (4{square}hydroxynonenal) and DNA oxidation (8{square}hydroxy{square}2{square}deoxyguanosine), were performed. We found that gastrodin treatment increased the levels of presynaptic SNAP25, synaptophysin, and postsynaptic PSD95, reduced phosphorylated tau protein Ser396, and APP-CTFs in N2a/APP cells. In addition, gastrodin reduced the levels of reactive oxygen species generation, lipid peroxidation, and DNA oxidation, reestablished mitochondrial membrane potential. Upregulated levels of phosphorylated-GSK-3{beta}, reduced levels of phosphorylated-ERK, and phosphorylated-JNK were involved the protective effect of gastrodin. In conclusion, we demonstrated a neuroprotective effect of gastrodin in N2a/APP cell line.

neuroscience↗

bioRxiv2022

Region- and variance-based DNA methylation analyses reveal novel disease genes and pathways for systemic lupus erythematosus

BackgroundSystemic lupus erythematosus (SLE) is a prototype autoimmune disease with unclear pathogenesis. DNA methylation is an important regulatory mechanism on gene expression, providing a key angle to understand disease mechanisms. To understand the pathways involved in SLE, and to develop biomarkers for its diagnosis and treatment, we analyzed DNA methylation profiles on blood cells from SLE patients and healthy controls. ResultsWe identified most differentially methylated regions (DMRs) in T cells, while majority of differentially variable sites (DVSs) were found in B cells, featuring hypervariability in enhancers. We observed a prominent T cell receptor (TCR) signaling cluster with consistent hypermethylation and a B cell receptor (BCR) cluster with highly increased variability in SLE. Genes involved in innate immunity were often found hypomethylated, while adaptive immunity genes were featured with hypermethylation. Using a machine learning approach, we identified 60 genes that accurately distinguished SLE patients from healthy individuals, which also showed correlation with disease activities. ConclusionsThis study highlights the role of lymphocyte receptor aberrations in the disease and identified a list of genes showing great potential as biomarkers and shedding new light on disease mechanisms, through novel analyses of methylation data.

bioinformatics↗

bioRxiv2022

Sequencing by avidity enables high accuracy with low reagent consumption

We present avidity sequencing - a novel sequencing chemistry that separately optimizes the process of stepping along a DNA template and the process of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar, and yield negligible dissociation rates. We demonstrate the use of avidites as a key component of a sequencing technology that surpasses Q40 accuracy and enables a diversity of applications that include single cell RNA-seq and whole human genome sequencing. We also show the advantages of this technology in sequencing through long homopolymers.

genomics↗

bioRxiv2022

Species-specific roles for the MAFA and MAFB transcription factors in regulatingislet β cell identity

Type 2 diabetes (T2D) is associated with compromised identity of insulin-producing pancreatic islet beta ({beta}) cells, characterized by inappropriate production of other islet cell-enriched hormones. Here we examined how hormone misexpression was influenced by the MAFA and MAFB transcription factors, closely related proteins that maintain islet cell function. Mice specifically lacking MafA in {beta} cells demonstrated broad, population-wide changes in hormone gene expression with an overall gene signature closely resembling islet gastrin (Gast)-positive cells generated under conditions of chronic hyperglycemia and obesity. A human {beta} cell line deficient in MAFB, but not one lacking MAFA, also produced a gastrin (GAST)-positive gene expression pattern. In addition, GAST was detected in human T2D {beta} cells with low levels of MAFB. Moreover, evidence is provided that human MAFB can directly repress GAST gene transcription. These results support a novel, species-specific role for MafA and MAFB in maintaining adult mouse and human {beta} cell identity, respectively, by repressing expression of Gast/GAST and other non-{beta} cell hormones.

cell biology↗

bioRxiv2022

Integrative Single Cell Multiomic Profiling Analysis Reveals HOX-PBX Gene Regulatory Network Contributing to the Survival of mTOR Hyperactive Cells

Lymphangioleiomyomatosis (LAM) is a rare, debilitating lung disease that predominantly affects women of reproductive age. LAM is characterized by the infiltration of the lungs by abnormally proliferating smooth muscle-like cells of unknown origin via an estrogen-dependent metastatic mechanism. LAM cells carry deleterious mutations of tuberous sclerosis complex (TSC1/TSC2) genes, resulting in hyperactivation of the mechanistic target of rapamycin complex 1 (mTORC1) and ultimately dysregulated cell growth. Sirolimus, an FDA approved mTORC1 inhibitor and current best-choice medication for LAM stabilizes lung function in most LAM patients. However, it requires sustained application and remains inefficacious in some patients. The greatest barriers to finding a cure for LAM include its undetermined origin and unclear underlying pathogenesis. Our study aims to advance knowledge on the origin of LAM, and ultimately serve as a premise for the development of novel therapeutic targets for LAM. Single cell RNA sequencing (scRNA-seq) is a powerful tool in biomedical research that informs gene expression differences at the cellular level and may provide insights into the most fundamental origin of LAM cells. Our scRNA-seq analysis of LAM cells revealed a unique population of cells (LAMCORE), expressing uterine-similar homeobox transcription factors (HOX) and Pre-B-cell leukemia homeobox 1 (PBX1), which are absent in normal lung, suggesting that the uterus is the primary origin of LAM. PBX1 is a transcription factor critical for female reproductive tract development and maintenance, and its overexpression is implicated in some female reproductive cancers. In this study we hypothesize that PBX1 promotes survival and lung colonization of LAM (TSC2-null) cells. Using LAM patient-derived cells, we validated the transcriptional profile, gene expression and protein levels of PBX1. We have the first functional evidence that PBX1 and its downstream targets are upregulated in LAM cells. In a mouse model of LAM, we monitored the effect of suppression of PBX1 by short hairpin RNA-mediated gene silencing on lung colonization and tumor growth. We also found that pharmacological suppression of PBX1 attenuates LAM lung colonization and promotes death of LAM cells in vivo and vitro. Our data collectively suggests that PBX1 is a critical regulator of LAM progression.

cancer biology↗

bioRxiv2022

Dysregulation of Acid Ceramidase-mediated Sphingolipid Metabolism Contributes to Tumor Progression in Tuberous Sclerosis Complex

Tuberous Sclerosis Complex (TSC) is disorder of multi-system benign neoplasia in the brain, heart, kidneys and lungs. Lymphangioleiomyomatosis (LAM) is a progressive pulmonary disease affecting exclusively women. Both are caused by mutations in TSC1 and TSC2, resulting in mTORC1 hyperactivation. Single cell RNA sequencing of LAM lungs identified activation of genes in the sphingolipid pathway. Independent validation studies showed that acid ceramidase (ASAH1) and dihydroceramide desaturase (DEGS1), key enzyme for regulating sphingolipid and ceramide metabolism, were significantly increased in TSC2-null cells, and their expression and activity were rapamycin-insensitive. TSC2 negatively regulated the biosynthesis of tumorigenic sphingolipids. Suppression of ASAH1 by shRNA or the inhibitor ARN14976 (17a) markedly decreased the viability of TSC2-null cells. In vivo, 17a significantly decreased the growth of Tsc2-null cell derived mouse xenografts. When combined with rapamycin, 17a more strongly inhibited the progression of renal cystadenomas in Tsc2+/- mice than either agent alone, evaluated by pathology and MRI. Collectively, our studies identify a rapamycin-insensitive disorder of sphingolipid metabolism in TSC2-null cells and tumors and validate the novel hypothesis that TSC2 regulates sphingolipid production and action via ASAH1. Targeting aberrant sphingolipid metabolism pathways may have therapeutic value in TSC and LAM, and possibly in mTORC1-hyperactive neoplasms.

cell biology↗

bioRxiv2022

Quercetin reduces APP expression, oxidative stress and mitochondrial dysfunction in the N2a/APPswe cells via ERK1/2 and AKT pathways

Abnormal amyloid-{beta} (A{beta}) abnormal accumulation and oxidative stress play important roles in Alzheimers disease (AD). Quercetin has been reported to possess antioxidant and anti-inflammatory properties, and thus of therapeutic interests for neurodegenerative disorders. In the present study, we aimed to characterize the mechanisms by which quercetin exerts neuroprotective effects in murine neuroblastoma N2a cells stably expressing human Swedishh mutant amyloid precursor protein (APP). Quercetin treatment exhibited low cytoxicity, attenuated APP expression and APP-induced oxidative neurotoxicity in N2a/APP cells. We found that quercetin effected via the down-regulation of phospho-extracellular signal{square}regulated protein kinase (p-ERK1/2) pathway and up-regulation of phospho-protein kinase B (p-AKT) pathway in N2a/APP cells. In addition, quercetin ameliorated the elevated levels of reactive oxygen species using DCFH-DA flow-cytometry in N2a/APP cells, lipid peroxidation using (4-HNE), and DNA oxidation (8-OHdG assays). Quercetin ameliorated the loss of mitochondrial membrane potential using JC-1 fluorescence assay in N2a/APP cells in a dose-dependent mannor. In conclusion, we domenstrated the neuroprotective effects of quercetin against the APP expression induced oxidative neurotoxicity, impairment of mitochondrial function and oxidative stress through inactivation of the ERK1/2 signaling pathway and activation of AKT signaling pathways.

neuroscience↗

bioRxiv2022

Guild-level microbiome signature associated with COVID-19 severity and prognosis

COVID-19 severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples collected from 300 in-hospital COVID-19 patients at time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), Redundancy Analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Random Forest model based on these 33 HQMAGs classified patients from different severity groups (average AUC = 0.79). Co-abundance network analysis found that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Random Forest regression showed that these 33 HQMAGs at admission had the capacity to predict 8 clinical parameters, which are predictors for COVID-19 prognosis, at Day 7 in hospital. Moreover, the dominance of Guild 1 over Guild 2 at admission predicted the death/discharge outcome of the critical patients (AUC = 0.92). Random Forest models based on these 33 HQMAGs classified patients with different COVID-19 symptom severity, and differentiated COVID-19 patients from healthy subjects, non-COVID-19, and pneumonia controls in three independent datasets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission.

microbiology↗

bioRxiv2022

Cryo-EM structure of the type III-E CRISPR-Cas effector gRAMP in complex with TPR-CHAT

The type III-E CRISPR-Cas effector protein, named gRAMP, is the largest single-unit CRISPR-Cas effector. A caspase-like peptidase (TPR-CHAT) gene often co-occurs with gRAMP gene clusters. However, the exact mechanism of the recognition and cleavage of target RNA of Sb-gRAMP, as well as the molecular architecture of the CRISPR-guided caspase complex, remains unclear. Here, we report the cryo-EM structures of the type III-E effector Sb-gRAMP-crRNA in a complex with TPR-CHAT, with and without target ssRNA at 3.0 and 2.9 [A], respectively. The overall structure of the gRAMP-crRNA-ssRNA-TPR-CHAT complex adopts an "L"-shaped conformation, consisting of a copy of gRAMP, a copy of TPR-CHAT, a 37-nt crRNA, and an 18-nt target ssRNA. The data presented in this manuscript reveal the mechanism of recognition of crRNA and target ssRNA by gRAMP, also, this work reports the structure of the CRISPR type III-E effector in complex with the binding partner TPR-CHAT, which provides vital clues for elucidating the functional relation between the CRISPR-Cas system and caspase peptidase.

biochemistry↗

bioRxiv2022

Recovery of structural integrity of epithelial monolayer in response to massive apoptosis-induced defects

Apoptosis exists ubiquitously in organisms and plays an essential role in maintaining the homeostasis of functional tissues. While the signaling pathway of cell apoptosis has been widely studied, the mechanism of how apoptotic cells regulate the structural homeostasis of a living tissue still remains largely elusive. Using a functional epithelial monolayer as a model system, we find that the integrity of the epithelium is interrupted by apoptosis-induced defects, with an increasing permeability to small molecules across the epithelium. The defects promote a structural reorganization through enhanced cell spreading and migratory dynamics, resulting in a quick recovery of epithelium integrity. Moreover, we show the epithelial monolayer remodeling is driven by local enhanced traction force after apoptosis, which triggers the process of fluidization and mesenchymal-like migration. Our results show the quick recovery of epithelial homeostasis when being interrupted by cell apoptosis, and indicate the importance of apoptosis-induced mechanical force in mediating cell behaviors to maintain the structural integrity of epithelium.

biophysics↗

bioRxiv2022

Revisiting the effects of Cas9 on p53-inactivating mutations reveals sex-biased genome editing by CRISPR-Cas9

CRISPR-Cas9 system has emerged as the dominant technology for gene editing and has great potential for large-scale clinical applications. One major concern is its off-target issue and other potential side effects after the introduction of exogenous CRISPR-Cas9 into cells. Several previous studies investigated CRISPR-Cas9 interactions with p53 mainly in non-transformed cells, such as RPE1 (retinal pigmented epithelium cells) and H9 (embryonic stem cells [ESC]). Recently, it has been reported that Cas9 alone can activate the p53 pathway and select for p53-inactivating mutations after studying hundreds of cancer cell lines. We reanalyzed the reported data of Cas9-associated p53-inactivating mutations and observed large significant sex difference when comparing Cas9 activities in p53-wildtype and p53-mutant cell lines. To expand the impact of this finding, we further examined all protein-coding genes screening by the CRISPR-Cas9 system in a large-scale dataset from the DepMap project. We highlight the p53 status-dependent sex bias of CRISPR-Cas9 effect across cancer cell types (genes including MYC, PIK3CA, KAT2B, KDM4E, SUV39H1, FANCB, TLR7, and APC2) and potential mechanisms (mediated by transcriptional factors including SOX9, FOXO4, LEF1, and RYBP) underlying this phenomenon, which suggest that the p53-dependent sex bias effect may need to be considered in future clinical applications, especially in cancer, when using this genome editing system.

genetics↗

bioRxiv2022

Identifying new regulators of evolutionarily conserved differential chromosome X dosage compensation

The active X chromosome in mammals is upregulated to balance its dosage to autosomes during evolution. However, it is elusive why the currently known dosage compensation machinery showed uneven and small influence on X genes, necessitating systemic investigation of X dosage in different angles and identification of new dosage regulators. Here, based on >20,000 transcriptomes, we identified two X gene groups (genome ploidy-sensitive [PSX] and ploidy-insensitive [PIX] genes), showing distinct but evolutionarily-conserved (in both primates and mouse) dosage compensations (termed X-over-Autosome dosage Ratio, or XAR). We then explored XAR in diseases and in stem cells, where XAR is potentially important. We demonstrated that XAR-PIX was downregulated while XAR-PSX upregulated across cancer types at both RNA and protein levels. In contrast, XAR-PIX was upregulated while XAR-PSX downregulated during stem cell differentiation. Interestingly, XAR-PIX, but not XAR-PSX, was significantly lower and associated with autoantibodies and inflammation in lupus patients, suggesting that insufficient dosage of PIX genes may contribute to lupus pathogenesis. We further identified and experimentally validated two new XAR regulators, TP53 and ATRX. Collectively, we provided insights to further unravel the mystery of X dosage compensation in mammals and its pathophysiological roles in human diseases.

cancer biology↗

bioRxiv2022

Three-dimensional structured illumination microscopy with enhanced axial resolution

We present two distinct, complementary methods for improving axial resolution in three-dimensional structured illumination microscopy (3D SIM) with minimal or no modification to the optical system. First, we show that placing a mirror directly opposite the sample enables 4-beam interference with higher spatial frequency content than 3D SIM illumination, offering near-isotropic imaging with [~]120 nm lateral and 160 nm axial resolution. Second, we develop an improved deep learning method that can be directly applied to 3D SIM data, obviating the need for additional hardware. This procedure results in [~]120 nm isotropic resolution and can be combined with denoising to facilitate volumetric imaging spanning dozens of time points. We demonstrate the potential of these advances by imaging a variety of cellular samples, delineating the nanoscale distribution of vimentin and microtubule filaments, observing the relative positions of caveolar coat proteins and lysosomal markers, and visualizing rich cytoskeletal dynamics within T-cells in the early stages of immune synapse formation.

cell biology↗