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Publications and source records attributed to Zhang, Q..
The authors have withdrawn their manuscript because the article needs to supplement the data of cell culture to clarify the mechanism. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Emerging evidence supports FDX1s important role in the development and progression of cancer, but no extensive cancer analysis is available to date. This study was the first to comprehensively explore the expression of FDX1 in 33 types of cancer and the significance of FDX1 in clinical prognosis by using bioinformatics techniques. Meanwhile, we analyzed the relationship between FDX1 and pathological stage, as well as immune cell infiltration. Based on this, the important role of FDX1 in tumor immunotherapy was proposed. The expression of FDX1 was significantly different between normal and tumor samples in 17 of 33 types of cancer. Besides, Cox regression analysis showed that FDX1 is a protective gene in Kidney renal clear cell carcinoma (KIRC), Cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC), Liver hepatocellular carcinoma (LIHC), Kidney renal papillary cell carcinoma (KIRP), Mesothelioma (MESO), and Thyroid carcinoma (THCA). Porphyrin and oxidative metabolism pathway regulating integrator complex was involved in the process. Furthermore, high expression of FDX1 promoted infiltration of Eosinophils and monocyte in Adrenocortical carcinoma (ACC) and Kidney Chromophobe (KICH) by affecting the tumor microenvironment (TME) and was significantly correlated with immune checkpoint genes. Our first pan-cancer analysis elucidates the expression characteristics of FDX1 across different cancers and highlights its potential value as a prognostic biomarker, laying a foundation for further study of its immunotherapy mechanism in various cancers.
Unbiased genetic screens implicated a number of uncharacterized genes in hearing loss, suggesting some biological processes required for auditory function remain unexplored. Loss of Kiaa1024L/Minar2, a previously understudied gene, caused deafness in mice, but how it functioned in hearing was unclear. Here we show that disruption of kiaa1024L/minar2 causes hearing loss in the zebrafish. Defects in mechanotransduction, longer and thinner hair bundles, and enlarged apical lysosomes in hair cells are observed in kiaa1024L/minar2 mutant. In cultured cells, Kiaa1024L/Minar2 is mainly localized to lysosomes and its overexpression recruits cholesterol and increases cholesterol labeling. Strikingly, an accessible pool of cholesterol is highly enriched in the hair bundle membrane, and loss of kiaa1024L/minar2 reduces cholesterol localization to the hair bundles. Decreasing cholesterol levels aggravates, while increasing cholesterol levels rescues hair cell defects in kiaa1024L/minar2 mutant. Therefore cholesterol plays an essential role in the hair bundles, and Kiaa1024L/Minar2 regulates cholesterol distribution and homeostasis to ensure normal hearing.
Sample preparation in genomics is a critical step that is often overlooked in molecular workflows and impacts the success of downstream genetic applications. This study explores the use of a recently developed focused ultrasound extraction (FUSE) technique to enable the rapid release of DNA from plant tissues for genetic analysis. FUSE generates a dense acoustic cavitation bubble cloud that pulverizes targeted tissue into acellular debris. This technique was applied to leaf samples of American chestnut (Castanea dentata), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), and chestnut oak (Quercus montana). We observed that FUSE can extract high quantities of DNA in 9-15 minutes, compared to the 30 minutes required for conventional DNA extraction. FUSE extracted DNA quantities of 24.33 {+/-} 6.51 ng/mg and 35.32 {+/-} 9.21 ng/mg from American chestnut and red maple, respectively, while conventional methods yielded 6.22 {+/-} 0.87 ng/mg and 11.51 {+/-} 1.95 ng/mg, respectively. The quality of the DNA released by FUSE allowed for successful amplification and next-generation sequencing. These results indicate that FUSE can improve DNA extraction efficiency for leaf tissues. Continued development of this technology aims to adapt to field-deployable systems to increase the cataloging of genetic biodiversity, particularly in low-resource biodiversity hotspots.
The scarcity of hematopoietic stem cells (HSCs) restricts their use in both clinical settings and experimental research. Here, we examined a recently developed method for expanding rigorously purified murine HSCs ex vivo. After three weeks of culture, only 0.1% of cells exhibited the input HSC phenotype, but these accounted for almost all functional long-term HSC activity. Input HSCs displayed varying potential for ex vivo self-renewal, with alternative outcomes revealed by single cell multimodal RNA- and ATAC-seq profiling. While most HSC progeny offered only transient in vivo reconstitution, these cells efficiently rescued mice from lethal myeloablation. The amplification of functional HSC activity allowed for long-term multilineage engraftment in unconditioned hosts that associated with a return of HSCs to quiescence. Thereby, our findings identify several key considerations for ex vivo HSC expansion, with major implications also for assessment of normal HSC activity. Key point: Ex vivo self-renewal is an intrinsic property of rare candidate HSCs, with implications for assessments of HSC activity by transplantation.
From 1 Jan 2022 to 15 June 2022, more than 2,100 cases of monkeypox have been reported in 42 countries. This unusual outbreak of monkeypox has raised new concerns in academia and the public. To keep abreast of the trend of the monkeypox epidemic, it is extremely urgent and important to surveille the accumulated genomic mutations and the change of the transmission ability of the pathogen, monkeypox virus (MPXV). We report a non-canonical RNA secondary structure, G-quadruplex (RG4), that surprisingly evolved stepwise with various variants. The RG4 motif is located in the coding sequence region of MPXV C9L gene that is functional in inhibiting host innate immune response. The evolution decreases the stability of this RG4 and promotes C9L protein level in living cells. Importantly, all the reported MPXV genomes in 2022 contain the most unstable RG4 variant, which may be the reason of the increasing spread of MPXV. These findings recommend that health authorities and researchers pay attention to the genomic evolution of MPXV.
Low-threshold mechanoreceptors (LTMRs) and their cutaneous end organs convert light mechanical forces acting on the skin into electrical signals that propagate to the central nervous system. In mouse hairy skin, hair follicle-associated longitudinal lanceolate complexes, which are end organs comprising of LTMR axonal endings that intimately associate with terminal Schwann cell (TSC) processes, mediate LTMR responses to hair deflection and skin indentation. Here, we characterized developmental steps leading to the formation of A{beta} RA-LTMR and A{delta}-LTMR lanceolate complexes. During early postnatal development, A{beta} RA-LTMRs and A{delta}-LTMRs extend and prune cutaneous axonal branches in close association with nascent TSC processes. Netrin-G1 is expressed in these developing A{beta} RA-LTMR and A{delta}-LTMR lanceolate endings, and Ntng1 ablation experiments indicate that Netrin-G1 functions in sensory neurons to promote lanceolate ending elaboration around hair follicles. The Netrin-G ligand (NGL-1), encoded by Lrrc4c, is expressed in TSCs, and ablation of Lrrc4c phenocopies the lanceolate complex deficits observed in Ntng1 mutants. Moreover, NGL-1-Netrin-G1 signaling is a general mediator of LTMR end organ formation across diverse tissue types demonstrated by the fact that A{beta} RA-LTMR endings associated with Meissner corpuscles and Pacinian corpuscles are also compromised in the Ntng1 and Lrrc4c mutant mice. Thus, axon-glia interactions mediated by NGL-1-Netrin-G1 signaling promote LTMR end organ formation. Significance statementOur sense of touch is essential for fundamental tasks ranging from object recognition to social exchange. Yet, touch remains one of the least understood senses at the developmental level. Here, we investigate the formation of lanceolate complexes, which are mechanosensory end organs associated with hair follicles. The axons of touch sensory neurons innervating hairy skin extend into the skin at late embryonic and neonatal times, prune excessive branches during early postnatal development, and closely associate with non-myelinating glial cells, called terminal Schwann cells (TSCs) during formation of mature endings around hair follicles. Moreover, NGL-1 and its receptor Netrin-G1 mediate a molecular dialogue between nascent TSCs and sensory neuron axonal endings to promote mechanosensory end organ formation in both hairy and non-hairy (glabrous) skin.
Microalgae are pivotal in maintaining water quality in the lakes and rivers of Qinghai-Tibet plateau. The optimum sewage treatment conditions for Desmodesmus sp. are, temperature: 20-25{degrees}C, light intensity: 3000-8000 lx, and pH: 7.0-7.5, identified based on orthogonal experiments. The maximum removal rate of total nitrogen, total phosphorus, and chemical oxygen demand was more than 95% in the actual sewage treatment. The sewage treatment capacity of Desmodesmus sp. from plateau is higher than that from plains under the same treatment conditions. To identify the differentially expressed genes and metabolites in Desmodesmus sp. in response to sewage treatment, a combination of metabolomics and transcriptomics was employed to the microalgae with and without sewage treatment. The results showed that the oxidative phosphorylation, photosynthesis, and propanoate metabolism pathways were the most significantly enriched pathways in sewage treatment. Further, the metabolism of adenosine diphosphate, 2-oxobutanoate, and succinate were significantly upregulated, downregulated, and both upregulated and downregulated, respectively, as shown by the combined transcriptome and metabolome analysis. Additionally, we found that sewage treatment could also induce numerous changes in the primary metabolism, such as carbohydrate, fatty acid biosynthesis, and amino acid metabolism when compared with control. Overall, our results should improve fundamental knowledge of molecular responses to Desmodesmus sp. in sewage treatment and contribute to the design of strategies in microalgae response to sewage treatment.
In the in vitro fertilization and embryo transfer (IVF-ET) treatments, blastocyst culture is the method of choice for the generation of the embryos. Blastocysts can present different growth, quality, availability, and morphological characteristics that can be used to evaluate them. Although extreme blastocyst formation failures have been associated with the alteration of a single gene, the molecular factors responsible for arrested embryos remain unknown. RNA-sequencing (RNA-seq) is a promising tool for facilitating transcriptomic studies in early human embryos, thus allowing the investigation of gene expression discrepancies associated with different morphological criteria. Herein, we performed transcriptome analyses of the different stages of arrested human embryos. We identified candidate genes and related cell signaling pathways potentially associated with either arrested or developed embryos. Specifically, the three genes (MOV10L1, DDX4, and FKBP6) related to both DNA methylation and piRNA metabolic pathway might be involved in embryo development. Additionally, the transcriptome of arrested early blastocysts was significantly different from developed late blastocysts. Although the gene expression profiles identified were not significantly different between low- and high-quality late blastocysts, a significant difference in the profiles of day 5 and day 6 available late blastocysts was observed, which may be related to the clinical pregnancy rate associated with IVF-ET. Furthermore, we show that some chimeric RNAs may be functional in blastocyst development. Our findings uncovered new molecular markers that can be used for embryonic development detection, which might act as a tool for blastocyst selection for subsequent transfer.
Zygotic genome activation (ZGA), a universal process in early embryogenesis that occurs during the maternal-to-zygotic transition, involves reprogramming in the zygotic nucleus that initiates global transcription. In recent decades, knowledge of this process has been acquired from research on various model organisms; however, a consensus explanation of the mechanism underlying the process, especially in relation to housekeeping gene reactivation, is lacking. Here, we used hybrids derived from two ascidian species (Ciona robusta and C. savignyi), which diverged >120 Mya with significant divergence among most orthologous genes, to symmetrically document the unique dynamics of ZGA in urochordates. We found two co-ordinated waves of ZGA, representing early developmental and housekeeping gene reactivation, during the 8-cell to 110-cell stage. Comparative analysis revealed the regulatory connection between maternal and zygotic genes as well as allelic-specific expression in a species-rather than parental-related manner, which was attributed to the divergence of cis-regulatory elements. Single-cell RNA sequencing revealed that spatial differential reactivation of paternal housekeeping genes was significantly correlated with the mechanical property of each cell type. These findings potentially provide a new system for understanding the evolution and adaptation of strategies regulating ZGA in basal chordates.
Light touch sensation begins with activation of low-threshold mechanoreceptor (LTMR) endings in the skin and propagation of their signals to the spinal cord and brainstem. We found that the clustered protocadherin gamma (Pcdhg) gene locus, which encodes 22 cell-surface homophilic binding proteins, is required in somatosensory neurons for normal behavioral reactivity to a range of tactile stimuli. Developmentally, distinct Pcdhg isoforms mediate LTMR synapse formation through neuron-neuron interactions and peripheral axonal branching through neuron-glia interactions. The Pcdhgc3 isoform mediates homophilic interactions between sensory axons and spinal cord neurons to promote synapse formation in vivo, and is sufficient to induce postsynaptic specializations in vitro. Moreover, loss of Pcdhgs and somatosensory synaptic inputs to the dorsal horn lead to fewer corticospinal synapses onto dorsal horn neurons. These findings reveal essential roles for Pcdhg isoform diversity in somatosensory neuron synapse formation, peripheral axonal branching, and step-wise assembly of central mechanosensory circuitry.
Omic-based technologies are of particular interest and importance for non-animal chemical hazard and risk characterization based on the premise that any apical endpoint change must be underpinned by some alterations measured at the omic levels. In this work we studied cellular responses to caffeine and coumarin by generating and integrating multi-omic data from transcriptomic, proteomic and phosphoproteomic experiments. We have shown that the methodology presented here is able to capture the complete chain of events from the first compound-induced changes at the phosphoproteome level to changes in gene expression induced by transcription factors and lastly to changes in protein abundance that further influence changes at the cellular level. In HepG2 cells we found the metabolism of lipids and general cellular stress to be dominant biological processes in response to caffeine and coumarin exposure, respectively. The phosphoproteomic changes were detected early in time, at very low concentrations and provided a fast adaptive cellular response to chemical exposure. Changes in protein abundance were found much less frequently than the transcriptomic changes and can be used, together with the transcriptomic changes, to facilitate a more complete understanding of pathway responses to chemical exposure. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/492410v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1e348c8org.highwire.dtl.DTLVardef@bf50c5org.highwire.dtl.DTLVardef@4fea36org.highwire.dtl.DTLVardef@998cb8_HPS_FORMAT_FIGEXP M_FIG C_FIG
Cell-type-specific gene expression is maintained in large part by transcription factors (TFs) selectively binding to distinct sets of sites in different cell types. Recent research works have provided evidence that such cell-type-specific binding is determined by TFs intrinsic sequence preferences, cooperative interactions with cofactors, cell-type-specific chromatin landscapes, and 3D chromatin interactions. However, computational prediction and characterization of cell-type-specific and shared binding sites is rarely studied. In this paper, we propose two computational approaches for predicting and characterizing cell-type-specific and shared binding sites by integrating multiple types of features, in which one is based on XGBoost and another is based on convolutional neural network (CNN). To validate the performance of our proposed approaches, ChIP-seq datasets of 10 binding factors were collected from the GM12878 (lymphoblastoid) and K562 (erythroleukemic) human hematopoietic cell lines, each of which was further categorized into cell-type-specific (GM12878-specific and K562-specific) and shared binding sites. Then, multiple types of features for these binding sites were integrated to train the XGBoost-based and CNN-based models. Experimental results show that our proposed approaches significantly outperform other competing methods on three classification tasks. To explore the contribution of different features, we performed ablation experiments and feature importance analysis. Consistent with previous studies, we find that chromatin features are major contributors in which chromatin accessibility is the best predictor. Moreover, we identified independent feature contribution for cell-type-specific and shared sites through SHAP values, observing that chromatin features play a main role in the cell-type-specific sites while motif features play a main role in the shared sites. Beyond these observations, we explored the ability of the CNN-based model to predict cell-type-specific and shared binding sites by excluding or including DNase signals, showing that chromatin accessibility significantly improves the prediction performance. Besides, we investigated the generalization ability of our proposed approaches to different binding factors in the same cellular environment or to the same binding factors in the different cellular environments.
Cell type composition of intact bulk tissues can vary across samples. Deciphering cell type composition and its changes during disease progression is an important step towards understanding disease pathogenesis. To infer cell type composition, existing cell type deconvolution methods for bulk RNA-seq data often require matched single-cell RNA-seq (scRNA-seq) data, generated from samples with similar clinical conditions, as reference. However, due to the difficulty of obtaining scRNA-seq data in diseased samples, only limited scRNA-seq data in matched disease conditions are available. Using scRNA-seq reference to deconvolve bulk RNA-seq data from samples with different disease conditions may lead to biased estimation of cell type proportions. To overcome this limitation, we propose an iterative estimation procedure, MuSiC2, which is an extension of MuSiC [1], to perform deconvolution analysis of bulk RNA-seq data generated from samples with multiple clinical conditions where at least one condition is different from that of the scRNA-seq reference. Extensive benchmark evaluations indicated that MuSiC2 improved the accuracy of cell type proportion estimates of bulk RNA-seq samples under different conditions as compared to the traditional MuSiC [1] deconvolution. MuSiC2 was applied to two bulk RNA-seq datasets for deconvolution analysis, including one from human pancreatic islets and the other from human retina. We show that MuSiC2 improves current deconvolution methods and provides more accurate cell type proportion estimates when the bulk and single-cell reference differ in clinical conditions. We believe the condition-specific cell type composition estimates from MuSiC2 will facilitate downstream analysis and help identify cellular targets of human diseases.
In the past decade, defective DNA repair has been increasingly linked with cancer progression. Human tumors with markers of defective DNA repair and increased replication stress have been shown to exhibit genomic instability and poor survival rates across tumor types. Here we utilize-omics data from two independent consortia to identify the genetic underpinnings of replication stress, therapy resistance, and primary carcinoma to brain metastasis in BRCA wildtype tumors. In doing so, we have defined a new pan-cancer class of tumors characterized by replicative instability (RIN). RIN is defined by genomic evolution secondary to replicative challenge. Our data supports a model whereby defective single-strand break repair, translesion synthesis, and non-homologous end joining effectors drive RIN. Collectively, we find that RIN accelerates cancer progression by driving copy number alterations and transcriptional program rewiring that promote tumor evolution. Statement of SignificanceDefining the genetic basis of genomic instability with wildtype BRCA repair effectors is a significant unmet need in cancer research. Here we identify and characterize a pan-cancer cohort of tumors driven by replicative instability (RIN). We find that RIN drives therapy resistance and distant metastases across multiple tumor types.
Cell-cell mechanical communications at large spatial scale (above hundreds of micrometers) have been increasingly recognized in recent decade, which shows importance in tissue-level assembly and morphodynamics. The involved mechanosensing mechanism and resulted physiological functions are still to be fully understood. Recent work showed that traction force sensation in the matrix induces cell communications for self-assembly. Here, based on the experimental model of cell directional migration on Matrigel hydrogel containing 0.5 mg/ml type I collagen, we studied the mechano-responsive pathways for cell distant communications. Airway smooth muscle (ASM) cells assembled network structure on the hydrogel, whereas stayed isolated individually when cultured on glass without force transmission. Cell directional migration, or network assembly was significantly attenuated by inhibited actomyosin activity, or inhibition of inositol 1,4,5-trisphosphate receptor (IP3R) calcium channel or SERCA pump on endoplasmic reticulum (ER) membrane, or L-type calcium channel on the plasma membrane. Inhibition of integrin {beta}1 with siRNA knockdown reduced cell directional migration and branching assembly, whereas inhibition of cell junctional N-cadherin with siRNA had little effect on distant attractions but blocked branching assembly. Our work demonstrated that the ER calcium channels and integrin are mechanosensing signals for cell mechanical communications regulated by actomyosin activity, while N-cadherin is responsible for traction force-induced cell stable connections in the assembly.
P-glycoprotein (Pgp) is a prototypical ABC transporter of great biological and clinical significance that confers cancer multidrug resistance and mediates the bioavailability and pharmacokinetics of many drugs1-3. Decades of structural and biochemical studies have provided insights into how Pgp binds diverse compounds4-9, but how they are translocated through the membrane has remained elusive. Here, we covalently attached a cyclic substrate to discrete sites of Pgp and determined multiple complex structures in inward- and outward-facing states by cryoEM. In conjunction with molecular dynamics simulations, our structures trace the substrate passage across the membrane and identify conformational changes in transmembrane helix 1 (TM1) as regulators of substrate transport. In mid-transport conformations, TM1 breaks at glycine 72. Mutation of this residue significantly impairs drug transport of Pgp in vivo, corroborating the importance of its regulatory role. Importantly, our data suggest that the cyclic substrate can exit Pgp without the requirement of a wide-open outward-facing conformation, diverting from the common efflux model for Pgp and other ABC exporters. The substrate transport mechanism of Pgp revealed here pinpoints critical targets for future drug discovery studies of this medically relevant system.
Feedback connections play a major role in many theories of brain function. Previous studies of feedback connections to early visual areas have mainly concentrated on the representation of central visual fields. Here, injections of tracers at different eccentricities in areas V1 and V2 revealed retinotopically organized feedback. Peripheral injections revealed projections from 15 areas that are not labeled by central injections. Connection strengths for the majority of projections vary significantly with eccentricity in a systematic fashion with respect to distance and origin; whereas projections to central and upper visual fields are significantly stronger from ventral stream areas, peripheral and lower field projections are stronger from the dorsal stream. Non-invasive functional connectivity suggests a similar anatomical organization in humans. These features are discussed with respect to the cognitive and perceptual roles of these feedback pathways.