Biology subjects

Tian, M.

Publications and source records attributed to Tian, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Microbial Peptidoglycan Engages Autophagy Receptor P62 to Induce Protective Mitophagy in the Liver

Although mitophagy is critical for maintaining mitochondrial integrity and hepatic homeostasis, the microbial-derived signals controlling this process remain unknown. Given the gut microbiotas profound influence on liver pathophysiology, identifying specific bacterial factors that directly regulate hepatocyte mitophagy could unlock novel therapeutic strategies. In this study, we identify bacterial peptidoglycan (PGN)--a conserved cell wall component--as a key activator of mitophagy that protects against hepatocyte death. Through both in vivo and in vitro studies, we demonstrate that either heat-killed Escherichia coli or purified PGN attenuates hepatocyte death. Mechanistically, PGN is internalized by hepatocytes, localizes to mitochondria, and initiates mitophagy via direct interaction with the autophagy adaptor p62/SQSTM1. Genetic ablation of p62 in hepatocytes completely abolishes PGN-induced mitophagy, underscoring the pathways essential role. Strikingly, therapeutic administration of PGN markedly alleviates carbon tetrachloride (CCl4)-induced hepatic fibrosis, reducing collagen deposition and suppressing hepatic stellate cell activation through enhanced autophagic flux. Our work unveils a previously unrecognized host-microbe crosstalk in which PGN acts as a mitophagy inducer, offering a potential therapeutic avenue for liver diseases driven by mitochondrial dysfunction.

cell biology↗

bioRxiv2025

Genome editing of papaya using both Cas9 and Cas12a

Papaya (Carica papaya L.) is an economically important tropical crop that produces papain and highly nutritious fruit, which are used in the grocery, cosmetic, pharmaceutical, and food processing industries. However, various destructive pathogens severely threaten its production. Furthermore, limited natural genetic variation restricts breeding efforts for crop improvement. Therefore, we turned to gene editing as a tool to address these problems. We utilized two CRISPR systems (Cas9 and Cas12a) and two papaya genes, CpPDS (phytoene desaturase) and CpMLO6 (Mildew Locus O 6), to establish efficient genome editing systems of papaya. The systems were delivered by an optimized protocol of Agrobacterium-mediated transformation (AMT) of embryogenic callus suspension cultures derived from hypocotyls. Accordingly, we transformed papaya with five plasmid constructs, each of which expressed one or two guide RNAs (gRNAs) for gene editing using either Cas9 or Cas12a. All except two T0 transgenic plants tested produced mutations with the majority containing indels of over 90%. Furthermore, successful mutation of the CpPDS gene using both Cas9 and Cas12a produced albino phenotypes as expected for disrupting a gene for carotenoid biosynthesis. Successful mutagenesis was achieved with seven out of eight gRNAs. Homozygous and/or biallelic mutants were generated from transformation using all five constructs, suggesting the feasibility of obtaining transgene-free homozygous segregating mutants by selfing in the second generation. Taken together, a robust and reliable papaya genome editing system was established, which enables genetic modification in various genomic environments to meet the diverse needs of basic scientific research and tropical crop improvement.

plant biology↗

bioRxiv2025

Atypical functional connectome in congenitally blind humans

The human cortex is organized along continuous functional gradients that capture systematic transitions in functional connectivity across the brain. These gradients describe large-scale organizational principles, including hierarchical transitions from unimodal to transmodal regions. Here, we provide the first characterization of cortical gradients in a large sample of congenitally blind (n = 41) and sighted (n = 44) adults to assess the relative contributions of intrinsic (genetic) and experiential factors to cortical gradient organization. Using resting-state fMRI, we compared functional connectome gradients and their association with cortical structure. Both groups exhibited similar principal gradients: unimodal to transmodal, somatosensory to visual, and frontoparietal segregation, demonstrating that the fundamental scaffold of cortical organization emerges largely independently of visual experience. However, blindness altered specific features of the functional connectome: the visual network was more segregated from the sensorimotor network and more integrated with transmodal and frontoparietal networks. Moreover, blind individuals showed reduced canonical hierarchical ordering within early visual areas, weaker structure-function coupling in visual and temporal regions, and altered functional areal boundaries in V1. These findings suggest that the development of large-scale cortical gradients reflects a genetically guided scaffold that is subsequently refined by sensory experience.

neuroscience↗

bioRxiv2025

Visual experience contributes to separation of face and language responses in the ventral stream

Human ventral occipitotemporal cortex (vOTC) contains specialized regions that support visual recognition of behaviorally-relevant categories, including faces, written language and places (e.g., 1-4). An open question is how experience interacts with innate constraints to enable functional specialization. We investigate this question by comparing vOTC function across sighted and congenitally blind adults. In sighted adults, a region in lateral vOTC called the fusiform face area (FFA) responds preferentially to faces, whereas distinct left-lateralized portions of vOTC respond to written language 1,2,5-12. In blind people, lateral vOTC responds to face touching, braille and speech, but their functional co-localization has not been tested 13-16. The same group of congenitally blind adults (n=20) touched faces and spatial layouts (Experiment 1) and performed a reading (braille) and spoken language task (Experiment 2). Sighted adults performed analogous tasks in the visual modality (n=28). Using within subject analyses, we replicate the separation of faces and written language in sighted adults: written language responses are found only in left vOTC and within that hemisphere they are separate from faces. By contrast, left and right vOTC responds to language in people born blind and in the left hemisphere face and language responses overlap. These findings suggest that visual experience contributes to segregating responses to face and language in vOTC. Co-localization of face and language responses suggests an innate predisposition for communication-relevant processing in lateral vOTC.

neuroscience↗

bioRxiv2024

Regulation of epigenetics and chromosome structure by human ORC2

We report a multi-omics study in a human cell line with mutations in three subunits of Origin Recognition Complex (ORC). The ORC subunits bind to DNA independent of each other in addition to as part of a common six-subunit ORC. DNA-bound ORC2 compacts chromatin and attracts repressive histone marks to focal areas of the genome, but ORC2 also activates chromatin at many sites and protects the genes from repressive marks. The epigenetic changes regulate hundreds of genes, including some epigenetic regulators, adding an indirect mechanism by which ORC2 regulates epigenetics without local binding. DNA-bound ORC2 also prevents the acquisition of CTCF at focal sites in the genome to regulate chromatin loops and indirectly affect epigenetics. Thus, our study reveals the genes and ORC1 regions bound by individual ORC subunits and suggests their role as epigenetics and chromosome structure regulators, independent of the role of the six-subunit ORC in DNA replication.

genomics↗

bioRxiv2024

Targeting SLC7A11-mediated cysteine metabolism for the treatment of trastuzumab resistant HER2 positive breast cancer

Trastuzumab resistance remains a challenge for HER2 positive breast cancer treatment. Targeting metabolic reprogramming would provide novel insights for therapeutic strategies. Here, we integrated metabolomics, transcriptomics and epigenomics data of trastuzumab sensitive and primary resistant HER2 positive breast cancer to identify metabolic alterations. Aberrant cysteine metabolism was discovered in trastuzumab primary resistant breast cancer at both circulating and intracellular levels. The inhibition of SLC7A11 and cysteine starvation could synergize with trastuzumab to induce ferroptosis. Mechanistically, increased H3K4me3 and decreased DNA methylation enhanced SLC7A11 transcription and cystine uptake in trastuzumab resistant breast cancer. The regulation of epigenetic modifications modulated cysteine metabolism and ferroptosis sensitivity. These results revealed an innovative approach for overcoming trastuzumab resistance by targeting specific amino acid metabolism.

cancer biology↗

bioRxiv2024

Optical profiling of NMDA receptor molecular diversity at synaptic and extrasynaptic sites

Neurotransmitter receptors are the linchpin of neuronal communication. These receptors often form large multimeric complexes that differ in their subunit composition, distribution and signaling properties. Studying individual subtypes in native tissues with subunit stoichiometry resolution remains challenging. This is the case of NMDA receptors (NMDARs), a class of glutamate-gated ion channels playing essential roles in brain development and plasticity. These receptors co-exist as multiple subtypes, with GluN1/GluN2A (GluN2A diheteromers), GluN1/GluN2B (GluN2B diheteromers) and GluN1/GluN2A/GluN2B (GluN2A/GluN2B triheteromers) receptors prevailing in the adult forebrain. Despite numerous investigations, the relative abundance and subcellular distribution of these subtypes remain contentious. Here, we designed a photochemical tool (Opto2B) enabling specific and reversible modulation of GluN2B diheteromers, while leaving other receptor subtypes unaffected (in particular GluN2A/GluN2B tri-heteromers). Using Opto2B, we established the differential contribution of GluN2B diheteromers to synaptic and extrasynaptic NMDAR pools during development. In particular, we show that in adult hippocampal CA1 pyramidal cells, GluN2A-receptors predominate in both pools, with no preferential contribution of GluN2B diheteromers to extrasynaptic currents. Our study clarifies decades of controversial research on extrasynaptic NMDARs and paves the way for interrogating NMDAR signaling diversity with unprecedented molecular and spatio-temporal resolution. Significance StatementPharmacological and genetic approaches, the gold standards for investigating receptor diversity, cannot easily distinguish between receptor populations containing one or more copies of the same subunit. For NMDARs, discriminating GluN2A/GluN2B triheteromers (containing one copy of GluN2A and one copy of GluN2B) from their diheteromeric counterparts (containing two copies of GluN2A or GluN2B) remains difficult. Here, we designed the first tool (Opto2B) allowing selective modulation of GluN2B diheteromers, leaving GluN2A/GluN2B triheteromers unaffected. Using Opto2B, we show that GluN2B diheteromers form a minor population in both synaptic and extrasynaptic compartments of the adult CA1 hippocampus, refuting the common belief of an enrichment of GluN2B diheteromers at extrasynaptic sites. This study should inform future drug discovery programs and studies on NMDAR molecular physiology.

neuroscience↗

bioRxiv2024

Multi-omics analysis reveals the mechanism of BnC07MYB3a is involved in seed coat color in Brassica napus L.

In rapeseed (Brassica napus), yellow-seeded varieties accumulate less flavonoid pigments (anthocyanins/proanthocyanidins) in their seed coats compared with black-seeded varieties. The yellow-seeded trait is associated with greatly improved seed oil yield, quality, and commercial value. Many R2R3 MYB activators have been characterized in rapeseed, but how MYB-type repressors affect pigment biosynthesis is not yet fully understood. In this study, we performed transcriptome sequencing and metabolomic analysis of B. napus varieties with extreme differences in seed coat color, combined with weighted gene co-expression network analysis. This analysis identified an R2R3-MYB-type transcription factor, BnC07MYB3a (BnaC07G0178800ZS), as a candidate regulator of the yellow-seeded trait in B. napus. Overexpressing BnC07MYB3a in Arabidopsis thaliana and B. napus downregulated the expression of flavonoid biosynthetic genes, resulting in significantly lower anthocyanin and proanthocyanidin accumulation than in the wild-type and a lighter seed coat color in transgenic plants. BnC07MYB3a directly binds to the promoter of the TRANSPARENT TESTA (TT) gene BnTT6 and represses its expression. BnC07MYB3a also physically interacts with BnA06bHLH92a and the WD40 transcription factor TRANSPARENT TESTA GLABRA1 (BnTTG1), suggesting that they might form a previously unidentified MYB-bHLH-WD40 transcription factor complex. Our results reveal the molecular mechanism and regulatory network of BnC07MYB3a in determining seed coat color in B. napus and provide a genetic resource for breeding yellow-seeded cultivars of B. napus.

molecular biology↗

bioRxiv2024

Preventive Effects of Pomegranate Seed Oil on Transient Middle Cerebral Artery Occlusion via the Keap1/Nrf2/NQO1 Pathway in the rats Cortex

Ischemic stroke remains a pressing challenge that needs to be solved. Energy metabolic failure is a critical factor contributing to mitochondrial dysfunction and oxidative stress in the pathogenesis of brain ischemia, leading to the generation of excessive reactive oxygen species. Pomegranate seed oil (PSO) exhibits antioxidant properties; however, its protective effects against cerebral ischemia/reperfusion injury and the underlying mechanisms remain unclear. In this study, a transient middle cerebral artery occlusion (tMCAO) rat model was employed to simulate cerebral ischemia/reperfusion injury. We investigated the mechanisms by which different concentrations of PSO modulate oxidative damage caused by cerebral ischemia/reperfusion injury through the Keap1/Nrf2/NQO1 pathway in cortex. SD male rats were randomly divided into four groups: Control, tMCAO+NaCl, tMCAO+LO (low concentration of PSO), tMCAO+MO (medium concentration of PSO), and tMCAO+HO (high concentration of PSO). Our findings suggest that low concentration of PSO exerts neuroprotective effects by activating Nrf2 and NQO1, thereby reducing oxidative stress. Furthermore, LO significantly improved neurological scores and reduced neuronal edema. Additionally, the results demonstrated an increase in superoxide dismutase (SOD) levels and a decrease in malondialdehyde (MDA) levels. In contrast, MO and HO exhibited suboptimal effects. To sum up, these results indicate that PSO activates neuroprotective pathways against oxidative stress following cerebral ischemia/reperfusion injury via the Keap1/Nrf2/NQO1 pathway, providing novel insights into potential preventive therapies for cerebral ischemia/reperfusion.

neuroscience↗

bioRxiv2024

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗

bioRxiv2024

PGSFusion streamlines polygenic score construction and epidemiological applications in biobank-scale cohorts

BackgroundThe polygenic score (PGS) is an estimate of an individuals genetic susceptibility to a specific complex trait and has been instrumental to the development of precision medicine. Clinically, the simplest form of PGS, which is calculated as a weighted sum of variant counts, has been widely applied to conduct disease risk classification. Unfortunately, despite the critical importance of PGS, there are few online resources available to biologists and epidemiologists to calculate PGS in a user-friendly manner. ResultsTo address this need, we have developed a web server, PGSFusion, that streamlines the construction of PGS using a large variety of methods targeting different epidemiological requirements. PGSFusion included 16 PGS methods in four categories, which are single-trait, annotation-based, multiple-trait, and cross-ancestry. In addition, PGSFusion also utilizes UK Biobank data to provide two kinds of in-depth analyses: i) prediction performance evaluation to display the consistency between PGS and specific traits and the effect size of PGS in different genetic risk groups; ii) joint effect analysis to investigate the interaction between PGS and covariates, as well as the genetic effect size in different subgroups of covariates. PGSFusion automatically identifies the required information in uploaded summary statistics files, provides a selection of suitable methods, and outputs calculated PGSs and their corresponding epidemiological results, all without requiring prior programming knowledge. To demonstrate the function of PGSFusion, we showcase three case studies in different application scenario, highlighting its versatility and values to researchers. ConclusionsOverall, PGSFusion presents an easy-to-use, effective, and extensible platform for PGS construction, promoting the accessibility and utility of PGS for researchers in the field of precision medicine.

bioinformatics↗

bioRxiv2024

Intercellular Signaling Pathways as Therapeutic Targets for Vascular Dementia Repair

Vascular dementia (VaD) is a white matter ischemic disease and the second-leading cause of dementia, with no direct therapy. Within the lesion site, cell-cell interactions dictate the trajectory towards disease progression or repair. To elucidate the underlying intercellular signaling pathways, a VaD mouse model was developed for transcriptomic and functional studies. The mouse VaD transcriptome was integrated with a human VaD snRNA-Seq dataset. A custom-made database encompassing 4053 human and 2032 mouse ligand-receptor (L-R) interactions identified significantly altered pathways shared between human and mouse VaD. Two intercellular L-R systems, Serpine2-Lrp1 and CD39-A3AR, were selected for mechanistic study as both the ligand and receptor were dysregulated in VaD. Decreased Seprine2 expression enhances OPC differentiation in VaD repair. A clinically relevant drug that reverses the loss of CD39-A3AR function promotes tissue and behavioral recovery in the VaD model. This study presents novel intercellular signaling targets and may open new avenues for VaD therapies.

neuroscience↗

bioRxiv2024

Spatial integration of sensory input and motor output in Pseudomonas aeruginosa chemotaxis through colocalized distribution

The opportunistic pathogen Pseudomonas aeruginosa serves as a model organism for studying multiple signal transduction pathways. The chemoreceptor cluster, a core component of the chemotaxis pathway, is assembled from hundreds of proteins. The unipolar distribution of receptor clusters has long been recognized, yet the precise mechanism governing their assembly remains elusive. Here, we directly observed the relative positions of the flagellar motor and chemoreceptor cluster using flagellar filament labeling and gene editing techniques. Surprisingly, we found that both are located at the same cell pole, with the distribution pattern controlled by the polar anchor protein FlhF. Additionally, the efficient assembly of the chemoreceptor cluster is partially dependent on the integrity of the motor structure. Furthermore, we discovered that overexpression of the chemotaxis regulatory protein CheY leads to high intracellular levels of the second messenger c-di-GMP, triggering cell aggregation. Therefore, the colocalization of the chemoreceptor cluster and flagellum in P. aeruginosa serves to avoid cross-pathway signaling interference, enabling cells to conduct various physiological activities in an orderly manner.

microbiology↗

bioRxiv2023

Engineering immunogens that select for specific mutations in HIV broadly neutralizing antibodies

Vaccine development targeting rapidly evolving pathogens such as HIV-1 requires induction of broadly neutralizing antibodies (bnAbs) with conserved paratopes and mutations, and, in some cases, the same Ig-heavy chains. The current trial-and-error search for immunogen modifications that improve selection for specific bnAb mutations is imprecise. To precisely engineer bnAb boosting immunogens, we used molecular dynamics simulations to examine encounter states that form when antibodies collide with the HIV-1 Envelope (Env). By mapping how bnAbs use encounter states to find their bound states, we identified Env mutations that were predicted to select for specific antibody mutations in two HIV-1 bnAb B cell lineages. The Env mutations encoded antibody affinity gains and selected for desired antibody mutations in vivo. These results demonstrate proof-of-concept that Env immunogens can be designed to directly select for specific antibody mutations at residue-level precision by vaccination, thus demonstrating the feasibility of sequential bnAb-inducing HIV-1 vaccine design.

immunology↗

bioRxiv2023

Integrating leaf gas exchange and chlorophyll fluorescence to reveal the long-term regulation of photosynthesis in situ

Understanding the diurnal and seasonal regulation of photosynthesis is an essential step in quantifying and modeling the impact of the environment on plant function. Although the dynamics of photosynthesis have been widely investigated in terms of CO2 exchange measurements, a more comprehensive view can be obtained when combining gas exchange and chlorophyll fluorescence (ChlF) measurements. However, such integrated measurements have been so far restricted to short term analysis using portable systems that combine IRGA and PAM-ChlF techniques. Here we introduce and demonstrate a new method for integrated, long-term and in situ measurements of leaf gas exchange and ChlF, based on an autonomous gas exchange system and a new miniature PAM- fluorometer. The method is used to simultaneously track the dynamics of the light and carbon reactions of photosynthesis at a 20-minute resolution in leaves of silver birch during summer time. The potential of the method is initially demonstrated using the ratio between electron transport and net assimilation (ETR/ANET). We successfully captured the diurnal patterns in the ETR/ANET during summer time, including a drastic increase in ETR/ANET upon a high-temperature period. We suggest that these measurements can provide valuable data to model and quantify the regulation of leaf photosynthesis in situ. HighlightWe introduce new integrated measurements to help resolve the seasonal and diurnal dynamics of photosynthesis regulation by combining long-term simultaneous measurements of gas exchange and chlorophyll fluorescence in field conditions.

plant biology↗

bioRxiv2023

TIPE drives a cancer stem-like phenotype by promoting glycolysis via PKM2/HIF-1alpha axis in melanoma

TIPE (TNFAIP8) has been identified as an oncogene and participates in tumor biology. However, how its role in the metabolism of tumor cells during melanoma development remains unclear. Here, we demonstrated that TIPE promoted glycolysis by interacting with pyruvate kinase M2 (PKM2) in melanoma. We found that TIPE induced PKM2 dimerization, thereby facilitating its translocation from the cytoplasm to the nucleus. TIPE-mediated PKM2 dimerization consequently promoted HIF-1 activation and glycolysis, which contributed to melanoma progression and increased its stemness features. Notably, TIPE specifically phosphorylated PKM2 at Ser 37 in an ERK-dependent manner. Consistently, the expression of TIPE was positively correlated with the levels of PKM2 Ser37 phosphorylation and cancer stem cell markers in melanoma tissues from clinical samples and tumor bearing mice. In summary, our findings indicate that the TIPE/PKM2/HIF-1 signaling pathway plays a pivotal role in promoting cancer stem cell properties by facilitating the glycolysis, which would provide a promising therapeutic target for melanoma intervention.

cancer biology↗

bioRxiv2023

TCM-CMap: A Novel Computational Methodology to Link Gene Perturbation to Therapeutic Targets in Complex TCM Prescriptions

Herbal medicine, especially Traditional Chinese medicine (TCM), is a valuable resource of natural products for drug discovery with obvious therapeutic effects. However, the mechanisms of action (MOAs) of herbal medicine are often unknown due to limited target information and the complexity of multiple ingredients and targets. This study developed a Herb-CMap algorithm to prioritize active ingredients and targets within herbal medicine by integrating transcriptomics- based gene perturbation data with a random walk algorithm. This methodology bridges the gap between gene perturbation of herbal medicine and its therapeutic target. Using the Suhuang antitussive capsule (Suhuang) for treating cough variant asthma (CVA) as a case study, we identify and experimentally verify that quercetin and luteolin directly interact with Il17a, Pik3cb, Pik3cd, Akt1, and Tnf. These interactions inhibit the IL-17 signaling pathway and inactivate PI3K, Akt, and NF- {kappa}B, preventing lung inflammation and treating CVA. Our findings demonstrate the potential of the Herb-CMap methodology to provide insights into the molecular MOAs of herbal medicine, thereby advancing drug discovery from herbal medicine.

systems biology↗

bioRxiv2023

Integrative analysis of DNA replication origins and ORC binding sites in human cells reveals a lack of overlap between them

Based on experimentally determined average inter-origin distances of [~]100 kb, DNA replication initiates from [~]50,000 origins on human chromosomes in each cell cycle. The origins are believed to be specified by binding of factors like the Origin Recognition Complex (ORC) or CTCF or other features like G-quadruplexes. We have performed an integrative analysis of 113 genome-wide human origin profiles (from five different techniques) and 5 ORC-binding profiles to critically evaluate whether the most reproducible origins are specified by these features. Out of [~]7.5 million union origins identified by all datasets, only 0.27% were reproducibly obtained in at least 20 independent SNS-seq datasets and contained in initiation zones identified by each of three other techniques (20,250 shared origins), suggesting extensive variability in origin usage and identification. 21% of the shared origins overlap with transcriptional promoters, posing a conundrum. Although the shared origins overlap more than union origins with constitutive CTCF binding sites, G-quadruplex sites and activating histone marks, these overlaps are comparable or less than that of known Transcription Start Sites, so that these features could be enriched in origins because of the overlap of origins with epigenetically open, promoter-like sequences. Only 6.4% of the 20,250 shared origins were within 1 kb from any of the [~]13,000 reproducible ORC binding sites in human cancer cells, and only 4.5% were within 1 kb of the [~]11,000 union MCM2-7 binding sites in contrast to the nearly 100% overlap in the two comparisons in the yeast, S. cerevisiae. Thus, in human cancer cell lines, replication origins appear to be specified by highly variable stochastic events dependent on the high epigenetic accessibility around promoters, without extensive overlap between the most reproducible origins and currently known ORC- or MCM-binding sites.

genomics↗