Biology subjects

Tian, R.

Publications and source records attributed to Tian, R..

87 records · Page 5Linked to original sources

bioRxiv2020

Lower Soil Carbon Loss Due to Persistent Microbial Adaptation to Climate Warming

Soil microbial respiration is an important source of uncertainty in projecting future climate and carbon (C) cycle feedbacks. Despite intensive studies for two decades, the magnitude, direction, and duration of such feedbacks are uncertain, and their underlying microbial mechanisms are still poorly understood. Here we examined the responses of soil respiration and microbial community structure to long-term experimental warming in a temperate grassland ecosystem. Our results indicated that the temperature sensitivity of soil microbial respiration (i.e., Q10) persistently decreased by 12.0{+/-}3.7% across 7 years of warming. Integrated metagenomic and functional analyses showed that microbial community adaptation played critical roles in regulating respiratory acclimation. Incorporating microbial functional gene abundance data into a microbially-enabled ecosystem model significantly improved the modeling performance of soil microbial respiration by 5-19%, compared to the traditional non-microbial model. Model parametric uncertainty was also reduced by 55-71% when gene abundances were used. In addition, our modeling analyses suggested that decreased temperature sensitivity could lead to considerably less heterotrophic respiration (11.6{+/-}7.5%), and hence less soil C loss. If such microbially mediated dampening effects occur generally across different spatial and temporal scales, the potential positive feedback of soil microbial respiration in response to climate warming may be less than previously predicted.

ecology↗

bioRxiv2019

Glucose metabolism promotes neonatal heart regeneration

The mammalian heart switches its main metabolic substrate from glucose to fatty acids shortly after birth. This metabolic switch coincides with the loss of regenerative capacity in the heart. However, it is unknown whether glucose metabolism itself regulates heart regeneration. Here, we report that glucose metabolism is a determinant of regenerative capacity in the neonatal mammalian heart. Cardiac-specific overexpression of Glut1, the embryonic form of constitutively active glucose transporter, resulted in an increase in glucose uptake and concomitant glycogen storage in postnatal heart. Upon cryoinjury, Glut1 transgenic hearts showed higher regenerative capacity with less fibrosis than non-transgenic control hearts. Interestingly, flow cytometry analysis revealed two distinct populations of ventricular cardiomyocytes: Tnnt2-high and Tnnt2-low cardiomyocytes, the latter of which showed significantly higher mitotic activity in response to high intracellular glucose in Glut1 transgenic hearts. Metabolic profiling shows that Glut1-transgenic hearts have a significant increase in the glucose metabolites upon injury, and inhibition of the nucleotide biosynthesis abrogated the regenerative advantage of high intra-cardiomyocyte glucose level. Our data suggest that the increased in glucose metabolism promotes cardiac regeneration in neonatal mouse heart.

developmental biology↗

bioRxiv2019

CRISPR-based screens uncover determinants of immunotherapy response and potential combination therapy strategies

Cancer cells commonly develop resistance to immunotherapy by loss of antigen expression. Combinatorial treatments that increase levels of the target antigen on the surface of cancer cells have the potential to restore efficacy to immunotherapy. Here, we use our CRISPR interference and CRISPR activation-based functional genomics platform to systematically identify pathways controlling cell-surface expression of the multiple myeloma immunotherapy antigen - B cell maturation antigen, BCMA. We discovered that pharmacological inhibition of HDAC7 and the Sec61 complex increased cell-surface BCMA, including in primary patient cells. Importantly, pharmacological Sec61 inhibition enhanced the anti-myeloma efficacy of a BCMA-targeted antibody-drug conjugate. A CRISPR interference CAR-T coculture screen enabled us to identify both antigen-dependent and -independent mechanisms controlling response of myeloma cells to BCMA-targeted CAR-T cells. Thus, our study demonstrates the potential of CRISPR screens to uncover mechanisms controlling response of cancer cells to immunotherapy and to suggest potential combination therapies. Key PointsO_LIUsing CRISPR screens, we systematically identify mechanisms increasing expression of the immunotherapy target BCMA and ADC efficacy. C_LIO_LIWe also identify antigen-independent mechanisms regulating response of cancer cells to BCMA-CAR-T cells. C_LI

cancer biology↗

bioRxiv2019

Extraordinary diversity of HLA class I gene expression in single cells contribute to the plasticity and adaptability of human immune system

HLA, the coding genes of human major histocompatibility (MHC) proteins, play a crucial role in the human adaptive immune system by presenting antigenic peptides to T cell receptors on T cells. HLA-A, HLA-B and HLA-C, these 3 Class I HLA genes are one of the most polymorphic loci in the human genome. For decades, HLA typing has been performed prior to tissue and stem cell transplantation. However, beyond the role in tissue matching, HLA has also been implicated in a wide array of autoimmune diseases and HLA genotypes and expression levels are closely associated with cancer patients prognosis as recent studies have revealed. Recently methods have been developed to perform HLA typing and HLA expression quantification together by using RNA-seq techniques. However, these bulk RNA-seq experiments are measuring an averaged signal of cell populations. Single-cell RNA-seq (scRNA-seq) has regained its popularity due to its power to reliably resolve single RNA transcriptomes at large scales. In our present study, we did HLA typing using three independent scRNA-seq datasets. Interestingly, we found that single cells from the same donor could be classified into different groups where each group has a distinct expressed HLA genotype (e.g., HLA-A, heterozygous or homozygous); in other words, HLA class I genes show abundant allele specific expression in single cells. This phenomenon has been repeatedly observed in a total of 14 donors from 3 independent datasets (one is breast epithelium, another two are multiple myeloma). Our systematic analysis of HLA class I gene expression using multiple scRNA-seq datasets has uncovered a putative mechanism, where by fine tuning HLA class I expressions both at the quantity and allele levels, our immune system is able to handle various internal challenges through single cells equipped with extraordinary diverse HLA expression patterns.

immunology↗

bioRxiv2019

Mitochondrial dysfunction is signaled to the integrated stress response by OMA1, DELE1 and HRI

In mammalian cells, mitochondrial dysfunction triggers the integrated stress response (ISR), in which eIF2 phosphorylation upregulates the transcription factor ATF4. However, how mitochondrial stress is relayed to the ISR is unknown. We found that HRI is the eIF2 kinase necessary and sufficient for this relay. Using an unbiased CRISPRi screen, we identified factors upstream of HRI: OMA1, a mitochondrial stress-activated protease, and DELE1, a little-characterized protein we found to be associated with the inner mitochondrial membrane. Mitochondrial stress stimulates the OMA1-dependent cleavage of DELE1, leading to its accumulation in the cytosol, where it interacts with HRI and activates its eIF2 kinase activity. Blockade of the OMA1-DELE1-HRI pathway is beneficial during some, but not all types of mitochondrial stress, and leads to an alternative response that induces specific molecular chaperones. Therefore, this pathway is a potential therapeutic target enabling fine-tuning of the ISR for beneficial outcomes in diseases involving mitochondrial dysfunction.

cell biology↗

bioRxiv2019

Compromised function of an ESCRT complex promotes endolysosomal escape of tau seeds and propagation of tau aggregation

Intercellular propagation of protein aggregation is emerging as a key mechanism in the progression of several neurodegenerative diseases, including Alzheimers Disease and frontotemporal dementia. However, we lack a systematic understanding of the cellular path-ways controlling prion-like propagation. To uncover such pathways, we performed CRISPR interference (CRISPRi) screens in a human cell-based model of propagation of tau aggregation. Our screens uncovered that knockdown of several components of the ESCRT machinery, including CHMP6, or CHMP2A in combination with CHMP2B (a gene linked to familial fronto-temporal dementia), promote propagation of tau aggregation. We found that knockdown of these genes caused damage to endolysosomal membranes, consistent with a role for the ESCRT pathway in endolysosomal membrane repair. Leakiness of the endolysosomal compartment significantly enhanced prion-like propagation of tau aggregation, likely by making tau seeds more available to pools of cytoplasmic tau. Together, these findings suggest that endolysosomal escape is a critical step in tau propagation.

cell biology↗

bioRxiv2019

Pan-genome analysis reveals the molecular basis of niche adaptation of Staphylococcus epidermidis strains

Staphylococcus epidermidis is the most commonly isolated species from human skin and the second leading cause of bloodstream infections. Here, we performed a large-scale comparative study without any pre-assigned reference to identify genomic determinants associated with their diversity and adaptation as a \"double-side spy\", a skin dominant colonization, and a successful pathogen. The pan-genome of S. epidermidis is open with 435 core proteins and a pan-genome size of 8034 proteins. Genome-wide phylogenetic tree shows that whole genome sequence is a powerful tool to analyze the complex evolutionary process of S. epidermidis and investigate the source of infection. Comparative genome analyses demonstrate the high diversity of antimicrobial resistances, especially mobile genetic elements. The complicated relationships of host-bacterium and bacterium-bacterium help S. epidermidis to play a vital role in balancing the epithelial microflora. The highly variable and dynamic nature of the S. epidermidis genome may be the result of its success in adapting to broad habitats, which is necessary to deal with complex environments. This study gives the general landscape of S. epidermidis pan-genome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible species.

microbiology↗

bioRxiv2019

Contraction of the ROS scavenging enzyme glutathione S-transferase gene family in cetaceans

Cetaceans are a group of marine mammals whose ancestors were adaptated for life on land. Life in an aquatic environment poses many challenges for air-breathing mammals. Diving marine mammals have adapted to rapid reoxygenation and reactive oxygen species (ROS)-mediated reperfusion injury. Here, we considered the evolution of the glutathione transferase (GST) gene family which has important roles in the detoxification of endogenously-derived ROS and environmental pollutants. We characterized the cytosolic GST gene family in 21 mammalian species; cetaceans, sirenians, pinnipeds, and their terrestrial relatives. All seven GST classes were identified, showing that GSTs are ubiquitous in mammals. Some GST genes are the product of lineage-specific duplications and losses, in line with a birth-and-death evolutionary model. We detected sites with signatures of positive selection that possibly influence GST structure and function, suggesting that adaptive evolution of GST genes is important for defending mammals from various types of noxious environmental compounds. We also found evidence for loss of alpha and mu GST subclass genes in cetacean lineages. Notably, cetaceans have retained a homolog of at least one of the genes GSTA1, GSTA4, and GSTM1; GSTs that are present in both the cytosol and mitochondria. The observed variation in number and selection pressure on GST genes suggest that the gene family structure is dynamic within cetaceans. Taken together, our results indicate that the cytosolic GST family in cetaceans reflects unique evolutionary dynamics related to oxygen-poor aquatic environments.

evolutionary biology↗

bioRxiv2019

CRISPR-based platform for multimodal genetic screens in human iPSC-derived neurons

CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biology. However, most previous CRISPR-based screens were conducted in cancer cell lines, rather than healthy, differentiated cells. Here, we describe a CRISPR interference (CRISPRi)-based platform for genetic screens in human neurons derived from induced pluripotent stem cells (iPSCs). We demonstrate robust and durable knockdown of endogenous genes in such neurons, and present results from three complementary genetic screens. First, a survival-based screen revealed neuron-specific essential genes and genes that improved neuronal survival upon knockdown. Second, a screen with a single-cell transcriptomic readout uncovered several examples of genes whose knockdown had strikingly cell-type specific consequences. Third, a longitudinal imaging screen detected distinct consequences of gene knockdown on neuronal morphology. Our results highlight the power of unbiased genetic screens in iPSC-derived differentiated cell types and provide a platform for systematic interrogation of normal and disease states of neurons.

cell biology↗

bioRxiv2018

Comparative genomics reveals contraction in cytosolic glutathione transferase genes in cetaceans: implications for oxidative stress adaptation

Cetaceans, a highly specialized group of aquatic mammals, experience oxidative stress induced by reactive oxygen species (ROS) production associated with the apnea/reoxygenation. The glutathione transferases (GST) family possesses multiple functions in detoxification and antioxidant defenses. However, the molecular evolution of GST family in cetaceans is still poorly investigated. Here, we characterized the GST gene family across 21 mammalian genomes including cetaceans and terrestrial relatives. Overall, 7 GST classes were identified, showing GSTs are ubiquitous and conservative to all mammals. Some of GSTs are lineage-specific duplication and loss, in line with a birth-and-death evolutionary model. We detected positive selection sites that possibly influence GST structure and function, suggesting adaptive evolution of GSTs is important for defending mammals from various types of noxious environmental compounds. There is evidence for loss of alpha and mu GST class in cetacean lineages when compared to their terrestrial relatives, consisting with the lower GST activities observed in cetaceans. Notably, we find that retained GSTA1, GSTA4 and GSTM1 in cetaceans, indicating a vital role in against lipid peroxidation and superoxide. Besides, variation in gene number, enzyme activity and selection pressure of GSTs between marine mammals suggests there is a divergent evolution of GSTs in aquatic species that might be associated to diving ability and oxidative status with different habitats. Summarily, our findings demonstrate that the GST family in cetaceans has been subject to evolutionary dynamics as response for their adaptations to oxidative stress, and highlighted the differential selection associated with different life history traits among mammals.

evolutionary biology↗

bioRxiv2018

Pleotropic effects of PPARD accelerate colorectal tumor progression and invasion

Colorectal carcinogenesis (CRC) progression requires additional molecular mechanisms to APC mutations/aberrant {beta}-catenin signaling. PPARD is a druggable ligand-activated nuclear receptor that regulates essential genes involved in cell fate. PPARD is upregulated in intestinal epithelial cells (IECs) of human colorectal adenomas and adenocarcinomas. The mechanistic significance of PPARD upregulation in CRC remains unknown. Here we show that targeted PPARD overexpression in IECs of mice strongly augmented {beta}-catenin activation via BMP7/TAK1 signaling, promoted intestinal tumorigenesis in Apcmin mice, and accelerated CRC progression and invasiveness in mice with IEC-targeted Apc{Delta}580 mutation. Human CRC invasive fronts had higher PPARD expression than their paired adenomas. A PPARD agonist (GW501516) enhanced APC{Delta}580 mutation-driven CRC, while a PPARD antagonist (GSK3787) suppressed it. Functional proteomics analyses and subsequent validation studies uncovered PPARD upregulation of multiple pro-invasive pathways that drive CRC progression (e.g. PDGFR{beta}, AKT1, CDK1 and EIF4G1). Our results identify novel mechanisms by which PPARD promotes CRC invasiveness and provide the rational for the development of PPARD antagonists to suppress CRC.

cancer biology↗

bioRxiv2017

PPARD regulation in gastric progenitor cells drives gastric tumorigenesis in mice

Little is known about the cell origin of gastric cancer. Peroxisome proliferator-activated receptor-delta (PPARD) is a druggable ligand-activated nuclear receptor that impacts protumorigenic cellular events. However, PPARDs role in tumorigenesis, especially gastric tumorigenesis, remains to be defined. We found that targeting PPARD overexpression in murine gastric progenitor cells (GPC), via a villin promoter, spontaneously induced gastric tumorigenesis that progressed to invasive adenocarcinoma. PPARD overexpression in GPC upregulated tumorigenic proinflammatory cytokine and CD44 expression, expanded GPC population in vivo, enhanced GPC self-renewal and proliferation in organoid cultures, and endowed these cells with tumorigenic properties. Our findings identify PPARD as a driver of gastric tumorigenesis via GPC transformation.

cancer biology↗

bioRxiv2017

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.\n\nBuilds onMavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchuir SO, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. eLife. 2016.\n\nImpact StatementWe organized a project-based course that used deep mutational scanning in multiple chemical conditions to resolve the inconsistencies between tolerance to mutations in laboratory conditions and sequence conservation over evolutionary timescales.

bioinformatics↗

bioRxiv2017

Quantitative Models Identify Histone Signatures Of Poised Genes Prior To Cellular Differentiation

BackgroundRecent studies have shown that histone marks are involved in pre-programming gene fates during cellular differentiation. Bivalent domains (marked by both H3K4me3 and H3K27me3) have been proposed to act in the histone pre-patterning of poised genes; however, bivalent genes could also resolve into monovalent silenced states during differentiation. Thus, the histone signatures of poised genes need to be more precisely characterized.\n\nResultsUsing a support vector machine (SVM), we show that the collective histone modification data from human blood hematopoietic cells (HSCs) could predict poised genes with fairly high predictive accuracy within the model of directed erythrocyte differentiation from HSCs. Surprisingly, models with single histone marks (e.g., H3K4me3 or H2A.Z) could reach comparable predictive powers to the full model built with all of the nine histone marks. We also derived an H2A.Z and H3K9me3-based Naive Bayesian model for inferring poised genes, and the validity of this model was supported by data from several other pluripotent/multipotent cells (including mouse ES cells).\n\nConclusionOur work represents a systematic quantitative study that verified that histone marks play a role in pre-programming the activation or repression of specific genes during cellular differentiation. Our results suggest that the relative quantities of H2A.Z modification and H3K9me3 modification are important in determining a corresponding genes fate during cellular differentiation.

bioinformatics↗

bioRxiv2017

Decoding directional genetic dependencies through orthogonal CRISPR/Cas screens

Genetic interaction studies are a powerful approach to identify functional interactions between genes. This approach can reveal networks of regulatory hubs and connect uncharacterised genes to well-studied pathways. However, this approach has previously been limited to simple gene inactivation studies. Here, we present an orthogonal CRISPR/Cas-mediated genetic interaction approach that allows the systematic activation of one gene while simultaneously knocking out a second gene in the same cell. We have developed this concept into a quantitative and scalable combinatorial screening platform that allows the parallel interrogation of hundreds of thousands of genetic interactions. We demonstrate that the established platform works robustly to uncover genetic interactions in human cancer cells and to interpret the direction of the flow of genetic information.

molecular biology↗