Biology subjects

Meng, L.

Publications and source records attributed to Meng, L..

84 records · Page 5Linked to original sources

bioRxiv2019

Engineering of Chimeric Antigen Receptor T Cells with integrin αEβ7 Results in Augmented Therapeutic Efficacy against E-cadherin positive tumor

Integrin E{beta}7 (CD103) can interact with E-cadherin and promote T cell retention in epithelial tissue. However, whether the expression of CD103 on chimeric antigen receptor (CAR)-T cells may augment T cell anti-tumor activity remains unknown. Using a preclinical model, we demonstrate that CD103 engineering of human CAR-T cells significantly improves their therapeutic effects on eliminating pre-established E-cadherin expressing tumor cells in immune deficient NOD.scid.Il2R{gamma}cnull (NSG) mice. Human T cells that were engineered with CAR containing 4-1BB and CD3zeta intracellular signaling domains (named BBz) expressed reduced level of CD103 in mice model. Ex vivo assays confirmed the effect of 4-1BB on repressing CD103 expression in CAR-T cells. On the other hand, we generated CD103 expressing CAR-T cells by introducing the E gene into the CAR structure (named CD103-BBz CAR-T cells). As compared to BBz CAR-T cells, CD103-BBz CAR-T cells produced higher levels of IL-2 and underwent greater expansion in cultures and acquired greater capacity to control the growth and metastasis of E-cadherin expressing lymphoma cells in NSG mice. This effect of CD103-BBz CAR-T cells was associated with their increased capacity to infiltrate into the tumor and persist in vivo, leading to significantly improved overall survival of lymphoma mice. Our findings suggest that engineering tumor-reactive T cells with CD103 may represent a novel strategy to improve adoptive T cells anti-tumor efficacy, and this strategy may have broad implication in the epithelial solid tumor treatment.\n\nHighlightsO_LICAR-T cells with 4-1BB costimulatory domain express reduced level of CD103\nC_LIO_LI4-1BB signaling antagonist TGF-{beta}1 induced CD103 expression\nC_LIO_LIEctopically expression of CD103 on CAR-T cells enhanced their anti-E-cadherin positive tumor capacity\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=83 SRC=\"FIGDIR/small/727446v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (19K):\norg.highwire.dtl.DTLVardef@d32377org.highwire.dtl.DTLVardef@1bd841corg.highwire.dtl.DTLVardef@12c5c98org.highwire.dtl.DTLVardef@173382d_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract:\n\nGraphic Summary: The co-stimulatory molecule 4-1BB within the CAR protein potently suppresses CD103 expression. Engineering CAR-T cells with CD103 significantly enhances their capacity to proliferate and infiltrate into the solid tumor, leading to augmented anti-tumor immunity.\n\nC_FIG

immunology↗

bioRxiv2019

High resolution single-cell chromatin 3D modeling reveals coherent chromatin aggregation with varied structures in controlling genome function stability

The genome 3D architecture is thought to be related to regulating gene expression levels in cells and can be explained by genome-wide chromatin interactions which have been explored by chromosome conformation capture based techniques, especially Hi-C. Based on single-cell Hi-C data, we developed a new method in constructing experimental consistent 3D intact genome structures for individual cells with a resolution of 10kb or higher. The modeled structures showed marked variations of 3D genome organization across different cells. However, chromosome loci marked by different proteins, such as CTCF and post-translationally modified histones, are consistently non-specifically aggregated in space. Interestingly, similar aggregations between active enhancers and active promoters were observed, especially for those separated by genomic regions of the scale of megabase or larger. Such long-range associations between active enhancers and promoters are strongly correlated with spatial aggregation of chromosome loci marked by different proteins. Through analyzing the 3D structures of intact genome, we proposed that coherent gene activation profiles among individual cells can be achieved by the consistent aggregation of protein marked loci instead of maintaining identical folded conformations.

biophysics↗

bioRxiv2019

A Novel Neoantigen Discovery Approach based on Chromatin High Order Conformation: Mapping the Neoantigen to 3D Genome

The high-throughput sequencing technology has yielded reliable and ultra-fast sequencing for DNA and RNA. For tumor cells of cancer patients, when combining the results of DNA and RNA sequencing, one can identify potential neoantigens that stimulate immune response of the T cells. However, when the somatic mutations are abundant, it is computationally challenging to efficiently prioritize the identified neoantigen candidates according to their ability of activating the T cell immuno-response. Numerous prioritization or prediction approaches have been proposed to address this issue but none of them considers the original DNA loci of the neoantigens from the perspective of 3D genome. Here we retrospect the DNA origins of the immune-positive and non-negative neoantigens in the context of 3D genome and discovered that 1) DNA loci of the immuno-positive neoantigens tend to cluster genome-wise. 2) DNA loci of the immuno-positive neoantigens tend to belong to active chromosomal compartment (compartment A) in some chromosomes. 3). DNA loci of the immuno-positive neoantigens tend to locate at specific regions in the 3D genome. We believe that the 3D genome information will help more precise neoantigen prioritization and discovery and eventually benefit precision and personalized medicine in cancer immunotherapy.

bioinformatics↗

bioRxiv2019

CTCF-mediated Chromatin Structures Dictate the Spatio-temporal Propagation of Replication Foci

Mammalian DNA replication is initiated at numerous replication origins, which are clustered into thousands of replication domains (RDs) across the genome. However, it remains unclear whether the replication origins within each RD are activated stochastically. To understand how replication is regulated at the sub-RD level, we directly visualized the spatio-temporal organization, morphology, and in situ epigenetic signatures of individual replication foci (RFi) across S-phase using super-resolution stochastic optical reconstruction microscopy (STORM). Importantly, we revealed a hierarchical radial pattern of RFi propagation that reverses its directionality from early to late S-phase, and is diminished upon caffeine treatment or CTCF knockdown. Together with simulation and bioinformatic analyses, our findings point to a CTCF-organized REplication Propagation (CoREP) model. The CoREP model suggests a non-random selection mechanism for replication activation mediated by CTCF at the sub-RD level, as well as the critical involvement of local chromatin environment in regulating replication in space and time.

cell biology↗

bioRxiv2018

Temporal modulation of host aerobic glycolysis determines the outcome of M. marinum infection

Macrophages are the first-line host defense where the invading Mycobacterium tuberculosis (Mtb) encounters. It has been recently reported that host aerobic glycolysis was elevated post the infection by a couple of virulent mycobacterial species. However, whether this metabolic transition is required for host defense against intracellular pathogens and the underlying mechanisms remain to be further investigated. By analyzing carbon metabolism, we found that macrophages infected by M. marinum, a surrogate mycobacterial specie to Mtb, showed a strong elevation of glycolysis. Next, three glycolysis inhibitors were examined for their ability to inhibit mycobacterial proliferation inside RAW264.7, a murine macrophage-like cell line. Among them, a glucose analog, 2-deoxyglucose (2-DG) displayed a protective effect on assisting host to resist mycobacterial infection, which was further validated in zebrafish-infection model. The phagocytosis of M. marinum was significantly decreased in macrophages pre-treated with 2-DG at concentrations of 0.5 and 1 mM, at which no inhibitory effect was posed on M. marinum growth in vitro. Moreover, 2-DG pre-treatment exerted a significant protective effect on zebrafish larvae to limit the proliferation of M. marinum, and such effect was correlated to tumor necrosis factor alpha (TNF-). On the contrary, the 2-DG treatment post infection did not restrain proliferation of M. marinum in WT zebrafish, and even accelerated bacterial replication in TNF--/- zebrafish. Together, modulation of glycolysis prior to infection boosts host immunity against M. marinum infection, indicating a potential intervention strategy to control mycobacterial infection.\n\nAuthor SummaryAs an intracellular pathogen, Mtb exploits multiple strategies to invade and hijack macrophages for its own advantages. Accordingly, recent investigations have shown that Mtb infection is accompanied with an alteration of host glucose metabolism. Macrophage and zebrafish infection models of M. marinum, facilitating our understanding towards mycobacterial pathogenesis, were applied in this study. We found that the pre-treatment of macrophages with a glucose analog, 2-DG, inhibited aerobic glycolysis and made host cells more inert to phagocytose the bud. In infected zebrafish larvae, bacterial load inside host pretreated with 2-DG remains at a significantly lower level compared to the untreated group. These findings imply that the modulation of host glycolysis regulates the fate of M. marinum infection, and indicate a promising metabolic target in TB intervention.

microbiology↗

bioRxiv2018

A giant ankyrin-B mechanism for neuro-diversity/divergence through stochastic ectopic axon projections

ANK2 is a high-confidence autism spectrum disorder (ASD) gene where affected individuals exhibit diverse symptoms with a wide range of IQ. We report a cellular mechanism resulting in stochastic brain connectivity that provides a rationale for both gain and loss of function due to ANK2 mutation. Deficiency of giant ankyrin-B (ankB), the neurospecific ANK2 mutation target, results in ectopic CNS axon tracts associated with increased axonal branching. We elucidate a mechanism limiting axon branching, whereby giant ankB is recruited by L1CAM to periodic axonal plasma membrane domains where it coordinates cortical microtubules and prevents microtubule stabilization of nascent axon branches. Heterozygous giant ankB mutant mice exhibit innate social deficits combined with normal/enhanced cognitive function. Thus, giant ankB-deficiency results in gain of aberrant structural connectivity with penetrant behavioral consequences that may contribute to both high and low-function ASD and other forms of neurodiversity/divergence.

neuroscience↗

bioRxiv2018

Atlas-CNV: a validated approach to call Single-Exon CNVs in the eMERGESeq gene panel

PurposeTo provide a validated method to confidently identify exon-containing copy number variants (CNVs), with a low false discovery rate (FDR), in targeted sequencing data from a clinical laboratory with particular focus on single-exon CNVs.\n\nMethodsDNA sequence coverage data are normalized within each sample and subsequently exonic CNVs are identified in a batch of samples (midpool), when the target log2 ratio of the sample to the batch median exceeds defined thresholds. The quality of exonic CNV calls is assessed by C-scores (Z-like scores) using thresholds derived from gold standard samples and simulation studies. We integrate an ExonQC threshold to lower FDR and compare performance with alternate software (VisCap).\n\nResultsThirteen CNVs were used as a truth set to validate Atlas-CNV and compared with VisCap. We demonstrated FDR reduction in validation, simulation and 10,926 eMERGESeq samples without sensitivity loss. Sixty-four multi-exon and 29 single-exon CNVs with high C-scores were assessed by MLPA.\n\nConclusionsAtlas-CNV is validated as a method to identify exonic CNVs in targeted sequencing data generated in the clinical laboratory. The ExonQC and C-score assignment can reduce FDR (identification of targets with high variance) and improve calling accuracy of single-exon CNVs respectively. We proposed guidelines and criteria to identify high confidence single-exon CNVs.

genomics↗

bioRxiv2018

The Expression of Inflammatory Genes in 3T3-L1 Adipocytes Exhibits a Memory to Stimulation by Macrophage Secretions

Obesity is characterized by increased output of inflammatory compounds from adipose tissue. Whilst the relative contribution of adipocytes and resident macrophages to this phenomenon is debated, there is no doubt that the secretions of each cell type can stimulate the expression of inflammatory genes in the other. We hypothesized that mechanisms must exist to prevent an escalating positive feedback loop between the two cell types, so that after an initial exposure to macrophage secretions, adipocytes would become desensitized to subsequent inflammatory stimulation.\n\nWe used microarrays to investigate the response of 3T3-L1 adipocytes to macrophage secretions (macrophage conditioned medium, MCM). MCM caused a rapid (<4 hours) and high amplitude (over 100-fold) rise in the expression of several inflammatory genes. For some genes, generally cytokines, expression returned to basal levels within 24 h following removal of the MCM, but other transcripts, notably those for acute phase proteins and extracellular matrix remodeling proteins, remained highly expressed even during the washout period.\n\nUnexpectedly, some cytokine genes (e.g., iNOS, IL-6) showed an enhanced expression to a second exposure of MCM, illustrating that the transcriptome response of 3T3-L1 adipocytes retains a memory to the first stimulus. We characterized the parameters that give rise to the memory phenomenon, finding that additional stimuli do not augment or abrogate the effect. The memory is preserved for several days after the initial exposure and it is not due to a change in sensitivity to the MCM but, rather, a change in the capacity of the signal-target system. The possible mechanisms of the memory are discussed, along with the physiological ramifications should the phenomenon be replicated in vivo.

biochemistry↗

bioRxiv2018

From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective

The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism for the formation of different chromatin structures in different cells and the sequence dependence of this process remain to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI forest and prairie genomic domains based on CGI density, which better segregates genomic elements along the genome than GC content. The genome is then divided into two sequentially, epigenetically, and transcriptionally distinct regions. These two types of megabase-sized domains spatially segregate, but to a different extent in different cell types. Overall, the forests and prairies gradually segregate from each other in development, differentiation, and senescence. The multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, thus helps define the cell identity. We propose that the phase separation of the 1D mosaic sequence in space, serving as a potential driving force, together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types and renders them distinct genomic properties. The mosaicity of the genome manifested in terms of alternative forests and prairies of a species could be related to its biological processes such as differentiation, aging and body temperature control.

biophysics↗

bioRxiv2017

Necroptosis promotes the Aging of the Male Reproductive System in Mice

Necroptosis is a form of programmed necrotic cell death in mammals that is mediated by a pair of kinases, RIP1 and RIP3, as well as the RIP3 substrate MLKL. We report here that male reproductive organs of both RIP3-and MLKL-knockout mice retain \"youthful\" morphology and function into advanced age, while those of age-matched wild type mice deteriorate. The RIP3 phosphorylation of MLKL, the activation marker of necroptosis, is detected in spermatogonial stem cells in the testes of old but not in young wild type mice. When the testes of young wild type mice are given a local necroptotic stimulus, their reproductive organs showed accelerated aging. Feeding of wild type mice with an RIP1 inhibitor prior to the normal onset of age-related changes in their reproductive organs blocked the appearance of signs of aging. Thus, necroptosis in testes promotes the aging-associated deterioration of the male reproductive system in mice.

cell biology↗

bioRxiv2016

Folding Principle of Chromosome Emerges from Mapping of Genome Features onto its 3D Structure

How chromosomes fold into 3D structures and how genome functions are affected or even controlled by their spatial organization remain challenging questions. Hi-C experiment has provided important structural insights for chromosome, and Hi-C data are used here to construct the 3D chromatin structure which are characterized by two spatially segregated chromatin compartments A and B. By mapping a plethora of genome features onto the constructed 3D chromatin model, we show vividly the close connection between genome properties and the spatial organization of chromatin. We are able to dissect the whole chromatin into two types of chromatin domains which have clearly different Hi-C contact patterns as well as different sizes of chromatin loops. The two chromatin types can be respectively regarded as the basic units of chromatin compartments A and B, and also spatially segregate from each other as the two chromatin compartments. Therefore, the chromatin loops segregate in the space according to their sizes, suggesting the excluded volume or entropic effect in chromatin compartmentalization as well as chromosome positioning. Taken together, these results provide clues to the folding principles of chromosomes, their spatial organization, and the resulted clustering of many genome features in the 3D space.

biophysics↗

bioRxiv2016

DNA Methylation Landscape Reflects the Spatial Organization of Chromatin in Different Cells

The relation between DNA methylation and chromatin structure is still largely unknown. By analyzing a large set of sequencing data, we observed a long-range power law correlation of DNA methylation with cell-class-specific scaling exponents in the range of thousands to millions of base pairs. We showed such cell-class-specific scaling exponents are caused by different patchiness of DNA methylation in different cells. By modeling the chromatin structure using Hi-C data and mapping the methylation level onto the modeled structure, we demonstrated the patchiness of DNA methylation is related to chromatin structure. The scaling exponents of the power law correlation is thus a display of the spatial organization of chromatin. Besides, the local correlation of DNA methylation is associated with nucleosome positioning and different between partially-methylated-domain and non-partially-methylated-domain, suggesting their different chromatin structures at several nucleosomes level. Our study provides a novel view of the spatial organization of chromatin structure from a perspective of DNA methylation, in which both long-range and local correlations of DNA methylation along the genome reflect the spatial organization of chromatin.

biophysics↗