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Biology subjects

Huang, F.

Publications and source records attributed to Huang, F..

At least 109 records · Page 6Linked to original sources
bioRxiv2020

The pleiotropic effects of the MNK1/2-eIF4E axis support immune suppression and metastasis in a model of postpartum breast cancer.

PurposeBreast cancer diagnosed within 10 years following childbirth is defined as postpartum breast cancer (PPBC) and is highly metastatic. Interactions between immune cells and other stromal cells within the involuting mammary gland are fundamental in facilitating an aggressive tumor phenotype. The MNK1/2-eIF4E axis promotes the translation of pro-metastatic mRNAs in tumor cells, but its role in modulating the function of non-tumor cells in the PPBC microenvironment, and in particular its activity in human PPBC, has not been explored. Experimental designWe used a combination of in vivo PPBC models and in vitro assays to study the effects of phospho-eIF4E deficiency on the pro-tumor function of select cells of the TME. Furthermore, we employed Imaging Mass Cytometry on PPBC and non-PPBC patient samples, to chart the expression of the MNK1/2-eIF4E axis components in the TME. ResultsHere, we show that phospho-eIF4E deficient (eIF4ES209A) PPBC mice are protected against lung metastasis and reveal differences in the lung immune microenvironment of the WT and eIF4ES209A mice. Moreover, we show that the expression of fibroblast-derived IL-33, an alarmin known to induce invasion, was repressed upon MNK1/2-eIF4E axis inhibition. Imaging Mass Cytometry results indicated that human PPBC contain phospho-eIF4E high-expressing tumor cells and CD8+ T cells displaying an activated dysfunctional phenotype. Finally, we block lung metastasis in PPBC mice, using combined MNK1/2 inhibition and anti-PD-1 therapy. ConclusionsThese findings implicate the involvement of the MNK1/2-eIF4E axis during PPBC metastasis and suggest a promising immunomodulatory route to enhance the efficacy of immunotherapy by blocking phospho-eIF4E. Translational relevancePostpartum breast cancer (PPBC) is highly aggressive. It is hypothesized that involution-induced changes in the postpartum breast microenvironment, which include an influx of inflammatory immune cells and activation of resident fibroblasts, facilitate the invasiveness of an existing neoplasm. We used imaging mass cytometry to do an in-depth profiling of the MNK1-eIF4E axis in the TME of a unique cohort of PPBC and non-PPBC patients. We observed patterns of phospho-eIF4E in non-tumor cells that were specific to the TME of PPBC. We also noted that the CD8+ T cells present in PPBC express an activated dysfunctional phenotype characterized by the co-expression of HLA-DR and PD-1. This study represents a first look at the expression of the MNK1-eIF4E axis in the stromal cells of metastatic breast cancer and has therapeutic implications as we show, in an animal model of PPBC, that MNK1/2 inhibition can be used to sensitize tumors to anti-PD1 immunotherapy.

cancer biology↗
bioRxiv2020

Relationship Between Neuroendocrine and Immune Gene Expression in Small Cell Lung Cancer

Small cell lung cancer (SCLC) is classified as a high-grade neuroendocrine (NE) tumor, but a subset of SCLC has been termed "variant" due to the loss of NE characteristics. In this study, we computed NE scores for patient-derived SCLC cell lines and xenografts, as well as human tumors. We aligned NE properties with transcription factor-defined molecular subtypes. Then we investigated the different immune phenotypes associated with high and low NE scores. We found repression of immune response genes as a shared feature between classic SCLC and pulmonary neuroendocrine cells of the healthy lung. With loss of NE fate, variant SCLC tumors regain cell-autonomous immune gene expression and exhibit higher tumor-immune interactions. Pan-cancer analysis revealed this NE lineage-specific immune phenotype in other cancers. Additionally, we observed MHC I re-expression in SCLC upon development of chemoresistance. These findings provide a new framework to guide design of treatment regimens in SCLC.

cancer biology↗
bioRxiv2020

The MNK1/2-eIF4E axis contributes to phenotype switching, melanoma progression, and resistance to immunotherapy.

Melanomas commonly undergo a phenotype switch, from a proliferative to an invasive state. Melanoma plasticity exhibited as phenotype switching contributes to immunotherapy resistance, however the mechanisms are not completely understood and thus therapeutically unexploited. Here, using a transgenic melanoma mouse model, we demonstrated a critical role of the MNK1/2-eIF4E axis in melanoma plasticity and resistance to immunotherapy. We showed that phospho-eIF4E deficient murine melanomas express high levels of melanocytic antigens, with similar results verified in patient melanomas. Mechanistically, we identified that phospho-eIF4E controls the translation of NGFR, a critical effector of phenotype switching. In patients with melanoma, the expression of MKNK1, the kinase for eIF4E, positively correlated with markers of immune exhaustion. Genetic ablation of phospho-eIF4E reprogrammed the immunosuppressive microenvironment, exemplified by lowered production of inflammatory factors and increased CD8+ T cell infiltrates. Blocking phospho-eIF4E, using MNK1/2 inhibitors, offers a new strategy to inhibit melanoma plasticity and improve the survival response to anti-PD-1 immunotherapy.

cancer biology↗
bioRxiv2020

An Efficient Method for Protein Crystallization

This paper has been withdrawn by bioRxiv because its content, including the author names, was fabricated and fraudulently submitted in what may have been an attempt to game citation statistics or other metrics.

biochemistry↗
bioRxiv2020

The ORF8 Protein of SARS-CoV-2 Mediates Immune Evasion through Potently Downregulating MHC-I

SARS-CoV-2 infection have caused global pandemic and claimed over 5,000,000 tolls1-4. Although the genetic sequences of their etiologic viruses are of high homology, the clinical and pathological characteristics of COVID-19 significantly differ from SARS5,6. Especially, it seems that SARS-CoV-2 undergoes vast replication in vivo without being effectively monitored by anti-viral immunity7. Here, we show that the viral protein encoded from open reading frame 8 (ORF8) of SARS-CoV-2, which shares the least homology with SARS-CoV among all the viral proteins, can directly interact with MHC-I molecules and significantly down-regulates their surface expression on various cell types. In contrast, ORF8a and ORF8b of SARS-CoV do not exert this function. In the ORF8-expressing cells, MHC-I molecules are selectively target for lysosomal degradation by an autophagy-dependent mechanism. As a result, CTLs inefficiently eliminate the ORF8-expressing cells. Our results demonstrate that ORF8 protein disrupts antigen presentation and reduces the recognition and the elimination of virus-infected cells by CTLs8. Therefore, we suggest that the inhibition of ORF8 function could be a strategy to improve the special immune surveillance and accelerate the eradication of SARS-CoV-2 in vivo.

microbiology↗
bioRxiv2020

A restriction-free method for gene reconstitution

This paper has been withdrawn by bioRxiv because its content, including the author names, was fabricated and fraudulently submitted in what may have been an attempt to game citation statistics or other metrics.

bioengineering↗
bioRxiv2020

The H-NS regulator plays a role in the stress induced by carbapenemase expression in Acinetobacter baumannii

Disruption of the histone-like nucleoid structuring protein (H-NS) was shown to affect the ability for Gram-negative bacteria to regulate genes associated with virulence, persistence, stress response, quorum sensing, biosynthesis pathways and cell adhesion. Here, we used the expression of metallo-{beta}-lactamases (MBLs) known to elicit envelope stress by the accumulation of toxic species in the periplasm to interrogate the role of H-NS in Acinetobacter baumannii, together with other stressors. Using a multidrug-resistant A. baumannii, we observed that H-NS plays a role in alleviating the stress triggered by MBL toxic precursors and counteract the effect of DNA-damaging agents, supporting its role in stress response. ImportanceCarbapenem-resistant A. baumannii (CRAB) is recognized as one of the most threatening gram-negative bacilli. H-NS is known to play a role in controlling the transcription of a variety of different genes, including those associated with stress response, persistence and virulence. In the present work, we uncovered a link between the role of H-NS in the A. baumannii stress response and its relationship with the envelope stress response and resistance to DNA-damaging agents. Overall, we posit a new role of H-NS, showing that H-NS serves to endure envelope stress that could also be a mechanism that alleviates the stress induced by MBL expression in A. baumannii. This could be an evolutionary advantage to further resist the action of carbapenems.

microbiology↗
bioRxiv2020

Efficient Method for Genomic DNA Mutagenesis in E. coli

This paper has been withdrawn by bioRxiv because its content, including the author names, was fabricated and fraudulently submitted in what may have been an attempt to game citation statistics or other metrics

bioengineering↗
bioRxiv2020

Variance lower bound on fluorescence microscopy image denoising

The signal to noise ratio of high-speed fluorescence microscopy is heavily influenced by photon counting noise and sensor noise due to the expected low photon budget. Denoising algorithms are developed to decrease these noise fluctuations in the microscopy data. One question arises: whether there exists a theoretical precision limit for the performance of a denoising algorithm. In this paper, combining Cramer-Rao Lower Bound with constraints and the low-pass-filter property of microscope systems, we develop a method providing a theoretical variance lower bound of microscopy image denoising. We show that this lower bound is influenced by photon count, readout noise, detection wavelength, effective pixel size and the numerical aperture of the microscope system. We demonstrate our development by comparing multiple state-of-the-art denoising algorithms to this bound. This theoretical bound provides a reference benchmark for microscopy denoising algorithms, and establishes a framework to incorporate additional prior knowledge into theoretical denoising performance limit calculation.

cell biology↗
bioRxiv2020

Low aflatoxin levels and flowering delay in Aspergillus flavus-resistant maize lines are correlated with increased corn earworm damage and enhanced seed fumonisin content

Preharvest mycotoxin contamination of field-grown crops is influenced not only by the host genotype, but also inoculum load, insect pressure and their confounding interactions with seasonal weather. In two field trials, we observed a preferred natural infestation of specific maize (Zea mays L.) genotypes by corn earworm (Helicoverpa zea Boddie) and investigated this unexpected interaction. These studies involved four maize lines with contrasting levels of resistance to Aspergillus flavus. The resistant lines had 7 to 14-fold greater infested ears than the susceptible lines. However, seed aflatoxin B1 levels, in mock- or A. flavus-inoculated ears were consistent with maize genotype resistance to A. flavus. Further, the corn earworm-infested ears had greater levels of fumonisin content in seeds than uninfested ears, indicating that the insect may have vectored native Fusarium verticillioides inoculum. The two maize lines with heavy infestation showed delayed flowering. The availability of young silk for egg-laying could have been a factor in the pervasive corn earworm damage of these lines. At the same time, H. zea larvae reared on AF-infused diet showed decreasing mass with increasing AF and >30% lethality at 250 ppb. In contrast, corn earworm was tolerant to fumonisin with no significant loss in mass even at 100 ppm, implicating the low seed aflatoxin content as a predominant factor for the prevalence of corn earworm infestation and the associated fumonisin contamination in A. flavus resistant lines. These results highlight the need for integrated strategies targeting mycotoxigenic fungi and their insect vectors to enhance the safety of crop commodities. IMPORTANCEAspergillus and Fusarium spp. not only cause ear rots in maize leading to crop loss, they can also contaminate the grain with carcinogenic mycotoxins. Incorporation of genetic resistance into breeding lines is an ideal solution for mycotoxin mitigation. However, the goal is fraught by a major problem. Resistance for AF or FUM accumulation is quantitative and contributed by several loci with small effects. Our work reveals that host phenology (flowering time) and insect vector-mycotoxin interactions can further confound breeding efforts. A host genotype even with demonstrable resistance can become vulnerable due to seasonal variation in flowering time or an outbreak of chewing insects. Incorporation of resistance to a single mycotoxin accumulation and not pairing it with insect resistance may not adequately ensure food safety. Diverse strategies including host-induced silencing of genes essential for fungal and insect pest colonization and broad-spectrum biocontrol systems need to be considered for robust mycotoxin mitigation.

plant biology↗
bioRxiv2020

The E. coli NudL enzyme is a Nudix hydrolase that cleaves CoA and its derivatives

The process of bacterial coenzyme A (CoA) degradation has remained unknown despite the otherwise detailed characterization of the CoA synthesis pathway over 30 years ago. Numerous enzymes capable of CoA degradation have been identified in other domains of life that belong to the Nudix superfamily of hydrolases, but the molecule responsible for this process in the model bacterial system of E. coli remains a mystery. We report here that E. coli contains two such Nudix enzymes capable of CoA degradation into 4-phosphopantetheine and 3,5-adenosine monophosphate. The E. coli enzymes NudC and NudL were cloned in various promoter-fusion constructs in order to purify them as soluble active enzymes and characterize their ability to catalyze the phosphohydrolysis of CoA. NudC, an enzyme known to hydrolyze NADH as its principal substrate, demonstrated the ability to hydrolyze CoA, among other coenzymes, at comparable rates to eukaryotic Nudix hydrolases. NudL, a previously uncharacterized enzyme, demonstrated the ability to cleave only CoA and CoA-related molecules at a rate orders of magnitude slower than its eukaryotic orthologs. NudC and NudL therefore represent a previously uncharacterized pathway of CoA degradation in the highly studied E. coli system. While the two enzymes display some substrate overlap, their respective activities imply that NudC may play a role as a general coenzyme hydrolase, while NudL specifically targets CoA. These data further suggest a role for these enzymes in the regulation of bacterial CoA-RNA.

biochemistry↗
bioRxiv2019

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g. deletion, translocation) or complex (e.g. chromothripsis, chromoplexy) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,833 tumor whole genome sequences (WGS), we introduce three complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early replicating regions and superenhancers, and are enriched in breast and ovarian cancers. Rigma comprise "chasms" of low-JCN deletions at late-replicating fragile sites in esophageal and other gastrointestinal (GI) adenocarcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold back inversions that are enriched in acral but not cutaneous melanoma and associated with a previously uncharacterized mutational process of non-APOBEC kataegis. Clustering of tumors according to genome graph-derived features identifies subgroups associated with DNA repair defects and poor prognosis.

genomics↗
bioRxiv2019

A novel antiviral lncRNA EDAL shields a T309 O-GlcNAcylation site to promote EZH2 degradation

The central nervous system (CNS) is vulnerable for viral infection, yet few host factors in the CNS are known to defend invasion by neurotropic viruses. We report here that multiple neurotropic viruses, including rabies virus (RABV), vesicular stomatitis virus (VSV), Semliki Forest virus (SFV) and herpes simplex virus 1 (HSV-1), elicit the neuronal expression of a host-encoded lncRNA EDAL. EDAL inhibits the replication of these neurotropic viruses in neuronal cells and RABV infection in mouse brains. EDAL binds to the conserved histone methyltransferase enhancer of zest homolog 2 (EZH2) and specifically causes EZH2 degradation via lysosomes, reducing the cellular H3K27me3 level. The antiviral function of EDAL resides in a 56-nt antiviral substructure through which its 18-nt helix-loop intimately contacts multiple EZH2 sites surrounding T309, a known O-GlcNAcylation site. EDAL positively regulate the transcription of Pcp4l1 encoding a 10 kDa peptide, which inhibits the replication of mutiple neurotropic viruses. Our findings proposed a model in which a neuronal lncRNA can exert an effective antiviral function via blocking a specific O-GlcNAcylation that determines EZH2 lysosomal degradation.

microbiology↗
bioRxiv2019

High-throughput sequencing analysis of bacterial diversity in raw and pasteurized goat milk

The aim of this study was to evaluate the microbial composition of both raw and pasteurized goat milk using high-throughput DNA sequencing. This analysis revealed that the dominant phylum found in the raw milk was Proteobacteria, and the dominant genus was Kluyvera; Proteobacteria and Kluyvera constituted up to 67.66% and 28.85% of the total bacteria population, respectively. The microorganisms in goat milk predominantly consist of Gram-negative bacteria. Notably, Akkermansia and Faecalibacterium were identified in goat milk for the first time. In addition, the results also indicate that some bacteria in pasteurized goat milk may exist in a viable but nonculturable (VBNC) state. This study provides a theoretical basis that may aid the community in better understanding bacterial diversity in goat milk. The results of this study will help us to improve the quality and safety of goat milk. ImportanceThe microbial diversity in goat milk and pasteurized goat milk at different refrigeration stages was described. Several bacterial species that have not previously been reported in goat milk were identified, including many VBNC bacteria. The findings provided the necessary microbial information for quality and safety of goat milk and dairy products.

microbiology↗
bioRxiv2019

Mining the human tonsillar microbiota as autoimmune modulator

Palatine tonsils are important lymphoid organs featuring constant cross-talks between the commensal microorganisms and immune system, and have been implicated as critical autoimmunity origins for immune-related diseases, including rheumatoid arthritis (RA), a common autoimmune disorder. However, there was no evidence to show link between tonsillar microbiota and RA. Here, we identified a significant dysbiosis of RA tonsillar microbiota, with loss of Streptococcus salivarius and its functional molecules salivaricins (a type of antibacterial peptides). Consistent with the niche-preference, S. salivarius and salivaricins administrated intranasally or intraorally conferred prophylactic and therapeutic efficacies against experimental arthritis. Moreover, we demonstrated, for the first time, that S. salivarius and salivaricins exerted immunosuppressive capacities via inhibiting CD4+effector T cell subsets and autoantibody production in mice and human. These results uncover a communication between tonsillar microbiota and host autoimmunity, and identify the active components from tonsillar microbes in modulating immune homeostasis.\n\nOne sentence summaryTonsillar microbiota regulate host autoimmunity via antibacterial peptides

microbiology↗
bioRxiv2019

Three dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval

Single-molecule localization microscopy is a powerful tool in visualizing organelle structures, interactions, and protein functions in biological research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. As imaging depth increases, photons emitted by fluorescent probes, the sole source of molecular positions, were scattered and aberrated, resulting in image artifacts and rapidly deteriorating resolution. We propose a method to allow constructing the in situ 3D response of single emitters directly from single-molecule dataset and therefore allow pin-pointing single-molecule locations with limit-achieving precision and uncompromised fidelity through whole cells and tissues. This advancement expands the routine applicability of super-resolution imaging from selected cellular targets near coverslips to intra- and extra-cellular targets deep inside tissues. We demonstrate this across a range of cellular-tissue architectures from mitochondrial networks, microtubules, and nuclear pores in 2D and 3D cultures, amyloid-{beta} plaques in mouse brains to developing cartilage in mouse forelimbs.

biophysics↗
bioRxiv2019

Chromosome level draft genomes of the fall armyworm, Spodoptera frugiperda (Lepidoptera: Noctuidae), an alien invasive pest in China

The fall armyworm (FAW), Spodoptera frugiperda (J.E. Smith) is a severely destructive pest native to the Americas, but has now become an alien invasive pest in China, and causes significant economic loss. Therefore, in order to make effective management strategies, it is highly essential to understand genomic architecture and its genetic background. In this study, we assembled two chromosome scale genomes of the fall armyworm, representing one male and one female individual procured from Yunnan province of China. The genome sizes were identified as 542.42 Mb with N50 of 14.16 Mb, and 530.77 Mb with N50 of 14.89 Mb for the male and female FAW, respectively. We predicted about 22,201 genes in the male genome. We found the expansion of cytochrome P450 and glutathione s-transferase gene families, which are functionally related to the intensified detoxification and pesticides tolerance. Further population analyses of corn strain (C strain) and rice strain (R strain) revealed that the Chinese fall armyworm was most likely invaded from Africa. These strain information, genome features and possible invasion source described in this study will be extremely important for making effective strategies to manage the fall armyworms.

genomics↗