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Introduction Although researchers have done intensive research on depression, its pathogenesis is still not fully explained. More and more evidence suggests that gut microbiota is closely related to the onset of depression; but its specific functional ways are not clearly identified. Objectives The purpose of our work was to find out how the gut microbiota was involved in the onset of depression, and to identify the potential ways to link the gut and brain in mice with depressive-like behaviors (DLB). Methods We used the chronic restraint stress (CRS)-induced depression model here. Gut microbiota compositions in fecal samples, lipid metabolism (in fecal, serum and hippocampus samples) and neurotransmitters in hippocampus samples were detected. Results We found that the 7 of 13 differential genera that significantly correlated with DLB belonged to phylum Firmicutes. The differential lipid metabolites in fecal samples mainly belonged to glycerophospholipids (GP) and fatty acids (FA) metabolism, and three important “metabolite type-bacterial taxa” correlated pairs were identified: “FA/GP-Firmicutes”, “FA/GP-Akkermansia”, and “FA/GP-Bifidobacterium”. The key differential lipid metabolites significantly correlated with DLB mainly belonged to FA and GP, and the DLB-related metagenomic genes were consistently enriched in GP metabolism and FA metabolism. Three significantly changed short-chain fatty acids (SCFAs) were significantly correlated with the majority of differential genera. Meanwhile, we found that the differential lipid metabolites in serum and hippocampus samples were mainly mapped into the GP metabolism, and there were four differential neurotransmitters from the tryptophan pathway in hippocampus samples. Conclusion Together, our findings could provide novel insights into the role of “microbiota-gut-brain” (MGB) axis in depression, and indicate that the gut microbiota might have a vital role in the onset of DLB by affecting the peripheral/central GP metabolism and tryptophan pathway. The “Firmicutes-SCFAs-GP metabolism-Tryptophan pathway” might be a possible way to link the gut and brain in depressed mice.

The potential toxicity of carbon quantum dots (CQDs) has received much attention because of their increasing biomedical applications. However, the impacts of CQDs on the gut–liver axis and gut microbiota of the host remain unclear. In this study, we investigated the effects of CQD chronic exposure (5 weeks) on the biodistribution, histopathology, antioxidant capacity, immune response, lipid metabolism, and gut microbiota composition in the common carp Cyprinus carpio at different concentrations (2 and 20 mg kg−1 body weight). The results demonstrated that CQDs heavily accumulated in the intestine and liver, severely damaging these organs. Superoxide dismutase and glutathione were reduced and malondialdehyde was increased in intestinal and liver tissues, and the nrf2/ho-1 signaling pathway was downregulated. In addition, CQDs activated toll-like receptor pathways to mediate inflammatory responses. Serum lipid levels were altered after CQD exposure, and srebp-1c, fas, hmgcr, and fxr expression was upregulated and cyp7a1 and cyp27a1 expression was downregulated in the intestine and liver. Interestingly, mttp and cpt-1α expression was upregulated and abca1, abcg8, and fgf19 expression was downregulated in the intestine, whereas their expression was opposite in the liver. Finally, 16S rRNA sequence analysis showed that gut microbiota diversity and richness were reduced, and the relative abundance of harmful bacteria increased and that of beneficial bacteria decreased. Bioinformatic analysis showed that the antioxidant capacity, immune response, and lipid metabolism also correlated with the relative abundance of gut microbial genera. In summary, this study provides reliable data for toxicological risk assessment of CQDs in aquatic ecosystems.

The fish pathogen Aeromonas hydrophila causes gastrointestinal tract infections and hemorrhagic septicemia and represents a widespread risk in aquaculture. This study aimed to determine whether compound probiotics could improve the intestinal barrier, immunity, and meat quality of common carp infected by A. hydrophila by feeding them compound probiotics. Carp were assigned to one of four groups: (1) control (no infection, no probiotics); (2) control + probiotic; (3) A. hydrophila infected; and (4) the A. hydrophila + probiotic group. At the beginning of the experiment, the carp were injected with either saline (0.86%) or A. hydrophila (4.87 × 107 CFU/mL). After 2 weeks of the feeding regime, results suggested that in A. hydrophila infected carp, dietary probiotics regulated the intestinal microflora as evidenced by a reduced abundance of Proteobacteria and increased amounts of Firmicutes and Fusobacteria in the intestine. In addition, dietary probiotics ameliorated both villus swelling and the decrease in villus height induced by A. hydrophila (P

Migratory birds are considered natural reservoirs of avian influenza A viruses (AIVs). To further our viral ecology knowledge and understand the subsequent risk posed by wild birds, we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River, China. We collected over 8000 samples and isolated 122 AIV strains. Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases. The results showed that the Yangtze River wintering wetlands functioned as a mixing ground, where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences; moreover, a portion of AIV gene segments were persistent inter-seasonally. Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes. In addition, we observed that viral gene segments in wintering wetlands were closely related to known North American isolates, indicating that intercontinental gene flow occurred. Notably, highly pathogenic H5 and low pathogenic H9 viruses, which usually circulate in poultry, were found to have crossed the poultry/wild bird interface, with the viruses introduced to wintering birds. Overall, this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands. Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.

Avian orthoavulavirus 13 (AOAV-13), formerly known as Avian paramyxovirus 13 (APMV-13), is found scatteredly in wild birds around the world. Although four complete genome sequences of AOAV-13 had been identified since the first discovery in Japan in 2003, the information available on the genetic variation and biological characteristics of AOAV-13 is still limited. In the present study, we isolated six AOAV-13 strains from fecal samples of wild migratory waterfowls during annual (2014-2018) viral surveillance of wild bird populations from wetland and domestic poultry of live bird markets (LBMs) in China. The phylogenetic analyses based on the HN and F genes showed that they had very close relationship and the molecular clock estimations showed a low evolutionary rate of AOAV-13. However, Bean goose/Hubei/V97-1/2015 is 1953 nt in size (ORF, 1, 776 nt), which is a unique size and longer than other reported AOAV-13 strains. Additionally, four repeats of conserved sequences "AAAAAT" was presented in the 5'-end trailer region of Swan goose/Hubei/VI49-1/2016, which is unprecedented in the AOAV-13. These findings highlight the importance of continuous monitoring the specific species of APMVs.

Males and females exhibit striking differences in the prevalence of metabolic traits including hepatic steatosis, a key driver of cardiometabolic morbidity and mortality. RNA methylation is a widespread regulatory mechanism of transcript turnover. Here, we show that presence of the RNA modification N6-methyladenosine (m6A) triages lipogenic transcripts for degradation and guards against hepatic triglyceride accumulation. In male but not female mice, this protective checkpoint stalls under lipid-rich conditions. Loss of m6A control in male livers increases hepatic triglyceride stores, leading to a more ‘feminized’ hepatic lipid composition. Crucially, liver-specific deletion of the m6A complex protein Mettl14 from male and female mice significantly diminishes sex-specific differences in steatosis. We further surmise that the m6A installing machinery is subject to transcriptional control by the sex-responsive BCL6–STAT5 axis in response to dietary conditions. These data show that m6A is essential for precise and synchronized control of lipogenic enzyme activity and provide insights into the molecular basis for the existence of sex-specific differences in hepatic lipid traits. Salisbury et al. show that hepatic lipogenic mRNA is regulated by m6A modifications in a sex-dependent and dietary-dependent manner, contributing to sex-specific differences in hepatic lipid metabolism.

The species composition of eight shrub communities were investigated in order to understand the species diversity of plant communities in buffer zone and wetland of Momianhe stream along a long-term mine waste area, Lanping county, Yunnan province, China. Dominant plant species and soil samples were collected to analysis heavy metal (Cu, Zn, Pb and Cd) accumulation characteristics. The results showed that 100% samples for Zn, Pb, Cd, and 87.5% samples for Cu in the investigated area exceeded the Yunnan geochemical background value of the heavy metals in the soil. There were 36 plants species in communities, among which Epilobium pyrricholophum, Elsholtzia argyi, Artemisia vestita, Tripogon chinensis were the dominant species. Plant species, the number of individuals, Ecological Dominance (Do), Shannon-Wiener index (H'), Simpson diversity index (Dsi) and Pielou evenness index (Epi) were affected by Cd and Cu contents of the soil and sediment. Therefore, the results indicate that Cu and Cd contents and ecological risk in the process of long-term vegetation restoration of small catchment in lead-zinc mine waste area should pay more attention.

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-2 genome from clinical specimens is limited by their low nucleic acid load and the complexity of the nucleic acid background. To address this issue, we modified and evaluated an approach by utilizing SARS-CoV-2-specific amplicon amplification and Oxford Nanopore PromethION platform. This workflow started with the throat swab of the COVID-19 patient, combined reverse transcript PCR, and multi-amplification in one-step to shorten the experiment time, then can quickly and steadily obtain high-quality SARS-CoV-2 genome within 24 h. A comprehensive evaluation of the method was conducted in 42 samples: the sequencing quality of the method was correlated well with the viral load of the samples; high-quality SARS-CoV-2 genome could be obtained stably in the samples with Ct value up to 39.14; data yielding for different Ct values were assessed and the recommended sequencing time was 8 h for samples with Ct value of less than 20; variation analysis indicated that the method can detect the existing and emerging genomic mutations as well; Illumina sequencing verified that ultra-deep sequencing can greatly improve the single read error rate of Nanopore sequencing, making it as low as 0.4/10,000 bp. In summary, high-quality SARS-CoV-2 genome can be acquired by utilizing the amplicon amplification and it is an effective method in accelerating the acquisition of genetic resources and tracking the genome diversity of SARS-CoV-2. Supplementary Information The online version contains supplementary material available at 10.1007/s12250-021-00378-8.

The avian influenza A (H7N9) virus is a zoonotic virus that is closely associated with live poultry markets. It has caused infections in humans in China since 2013. Five waves of the H7N9 influenza epidemic occurred in China between March 2013 and September 2017. H7N9 with low-pathogenicity dominated in the first four waves, whereas highly pathogenic H7N9 influenza emerged in poultry and spread to humans during the fifth wave, causing wide concern. Specialists and officials from China and other countries responded quickly, controlled the epidemic well thus far, and characterized the virus by using new technologies and surveillance tools that were made possible by their preparedness efforts. Here, we review the characteristics of the H7N9 viruses that were identified while controlling the spread of the disease. It was summarized and discussed from the perspectives of molecular epidemiology, clinical features, virulence and pathogenesis, receptor binding, T-cell responses, monoclonal antibody development, vaccine development, and disease burden. These data provide tools for minimizing the future threat of H7N9 and other emerging and re-emerging viruses, such as SARS-CoV-2.

RNA-binding proteins (RBPs) are critical regulators of transcription and translation that are often dysregulated in cancer. Although RBPs are increasingly recognized as being important for normal hematopoiesis and for hematologic malignancies as oncogenes or tumor suppressors, RBPs that are essential for the maintenance and survival of leukemia remain elusive. Here we show that YBX1 is specifically required for maintaining myeloid leukemia cell survival in an N6-methyladenosine (m6A)-dependent manner. We found that expression of YBX1 is significantly upregulated in myeloid leukemia cells, and deletion of YBX1 dramatically induces apoptosis and promotes differentiation coupled with reduced proliferation and impaired leukemic capacity of primary human and mouse acute myeloid leukemia cells in vitro and in vivo. Loss of YBX1 has no obvious effect on normal hematopoiesis. Mechanistically, YBX1 interacts with insulin-like growth factor 2 messenger RNA (mRNA)-binding proteins (IGF2BPs) and stabilizes m6A-tagged RNA. Moreover, YBX1 deficiency dysregulates the expression of apoptosis-related genes and promotes mRNA decay of MYC and BCL2 in an m6A-dependent manner, which contributes to the defective survival that results from deletion of YBX1. Thus, our findings have uncovered a selective and critical role of YBX1 in maintaining myeloid leukemia survival, which might provide a rationale for the therapeutic targeting of YBX1 in myeloid leukemia.

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi-omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets. Methods: We have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers. Results: MLL-r cells feature an extensive remodeling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodeling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodeling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology. Conclusions: Apart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.

Therapeutic interference of the programmed cell death protein 1(PD-1)/immunosuppressive programmed cell death ligand 1 (PD-L1) signaling pathway by monoclonal antibodies has achieved spectacular success for treating various tumors. However, the development of small molecule inhibitors of PD-1/PD-L1 has lagged far behind due to the challenge of targeting the highly hydrophobic and relatively flat binding interface, despite the benefits small molecule can bring over therapeutic antibodies. This technical challenge provokes the adoption of different strategies in searching for small, medium-sized, and large molecule modulators (e.g., degraders, downregulators, and covalent inhibitors) of the PD-1/PD-L1 protein-protein interaction. In this review article, we discuss latest advances in the development of PD-L1 modulators, with a focus on degraders, downregulators, and covalent inhibitors.

We have surveyed avian influenza virus (AIV) genomes from live poultry markets within China since 2014. Here we present a total of 16,091 samples that were collected from May 2016 to February 2019 in 23 provinces and municipalities in China. We identify 2048 AIV-positive samples and perform next generation sequencing. AIV-positive rates (12.73%) from samples had decreased substantially since 2016, compared to that during 2014–2016 (26.90%). Additionally, H9N2 has replaced H5N6 and H7N9 as the dominant AIV subtype in both chickens and ducks. Notably, novel reassortants and variants continually emerged and disseminated in avian populations, including H7N3, H9N9, H9N6 and H5N6 variants. Importantly, almost all of the H9 AIVs and many H7N9 and H6N2 strains prefer human-type receptors, posing an increased risk for human infections. In summary, our nation-wide surveillance highlights substantial changes in the circulation of AIVs since 2016, which greatly impacts the prevention and control of AIVs in China and worldwide., In this study, the authors present a genomic surveillance of avian influenza genomes sampled from live poultry markets in China. They report that a number of variants have emerged since 2016 that pose an increased risk to humans. They highlight the importance of continuous genome surveillance of circulating influenza strains.

It has been reported that allergen dosage can impact the differentiation of dendritic cells (DCs)-mediated T cells. However, the mechanisms of such dose-dependent differentiation are poorly understood. In this study, bone marrow-derived immature DCs stimulated with Ovalbumin (OVA) of different concentrations (0, 10, 100, 1000, 10000μg/ml, respectively). DCs were then co-cultured with naive T cells. RNA-sequencing detection and DNA methylation of DCs were performed. We show that when DCs were stimulated with low-dose (10μg/ml), 77 genes were up-regulated and 87 genes down-regulated. Most activated genes were related to ribosome synthesis and ion channel inhibition. At the medium-dose (100μg/ml), 339 genes were up-regulated and 168 genes down-regulated. Most activated genes involved cytokine synthesis and regulation of immune responses. At high-dose (10000μg/ml), 2497 genes were up-regulated and 1156 genes down-regulated. TNF signaling pathway, NF-kappa B signaling pathway, antigen processing and presentation signaling pathway were mostly up-regulated. The related co-stimulators, co-inhibitory molecules, inhibitory cytokines, negative regulating enzymes were highly expressed. The monocarbate, coenzyme, fatty acid, glucolipid, starch, sucrose and other metabolism-related signaling pathways were down-regulated. The profiles of DNA methylation and RNA synthesis of DCs varied with different doses of OVA, which serves to induce T cells to differentiate in various directions.

N6-methyladenosine (m6A) is the most prevalent internal RNA modification in mammals that regulates homeostasis and function of modified RNA transcripts. Here, we aimed to investigate the role of YTH m6A RNA-binding protein 1 (YTHDF1), a key regulator of m6A methylation in gastric cancer tumorigenesis. Multiple bioinformatic analyses of different human cancer databases identified key m6A-associated genetic mutations that regulated gastric tumorigenesis. YTHDF1 was mutated in about 7% of patients with gastric cancer, and high expression of YTHDF1 was associated with more aggressive tumor progression and poor overall survival. Inhibition of YTHDF1 attenuated gastric cancer cell proliferation and tumorigenesis in vitro and in vivo. Mechanistically, YTHDF1 promoted the translation of a key Wnt receptor frizzled7 (FZD7) in an m6A-dependent manner, and mutated YTHDF1 enhanced expression of FZD7, leading to hyperactivation of the Wnt/β-catenin pathway and promotion of gastric carcinogenesis. Our results demonstrate the oncogenic role of YTHDF1 and its m6A-mediated regulation of Wnt/β-catenin signaling in gastric cancer, providing a novel approach of targeting such epigenetic regulators in this disease. Significance: This study provides a rationale for controlling translation of key oncogenic drivers in cancer by manipulating epigenetic regulators, representing a novel and efficient strategy for anticancer treatment.

Aim: To comprehensively understand microbiota-regulated lincRNA–miRNA–mRNA networks in psychiatric disorders. Materials & methods: Integrated analyses of lincRNAs, mRNAs and miRNAs, obtained by microarray analysis of hippocampus from specific pathogen-free, germ-free and colonized germ-free mice, were performed. Results: Expression of 139 mRNAs, seven miRNAs and one lincRNA was restored following colonization. The restored transcripts were mainly involved in CREB and Ras/MAPK signaling pathways. RNA transcription and post-transcriptional regulation were the primary perturbed functions. Finally, 12 lincRNAs, six miRNAs and 47 mRNAs were included in a lincRNA–miRNA–mRNA network, and lincRNA0926-miR-190a-5p-Celf4 interactions may play a pivotal role in this regulatory network. Conclusion: This study provides clues for understanding the molecular basis of gut microbiota–brain interactions in depressive- and anxiety-like behaviors.

The cadmium (Cd) pollution of farmland soil is serious in the world. The present study investigated the effects of intercropping Vicia faba and the hyperaccumulator Sonchus asper on the Cd accumulation and root responses (morphology and secreted organic acids) of plants grown on soil from a mining area in Yunnan Province, China, under different Cd stress levels (0, 50, 100, and 200 mg kg–1). Intercropping increased the biomass of both S. asper and V. faba, as well as the Cd accumulation and Cd transfer coefficient from roots to shoots of S. asper, but decreased those of V. faba in the 200 mg kg–1 Cd treatment. The Cd concentrations in roots, shoots, and grains from intercropped V. faba plants were positively correlated (P

Snapdragon (Antirrhinum majus L.) is a popular ornamental and model plant species, and the recently released reference genome could greatly boost its utilization in fundamental research. However, the lack of an efficient genetic transformation system is still a major limiting factor for its full application in genetic and molecular studies. In this study, a simple method for quick regeneration and efficient Agrobacterium-mediated transformation of snapdragon was developed. Cotyledon petiole and hypocotyl explants derived from two-week-old seedlings were cultured on MS media supplemented with 2 mg/L zeatin (ZT), 0.2 mg/L 1-naphthaleneacetic acid (NAA), and 2 mg/L AgNO3, and adventitious shoots were regenerated through organogenesis with an average regeneration of 48.00% and 41.33%, respectively. By contrast, the regeneration frequency was only 22.67% for cotyledon petiole and 25.67% for hypocotyl explants in the absence of AgNO3. Moreover, the application of AgNO3 promoted indirect shoot organogenesis, while direct shoot organogenesis occurred in the absence of AgNO3 from both hypocotyl or cotyledon petiole explants. Agrobacterium-mediated genetic transformation systems were developed with this high-efficient regeneration system. The transformation efficiency has been improved from 0 to 1% through the direct shoot organogenesis to 3 to 4% via the indirect shoot organogenesis. This efficient regeneration and genetic transformation method could be important for future use of snapdragon as a model plant to address some fundamental questions which are hard to be solved by using other model plant species, and to accelerate the breeding process through CRISPR/Cas9 genome editing. Genetic transformation of snapdragon was significantly improved by applying AgNO3 to induce indirect organogenesis, which will substantially facilitate its fundamental research as well as molecular breeding.

Novel small molecule compounds based on various scaffolds including chalcone, flavonoid, and resorcinol dibenzyl ether were designed and tested for their inhibitory activity against the Programmed Cell Death-1/Programmed Cell Death-Ligand 1 (PD-1/PD-L1) pathway. Among them, compound

N6-Methyladenosine (m6A) is the most abundant modification of mammalian mRNAs. RNA methylation fine tunes RNA stability and translation, altering cell fate. The fat mass- and obesity-associated protein (FTO) is an m6A demethylase with oncogenic properties in leukemia. Here, we show that FTO expression is suppressed in ovarian tumors and cancer stem cells (CSC). FTO inhibited the self-renewal of ovarian CSC and suppressed tumorigenesis in vivo, both of which required FTO demethylase activity. Integrative RNA sequencing and m6A mapping analysis revealed significant transcriptomic changes associated with FTO overexpression and m6A loss involving stem cell signaling, RNA transcription, and mRNA splicing pathways. By reducing m6A levels at the 3′UTR and the mRNA stability of two phosphodiesterase genes (PDE1C and PDE4B), FTO augmented second messenger 3′, 5′-cyclic adenosine monophosphate (cAMP) signaling and suppressed stemness features of ovarian cancer cells. Our results reveal a previously unappreciated tumor suppressor function of FTO in ovarian CSC mediated through inhibition of cAMP signaling. Significance: A new tumor suppressor function of the RNA demethylase FTO implicates m6A RNA modifications in the regulation of cyclic AMP signaling involved in stemness and tumor initiation.

The absence of alloantibodies is a feature of transplantation tolerance. Although the lack of T cell help has been evoked to explain this absence, herein we provide evidence for B cell-intrinsic tolerance mechanisms. Using a murine model of heart tolerance, we showed that alloreactive B cells were not deleted but rapidly lost their ability to differentiate into germinal center B cells and secrete donor-specific antibodies. We inferred that tolerant alloreactive B cells retained their ability to sense alloantigen because they continued to drive T cell maturation into CXCR5+PD-1+ T follicular helper cells. Unexpectedly, dysfunctional alloreactive B cells acquired the ability to inhibit antibody production by new naive B cells in an antigen-specific manner. Thus, tolerant alloreactive B cells contribute to transplantation tolerance by foregoing germinal center responses while retaining their ability to function as antigen-presenting cells and by actively suppressing de novo alloreactive B cell responses.

Over 170 chemical modifications have been identified in protein-coding and noncoding RNAs and shown to exhibit broad impacts on gene expression. Dysregulation of RNA modifications caused by aberrant expression of or mutations in RNA modifiers aberrantly reprograms the epitranscriptome and skews global gene expression, which in turn leads to tumorigenesis and drug resistance. Here we review current knowledge of the functions and underlying mechanisms of aberrant RNA modifications in human cancers, particularly several common RNA modifications, including N6-methyladenosine (m6A), A-to-I editing, pseudouridine (ψ), 5-methylcytosine (m5C), 5-hydroxymethylcytosine (hm5C), N1-methyladenosine (m1A), and N4-acetylcytidine (ac4C), providing insights into therapeutic implications of targeting RNA modifications and the associated machineries for cancer therapy.

Late blight is a potentially devastating disease of potato. Dimethomorph has been widely used for preventing and controlling this disease. However, there is little information on dimethomorph resid...

Background Depression is a highly prevalent mental illness that severely impacts the quality of life of affected individuals. Our recent studies demonstrated that diterpene ginkgolides (DG) have antidepressant effects in mice. However, the underlying molecular mechanisms remained much unclear. Methods In this study, we assessed the antidepressant effects of chronic DG therapy in rats by evaluating depression-related behaviors, we also examined potential side effects using biochemical indicators. Furthermore, we performed an in-depth molecular network analysis of gene-protein-metabolite interactions on the basis of metabolomics. Results Chronic DG treatment significantly ameliorated the depressive-like behavioral phenotype. Furthermore, the neurotrophin signaling-related NT3-TrkA and Ras-MAPK pathways may play an important role in the antidepressant effect of DG in the hippocampus. Conclusion These findings provide novel insight into the mechanisms underlying the antidepressant action of DG, and should help advance the development of new therapeutic strategies for depression.

N6-Methyladenosine (m6A) RNA modification has emerged in recent years as a new layer of regulatory mechanism controlling gene expression in eukaryotes. As a reversible epigenetic modification found not only in messenger RNAs but also in non-coding RNAs, m6A affects the fate of the modified RNA molecules and plays important roles in almost all vital bioprocesses, including cancer development. Here we review the up-to-date knowledge of the pathological roles and underlying molecular mechanism of m6A modifications (in both coding and non-coding RNAs) in cancer pathogenesis and drug response/resistance, and discuss the therapeutic potential of targeting m6A regulators for cancer therapy.

Epigenetic mRNA modification is an evolving field. N6-methyladenosine (m6A) is the most frequent internal transcriptional modification in eukaryotic messenger RNAs (mRNAs). This review will discuss the functions of the m6A mRNA machinery, including its "writers" that are components of the methyltransferase complex, its "readers" and its "erasers" (specifically FTO and ALKBH5) in cancer. The writers deposit the m6A and include METTL3, METTL14, WTAP, VIRMA, and RBM15. M6A methylation is removed by the m6A demethylases (FTO and ALKBH5). Lastly, the most diverse members are the readers that can contribute to mRNA splicing, stability, translation, and nuclear export. Many of these functions continue to be elucidated. The dysregulation of this machinery in various malignancies and the associated impact on tumorigenesis and drug response will be discussed herein with a focus on solid tumors. It is clear that, by contributing to either mRNA stability or translation, there are downstream targets that are impacted, contributing to cancer progression and the self-renewal ability of cancer stem cells.

MicroRNAs (miRNAs) and N6-methyladenosine (m6A) are known to serve as key regulators of acute myeloid leukemia (AML). Our previous microarray analysis indicated miR-550-1 was significantly downregulated in AML. The specific biological roles of miR-550-1 and its indirect interactions and regulation of m6A in AML, however, remain poorly understood. At the present study, we found that miR-550-1 was significantly down-regulated in primary AML samples from human patients, likely owing to hypermethylation of the associated CpG islands. When miR-550-1 expression was induced, it impaired AML cell proliferation both in vitro and in vivo, thus suppressing tumor development. When ectopically expressed, miR-550-1 drove the G0/1 cell cycle phase arrest, differentiation, and apoptotic death of affected cells. We confirmed mechanistically that WW-domain containing transcription regulator-1 (WWTR1) gene was a downstream target of miR-550-1. Moreover, we also identified Wilms tumor 1-associated protein (WTAP), a vital component of the m6A methyltransferase complex, as a target of miR-550-1. These data indicated that miR-550-1 might mediate a decrease in m6A levels via targeting WTAP, which led to a further reduction in WWTR1 stability. Using gain- and loss-of-function approaches, we were able to determine that miR-550-1 disrupted the proliferation and tumorigenesis of AML cells at least in part via the direct targeting of WWTR1. Taken together, our results provide direct evidence that miR-550-1 acts as a tumor suppressor in the context of AML pathogenesis, suggesting that efforts to bolster miR-550-1 expression in AML patients may thus be a viable clinical strategy to improve patient outcomes.

N6-Methyladenosine (m6A) is the most prevalent internal RNA modification in mRNA, and has been found to be highly conserved and hard-coded in mammals and other eukaryotic species. The importance of m6A for gene expression regulation and cell fate decisions has been well acknowledged in the past few years. However, it was only until recently that the mechanisms underlying the biogenesis and specificity of m6A modification in cells were uncovered. We review up-to-date knowledge on the biogenesis of the RNA m6A modification, including the cis-regulatory elements and trans-acting factors that determine general de novo m6A deposition and modulate cell type-specific m6A patterns, and we discuss the biological significance of such regulation.

To assess root metabolic differences of maize varieties in their response to lead (Pb) stress, the lead-tolerant variety Huidan No. 4 and the lead-sensitive variety Ludan No. 8 were tested under Pb-free and Pb-stressed conditions. Changes in metabolites were measured using ultra-performance liquid chromatography–mass spectrometry. Pb stress changed the levels of the amino acids proline, glutamine, lysine, and arginine in both varieties, whereas glutamate and phenylalanine levels changed only in Huidan No. 4. Pb stress altered cystine, valine, methionine, and tryptophan levels only in Ludan No. 8. Therefore, the synthesis and decomposition of amino acids may affect the response of maize to Pb stress. The degree of change in differential metabolites for Huidan No. 4 was greater than that for Ludan No. 8. In cell wall subcellular components, increases in superoxide dismutase (SOD), peroxidases (PODs), and Pb concentrations were greater in Huidan No. 4 than in Ludan No. 8. Therefore, the greater Pb tolerance of Huidan No. 4 could be due to better sequestration of Pb in cell walls and more effective removal of reactive oxygen species (ROS) from the plant. The levels of certain metabolites only increased in Ludan No. 8, indicating that Pb-sensitive varieties may use different metabolic pathways to cope with Pb stress. Both varieties showed increased levels of some metabolites related to antioxidant protection and osmotic regulation. This study provides an understanding of maize Pb tolerance mechanisms and a basis for further development of tools for use in maize breeding.

Cobalt is a transition metal located in the fourth row of the periodic table and is a neighbor of iron and nickel. It has been considered an essential element for prokaryotes, human beings, and other mammals, but its essentiality for plants remains obscure. In this article, we proposed that cobalt (Co) is a potentially essential micronutrient of plants. Co is essential for the growth of many lower plants, such as marine algal species including diatoms, chrysophytes, and dinoflagellates, as well as for higher plants in the familyFabaceaeorLeguminosae. The essentiality to leguminous plants is attributed to its role in nitrogen (N) fixation by symbiotic microbes, primarily rhizobia. Co is an integral component of cobalamin or vitamin B12, which is required by several enzymes involved in N2fixation. In addition to symbiosis, a group of N2fixing bacteria known as diazotrophs is able to situate in plant tissue as endophytes or closely associated with roots of plants including economically important crops, such as barley, corn, rice, sugarcane, and wheat. Their action in N2fixation provides crops with the macronutrient of N. Co is a component of several enzymes and proteins, participating in plant metabolism. Plants may exhibit Co deficiency if there is a severe limitation in Co supply. Conversely, Co is toxic to plants at higher concentrations. High levels of Co result in pale-colored leaves, discolored veins, and the loss of leaves and can also cause iron deficiency in plants. It is anticipated that with the advance of omics, Co as a constitute of enzymes and proteins and its specific role in plant metabolism will be exclusively revealed. The confirmation of Co as an essential micronutrient will enrich our understanding of plant mineral nutrition and improve our practice in crop production.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the most important emerging pathogen worldwide, but its early transcriptional dynamics and host immune response remain unclear. Herein, the expression profiles of viral interactions with different types of hosts were comprehensively dissected to shed light on the early infection strategy of SARS-CoV-2 and the host immune response against infection. SARS-CoV-2 was found to exhibit a two-stage transcriptional strategy within the first 24 h of infection, comprising a lag phase that ends with the virus being paused and a log phase that starts when the viral load increases rapidly. Interestingly, the host innate immune response was found not to be activated (latent period) until the virus entered the log stage. Noteworthy, when intracellular immunity is suppressed, SARS-CoV-2 shows a correlation with dysregulation of metal ion homeostasis. Herein, the inhibitory activity of copper ions against SARS-CoV-2 was further validated in in vitro experiments. Coronavirus disease 2019-related genes (including CD38, PTX3, and TCN1) were also identified, which may serve as candidate host-restricted factors for interventional therapy. Collectively, these results confirm that the two-stage strategy of SARS-CoV-2 effectively aids its survival in early infection by regulating the host intracellular immunity, highlighting the key role of interferon in viral infection and potential therapeutic candidates for further investigations on antiviral strategies.

Container crop production has become increasingly popular over the last 50 years. A major component of container or potting media is peat. Peatlands are a natural carbon sink, and peat is a nonrenewable natural resource. Peat harvesting has become an important environmental issue. There is a growing effort to explore alternative organic materials to completely or partially replace peat as a medium component. Biochar is a carbon-rich product that has gained increasing interest as a component of growing media. In the present study, biochar was produced from rice straw. Peat/perlite/biochar (PPB, 40/30/30 v/v) and peat/perlite/biochar/vermicompost (PPBC, 30/30/35/5 v/v) were evaluated relative to a basal or control medium of peat/perlite (PP, 70:30 v/v). Alpinia (Alpinia zerumbet ‘Variegata Dwarf’) was used as a test plant. Amending biochar and biochar–compost mix increased the pH of the growing media. Hydrophysical properties including container capacity, bulk density, air space and total porosity were all within or near the standard ranges for soilless growing media. Chlorophyll a and b contents of A. zerumbet plants grown in PPB medium were reduced by more than 20% and 28%, respectively, compared to those grown in PP or PPBC media. The net photosynthetic rate of PPB-grown plants was more than 28% lower than those grown in PP and PPBC media. As a result, shoot and root dry weights of plants produced in PPB medium were more than 42% and 22% less, respectively, than those grown in PP and PPBC media. Although visual quality of PPB-grown plants was lower, they still exhibited marketable quality, which was largely due to the fact that their side shoots, leaf numbers, leaf areas, leaf thickness, and shoot diameters were comparable to those produced in PP and PPBC media. The present study showed that in a peat/perlite basal medium, substitution of peat by biochar derived from rice straw at 30% affected the growth of A. zerumbet plants, mainly in dry matter accumulation, but the plants were still marketable. On the other hand, plants grown in the same basal medium with peat replaced by the biochar at 35% plus an amendment of compost at 5% were comparable to those grown in the control medium. As the value of ornamental plants depends on their aesthetic appearance, a potting medium comprised of peat/perlite/biochar/vermicompost at 30/30/35/5 by volume is recommended for the production of A. zerumbet plants. The substitution of peat at 35% suggests that peat use can be reduced in the formulation of potting media, thus contributing to the conservation of peatlands.

Insulin receptor substrate-1 (IRS-1) is reported to play a critical role in the development, progression, invasion and metastasis of several types of tumors and is abnormally expressed in nasopharyngeal carcinoma (NPC). Although IRS-1 is predicted to be targeted by microRNA (miR)-144, the biological roles and potential mechanisms of miR-144 in NPC remain unclear. In the present study, the expression levels of miR-144 and IRS-1 in several NPC cell lines were first examined, and found that they were negatively correlated. Following the introduction of the miR-144 mimic, IRS-1 was downregulated at the protein level without affecting the mRNA level. The Cell Counting Kit-8 assay showed that the miR-144 mimic and siRNA targeting IRS-1 mRNA significantly decreased cell proliferation by arresting the cell cycle at the G1/G0 phase. The malignant behaviours of NPC cell lines, including migration, invasion and tumour formation in soft agar, were then analyzed after regulating miR-144 levels; as expected, the results showed that both the miR-144 mimic and siIRS-1 decreased these malignant behaviours. Furthermore, the downregulation of IRS-1 by miR-144 decreased the expression level of dishevelled 2 (Dvl2) protein without affecting its mRNA level, and Dvl2 overexpression abolished the inhibitory effect of the miR-144 mimic in NPC, indicating that miR-144 potentially regulates NPC by indirectly regulating Dvl2. Taken together, the present study results suggest that miR-144 acts as a tumour suppressor in NPC cell lines by regulating IRS-1 and Dvl2, which indicates that it is a potential therapeutic target for NPC treatment.

Protein-coding and noncoding RNAs can be decorated with a wealth of chemical modifications, and such modifications coordinately orchestrate gene expression during normal hematopoietic differentiation and development. Aberrant expression and/or dysfunction of the relevant RNA modification modulators/regulators (“writers,” “erasers,” and “readers”) drive the initiation and progression of hematopoietic malignancies; targeting these dysregulated modulators holds potent therapeutic potential for the treatment of hematopoietic malignancies. In this review, we summarize current progress in the understanding of the biological functions and underlying mechanisms of RNA modifications in normal and malignant hematopoiesis, with a focus on the N6-methyladenosine modification, as well as discuss the therapeutic potential of targeting RNA modifications for the treatment of hematopoietic malignancies, especially acute myeloid leukemia.

Shunjie Bai,1,* Jing Xie,2,* Huili Bai,3 Tian Tian,4 Tao Zou,5,6 Jian-Jun Chen7 1Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 2Department of Endocrinology, the Fourth People’s Hospital of Chongqing, Chongqing University Central Hospital, Chongqing, People’s Republic of China; 3The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People’s Republic of China; 4Department of Neurology, the Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People’s Republic of China; 5Department of Psychiatry, the Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People’s Republic of China; 6Shanghai Key Laboratory of Forensic Medicine, Academy of Forensic Science, Shanghai, People’s Republic of China; 7Institute of Life Sciences, Chongqing Medical University, Chongqing, People’s Republic of China*These authors contributed equally to this workCorrespondence: Jian-Jun ChenInstitute of Life Sciences, Chongqing Medical University, 1 Yixueyuan Road, Yuzhong District, Chongqing, 400016, People’s Republic of ChinaEmail chenjianjun@cqmu.edu.cnTao ZouDepartment of Psychiatry, The Affiliated Hospital of Guizhou Medical University, Yunyan District, Guiyang, Guizhou Province, 550004, People’s Republic of ChinaEmail zoutaozou@tom.comBackground: Although many works have been conducted to explore the biomarkers for diagnosing major depressive disorder (MDD), the widely accepted biomarkers are still not identified. Thus, the combined application of serum metabolomics and fecal microbial communities was used to identify gut microbiota-derived inflammation-related serum metabolites as potential biomarkers for MDD.Methods: MDD patients and healthy controls (HCs) were included in this study. Both serum samples and fecal samples were collected. The liquid chromatography mass spectrometry (LC-MS) was used to detect the metabolites in serum samples, and the 16S rRNA gene sequencing was used to analyze the gut microbiota compositions in fecal samples.Results: Totally, 60 MDD patients and 60 HCs were recruited. The 24 differential serum metabolites were identified, and 10 of these were inflammation-related metabolites. Three significantly affected inflammation-related pathways were identified using differential metabolites. The 17 differential genera were identified, and 14 of these genera belonged to phyla Firmicutes. Four significantly affected inflammation-related pathways were identified using differential genera. Five inflammation-related metabolites (LysoPC(16:0), deoxycholic acid, docosahexaenoic acid, taurocholic acid and LysoPC(20:0)) were identified as potential biomarkers. These potential biomarkers had significant correlations with genera belonged to phyla Firmicutes. The panel consisting of these biomarkers could effectively distinguish MDD patients from HCs with an area under the curve (AUC) of 0.95 in training set and 0.92 in testing set.Conclusion: These findings suggested that the disturbance of phyla Firmicutes might be involved in the onset of depression by regulating host’s inflammatory response, and these potential biomarkers could be useful for future investigating the objective methods for diagnosing MDD.Keywords: major depressive disorder, gut microbiota, biomarkers, inflammation, metabolite

Alpinia zerumbet (Zingiberaceae) is a unique ornamental and medicinal plant primarily used in food ingredients and traditional medicine. While organic amendments such as biochar (BC) and compost (Co) have been demonstrated to improve plant productivity, no studies have examined their effects on the growth, physiology, and secondary metabolites of A. zerumbet. This study evaluated the impact of the amendment of BC, Co, or a biochar and compost mixture (BC+Co) on modifying and improving the growth, photosynthesis, antioxidant status, and secondary metabolism of A. zerumbet grown on sandy loam soil. The morpho-physiological and biochemical investigation revealed variation in the response of A. zerumbet to organic amendments. The amendment of BC and BC+Co significantly increased net photosynthetic rates of plants by more than 28%, chlorophyll a and b contents by 92 and 78%, respectively, and carboxylation efficiency by 50% compared with those grown in the sandy loam soil without amendment. Furthermore, the amendment significantly decreased plant oxidative stress, measured as leaf free proline and glycine betaine. Enzymatic antioxidant activity, total phenols, and flavonoids also varied in their response to the organic amendments. In conclusion, this study shows that BC and/or Co amendments are an efficient and sustainable method for improving the metabolite contents and reducing oxidative stress in A. zerumbet.

‘Liuyuezaoyou’ is an early-ripening cultivar selected from a bud mutation of Citrus grandis Osbeck ‘Guanximiyou’. They were designated here as MT and WT, respectively. The fruit of MT matures about 45 days earlier than WT, which was accompanied by significant changes in key phytohormones, sugar compounds and organic acids. Recent studies have showed that microRNAs (miRNAs) play an important role in regulation of fruit ripening process. The aim of this study was to compare MT fruits with WT ones to uncover if miRNAs were implicated in the ripening of C. grandis. Fruits of both WT and MT at four developmental stages were analyzed using high-throughput sequencing and RT-PCR. Several independent miRNA libraries were constructed and sequenced. A total of 747 known miRNAs were identified and 99 novel miRNAs were predicted across all libraries. The novel miRNAs were found to have hairpin structures and possess star sequences. These results showed that transcriptome and miRNAs are substantially involved in a complex and comprehensive network in regulation of fruit ripening of this species. Further analysis of the network model revealed intricate interactions of miRNAs with mRNAs during the fleshy fruit ripening process. Several identified miRNAs have potential targets. These include auxin-responsive protein IAA9, sucrose synthase 3, V-type proton ATPase, NCED1 (ABA biosynthesis) and PL1/5 (pectate lyase genes), as well as NAC100 putative coordinated regulation networks, whose interactions with respective miRNAs may contribute significantly to fruit ripening of C. grandis.

This study aimed to identify the disease-causing gene of three Chinese families with glaucoma. Whole exome sequencing was performed on the probands and detected three different variants (c.405C>A (p.Cys135Ter), c.851G>T (p.Ser284Ile), and c.392C>T (p.Ser131Leu)) in FOXC1 as a causative gene of glaucoma, and Sanger sequencing was performed for verification and cosegregation analysis. Three in silico tools all predicted these two missense variants to be probably disease-causing. Western blot analysis, immunofluorescence, and dual-luciferase assay were further used to evaluate the effect of FOXC1 missense variants, and demonstrated that the two variants resulted in decreased transactivation activity of FOXC1 although the variants had no effect on the protein amount and the nucleus subcellar localization of FOXC1 compared with the wild type, which implies that both of two variants may be probably pathogenic. In this study, we reported two novel FOXC1 variants as well as a reported variant and the phenotypes associated to these variants, which expands the spectrum and relevant phenotypes of FOXC1 variants. Additionally, the functional analysis of FOXC1 variants provides further insight into the possible pathogenesis of anterior segment anomaly related to FOXC1.

Mutant isocitrate dehydrogenase (IDH) 1 and 2 play a pathogenic role in cancers, including acute myeloid leukemia (AML), by producing oncometabolite 2-hydroxyglutarate (2-HG). We recently reported that tyrosine phosphorylation activates IDH1 R132H mutant in AML cells. Here, we show that mutant IDH2 (mIDH2) R140Q commonly has K413 acetylation, which negatively regulates mIDH2 activity in human AML cells by attenuating dimerization and blocking binding of substrate (α-ketoglutarate) and cofactor (NADPH). Mechanistically, K413 acetylation of mitochondrial mIDH2 is achieved through a series of hierarchical phosphorylation events mediated by tyrosine kinase FLT3, which phosphorylates mIDH2 to recruit upstream mitochondrial acetyltransferase ACAT1 and simultaneously activates ACAT1 and inhibits upstream mitochondrial deacetylase SIRT3 through tyrosine phosphorylation. Moreover, we found that the intrinsic enzyme activity of mIDH2 is much higher than mIDH1, thus the inhibitory K413 acetylation optimizes leukemogenic ability of mIDH2 in AML cells by both producing sufficient 2-HG for transformation and avoiding cytotoxic accumulation of intracellular 2-HG.

The microbiota–gut–brain axis has been considered to play an important role in the development of depression, but the underlying mechanism remains unclear. The gastrointestinal tract is home to trillions of microbiota and the colon is considered an important site for the interaction between microbiota and host, but few studies have been conducted to evaluate the alterations in the colon. Accordingly, in this study, we established a chronic social defeated stress (CSDS) mice model of depression. We applied 16S rRNA gene sequencing to assess the gut microbial composition and gas and liquid chromatography–mass spectroscopy to identify fecal metabolites and colonic lipids, respectively. Meanwhile, we used Spearman’s correlation analysis method to evaluate the associations between the gut microbiota, fecal metabolites, colonic lipids, and behavioral index. In total, there were 20 bacterial taxa and 18 bacterial taxa significantly increased and decreased, respectively, in the CSDS mice. Further, microbial functional prediction demonstrated a disturbance of lipid, carbohydrate, and amino acid metabolism in the CSDS mice. We also found 20 differential fecal metabolites and 36 differential colonic lipids (in the category of glycerolipids, glycerophospholipids, and sphingolipids) in the CSDS mice. Moreover, correlation analysis showed that fecal metabolomic signature was associated with the alterations in the gut microbiota composition and colonic lipidomic profile. Of note, three lipids [PC(16:0/20:4), PG(22:6/22:6), and PI(18:0/20:3), all in the category of glycerophospholipids] were significantly associated with anxiety- and depression-like phenotypes in mice. Taken together, our results indicated that the gut microbiota might be involved in the pathogenesis of depression via influencing fecal metabolites and colonic glycerophospholipid metabolism.

B-cell precursor acute lymphoblastic leukemia (BCP-ALL) with mixed-lineage leukemia gene rearrangement (MLL-r) is a poor-prognosis subtype for which additional therapeutic targets are urgently needed. Currently no multi omics data set for primary MLL r patient cells exists that integrates transcriptomics, proteomics and glycomics to gain an inclusive picture of theranostic targets.MethodsWe have integrated transcriptomics, proteomics and glycomics to i) obtain the first inclusive picture of primary patient BCP-ALL cells and identify molecular signatures that distinguish leukemic from normal precursor B-cells and ii) better understand the benefits and limitations of the applied technologies to deliver deep molecular sequence data across major cellular biopolymers.ResultsMLL-r cells feature an extensive remodelling of their glycocalyx, with increased levels of Core 2-type O-glycans and complex N-glycans as well as significant changes in sialylation and fucosylation. Notably, glycosaminoglycan remodelling from chondroitin sulfate to heparan sulfate was observed. A survival screen, to determine if glycan remodelling enzymes are redundant, identified MGAT1 and NGLY1, essential components of the N-glycosylation/degradation pathway, as highly relevant within this in vitro screening. OGT and OGA, unique enzymes that regulate intracellular O-GlcNAcylation, were also indispensable. Transcriptomics and proteomics further identified Fes and GALNT7-mediated glycosylation as possible therapeutic targets. While there is overall good correlation between transcriptomics and proteomics data, we demonstrate that a systematic combined multi-omics approach delivers important diagnostic information that is missed when applying a single omics technology.ConclusionsApart from confirming well-known MLL-r BCP-ALL glycoprotein markers, our integrated multi-omics workflow discovered previously unidentified diagnostic/therapeutic protein targets.Graphical abstract

Whether and how m6A modifications regulate NK cell immunity remain unknown. Here, Ma et al. show that NK cell proliferation, survival, and effector functions are positively controlled by the RNA m6A reader YTHDF2., N6-methyladenosine (m6A) is the most prevalent posttranscriptional modification on RNA. NK cells are the predominant innate lymphoid cells that mediate antiviral and antitumor immunity. However, whether and how m6A modifications affect NK cell immunity remain unknown. Here, we discover that YTHDF2, a well-known m6A reader, is upregulated in NK cells upon activation by cytokines, tumors, and cytomegalovirus infection. Ythdf2 deficiency in NK cells impairs NK cell antitumor and antiviral activity in vivo. YTHDF2 maintains NK cell homeostasis and terminal maturation, correlating with modulating NK cell trafficking and regulating Eomes, respectively. YTHDF2 promotes NK cell effector function and is required for IL-15–mediated NK cell survival and proliferation by forming a STAT5–YTHDF2 positive feedback loop. Transcriptome-wide screening identifies Tardbp to be involved in cell proliferation or survival as a YTHDF2-binding target in NK cells. Collectively, we elucidate the biological roles of m6A modifications in NK cells and highlight a new direction to harness NK cell antitumor immunity., Graphical Abstract

The fungus gnat is a major pest of chive in China. Its control has been relied heavily on the application of clothianidin. Due to the intensive application, its control efficacy become reduced. The present study was intended to evaluate co-drenching of clothianidin with hexaflumuron on absorption and dissipation of clothianidin in chive plants and soils and determine the effect of such application on control efficacies. Chive production fields in Guangdong and Hubei Provinces were drenched with clothianidin alone and a mixture of clothianidin and hexaflumuron at low application rates. Concentrations of clothianidin in chive plants and soils were analyzed by HPLC. Results showed that co-application had higher control efficacies against the fungus gnat than clothianidin alone. The co-application enhanced clothianidin absorption and dissipation and extended the half-lives of clothianidin in chive. It was likely that hexaflumuron protected chive roots from larva damage, and healthy roots absorbed more clothianidin, resulting in the extension of the half-lives. Additionally, the terminal residues of clothianidin in chive after 14 days of application were lower than the maximum residue limit in chive set by the Codex Alimentarius Commission. This study for the first time documented that co-application of clothianidin and hexaflumuron improved chive plants in absorption and dissipation of clothianidin and enhanced fungus gnat control efficacies.

Novel dual HDAC3/tubulin inhibitors were designed and efficiently synthesized by combining the pharmacophores of SMART (tubulin inhibitor) and MS-275 (HDAC inhibitor), among which compound 15c was found to be the most potent and balanced HDAC3/tubulin dual inhibitor with high HDAC3 activity (IC50 = 30 nM) and selectivity (SI > 1000) as well as excellent antiproliferative potency against various cancer cell lines, including an HDAC-resistant gastric cancer cell line (YCC3/7) with IC50 values in the range of 30-144 nM. Compound 15c inhibited B16-F10 cancer cell migration and colony formation. In addition, 15c demonstrated significant in vivo antitumor efficacy in a B16-F10 melanoma tumor model with a better TGI (70.00%, 10 mg/kg) than that of the combination of MS-275 and SMART. Finally, 15c presented a safe cardiotoxicity profile and did not cause nephro-/hepatotoxicity. Collectively, this work shows that compound 15c represents a novel tubulin/HDAC3 dual-targeting agent deserving further investigation as a potential anticancer agent.

Summary This protocol describes how to evaluate cellular metabolic state, including the glycolytic activity, in live CD34+ hematopoietic stem/progenitor cells (HSPCs) upon depletion of a specific target gene. We detail the procedure of enriching mononuclear cells from human umbilical cord blood samples, isolation of CD34+ HSPCs using positive immunomagnetic separation, and the analysis of glycolytic activity in lentivirally transduced CD34+ HSPCs using Seahorse Assay. This protocol can be applied to evaluate potential aerobic glycolysis gene targets for cancer therapy. For complete details on the use and execution of this protocol, please refer to Qing et al. (2021)., Graphical abstract, Highlights • Preparation of umbilical cord blood mononuclear cells (UCB MNCs) from human samples • Isolation of CD34+ HSPCs from UCB MNCs by positive immunomagnetic separation • Detailed protocol for lentiviral transduction of CD34+ HSPCs • Optimized procedure to assess glycolytic rates in CD34+ HSPCs via Seahorse Assay, This protocol describes how to evaluate cellular metabolic state, including the glycolytic activity, in live CD34+ hematopoietic stem/progenitor cells (HSPCs) upon depletion of a specific target gene. We detail the procedure of enriching mononuclear cells from human umbilical cord blood samples, isolation of CD34+ HSPCs using positive immunomagnetic separation, and the analysis of glycolytic activity in lentivirally transduced CD34+ HSPCs using Seahorse Assay. This protocol can be applied to evaluate potential aerobic glycolysis gene targets for cancer therapy.

ZEB1 (a positive enhancer) and KLF5 (a negative silencer) affect transcription factors and play inherently conserved roles in tumorigenesis and multidrug resistance. In humans, the rs2295080T-allele at the mTOR promoter locus has been associated with human cancer risk; however, the 63 bp spacing of another SNP rs2295079 has not been identified. Here, we discovered, for the first time, that rs2295079 (-78C/G) and rs2295080 (-141G/T) formed linkage haplotypes, with Ht1 (-78C/-141G) and Ht2 (-78G/-141T) being dominant, which were associated with distinct susceptibility to breast cancer, response to paclitaxel, and clinical outcomes in breast cancer. At the cellular level, compared with Ht1, Ht2 exhibits a much stronger effect on promoting mTOR expression, leading to enhanced tumor cell growth and strengthened resistance to PTX treatment. Mechanistically, the -141T allele of Ht2 creates a novel ZEB1-binding site; meanwhile, the -78C allele of Ht1 exists as an emerging KLF5-binding site, which synergistically induces promote/inhibit mTOR expression, cell proliferation, and excretion of cytotoxic drugs through the ZEB1/KLF5–mTOR–CCND1/ABCB1 cascade, thereby affecting the response to paclitaxel treatment in vivo and in vitro. Our results suggest the existence of a ZEB1/KLF5–mTOR–CCND1/ABCB1 axis in human cells that could be involved in paclitaxel response pathways and functionally regulate interindividualized breast cancer susceptibility and prognosis. Implications: This study highlights the function of haplotypes of mTOR -78C/-141G and -78G/-141T, in affecting breast cancer susceptibility and paclitaxel response regulated by ZEB1/KLF5–mTOR–CCND1/ABCB1 axis.

Dendrobium officinale Kimura et Migo is a famous traditional Chinese medicinal plant. It produces various phytochemicals, particularly polysaccharides, which have nutraceutical and pharmaceutical values. To increase its biomass production and polysaccharide content, our breeding program has generated a series of polyploid cultivars through colchicine treatment of protocorm-like bodies (PLBs). The present study compared two tetraploid cultivars, 201-1-T1 and 201-1-T2, with their diploid parental cultivar, 201-1, in an established in vitro culture system. Tetraploid ‘201-1-T1’ and ‘201-1-T2’ had shorter leaves and shorter and thicker stems and roots, and they produced higher biomass compared with the diploid cultivar. The length and width of stomata significantly increased, but stomatal density decreased in tetraploid cultivars. The PLB induction rates from the stem node explants of the tetraploid cultivars were significantly higher than those of diploid. However, the PLB proliferation of tetraploids was lower than that of the diploid. The mean number of plantlets regenerated from tetraploid PLBs was also lower than that of the diploid after 4 months of culture. Polysaccharide contents in stems, leaves, and roots of 6-month-old tetraploid plantlets were significantly higher than those of diploids. The polysaccharide content in the stem of ‘201-1-T1’ was 12.70%, which was a 2-fold increase compared with the diploid cultivar. Our results showed that chromosome doubling could be a viable way of improving D. officinale in biomass and polysaccharide production.

Gut microbiota can affect multiple brain functions and cause behavioral alterations through the microbiota-gut-brain axis. In our previous study, we found that the absence of gut microbiota can influence the expression of microRNAs and mRNAs in the hippocampal region of the germ-free (GF) mice. Long non-coding RNAs (lncRNAs) are increasingly being recognized as an important functional transcriptional regulator in the brain. In the present study, we aim to identify possible biological pathways and functional networks for lncRNA-associated transcript of the gut microbiota in relation to the brain function. The profiles of lncRNA and mRNA from specific pathogen-free (SPF), colonized GF (CGF), and GF mice were generated using the Agilent Mouse LncRNA Array v2.0. Differentially expressed (DE) lncRNAs and mRNAs were identified, and lncRNA target genes were also predicted. Ingenuity pathway analysis (IPA) was performed to analyze related signaling pathways and biological functions associated with these dysregulated mRNAs and target genes. Validation with quantitative real-time PCR was performed on several key genes. Compared with SPF mice a total of 2230 DE lncRNAs were found in GF mice. Among these, 1355 were upregulated and 875 were downregulated. After comparing the target genes of DE lncRNAs with mRNA datasets, 669 overlapping genes were identified. IPA core analyses revealed that most of these genes were highly associated with cardiac hypertrophy, nuclear factors of activated T cells (NFAT) gonadotropin-releasing hormone (GnRH), calcium, and cAMP-response element-binding protein (CREB) signaling pathways. Additionally, mRNA expression levels of APP, CASP9, IGFBP2, PTGDS, and TGFBR2 genes that are involved in central nervous system functions were significantly changed in the GF mouse hippocampus. Through this study, for the first time, we describe the effect of gut microbiota on the hippocampal lncRNA regulation. This will help in enhancing the overall knowledge about microbiota-gut-brain axis.

Epigenetics is the study of heritable changes in gene expression without changing the DNA sequence - a change in phenotype without a change in genotype. Epigenetic abnormalities can lead to serious diseases such as cancer in organisms. Histone methylation is one of the several manifestations of epigenetics, and requires specific enzymes to catalyze, for example, G9a, which is a histone methyl transferase. G9a catalyzes the methylation of histone 3 lysine 9 (H3K9) and histone 3 lysine 27 (H3K27). In addition, G9a also plays an essential role in DNA replication, damage and repair, and gene expression by regulating DNA methylation. Moreover, G9a has been found to be overexpressed in many tumor cells and is associated with the occurrence and development of tumors. Because of its unique characteristics, G9a has become a very promising target for anti-cancer agents. Over the last decade, dozens of G9a inhibitors have been discovered as potential anticancer therapeutic agents. In this review, we summarize and classify current G9a inhibitors, the challenges and future direction are also discussed in detail.