Epitranscriptic regulation of HRAS by N6-methyladenosine drives tumor progression.

Overexpression of Ras, in addition to the oncogenic mutations, occurs in various human cancers. However, the mechanisms for epitranscriptic regulation of RAS in tumorigenesis remain unclear. Here, we report that the widespread N6-methyladenosine (m6A) modification of HRAS, but not KRAS and NRAS, is higher in cancer tissues compared with the adjacent tissues, which results in the increased expression of H-Ras protein, thus promoting cancer cell proliferation and metastasis. Mechanistically, three m6A modification sites of HRAS 3' UTR, which is regulated by FTO and bound by YTHDF1, but not YTHDF2 nor YTHDF3, promote its protein expression by the enhanced translational elongation. In addition, targeting HRAS m6A modification decreases cancer proliferation and metastasis. Clinically, up-regulated H-Ras expression correlates with down-regulated FTO and up-regulated YTHDF1 expression in various cancers. Collectively, our study reveals a linking between specific m6A modification sites of HRAS and tumor progression, which provides a new strategy to target oncogenic Ras signaling.

LCDR regulates the integrity of lysosomal membrane by hnRNP K-stabilized LAPTM5 transcript and promotes cell survival.

Lysosome plays important roles in cellular homeostasis, and its dysregulation contributes to tumor growth and survival. However, the understanding of regulation and the underlying mechanism of lysosome in cancer survival is incomplete. Here, we reveal a role for a histone acetylation-regulated long noncoding RNA termed lysosome cell death regulator (LCDR) in lung cancer cell survival, in which its knockdown promotes apoptosis. Mechanistically, LCDR binds to heterogenous nuclear ribonucleoprotein K (hnRNP K) to regulate the stability of the lysosomal-associated protein transmembrane 5 (LAPTM5) transcript that maintains the integrity of the lysosomal membrane. Knockdown of LCDR, hnRNP K, or LAPTM5 promotes lysosomal membrane permeabilization and lysosomal cell death, thus consequently resulting in apoptosis. LAPTM5 overexpression or cathepsin B inhibitor partially restores the effects of this axis on lysosomal cell death in vitro and in vivo. Similarly, targeting LCDR significantly decreased tumor growth of patient-derived xenografts of lung adenocarcinoma (LUAD) and had significant cell death using nanoparticles (NPs)-mediated systematic short interfering RNA delivery. Moreover, LCDR/hnRNP K/LAPTM5 are up-regulated in LUAD tissues, and coexpression of this axis shows the increased diagnostic value for LUAD. Collectively, we identified a long noncoding RNA that regulates lysosome function at the posttranscriptional level. These findings shed light on LCDR/hnRNP K/LAPTM5 as potential therapeutic targets, and targeting lysosome is a promising strategy in cancer treatment.

The diversity and biogeography of abundant and rare intertidal marine microeukaryotes explained by environment and dispersal limitation.

Benthic microeukaryotes are key ecosystem drivers in marine sandy beaches, an important and dynamic environment; however, little is known about their diversity and biogeography on a large spatial scale. Here, we investigated the community composition and geographical distributions of benthic microeukaryotes using high-throughput sequencing of the 18S rRNA gene and quantified the contributions of environmental factors and spatial separation on the distribution patterns of both rare and abundant taxa. We collected 36 intertidal samples at 12 sandy beaches from four regions that spanned distances from 0.001 to 12,000 km. We found 12,890 operational taxonomic units (OTUs; 97% sequence identity level) including members of all eukaryotic super-groups and several phyla of uncertain position. Arthropoda and Diatomeae dominated the sequence reads in abundance, but Ciliophora and Discoba were the most diverse groups across all samples. About one-third of the OTUs could not be definitively classified at a similarity level of 80%, supporting the view that a large number of rare and minute marine species may have escaped previous characterization. We found generally similar geographical patterns for abundant and rare microeukaryotic sub-communities, and both showed a significant distance-decay similarity trend. Variation partitioning showed that both rare and abundant sub-communities exhibited a slightly stronger response to environmental factors than spatial (distance) factors. However, the abundant sub-community was strongly correlated with variations in spatial, environmental and sediment grain size factors (66% of variance explained), but the rare assemblage was not (16%). This suggests that different or more complex mechanisms generate and maintain diversity in the rare biosphere in this habitat.

m6A modification enhances the stability of CDC25A promotes tumorigenicity of esophagogastric junction adenocarcinoma via cell cycle.

N6-Methyladenosine (m6A) modification and its regulators play critical roles in human cancers, but their functions and regulatory mechanisms in adenocarcinoma of the esophagogastric junction (AEG) remain unclear. Here, we identified that IGF2BP3 is the most significantly up-regulated m6A regulator in AEG tumors versus paired normal adjacent tissues from the expression profile of m6A regulators in a large cohort of AEG patients. Silencing IGF2BP3 inhibits AEG progression in vitro and in vivo. By profiling transcriptome-wide targets of IGF2BP3 and the m6A methylome in AEG, we found that IGF2BP3-mediated stabilization and enhanced expression of m6A-modified targets, including targets of the cell cycle pathway, such as CDC25A, CDK4, and E2F1, are critical for AEG progression. Mechanistically, the increased m6A modification of CDC25A accelerates the G1-S transition. Clinically, up-regulated IGF2BP3, METTL3, and CDC25A show a strong positive correlation in TCGA pan-cancer, including AEG. In conclusion, our study highlights the role of post-transcriptional regulation in modulating AEG tumor progression and elucidates the functional importance of the m6A/IGF2BP3/CDC25A axis in AEG cells.

Biocontrol mechanism of Bacillus siamensis sp. QN2MO-1 against tomato fusarium wilt disease during fruit postharvest and planting.

Tomato fusarium wilt caused by Fusarium oxysporum f. sp. lycopersici (Fol) is a highly destructive disease, resulting in severe economic losses of global tomato production annually. An eco-friendly alternative to chemical fungicide using biological control agents (BCAs) is urgently needed. Here, Bacillus siamensis QN2MO-1 was isolated from Noli fruit and had a strong antagonistic activity against Fol in vitro and in vivo. Strain QN2MO-1 also exhibited a broad-spectrum antifungal activity against the selected 14 phytopathogenic fungi. The crude protein produced by strain QN2MO-1 could inhibit the spore germination of Fol and destroy the spore structure. It was closely related with the generation of chitinase and ß-1,3-glucanase secreted by strain QN2MO-1. In a pot experiment, the application of B. siamensis QN2MO-1 effectively alleviated the yellowing and wilting symptoms of tomato plants. The disease index and incidence rate were decreased by 72.72% and 80.96%, respectively. The rhizospheric soil in tomato plants owed a high abundance of microbial community. Moreover, strain QN2MO-1 also enhanced the plant growth and improved the fruit quality of tomato. Therefore, B. siamensis QN2MO-1 will be explored as a potential biocontrol agent and biofertilizer.

HUNK inhibits epithelial-mesenchymal transition of CRC via direct phosphorylation of GEF-H1 and activating RhoA/LIMK-1/CFL-1.

Epithelial-mesenchymal transition (EMT) is associated with the invasive and metastatic phenotypes in colorectal cancer (CRC). However, the mechanisms underlying EMT in CRC are not completely understood. In this study, we find that HUNK inhibits EMT and metastasis of CRC cells via its substrate GEF-H1 in a kinase-dependent manner. Mechanistically, HUNK directly phosphorylates GEF-H1 at serine 645 (S645) site, which activates RhoA and consequently leads to a cascade of phosphorylation of LIMK-1/CFL-1, thereby stabilizing F-actin and inhibiting EMT. Clinically, the levels of both HUNK expression and phosphorylation S645 of GEH-H1 are not only downregulated in CRC tissues with metastasis compared with that without metastasis, but also positively correlated among these tissues. Our findings highlight the importance of HUNK kinase direct phosphorylation of GEF-H1 in regulation of EMT and metastasis of CRC.

DMDRMR promotes angiogenesis via antagonizing DAB2IP in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) patients are highly angiogenic and treated by targeted therapies against VEGFA/VEGFR signaling pathway. However, tumors with such targeted therapies remain a significant clinic challenge. Understanding the underlying mechanism against angiogenesis is highly desired. Here, we demonstrated that the lncRNA DMDRMR serves as a sponge of miR-378a-5p to increase EZH2 and SMURF1 expression, thus promoting EZH2-mediated transcriptional repression of DAB2IP and SMURF1-mediated degradation of DAB2IP. Consequently, this axis activates VEGFA/VEGFR2 signaling pathway, resulting in angiogenesis and resistance of tumor cells to sunitinib in ccRCC. Moreover, the competing endogenous RNA regulatory axis of DMDRMR is clinically relevant to ccRCC pathogenesis and prognosis of patients with ccRCC. Our results support that the DMDRMR/miR-378a-5p/DAB2IP axis may serve as a novel target for combination diagnosis or therapy of ccRCC patients. Our findings may have highly clinical relevance for future translation to develop the targeted therapies for patients with ccRCC.

Epigenetic effects of silver nanoparticles and ionic silver in Tetrahymena thermophila.

The widespread use of silver nanoparticles (Ag NPs) has raised substantial health risks, but little is known about the epigenetic toxicity induced by Ag+ and Ag NPs. This study characterized physiological and lncRNA profiles to explore the toxic effects and epigenetic mechanisms in Tetrahymena thermophila on exposure to Ag+ (in the form of AgNO3) and different Ag NPs for 24 h. The Ag NPs studied varied in size (10 nm and 80 nm) and surface coating (citrate and polyvinylpyrrolidone). We found that both Ag+ and Ag NPs elicited strong growth-inhibiting effects on T. thermophila. The toxicity was mainly caused by high reactive oxygen species (ROS) levels, leading to lipid peroxidation and mitochondrial dysfunction. To combat the oxidative stress, the protist activated an antioxidative response, increasing the activity of glutathione peroxidase and other antioxidants. Notably, 1250 lncRNAs were differentially expressed under Ag+ or Ag NPs exposure relative to the non-exposure control, which were clustered into 15 expression modules in weighted gene co-expression network analysis. These gene modules exhibited toxicant-specific expression patterns, potentially playing regulatory roles, via their co-expressed mRNAs, to inhibit cell growth, activate cell membrane cation channel, and promote oxidoreductase activity. This research illuminates how post-transcriptional mechanisms of a ciliated protozoan regulate responses to Ag+ and Ag NPs toxicities.

Analysis and verification of N6-methyladenosine-modified genes as novel biomarkers for clear cell renal cell carcinoma.

N6-methyladenosine (m6A) has been involved in diverse biological processes in cancer, but its function and clinical value in clear cell renal cell carcinoma (ccRCC) remain largely unknown. In this study, we found that 1453 m6A-modified differentially expressed genes (DEGs) of ccRCC were mainly enriched in cell cycle, PI3K-AKT, and p53 signaling pathways. Then we constructed a co-expression network of the 1453 m6A-modified DEGs and identified a most clinically relevant module, where NUF2, CDCA3, CKAP2L, KIF14, and ASPM were hub genes. NUF2, CDCA3, and KIF14 could combine with a major RNA m6A methyltransferase METTL14, serving as biomarkers for ccRCC. Real-time quantitative PCR assay confirmed that NUF2, CDCA3, and KIF14 were highly expressed in ccRCC cell lines and ccRCC tissues. Furthermore, these three genes were modified by m6A and negatively regulated by METTL14. This study revealed that NUF2, CDCA3, and KIF14 were m6A-modified biomarkers, representing a potential diagnostic, prognostic, and therapeutic target for ccRCC.Abbreviations: m6A: N6-methyladenosine; ccRCC: clear cell renal cell carcinoma; DEGs: differentially expressed genes; NUF2: NUF2 component of NDC80 kinetochore complex; CDCA3: cell division cycle associated 3; CKAP2L: cytoskeleton associated protein 2 like; KIF14: kinesin family member 14; ASPM: assembly factor for spindle microtubules; METTL14: methyltransferase 14; OS: overall survival; FPKM: fragments per kilobase million; GEO: gene expression omnibus; TCGA: the Cancer Genome Atlas; RMA: robust multi-array average expression measure; WGCNA: weighted gene co-expression network analysis; GO: gene ontology; KEGG: kyoto encyclopedia of genes and genomes; ROC: receiver operating characteristic curve; AUC: area under the curve; RIP: RNA immunoprecipitation; qPCR: real-time quantitative PCR.

DMDRMR-Mediated Regulation of m6A-Modified CDK4 by m6A Reader IGF2BP3 Drives ccRCC Progression.

Aberrant N 6-methyladenosine (m6A) modification has emerged as a driver of tumor initiation and progression, yet how long noncoding RNAs (lncRNA) are involved in the regulation of m6A remains unknown. Here we utilize data from 12 cancer types from The Cancer Genome Atlas to comprehensively map lncRNAs that are potentially deregulated by DNA methylation. A novel DNA methylation-deregulated and RNA m6A reader-cooperating lncRNA (DMDRMR) facilitated tumor growth and metastasis in clear cell renal cell carcinoma (ccRCC). Mechanistically, DMDRMR bound insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) to stabilize target genes, including the cell-cycle kinase CDK4 and three extracellular matrix components (COL6A1, LAMA5, and FN1), by specifically enhancing IGF2BP3 activity on them in an m6A-dependent manner. Consequently, DMDRMR and IGF2BP3 enhanced the G1-S transition, thus promoting cell proliferation in ccRCC. In patients with ccRCC, high coexpression of DMDRMR and IGF2BP3 was associated with poor outcomes. Our findings reveal that DMDRMR cooperates with IGF2BP3 to regulate target genes in an m6A-dependent manner and may represent a potential diagnostic, prognostic, and therapeutic target in ccRCC. SIGNIFICANCE: This study demonstrates that the lncRNA DMDRMR acts as a cofactor for IGF2BP3 to stabilize target genes in an m6A-dependent manner, thus exerting essential oncogenic roles in ccRCC.

Patterns and Processes in Marine Microeukaryotic Community Biogeography from Xiamen Coastal Waters and Intertidal Sediments, Southeast China.

Microeukaryotes play key roles in the structure and functioning of marine ecosystems. Little is known about the relative importance of the processes that drive planktonic and benthic microeukaryotic biogeography in subtropical offshore areas. This study compares the microeukaryotic community compositions (MCCs) from offshore waters (n = 12) and intertidal sediments (n = 12) around Xiamen Island, southern China, using high-throughput sequencing of 18S rDNA. This work further quantifies the relative contributions of spatial and environmental variables on the distribution of marine MCCs (including total, dominant, rare and conditionally rare taxa). Our results showed that planktonic and benthic MCCs were significantly different, and the benthic richness (6627 OTUs) was much higher than that for plankton (4044 OTUs) with the same sequencing effort. Further, we found that benthic MCCs exhibited a significant distance-decay relationship, whereas the planktonic communities did not. After removing two unique sites (N2 and N3), however, 72% variation in planktonic community was explained well by stochastic processes. More importantly, both the environmental and spatial factors played significant roles in influencing the biogeography of total and dominant planktonic and benthic microeukaryotic communities, although their relative effects on these community variations were different. However, a high proportion of unexplained variation in the rare taxa (78.1-97.4%) and conditionally rare taxa (49.0-81.0%) indicated that more complex mechanisms may influence the assembly of the rare subcommunity. These results demonstrate that patterns and processes in marine microeukaryotic community assembly differ among the different habitats (coastal water vs. intertidal sediment) and different communities (total, dominant, rare and conditionally rare microeukaryotes), and provide novel insight on the microeukaryotic biogeography and ecological mechanisms in coastal waters and intertidal sediments at local scale.