Hydrolytic endonucleolytic ribozyme (HYER) is programmable for sequence-specific DNA cleavage.

Ribozymes are catalytic RNAs with diverse functions including self-splicing and polymerization. This work aims to discover natural ribozymes that behave as hydrolytic and sequence-specific DNA endonucleases, which could be repurposed as DNA manipulation tools. Focused on bacterial group II-C introns, we found that many systems without intron-encoded protein propagate multiple copies in their resident genomes. These introns, named HYdrolytic Endonucleolytic Ribozymes (HYERs), cleaved RNA, single-stranded DNA, bubbled double-stranded DNA (dsDNA), and plasmids in vitro. HYER1 generated dsDNA breaks in the mammalian genome. Cryo-electron microscopy analysis revealed a homodimer structure for HYER1, where each monomer contains a Mg2+-dependent hydrolysis pocket and captures DNA complementary to the target recognition site (TRS). Rational designs including TRS extension, recruiting sequence insertion, and heterodimerization yielded engineered HYERs showing improved specificity and flexibility for DNA manipulation.

RBM45 reprograms lipid metabolism promoting hepatocellular carcinoma via Rictor and ACSL1/ACSL4.

Reprogramming of lipid metabolism during hepatocarcinogenesis is not well elucidated. Here, we aimed to explore pivotal RNA-binding motif proteins (RBMs) in lipid metabolism and their therapeutic potential in hepatocellular carcinoma (HCC). Through bioinformatic analysis, we identified RBM45 as a critical gene of interest among differentially expressed RBMs in HCC, with significant prognostic relevance. RBM45 influenced the malignant biological phenotype and lipid metabolism of HCC cells. Mechanically, RBM45 promotes de novo lipogenesis in HCC by directly targeting two key enzymes involved in long-chain fatty acid synthesis, ACSL1 and ACSL4. RBM45 also targets Rictor, which has been demonstrated to modulate lipid metabolism profoundly. RBM45 also aided lipid degradation through activating a key fatty acid ß oxidation enzyme, CPT1A. Thus, RBM45 boosted lipid synthesis and decomposition, indicating an enhanced utility of lipid fuels in HCC. Clinically, body mass index was positively correlated with RBM45 in human HCCs. The combination of a PI3K/AKT/mTOR pathway inhibitor in vitro or Sorafenib in orthotopic liver cancer mouse models with shRBM45 has a more significant therapeutic effect on liver cancer than the drug alone. In summary, our findings highlight the versatile roles of RBM45 in lipid metabolism reprogramming and its therapeutic potential in HCC. Lipids induced RBM45 expression. In turn, RBM45 promoted the utility of lipid in HCCs through accelerating both de novo lipogenesis and fatty acid ß oxidation, which required the participation of Rictor, a core component of mTORC2 that has been demonstrated to modulate lipid metabolism potently, as well as ACSL1/ACSL4, two key enzymes of long-chain fatty acid synthesis. When the first-line chemotherapy drug sorafenib is combined with a PI3K/AKT/mTOR pathway inhibitor (MK2206 is an AKT inhibitor, rapamycin is a mTOR inhibitor, and inhibiting RBM45 can significantly inhibit Rictor), cell cycle, proliferation, lipid metabolism reprogramming, and hepatocarcinogenesis can be significantly inhibited, while apoptosis can be significantly enhanced.

Neuroprotective effects of an engineered Escherichia coli Nissle 1917 on Parkinson's disease in mice by delivering GLP-1 and modulating gut microbiota.

Considerable evidence suggests that insulin resistance is closely linked to Parkinson's disease (PD), leading to agents aiming at treating diabetes can be regarded as new neuroprotective strategies in PD, notably glucagon-like peptide-1 (GLP-1). However, the extremely short half-life of GLP-1 due to degradation by the ubiquitous proteolytic enzyme limits its clinical application. In this study, we engineered the recombinant integrant probiotic strain Escherichia coli Nissle 1917 (EcN) to create a strain EcN-GLP-1 that effectively delivers the heterologous GLP-1 molecule. Subsequently, we assessed its neuroprotective effects on 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP)-induced PD mice. We demonstrated that EcN-GLP-1 treatment could improve motor deficits, increase tyrosine hydroxylase-positive neurons, suppress microglia and astrocyte activation, reduce brain and colon inflammation, and ameliorate colonic barrier function damaged by MPTP induction. Meanwhile, we confirmed that the oral administration of EcN-GLP-1 could restore the disturbance of gut microbiota in the MPTP-induced PD mice, by reducing the relative abundances of Akkermansia and Oscillospira, and increasing the level of Prevotella in the gut. These results support further development of an engineered probiotic platform in which production of GLP-1 for gut-brain disorders, such as PD.

METTL5-mediated 18S rRNA m6A modification promotes oncogenic mRNA translation and intrahepatic cholangiocarcinoma progression.

Intrahepatic cholangiocarcinoma (ICC) is a deadly cancer with rapid tumor progression. While hyperactive mRNA translation caused by mis-regulated mRNA or tRNA modifications promotes ICC development, the role of rRNA modifications remains elusive. Here, we found that 18S rRNA m6A modification and its methyltransferase METTL5 were aberrantly upregulated in ICC and associated with poorer survival (log rank test, p < 0.05). We further revealed the critical role of METTL5-mediated 18S rRNA m6A modification in regulation of ICC cell growth and metastasis using loss- and gain-of function assays in vitro and in vivo. The oncogenic function of METTL5 is corroborated using liver-specific knockout and overexpression ICC mouse models. Mechanistically, METTL5 depletion impairs 18S rRNA m6A modification that hampers ribosome synthesis and inhibits translation of G-quadruplex-containing mRNAs that are enriched in the transforming growth factor (TGF)-ß pathway. Our study uncovers the important role of METTL5-mediated 18S rRNA m6A modification in ICC and unravels the mechanism of rRNA m6A modification-mediated oncogenic mRNA translation control.

PLANET: A Multi-objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction.

Predicting protein-ligand binding affinity is a central issue in drug design. Various deep learning models have been published in recent years, where many of them rely on 3D protein-ligand complex structures as input and tend to focus on the single task of reproducing binding affinity. In this study, we have developed a graph neural network model called PLANET (Protein-Ligand Affinity prediction NETwork). This model takes the graph-represented 3D structure of the binding pocket on the target protein and the 2D chemical structure of the ligand molecule as input. It was trained through a multi-objective process with three related tasks, including deriving the protein-ligand binding affinity, protein-ligand contact map, and ligand distance matrix. Besides the protein-ligand complexes with known binding affinity data retrieved from the PDBbind database, a large number of non-binder decoys were also added to the training data for deriving the final model of PLANET. When tested on the CASF-2016 benchmark, PLANET exhibited a scoring power comparable to the best result yielded by other deep learning models as well as a reasonable ranking power and docking power. In virtual screening trials conducted on the DUD-E benchmark, PLANET's performance was notably better than several deep learning and machine learning models. As on the LIT-PCBA benchmark, PLANET achieved comparable accuracy as the conventional docking program Glide, but it only spent less than 1% of Glide's computation time to finish the same job because PLANET did not need exhaustive conformational sampling. Considering the decent accuracy and efficiency of PLANET in binding affinity prediction, it may become a useful tool for conducting large-scale virtual screening.

Cross-talk between Myeloid and B Cells Shapes the Distinct Microenvironments of Primary and Secondary Liver Cancer.

The tumor microenvironment is distinctive in primary and secondary liver cancer. B cells represent an important component of immune infiltrates. Here, we demonstrated that B cells are an important regulator in hepatocellular carcinoma (HCC) and colorectal cancer liver metastasis (CRLM) microenvironments. B cells displayed distinct developmental trajectories in HCC and CRLM. Single-cell analysis revealed that IgG+ plasma cells preferentially accumulated in HCC, whereas IgA+ plasma cells were preferentially enriched in CRLM. Mechanistically, IgG+ plasma cells in HCC were recruited by tumor-associated macrophages via the CXCR3-CXCL10 axis, whereas IgA+ plasma cells in CRLM were recruited by metastatic tumor cells via CCR10-CCL28 signaling. Functionally, IgG+ plasma cells preferentially promoted protumorigenic macrophages formation in HCC, and IgA+ plasma cells preferentially induced granulocytic myeloid-derived suppressor cells activation in CRLM. Clinically, increased infiltration of IgG+ plasma cells and macrophages in HCC was correlated to worse survival, whereas increased intratumoral IgA+ plasma cells and neutrophils in CRLM indicated poor prognosis. Taken together, this study demonstrated plasma and myeloid cell-mediated immunosuppression in HCC and CRLM, suggesting that selectively modulating primary or secondary tumor-related immunosuppressive regulatory networks might reprogram the microenvironment and provide an immunotherapeutic strategy for treating liver cancer. SIGNIFICANCE: The immunomodulatory patterns of tumor-infiltrating B cells are distinct in primary and secondary liver cancer, with plasma cells mediating important physiologic processes that drive cancer progression.

Unveiling alkali metal poisoning of CrMn catalyst for selective catalytic reduction of NOx with NH3: An experimental and theoretical study.

Alkali metal poisoning has been an intricate and unsolved issue confining the catalytic activity of NH3-SCR catalysts up to now. Herein, the effect of NaCl and KCl on catalytic activity of CrMn catalyst for NH3-SCR of NOx was systematically investigated to clarify the alkali metal poisoning by combined experiments and theoretical calculations. It unveiled that NaCl/KCl could deactivate CrMn catalyst due to the decrease in specific surface area, electron transfer (Cr5++Mn3+↔Cr3++Mn4+), redox ability and oxygen vacancy and NH3/NO adsorption. In addition, NaCl cut off E-R mechanism reactions by inactivating surface Brønsted/Lewis acid sites. DFT calculations revealed that (1) Na and K could weaken MnO bond, (2) competitive adsorption between Cl and NH3 was a main reason weakening Lewis acid, (3) Cl adsorption was also a major cause diminishing Brønsted acid and oxygen vacancy, (4) Both Na and K seriously impeded NO adsorption/activation, (5) NaCl/KCl increased the reaction heat of H2O desorption (rate-determining step) in E-R mechanism reactions and KCl elevated its energy barrier in L-H mechanism reactions. Thus, this study provides the deep understanding of alkali metal poisoning and a well strategy to synthesize NH3-SCR catalysts with outstanding alkali metal resistance.

The compact Casπ (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation.

CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation.

(Sr, Ca)AlSiN3:Eu2+ Phosphor-Doped YAG:Ce3+ Transparent Ceramics as Novel Green-Light-Emitting Materials for White LEDs.

In this work, based on Y3Al5O12:Ce3+ (YAG:Ce3+) transparent ceramic and (Sr, Ca)AlSiN3:Eu2+ phosphors, novel green-light-emitting materials were systematically studied. YAG:Ce3+ transparent ceramics with different doping-concentrations, from 0% to 1% (Sr, Ca)AlSiN3:Eu2+ phosphors, were fabricated by dry pressing and vacuum sintering. The serial phosphor ceramics had 533 nm green-light emission when excited by 460 nm blue light. The PL, PLE, and chromaticity performances were measured, indicating that more of the green-light component was emitted with the increase in doping concentration. The addition of (Sr, Ca)AlSiN3:Eu2+ phosphor increased the green-light wavelength area and improved the quantum yield (QY) of the YAG:Ce3+ ceramic matrix. The phase composition, microstructure, crystal-field structure and phosphor distribution of (Sr, Ca)AlSiN3:Eu2+ phosphor-doped YAG:Ce3+ transparent ceramics were investigated, to explore the microscopic causes of the spectral changes. Impressively, (Sr, Ca)AlSiN3:Eu2+ phosphors were distributed homogeneously, and the pinning effect of phosphor caused the suppression of grain growth. The novel materials could provide an effective strategy for full-spectrum white lighting and displaying applications in the future.

Eliminating METTL1-mediated accumulation of PMN-MDSCs prevents hepatocellular carcinoma recurrence after radiofrequency ablation.

BACKGROUND AND AIMS: Radiofrequency ablation (RFA) is an important curative therapy in hepatocellular carcinoma (HCC), but recurrence rate remains as high as all the other HCC therapeutic modalities. Methyltransferase 1 (METTL1), an enzyme for m 7 G tRNA modification, was reported to promote HCC development. Here, we assessed the role of METTL1 in shaping the immunosuppressive tumor microenvironment after insufficient RFA (iRFA). APPROACH AND RESULTS: By immunohistochemistry and multiplex immunofluorescence (mIF) staining, we showed that METTL1 expression was enhanced in post-RFA recurrent HCC, accompanied by increased CD11b + CD15 + polymorphonuclear-myeloid-derived suppressor cells (PMN-MDSCs) and decreased CD8 + T cells. Mechanistically, heat-mediated METTL1 upregulation enhanced TGF-ß2 translation to form the immunosuppressive environment by induction of myeloid-derived suppressor cell. Liver-specific overexpression or knockdown of Mettl1 significantly affected the accumulation of PMN-MDSCs and subsequently affected CD8 + T cell infiltration. Complete RFA successfully eliminated the tumor, whereas iRFA-treated mice exhibited enhanced tumor growth and metastasis with increased PMN-MDSC accumulation and decreased CD8 + T cells compared to sham surgery. Interrupting METTL1-TGF-ß2-PMN-MDSC axis by anti-Ly6G antibody, or knockdown of hepatoma-intrinsic Mettl1 or Tgfb2 , or TGF-ß signaling blockade significantly mitigated tumor progression induced by iRFA and restored CD8 + T cell population. CONCLUSIONS: Our study sheds light on the pivotal role of METTL1 in modulating an immunosuppressive microenvironment and demonstrated that interrupting METTL1-TGF-ß2-PMN-MDSC axis could be a therapeutic strategy to restore antitumor immunity and prevent HCC recurrence after RFA treatment, meriting further clinical studies.

RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications.

RNA modification is a dynamic and reversible process regulated by a series of writers, erasers and readers (WERs). Abnormal changes of WERs will disrupt the RNA modification homeostasis of their target genes, leading to the dysregulation of RNA metabolisms such as RNA stability and translation, and consequently to diseases such as cancer. A public repository hosting the regulatory relationships between WERs and their target genes will help in understanding the roles of RNA modifications in various physiological and pathological conditions. Previously, we developed a database named 'm6A2Target' to host targets of WERs in m6A, one of the most prevalent RNA modifications in eukaryotic cells. To host all RNA modification (RM)-related WER-target associations, we hereby present an updated database, named 'RM2Target' (http://rm2target.canceromics.org/). In this update, RM2Target encompasses 1 619 653 WER-target associations for nine RNA modifications in human and mouse, including m6A, m6Am, m5C, m5U, m1A, m7G, pseudouridine, 2'-O-Me and A-to-I. Extensive annotations of target genes are available in RM2Target, including but not limited to basic gene information, RNA modifications, RNA-RNA/RNA-protein interactions and related diseases. Altogether, we expect that RM2Target will facilitate further downstream functional and mechanistic studies in the field of RNA modification research.

Elucidating the facet-dependent reactivity of CrMn catalyst for selective catalytic reduction of NOx with NH3.

The facet-dependent reactivity of CrMn catalysts was still unclear, hindering the further enhancement of their low-temperature SCR performance. Herein, the facet-dependent reactivity of CrMn1.5O4 catalyst for NH3-SCR of NOx was innovatively illustrated by numerous characterizations and density functional theory (DFT) calculations. Exposed (100) facet of CrMn1.5O4 catalyst exhibited best low-temperature SCR activity with ≥90 % NO conversion within 148-296 °C and 2.86 × 10-3 mol/(g·s) reaction rate within 160-240 °C. The characterizations revealed that (100) facet could induce the increase of BET specific area, electron transfer, concentration of Mn4+ and Oα, surface acidity, redox ability, NH3 and NOx adsorption/activation capacity. Subsequently, DFT calculations demonstrated that (100) facet exhibited the strongest affinity for NH3 and NO due to its unique 3O3c-Mn5c-2O4c bond and abundant charges transfer near the active adsorption sites, and Brønsted acid and oxygen vacancies were most easily formed on (100) facet. Furthermore, H2O formation as the rate determining step easily occurred on (100) facet. Eventually, we successfully improved the low-temperature SCR activity of CrMn1.5O4 catalyst by further tailoring highly active (100) facet from 0.754 to 0.865. This work provides the deeper understanding of facet-dependent reactivity and a good strategy to improve the catalytic activity of the catalysts.

TIGER: A Web Portal of Tumor Immunotherapy Gene Expression Resource.

Immunotherapy is a promising cancer treatment method; however, only a few patients benefit from it. The development of new immunotherapy strategies and effective biomarkers of response and resistance is urgently needed. Recently, high-throughput bulk and single-cell gene expression profiling technologies have generated valuable resources. However, these resources are not well organized and systematic analysis is difficult. Here, we present TIGER, a tumor immunotherapy gene expression resource, which contains bulk transcriptome data of 1508 tumor samples with clinical immunotherapy outcomes and 11,057 tumor/normal samples without clinical immunotherapy outcomes, as well as single-cell transcriptome data of 2,116,945 immune cells from 655 samples. TIGER provides many useful modules for analyzing collected and user-provided data. Using the resource in TIGER, we identified a tumor-enriched subset of CD4+ T cells. Patients with melanoma with a higher signature score of this subset have a significantly better response and survival under immunotherapy. We believe that TIGER will be helpful in understanding anti-tumor immunity mechanisms and discovering effective biomarkers. TIGER is freely accessible at http://tiger.canceromics.org/.

Identification of DNA methylation signatures for hepatocellular carcinoma detection and microvascular invasion prediction.

BACKGROUND AND AIM: Preoperative evaluation of microvascular invasion (MVI) in patients with hepatocellular carcinoma (HCC) is important for surgical strategy determination. We aimed to develop and establish a preoperative predictive model for MVI status based on DNA methylation markers. METHODS: A total of 35 HCC tissues and the matched peritumoral normal liver tissues as well as 35 corresponding HCC patients' plasma samples and 24 healthy plasma samples were used for genome-wide methylation sequencing and subsequent methylation haplotype block (MHB) analysis. Predictive models were constructed based on selected MHB markers and 3-cross validation was used. RESULTS: We grouped 35 HCC patients into 2 categories, including the MVI- group with 17 tissue and plasma samples, and MVI + group with 18 tissue and plasma samples. We identified a tissue DNA methylation signature with an AUC of 98.0% and a circulating free DNA (cfDNA) methylation signature with an AUC of 96.0% for HCC detection. Furthermore, we established a tissue DNA methylation signature for MVI status prediction, and achieved an AUC of 85.9%. Based on the MVI status predicted by the DNA methylation signature, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the predicted MVI- group than that in the predicted MVI + group. CONCLUSIONS: In this study, we identified a cfDNA methylation signature for HCC detection and a tissue DNA methylation signature for MVI status prediction with high accuracy.

Predicting Pyrolysis of a Wide Variety of Petroleum Coke Using an Independent Parallel Reaction Model and a Backpropagation Neural Network.

In this work, the pyrolysis behavior and gaseous products of petroleum coke were investigated by nonisothermal thermogravimetric analysis (TGA) and thermogravimetry-mass spectrometry (TG-MS). Then, the pyrolysis kinetics of six kinds of petroleum coke (Fushun (FS), Fuyu (FY), Wuhan (WH), Zhenhai (ZH), Qilu (QL), and Shijiazhuang (SJZ)) were determined by an independent parallel reaction (IPR) model, and the kinetic parameters (activation energy and preexponential factor) were obtained. In addition, an efficient backpropagation neural network (BPNN) was developed to predict the thermal data of six kinds of petroleum coke. The BPNN-predicted thermal data were used to calculate the kinetic parameters based on the IPR model, and the results were compared with the ones calculated using experimental data. The results showed that the pyrolysis process of six kinds of petroleum coke was divided into three stages, of which stage II (250-900 °C) had the significant mass loss, corresponding to the devolatilization of petroleum coke. MS fragmented ion intensity analysis indicated that the main pyrolysis products were methane CH x (m/z = 13, 14, 15, and 16), aliphatic hydrocarbon C3H5, H2, CO, CO2, and H2O. The thermal data predicted by the IPR, BPNN, and BPNN-IPR (BPNN combined with IPR) models were in good agreement with the experimental data. Most importantly, it was concluded that the BPNN-predicted data can be further applied to calculate the kinetic parameters using the IPR kinetic model.

PSMA-specific degradable dextran for multiplexed immunotargeted siRNA therapeutics against prostate cancer.

Small interfering RNA (siRNA) is ideal for gene silencing through a sequence-specific RNA interference process. The redundancy and complexity of molecular pathways in cancer create a need for multiplexed targeting that can be achieved with multiplexed siRNA delivery. Here, we delivered multiplexed siRNA with a PSMA-targeted biocompatible dextran nanocarrier to downregulate CD46 and PD-L1 in PSMA expressing prostate cancer cells. The selected gene targets, PD-L1 and CD46, play important roles in the escape of cancer cells from immune surveillance. PSMA, abundantly expressed by prostate cancer cells, allowed the prostate cancer-specific delivery of the nanocarrier. The nanocarrier was modified with acid cleavable acetal bonds for a rapid release of siRNA. Cell imaging and flow cytometry studies confirmed the PSMA-specific delivery of CD46 and PD-L1 siRNA to high PSMA expressing PC-3 PIP cells. Immunoblot, qRT-PCR and flow cytometry methods confirmed the downregulation of CD46 and PD-L1 following treatment with multiplexed siRNA.

VEGF Overexpression Significantly Increases Nanoparticle-Mediated siRNA Delivery and Target-Gene Downregulation.

The availability of nanoparticles (NPs) to deliver small interfering RNA (siRNA) has significantly expanded the specificity and range of 'druggable' targets for precision medicine in cancer. This is especially important for cancers such as triple negative breast cancer (TNBC) for which there are no targeted treatments. Our purpose here was to understand the role of tumor vasculature and vascular endothelial growth factor (VEGF) overexpression in a TNBC xenograft in improving the delivery and function of siRNA NPs using in vivo as well as ex vivo imaging. We used triple negative MDA-MB-231 human breast cancer xenografts derived from cells engineered to overexpress VEGF to understand the role of VEGF and vascularization in NP delivery and function. We used polyethylene glycol (PEG) conjugated polyethylenimine (PEI) NPs to deliver siRNA that downregulates choline kinase alpha (Chkα), an enzyme that is associated with malignant transformation and tumor progression. Because Chkα converts choline to phosphocholine, effective delivery of Chkα siRNA NPs resulted in functional changes of a significant decrease in phosphocholine and total choline that was detected with 1H magnetic resonance spectroscopy (MRS). We observed a significant increase in NP delivery and a significant decrease in Chkα and phosphocholine in VEGF overexpressing xenografts. Our results demonstrated the importance of tumor vascularization in achieving effective siRNA delivery and downregulation of the target gene Chkα and its function.

A systematic review of the quality of reporting and risk of bias for randomized crossover trials in digestive disease journals.

BACKGROUND: The quality of randomized crossover studies on digestive diseases is unclear. We aimed to review crossover trials in digestive disease journals and evaluate their reporting quality and risk of bias. METHODS: We searched the PubMed, Web of Science, and Scopus databases for all crossover trials in 39 digestive journals between January 2011 and September 2021. Reporting adherence was based on the CONSORT 2010 statement: extension to randomized crossover trials published in July 2019. A newly released Cochrane risk of bias tool 2.0 extension for crossover trials was applied to assess the risk of bias. RESULTS: In total, 173 studies were included in the analysis, and 16.2% were published following the CONSORT statement extension. The crossover design was not only widely used in drug efficacy trials (48.6%) but also in endoscopic ultrasound trials (23.7%) and dietary studies (17.9%) in the field of digestive diseases. The overall reporting adherence was 37.6% for full texts and 43.4% for abstracts. The proportions of trials with low, some concerns, and high risk of bias were 13.9%, 15.6%, and 70.5%, respectively. The difference in reporting adherence and high risk of bias between pre- and post-CONSORT was not significant. Having a sample size plan, defining primary end points, and pre-registration showed higher reporting adherence and lower risk of bias than those who did not. CONCLUSION: These findings demonstrated the inadequate quality of randomized crossover trials for digestive diseases. Compliance with the CONSORT extension for crossover trials must be strengthened and improved (PROSPERO CRD: 42021248723).

MeRIPseqPipe: an integrated analysis pipeline for MeRIP-seq data based on Nextflow.

SUMMARY: MeRIPseqPipe is an integrated and automatic pipeline that can provide users a friendly solution to perform in-depth mining of MeRIP-seq data. It integrates many functional analysis modules, range from basic processing to downstream analysis. All the processes are embedded in Nextflow with Docker support, which ensures high reproducibility and scalability of the analysis. MeRIPseqPipe is particularly suitable for analyzing a large number of samples at once with a simple command. The final output directory is structured based on each step and tool. And visualization reports containing various tables and plots are provided as HTML files. AVAILABILITY AND IMPLEMENTATION: MeRIPseqPipe is freely available at https://github.com/canceromics/MeRIPseqPipe. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

METTL1 promotes hepatocarcinogenesis via m7 G tRNA modification-dependent translation control.

BACKGROUND: N7 -methylguanosine (m7 G) modification is one of the most common transfer RNA (tRNA) modifications in humans. The precise function and molecular mechanism of m7 G tRNA modification in hepatocellular carcinoma (HCC) remain poorly understood. METHODS: The prognostic value and expression level of m7 G tRNA methyltransferase complex components methyltransferase-like protein-1 (METTL1) and WD repeat domain 4 (WDR4) in HCC were evaluated using clinical samples and TCGA data. The biological functions and mechanisms of m7 G tRNA modification in HCC progression were studied in vitro and in vivo using cell culture, xenograft model, knockin and knockout mouse models. The m7 G reduction and cleavage sequencing (TRAC-seq), polysome profiling and polyribosome-associated mRNA sequencing methods were used to study the levels of m7 G tRNA modification, tRNA expression and mRNA translation efficiency. RESULTS: The levels of METTL1 and WDR4 are elevated in HCC and associated with advanced tumour stages and poor patient survival. Functionally, silencing METTL1 or WDR4 inhibits HCC cell proliferation, migration and invasion, while forced expression of wild-type METTL1 but not its catalytic dead mutant promotes HCC progression. Knockdown of METTL1 reduces m7 G tRNA modification and decreases m7 G-modified tRNA expression in HCC cells. Mechanistically, METTL1-mediated tRNA m7 G modification promotes the translation of target mRNAs with higher frequencies of m7 G-related codons. Furthermore, in vivo studies with Mettl1 knockin and conditional knockout mice reveal the essential physiological function of Mettl1 in hepatocarcinogenesis using hydrodynamics transfection HCC model. CONCLUSIONS: Our work reveals new insights into the role of the misregulated tRNA modifications in liver cancer and provides molecular basis for HCC diagnosis and treatment.