The common marmoset has emerged as an increasingly valuable non-human primate model in neuroscience and biomedical research. Recombinant adeno-associated viruses (AAVs) are powerful tools for gene delivery and gene therapy. However, a systematic comparison of different AAV capsids and delivery routes remains lacking in marmosets. In this study, we constructed a barcoded AAV library comprising 21 capsid variants and administered it to marmosets via intravenous, intraventricular, and intrastriatal injections. To evaluate the AAV tropism, we quantified vector DNA, viral RNA abundance, and tdTomato signals in the marmoset brain and other tissues. Intravenous administration led to limited brain transduction, while intraventricular and intrastriatal administrations demonstrated high transduction efficiency in the marmoset brain. Notably, some AAV capsids exhibited distinct transduction patterns in the marmoset brain. These results offer valuable guidance for optimizing AAV-based gene delivery strategies in marmoset models and support their utility in both basic neuroscience research and potential therapeutic applications.

This file includes: Materials and Methods; Figures. S1 to S22; Tables. S1, S2, S3, S4, S5 and S7; Original Western-blot images

As systematic comparisons of editing efficiency and specificity seldom keep pace with rapid developments in RNA-guided nucleases (RGNs), the current study examined 50 such editing systems and characterized the off-target effects and genomic structural impacts of a subset of high-efficiency RGNs. Among them, AsCas12a-Ultra, LbCpf1, and AsCas12a-Plus demonstrated similar or higher efficiency compared to SpCas9, while the relatively high efficiency and small size of enOsCas12f1 together support its suitability for in vivo delivery. AsCpf1-YH and FnCpf1 exhibited the lowest single-guide RNA-dependent (sgRNA-dependent) off-target risks, whereas DpFNuc showed the highest. Genomic structural analysis revealed that enCas12f-HKRA frequently introduces chromosomal translocations, while Cas12j-SF05 poses a lower risk of such mutations. Notably, the high-efficiency RGNs were associated with translocation hotspots. Additionally, enRhCas12f1 and SpaCas12f1 had the lowest cytotoxicity, while enAsCpf1-HF strongly inhibited cell proliferation. This study establishes the first multidimensional performance evaluation framework for RGNs, providing a data-driven tool to support precise genome editing.

Lung cancer remains a leading cause of cancer-related mortality worldwide, with nonsmall cell lung cancer (NSCLC) accounting for approximately 85% of cases. Herein, we develop a split G-quadruplex-programmed fluorescent platform integrating exonuclease III (Exo-III)-assisted dual signal amplification for ultrasensitive detection of the NSCLC-related miRNA let-7a. This platform incorporates two synergistic background-suppression strategies: immobilization of sensing components on a microplate to remove interfering substances and enzymatic cleavage byproducts, and the employment of malachite green as an aggregation-induced emission fluorophore that activates only upon specific G-quadruplex binding. The Exo-III-mediated dual recycling mechanism substantially enhances detection sensitivity. Under optimized conditions, the platform achieves an exceptionally low detection limit of 0.76 fM with a wide linear range from 1 fM to 50 nM. The method exhibits excellent specificity for discriminating let-7a from homologous miRNAs, high recovery rates (97.6-104.3%) in serum samples, and strong correlation with qRT-PCR. This simple, robust platform holds great promise for early NSCLC diagnosis and clinical monitoring.

Verrucomicrobiota are widely distributed across various habitats but are difficult to culture. Some previous multiomics analyses reported that Verrucomicrobiota have outstanding metabolic capacity for organic matter degradation and are able to degrade and synthesize polysaccharides, two activities that could contribute significantly to the Earth's carbon cycle. Here, we isolated from marine sediment two novel strains, Thalassobacterium maritimum SDUM461003T and Thalassobacterium sedimentorum SDUM461004T, that represent a new genus of the difficult-to-culture phylum Verrucomicrobiota. Genome analysis, functional annotation, and experimental verification revealed that these two strains degrade polysaccharides and antibiotics, including some complex sulfated polysaccharides (SPs), primarily fucoidan and chondroitin sulfate. Moreover, electron microscopy images revealed that these bacteria can synthesize and store large amounts of glycogen. These polysaccharide degradation and synthesis capacities also exist but differ under nitrogen-deficient conditions, indicating that Verrucomicrobiota may have the potential to maintain their normal metabolism by nitrogen fixation under aerobic conditions. Given that polysaccharides and their degradation products are particularly crucial carbon sources for marine microorganisms, Verrucomicrobiota are thought to be important contributors to biogeochemical cycling in the ocean. IMPORTANCE:Verrucomicrobiota are widely distributed and able to utilize a variety of difficult-to-biodegrade polysaccharides, which have a significant impact on the marine carbon cycle. However, there are not enough pure culture strains of Verrucomicrobiota, as hard-to-cultivate bacteria, for us to study. Here, our study reports a new genus in the phylum Verrucomicrobiota and investigates their ability to degrade and synthesize a variety of polysaccharides as well as the mechanism of utilizing difficult-to-degrade polysaccharides. We also explored their special performance on carbon utilization in marine nitrogen-deficient environments. This contributes to deepening our understanding of the involvement of marine microorganisms in the marine carbon cycle.

The liver exhibits extensive circadian regulation among organs. Epidemiological studies have substantiated that disruptions in circadian rhythm constitute a risk factor for the oncogenesis of liver cancer. Nonetheless, the molecular underpinnings of how circadian dysregulation influences liver cancer progression remain elusive. Our research aims to elucidate these mechanisms and develop a predictive model for prognosis and treatment responsiveness. Our multi-omics analysis revealed extensive dysregulation of liver circadian genes (LCGs) in liver cancer. Employing machine learning algorithms, we pinpointed four pivotal dysregulated LCGs. Through the integration of single-cell, bulk, and spatial transcriptomics, we further elucidated the interconnections between LCGs dysregulation and the tumor microenvironment. In vivo and in vitro experiments demonstrated that RBM17, identified as a crucial dysregulated LCG, promotes the progression of liver cancer and cisplatin resistance by facilitating cancer stem cell phenotype. The circadian prognosis scores (CPS), based on these four genes, effectively reflected the prognosis of liver cancer patients and their responses to various therapeutic interventions. Mechanism of Action (MOA) analysis suggested that high CPS level may sensitize tumors to cell cycle-targeted therapies. Collectively, our findings provide new insights into the interplay between liver circadian gene regulation and liver cancer progression, and propose novel therapeutic targets for liver cancer.

ADAR is highly expressed and correlated with poor prognosis in hepatocellular carcinoma (HCC), yet the role of its constitutive isoform ADARp110 in tumorigenesis remains elusive. We investigated the role of ADARp110 in HCC and underlying mechanisms using clinical samples, a hepatocyte-specific Adarp110 knock-in mouse model, and engineered cell lines. ADARp110 is overexpressed and associated with poor survival in both human and mouse HCC. It creates an immunosuppressive microenvironment by inhibiting total immune cells, particularly cytotoxic GZMB + CD8 + T cells infiltration, while augmenting Treg cells, MDSCs, and exhausted CD8 + T cells ratios. Mechanistically, ADARp110 interacts with SNRPD3 and RNPS1 to stabilize CD24 mRNA by inhibiting STAU1-mediated mRNA decay. CD24 protects HCC cells from two indispensable mechanisms: macrophage phagocytosis and oxidative stress. Genetic knockdown or monoclonal antibody treatment of CD24 inhibits ADARp110-overexpressing tumor growth. Our findings unveil different mechanisms for ADARp110 modulation of tumor immune microenvironment and identify CD24 as a promising therapeutic target for HCCs.

RNA modification, as a crucial post-transcriptional regulatory mechanism, plays a pivotal role in normal physiological processes and is closely associated with the onset and progression of various human diseases. Recent studies have highlighted significant alterations in the level of RNA modifications, including m6A, m6Am, m1A, m5C, m7G, ac4C, Ψ, and A-to-I editing, across multiple diseases. These findings suggest the potential of RNA modifications and their regulatory factors as biomarkers for early disease diagnosis and prognosis. This review provides an overview of statistical methods, machine learning techniques employed in identifying disease diagnostic and prognostic biomarkers, along with relevant evaluation metrics and bioinformatics tools. We further explore the types of common RNA modifications, the modifying proteins involved, and the underlying mechanisms of modification. The focus of this paper is on the application of machine learning algorithms in discovering RNA modification-related biomarkers, particularly for disease diagnosis and prognosis. By reviewing recent advancements in the identification of disease biomarkers, and analyzing the prospects and challenges of their clinical application, we aim to offer insights into the mining methods of RNA modifications and their associated factors as disease diagnostic or prognostic biomarkers, providing a valuable reference for future research and clinical practice.

The SPARDA system,a short Argonaute-based bacterial defense mechanism,employs guide RNA to recognize invad-ing complementary DNA and degrade both invader and the host genome,leading to cell death or dormancy.A recent paper published in Cell Research elucidated the activation mechanism of Novosphingopyxis baekryungensis NbaSPARDA by capturing cryo-EM snapshots,demonstrating that guide RNA-target DNA heteroduplex formation triggers filament assembly and subsequent activation of collateral nuclease activity on environmental nucleic acids.

Plant benzylisoquinoline alkaloids (BIAs) are a group of plant-specialized metabolites with significant pharmacological properties. In lotus (Nelumbo nucifera), BIAs accumulate primarily in the leaf blade and plumule organs. The two organs, however, accumulate quite different types of BIAs, within the former primarily aporphine-type BIAs, while the latter predominantly bis-BIAs. Herein, we demonstrate that the spatial regulation of BIA biosynthesis in lotus is coordinately controlled through the NnMYC2-NnMYB14-NnCYP80 modules. Genome-wide screening of lotus CYP80 genes discovered two tandemly arrayed yet tissue-specific NnCYP80s that are identical to the previously reported NnCYP80G and NnCYP80A, respectively. NnCYP80G is expressed primarily in the lotus laminae, while NnCYP80A is expressed particularly in the plumules. Our enzyme assays confirmed the proaporphine synthase activity of NnCYP80G and the bis-BIA synthase activity of NnCYP80A, and revealed the aporphine synthase activity of NnCYP80G by efficiently converting the (R)-reticuline substrate into corytuberine. In addition, we characterized an R2R3 MYB transcription factor (TF) NnMYB14, which binds directly to the NnCYP80G and NnCYP80A promoters and positively regulates their expression. NnMYC2, the core regulator in the JA signaling pathway, acts very upstream of NnMYB14, by binding directly to the NnMYB14 promoter and inducing its expression. Our results resolved that the organ-specific accumulation of BIAs in lotus is attributed to the tissue-specially expressed NnCYP80G and NnCYP80A genes, and the NnMYC2-NnMYB14 TF module could positively regulate the NnCYP80G and NnCYP80A expression and the lotus BIA biosynthesis.