Types of nuclear localization signals and mechanisms of protein import into the nucleus

In-vitro evaluation of cationic Lipopeptides as adjuvant candidate for DNA plasmid vaccine

Lipopeptides with different fatty acids (palmitic, palmitoleic, stearic, oleic, and linoleic acids) conjugated to CHSPKKKRKV were synthesised by a solid-phase peptide method using the Fmoc strategy (Fmoc-SPPS) on 2-CTC (2-chlorotritylchloride) resin. The lipopeptides were purified by RP-HPLC and characterised by ToF-ESI-MS and 1D-NMR. The capability of the lipopeptide to interact with the plasmid was evaluated by DNA agarose gel electrophoresis. The particle size of the lipopeptide/DNA complexes was determined by dynamic light scattering assay and TEM analysis. The biological activities including cytotoxicity, nitrite oxide (NO) release, and IL-6 and TNF-α production were evaluated in RAW 264.7 cells. ToF-ESI-MS revealed [M + 2H]2+ and [M + 3H]3+ ion peaks which were validated by 1H NMR and 13C NMR, confirming the lipopeptide molecular structure. All lipopeptides condensed and protected the DNA plasmid from enzymatic degradation at the lipopeptide/DNA mass ratio of 2:1. In addition, the size of the cationic lipopeptide/DNA complexes ranged from ∼250 to 700 nm. The lipopeptides showed moderate cytotoxicity with IC50 values ranging from 120 to 190 ppm, induced NO release (275-1060 ppm) and IL-6 (40-497 pg) and TNF-α (150-270 pg) production with the highest level achieved by C(18,0)-CHSPKKKRKV. In conclusion, CHSPKKKRKV-based lipopeptides with different fatty acids are potential adjuvant candidates but further evaluation in animal models is required.

CXXC5 is a ubiquitinated protein and is degraded by the ubiquitin-proteasome pathway

CXXC5, as a member of the zinc-finger CXXC family proteins, interacts with unmodified CpG dinucleotides to modulate the expression of genes involved in cellular proliferation, differentiation, and death in physiology and pathophysiology. Various signaling pathways, including mitogenic 17β-estradiol (E2), contribute to the expression and synthesis of CXXC5. However, how signaling pathways modulate protein levels of CXXC5 in cells is largely unknown. We previously reported that some key regulators, including retinoblastoma 1 and E74-like ETS transcription factor 1, of the G1 to S phase transitions are involved in the expression of CXXC5 in estrogen-responsive MCF-7 cells, derived from a breast adenocarcinoma. We, therefore, predict that the synthesis of CXXC5 is regulated in a cell cycle-dependent manner. We report here that although E2 in synchronized MCF-7 cells augments both transcription and synthesis of CXXC5 in the G1 phase, CXXC5 protein levels are primarily mediated by ubiquitination independently of cell cycle phases. Utilizing the bioUbiquitination approach, which is based on cellular biotinylation of ubiquitin, in HEK293FT cells derived from immortalized human embryonic kidney cells, followed by sequential immunoprecipitation coupled mass spectrometry analyses, we identified ubiquitinated lysine residues of CXXC5. We show in both MCF-7 and HEK293FT cells that the ubiquitinated lysine residues contribute to the degradation of CXXC5 through the ubiquitin-proteasome pathway.

Age-associated interplay between zinc deficiency and Golgi stress hinders microtubule-dependent cellular signaling and epigenetic control

Golgi abnormalities have been linked to aging and age-related diseases, yet the underlying causes and functional consequences remain poorly understood. This study identifies the interaction between age-associated zinc deficiency and Golgi stress as a critical factor in cellular aging. Senescent Golgi bodies from human fibroblasts show a fragmented Golgi structure, associated with a decreased interaction of the zinc-dependent Golgi-stacking protein complex Golgin45-GRASP55. Golgi stress is increased, and functions such as glycosylation and vesicle transport are impaired. These disturbances promote Golgi and perinuclear microtubule disassembly and subsequent mislocalization of intracellular proteins associated with cellular signaling and epigenetic control. Pharmacological induction of Golgi stress or zinc deficiency, or ablation of the Golgi-associated zinc transporter gene Zip13 in mouse fibroblasts, replicate the characteristics of cellular senescence, emphasizing the critical role of Golgi-zinc homeostasis. These findings highlight the importance of adequate zinc intake and suggest targeting Golgi dysfunction as a therapeutic strategy for alleviating age-related cellular decline.

The dual-targeted transcription factor BAI1 orchestrates nuclear and plastid gene transcription in land plants

Coordinated gene transcription in plastids and nuclei is necessary for the photosynthetic apparatus assembly during chloroplast biogenesis. Despite the identification of several transcription factors regulating nuclear-encoded photosynthetic gene transcription, transcription factors regulating plastid gene transcription are barely reported. Here, we report that BAI1 ("albino" in Chinese), a nucleus-plastid dual-targeted C2H2-type zinc-finger transcription factor in Arabidopsis, positively regulates and tunes the transcription of both nuclear and plastid genes. Knockout of BAI1 blocks chloroplast formation, producing albino seedlings and lethality. In plastids, BAI1 is a newly identified functional component of the pTAC (transcriptionally active chromosome complex), which interacts with another pTAC component, pTAC12/PAP5/HMR, to allow the effective assembly of plastid-encoded RNA polymerase (PEP) complexes. The transcript levels of PEP-dependent genes were reduced in the bai1 mutant. In contrast, the accumulation of nuclear-encoded RNA polymerase (NEP)-dependent transcripts was increased, suggesting that BAI1 is critical in maintaining PEP activity. BAI1 directly binds to the promoter regions of nuclear genes RbcSs and a plastid gene RbcL to activate their expression for RubisCO assembly. AtBAI1 homologs TaBAI1, GmBAI1a, and GmBAI1b from monocots and dicots can fully complement the defects of the Arabidopsis bai1 mutant. In contrast, Physcomitrium patens BAI1 (PpBAI1) only partially complements the bai1 mutant. Phylogenetic analysis of BAI1 and HMR uncovered that both components arose from late-diverging streptophyte algae, following a conserved evolutionary path during terrestrialization. In summary, this work unveils a BAI1-mediated transcription regulatory mechanism synchronizing the transcription of nuclear and plastid genes, necessary for hybrid photosynthetic complex assembly. This could be an intrinsic feature facilitating plant terrestrialization.

The ESCRT protein CHMP5 promotes T cell leukemia by enabling BRD4-p300-dependent transcription

Addiction to oncogene-rewired transcriptional networks is a therapeutic vulnerability in cancer cells, underscoring a need to better understand mechanisms that relay oncogene signals to the transcriptional machinery. Here, using human and mouse T cell acute lymphoblastic leukemia (T-ALL) models, we identify an essential requirement for the endosomal sorting complex required for transport protein CHMP5 in T-ALL epigenetic and transcriptional programming. CHMP5 is highly expressed in T-ALL cells where it mediates recruitment of the coactivator BRD4 and the histone acetyl transferase p300 to enhancers and super-enhancers that enable transcription of T-ALL genes. Consequently, CHMP5 depletion causes severe downregulation of critical T-ALL genes, mitigates chemoresistance and impairs T-ALL initiation by oncogenic NOTCH1 in vivo. Altogether, our findings uncover a non-oncogene dependency on CHMP5 that enables T-ALL initiation and maintenance.

Influences of chain length and conformation of guanidinylated linear synthetic polypeptides on nuclear delivery of siRNA with potential application in transcriptional gene silencing

Transcriptional gene silencing (TGS) mediated by siRNA holds promise for long-term silencing efficacy, determined by effective nuclear delivery of siRNA. However, non-viral vectors for this purpose are limited. In this work, we synthesized guanidinylated linear synthetic polypeptides (GLSPs) to explore how chain length and conformation impact siRNA delivery, especially nuclear entry. Results show that helical conformations, particularly right-handed ones, enhance siRNA loading and silencing efficiency compared to unordered structures. Increasing chain length also improves these aspects. The endocytic pathways of carrier/siRNA nanocomplexes (NCs) are mainly determined by conformation, regardless of length. Notably, some NCs derived from right-handed helices can enter cells via direct membrane penetration, like bioactivity of cell penetrating peptides (CPPs). When the peptide chain of GLSPs is long enough, all vectors can rapidly deliver siRNA to the nucleus, similar to bioactivity of nuclear localization signal peptides (NLSPs). Interestingly, helicity of the vectors aids endosomal escape of NCs. Moreover, delivering siRNA to the nucleus via GLSPs induces TGS associated with DNA promoter methylation or histone deacetylation. This study clarifies the structure-activity relationship of GLSPs in siRNA delivery, providing new insights for designing non-viral carriers for TGS.

The Third Pillar of Precision Medicine - Precision Delivery

Precision Medicine is thought of as having two main pillars: Precision Diagnosis and Precision Therapy. However, for Precision Medicine to reach its full potential, a third pillar is needed that we propose to call Precision Delivery. In the laboratory, many therapies show great efficacy when tested directly with target cells. However, upon clinical translation, they are often given via intravenous or oral administration, resulting in their systemic distribution. To ensure therapies reach target sites at the correct therapeutic levels, they are often given at higher concentrations. However, this can be associated with off-target effects, side-effects, and unwanted interactions. Delivery strategies can help mitigate this by "spatially re-coupling" therapies in vivo with target cells. This review explains the concept of Precision Delivery, which can be thought of as three interconnected, but independent, modules: targeted delivery, microenvironment modulation, and cellular interactions. While locoregional approaches directly deliver therapies into target tissues through endovascular, endoluminal, percutaneous, and implantation techniques, microenvironment modulation technologies facilitate the movement of therapies across biological barriers and through tissue matrices, so optimized therapies can reach and interact with target cells. We highlight new innovations driving advances in Precision Delivery, while also discussing the considerations and challenges that Precision Delivery faces as it becomes increasingly integrated into treatment workflows.

Genome-wide characterization of citrus remorin genes identifies an atypical remorin CsREM1.1 responsible for fruit disease resistance

Remorins (REMs) are plant-specific proteins associated with plasma membrane (PM) and exhibit diverse biological functions. However, the roles of remorins in fruit crops and fruit disease resistance remain unexplored. Here, we performed a genome-wide characterization of remorin genes from citrus (Citrus sinensis) and identified an atypical remorin CsREM1.1 responsible for fruit resistance to Penicillium digitatum (Pd), a notorious postharvest fungal pathogen of citrus. Ten remorin genes were identified in the C. sinensis genome and they were categorized into five groups. A lot of cis-elements involved in hormone and stress responsiveness were exhibited in the promoter regions of citrus remorin genes. Reverse transcription-quantitative PCR (RT-qPCR) analysis showed that the majority of citrus remorin genes, especially CsREM1.1, were significantly induced in citrus fruit upon Pd infection. Unlike typical remorins, CsREM1.1 exhibited nuclear localization in addition to its traditional PM localization. Transient expression of CsREM1.1 in the model plant Nicotiana benthamiana suppressed plant cell death triggered by BAX, an important pro-apoptotic factor, and enhanced plant resistance to Botrytis cinerea. Moreover, transient overexpression or silencing of CsREM1.1 in citrus fruit indicated the important contribution of CsREM1.1 in fruit resistance to Pd. Our study increases the understanding of plant remorins and provides valuable insights for future research on fruit disease resistance.

The membrane-associated β2e-subunit of voltage-gated calcium channels translocates to the nucleus and regulates gene expression

The β-subunit (Cavβ) is a central component of the voltage-gated calcium channel complex. It lacks transmembrane domains and exhibits both channel-related and non-related functions. Previous studies have shown that, in the absence of the Cavα1 pore-forming subunit, electrostatic interactions between the N-terminus of Cavβ2e and the plasma membrane mediate its anchoring to the cell surface. Here, we demonstrate that, upon phospholipase C activation, Cavβ2e dissociates from the plasma membrane and homogeneously distributes between the cytosol and the nucleus. Mutagenesis analysis identified critical residues in the N-terminus of the protein, including a stretch of positively charged amino acids and a dileucine motif, which serve as nuclear import and export signals, respectively. Fusion of the Cavβ2e N-terminus to a trimeric YFP chimeric construct shows that this segment suffices for nuclear shuttling. Thus, the N-terminus of Cavβ2e emerges as a regulatory hotspot region controlling the subcellular localization of the protein. Quantitative mass spectrometry analysis revealed that the heterologous expression of a nuclear-enriched Cavβ2e mutant regulates gene expression. Our findings demonstrate the presence of active nuclear localization signals in Cavβ2e that enables its nuclear targeting and regulation of protein expression. Furthermore, they establish the membrane-associated Cavβ2e as a novel signaling mediator within the phospholipase C cascade.

Hairpin Internal Nuclear Localization Signals in CRISPR-Cas9 Enhance Editing in Primary Human Lymphocytes

The incorporation of nuclear localization signal (NLS) sequences at one or both termini of CRISPR enzymes is a widely adopted strategy to facilitate genome editing. Engineered variants of CRISPR enzymes with diverse NLS sequences have demonstrated superior performance, promoting nuclear localization and efficient DNA editing. However, limiting NLS fusion to the CRISPR protein's termini can negatively impact protein yield via recombinant expression. Here we present a distinct strategy involving the installation of hairpin internal NLS sequences (hiNLS) at rationally selected sites within the backbone of CRISPR-Cas9. We evaluated the performance of these hiNLS Cas9 variants by editing genes in human primary T cells following the delivery of ribonucleoprotein enzymes via either electroporation or co-incubation with amphiphilic peptides. We show that hiNLS Cas9 variants can improve editing efficiency in T cells compared with constructs with terminally fused NLS sequences. Furthermore, many hiNLS Cas9 constructs can be produced with high purity and yield, even when these constructs contain as many as nine NLS. These hiNLS Cas9 constructs represent a key advance in optimizing CRISPR effector design and may contribute to improved editing outcomes in research and therapeutic applications.

PAMAM-Based DNA Fluorescence Nanoprobe for Rapid Whole Cellular APE1 Detection and Imaging

Apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/ref-1, APE1), a vital protein for DNA repair and cellular redox regulation, is frequently overexpressed in tumor cells, underscoring the importance of developing sensitive detection methods for early cancer diagnosis. However, the rapid detection and visualization of nuclear APE1 in tumor cells are still challenging. In this study, we successfully developed a novel DNA fluorescent nanoprobe based on polyamidoamine (PAMAM) for the rapid detection of cytoplasmic and nuclear APE1. The PAMAM surface was modified with arginine (Arg), named PR, and its hydrophobic core encapsulated the 1,6,7,12-tetrachloroperylene tetracarboxylic acid dianhydride (TA) dye to construct fluorescent nanoparticles (TPR). Furthermore, an APE1-responsive dsDNA (SP) was linked on the TPR surface, containing apurinic/apyrimidinic sites (AP sites) and the black hole quencher 2 (BHQ2) and ensuring that fluorescence remains off in the absence of APE1. TPR-SP exhibited a detection range of 0.125-25 U mL-1 and a detection limit as low as 0.03 U mL-1. Compared with the Arg-free nanoprobes (TP-SP), TPR-SP significantly accelerated endocytosis and nuclear penetration, reducing the APE1 detection time to one-quarter (from 2 to 0.5 h). Notably, the APE1 signal in the whole nucleus can also be significantly detected. Thus, the TPR nanoprobe achieves the rapid enrichment and amplification of fluorescence signals, leading to highly sensitive whole cellular APE1 detection. This innovative and efficient detection method greatly expands the technological means for early cancer detection.

Heat inducible nuclear translocation of Kdm6bb drives temperature dependent sex reversal in Nile tilapia

Understanding the primary molecular events driving temperature-dependent sex reversal (TSR) has proven challenging, particularly in distinguishing these from secondary effects of sexual differentiation. The mechanisms translating temperature into a sex-determining signal in fish are still largely unknown. Through combined transcriptomic and genome-wide histone methylation analyses of gonads in Nile tilapia (Oreochromis niloticus) exposed to normal and elevated temperatures, we observed significant upregulation of male-promoting genes (amh, dmrt1, gsdf) and suppression of female-promoting genes (wt1a and foxl3) at high temperature. These changes were correlated with methylation changes in H3K27 and H3K4 in the promoter regions of these genes. Among the histone methylation enzymes induced by high temperature, we identified the H3K27 demethylase Kdm6bb to be a key factor. Gene deletion and biochemical studies confirmed that Kdm6bb significantly impacts the H3K27 methylation level, that influences sex determination. Crucially, we discovered that the TSR function of Kdm6bb is mediated by the alternative inclusion of a previously unrecognized intron, enabling nuclear translocation of the demethylase to perform its function. Our findings refute the previously proposed "translation deficiency" mechanism of kdm6bb, and highlight the critical role of mRNA alternative splicing and subcellular localization of the demethylase in temperature-induced sex reversal.

ABCF1-K430-Lactylation promotes HCC malignant progression via transcriptional activation of HIF1 signaling pathway

Lysine lactylation plays critical roles in various diseases, including cancer. Our previous study showed that lactylation of non-histone ABCF1 may be involved in hepatocellular carcinoma (HCC) progression. In this study, we evaluated the prognostic value of ABCF1-K430la in HCC using immunohistochemical staining and performed amino acid point mutations, multi-omics crossover, and biochemical experiments to investigate its biological role and underlying mechanism. Additionally, we performed molecular docking on lactylation sites. ABCF1-K430la was highly expressed in HCC tissues and correlated with poor patient prognosis. Functionally, ABCF1-K430la promoted HCC growth and lung metastasis. Mechanistically, upon lactylation, E2 ubiquitin ligase activity of ABCF1 remained unaffected, and ABCF1 entered the nucleus, bound to the KDM3A promoter to upregulate its expression, and activated the KDM3A-H3K9me2-HIF1A axis, challenging the notion that ABCF1 functions exclusively in cytoplasmic protein translation. Notably, we discovered the existence of a lactate-ABCF1(430Kla)-HIF1A-lactate in HCC. A small-molecule drug screen targeting ABCF1-K430la revealed that tubuloside A inhibits ABCF1-K430la and suppresses HCC development. These findings demonstrate that elevated ABCF1-K430la expression promotes HCC development, suggesting it as a potential prognostic biomarker and therapeutic target for HCC.

Exploring the Cytoplasmic Retention of CRISPR-Cas9 in Eukaryotic Cells: The Role of Nuclear Localization Signals and Ribosomal Interactions

Cas9 must be localized to the nucleus to access the genome of mammalian cells. For most proteins, adding a single nuclear localization signal (NLS) is sufficient to promote nuclear entry. However, Cas9 nuclear entry appears to be inefficient as multiple NLSs are typically added to Cas9. Here, we found that three different Cas9 variants interact with the ribosome in HEK293T cells, and that this interaction is RNA mediated. Following immunoprecipitation-mass spectrometry of cytoplasmic-localized Cas9-0NLS and nuclear-localized Cas9-4NLS constructs, we identified novel Cas9 interactors in postmitotic neurons, including KEAP1 and additional ribosomal subunits, the latter were enriched in Cas9-0NLS samples. Collectively, our results suggest that Cas9 is sequestered in the cytoplasm of mammalian cells, in part, via interaction with the ribosome. Increasing the number of NLSs on Cas9 and/or increasing the amount of cytoplasmic guide RNA has the potential to outcompete ribosomal RNA binding and promote efficient nuclear localization of CRISPR-Cas9 variants.

Efficient Intracellular Delivery of CRISPR-Cas9 Ribonucleoproteins Using Dendrimer Nanoparticles for Robust Genomic Editing

CRISPR-Cas9, a flexible and efficient genome editing technology, is currently limited by the challenge of delivering the large ribonucleoprotein complex intracellularly and into the nucleus. Existing delivery techniques/vectors are limited by their toxicity, immunogenicity, scalability, and lack of specific cell-targeting ability. This study presents a neutral, non-toxic dendrimer conjugate construct that shows promise in overcoming these limitations. We covalently-conjugated S. pyogenes Cas9-2NLS (Cas9-nuclear localization sequence) endonuclease to a hydroxyl PAMAM dendrimer through a glutathione-sensitive disulfide linker via highly specific inverse Diels-alder click reaction (IEDDA), and a single guide RNA (sgRNA) was complexed to the Cas9-dendrimer conjugate nano-construct (D-Cas9). D-Cas9- RNP produces robust genomic deletion in vitro of GFP in HEK293 cells (~100%) and VEGF in a human pigmental epithelium cell line (ARPE-19) (20%). The uptake of the D-Cas9-RNP constructs on similar timescales as small molecules highlights the robustness of the biophysical mechanisms enabling the dendrimer to deliver payloads as large as Cas9, while retaining payload functionality. This promising conjugation approach enabled better stability to the neutral construct. Combined with recent advances in hydroxyl dendrimer delivery technologies in the clinic, this approach may lead to advances in 'neutral' dendrimer-enabled non-toxic, cell-specific, highly efficient in vitro and in vivo genome editing.

Phosphate-dependent nuclear export via a non-classical NES class recognized by exportin Msn5

Gene expression in response to environmental stimuli is dependent on nuclear localization of key signaling components, which can be tightly regulated by phosphorylation. This is exemplified by the phosphate-sensing transcription factor Pho4, which requires phosphorylation for nuclear export by the yeast exportin Msn5. Here, we present a high resolution cryogenic-electron microscopy structure showing the phosphorylated 35-residue nuclear export signal of Pho4, which binds the concave surface of Msn5 through two Pho4 phospho-serines that align with two Msn5 basic patches. These findings characterize a mechanism of phosphate-specific recognition mediated by a non-classical signal distinct from that for Exportin-1. Furthermore, the discovery that unliganded Msn5 is autoinhibited explains the positive cooperativity of Pho4/Ran-binding and proposes a mechanism for Pho4's release in the cytoplasm. These findings advance our understanding of the diversity of signals that drive nuclear export and how cargo phosphorylation is crucial in regulating nuclear transport and controlling cellular signaling pathways.

Deep learning prioritizes cancer mutations that alter protein nucleocytoplasmic shuttling to drive tumorigenesis

Genetic variants can affect protein function by driving aberrant subcellular localization. However, comprehensive analysis of how mutations promote tumor progression by influencing nuclear localization is currently lacking. Here, we systematically characterize potential shuttling-attacking mutations (SAMs) across cancers through developing the deep learning model pSAM for the ab initio decoding of the sequence determinants of nucleocytoplasmic shuttling. Leveraging cancer mutations across 11 cancer types, we find that SAMs enrich functional genetic variations and critical genes in cancer. We experimentally validate a dozen SAMs, among which R14M in PTEN, P255L in CHFR, etc. are identified to disrupt the nuclear localization signals through interfering their interactions with importins. Further studies confirm that the nucleocytoplasmic shuttling altered by SAMs in PTEN and CHFR rewire the downstream signaling and eliminate their function of tumor suppression. Thus, this study will help to understand the molecular traits of nucleocytoplasmic shuttling and their dysfunctions mediated by genetic variants.

Cas9-mediated gene-editing frequency in microalgae is doubled by harnessing the interaction between importin α and phytopathogenic NLSs

Pathogen-derived nuclear localization signals (NLSs) enable vigorous nuclear invasion in the host by the virulence proteins harboring them. Herein, inspired by the robust nuclear import mechanism, we show that NLSs originating from the plant infection-associated Agrobacterium proteins VirD2 and VirE2 can be incorporated into the Cas9 system as efficient nuclear delivery enhancers, thereby improving the low gene-editing frequency in a model microalga, Chlamydomonas reinhardtii, caused by poor nuclear localization of the bulky nuclease. Prior to evaluation of the NLSs, IPA1 (Cre04.g215850) was first defined in the alga as the nuclear import-related importin alpha (Impα) that serves as a counterpart adaptor protein of the NLSs, based on extensive in silico analyses considering the protein's sequence, tertiary folding behavior, and structural basis when interacting with a well-studied SV40TAg NLS. Through precursive affinity explorations, we reproducibly found that the NLSs mediated the binding between the Cas9 and Impα with nM affinities and visually confirmed that the fusion of the NLSs strictly localized the peptide-bearing cargoes in the microalgal nucleus without compensating for their cleavage ability. When employed in a real-world application, the VirD2 NLS increases the mutation frequency (~1.12 × 10-5) over 2.4-fold compared to an archetypal SV40TAg NLS (~0.46 × 10-5) when fused with Cas9. We demonstrate the cross-species versatility of the Impα-dependent strategy by successfully applying it to an industrial alga, Chlorella Sp. HS2. This work, focused on affinity augmentation, provides insights into increasing the frequency of gene editing, which can be advantageously used in programmable mutagenesis with broad applicability.

Protein codes promote selective subcellular compartmentalization

Cells have evolved mechanisms to distribute ~10 billion protein molecules to subcellular compartments where diverse proteins involved in shared functions must assemble. In this study, we demonstrate that proteins with shared functions share amino acid sequence codes that guide them to compartment destinations. We developed a protein language model, ProtGPS, that predicts with high performance the compartment localization of human proteins excluded from the training set. ProtGPS successfully guided generation of novel protein sequences that selectively assemble in the nucleolus. ProtGPS identified pathological mutations that change this code and lead to altered subcellular localization of proteins. Our results indicate that protein sequences contain not only a folding code but also a previously unrecognized code governing their distribution to diverse subcellular compartments.

Cdk6's functions are critically regulated by its unique C-terminus

The vital cell cycle machinery is tightly regulated and alterations of its central signaling hubs are a hallmark of cancer. The activity of CDK6 is controlled by interaction with several partners including cyclins and INK4 proteins, which have been shown to mainly bind to the amino-terminal lobe. We analyzed the impact of CDK6's C-terminus on its functions in a leukemia model, revealing a central role in promoting proliferation. C-terminally truncated Cdk6 (Cdk6 ΔC) shows reduced nuclear translocation and therefore chromatin interaction and fails to enhance proliferation and disease progression. The combination of proteomic analysis and protein modeling highlights that Cdk6's C-terminus is essential for protein flexibility and for its binding potential to cyclin D, p27Kip1 and INK4 proteins but not cyclin B. We demonstrate that the C-terminus is a unique and essential part of the CDK6 protein, regulating interaction partner binding and therefore CDK6's functionality.

Enhancing non-viral DNA delivery systems: Recent advances in improving efficiency and target specificity

DNA-based therapies are often limited by challenges such as stability, long-term integration, low transfection efficiency, and insufficient targeted DNA delivery. This review focuses on recent progress in the design of non-viral delivery systems for enhancing targeted DNA delivery and modulation of therapeutic efficiency. Cellular uptake and intracellular trafficking mechanisms play a crucial role in optimizing gene delivery efficiency. There are two main strategies employed to improve the efficiency of gene delivery vectors: (i) explore different administration routes (e.g., mucosal, intravenous, intramuscular, subcutaneous, intradermal, intratumoural, and intraocular) that best facilitates optimal uptake into the targeted cells and organs and (ii) modify the delivery vectors with cell-specific ligands (e.g., natural ligands, antibodies, peptides, carbohydrates, or aptamers) that enable targeted uptake to specific cells with higher specificity and improved biodistribution. We describe how recent progress in employing these DNA delivery strategies is advancing the field and increasing the clinical translation and ultimate clinical application of DNA therapies.

From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models

Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biology-studying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights and feature visualizer.

Subcellular Enrichment Patterns of New Genes in Drosophila Evolution

The evolutionary patterns of proteins within subcellular compartments underlie the innovation and diversification foundation of the living eukaryotic organism. The location of proteins in subcellular compartments promotes the formation of network interaction modules, which in turn reshape the architecture of higher-level protein-protein interaction networks. Here, we conducted the most up-to-date gene age dating of Drosophila melanogaster by employing recently available long-read sequencing genomes as references. We found that an elevated gene fixation in the most recent common ancestor of Drosophila genus predated the divergence between two Drosophila subgenera, and a significant tendency of these genes in D. melanogaster encode proteins that localize to the extracellular matrix, accompanying the adaptive radiation of Drosophila species. Proteins encoded by genes located in the extracellular space exhibit higher sequence divergence, suggesting a rapid evolutionary process. We also observed that proteins encoded by genes originating from the same evolutionary branches tend to co-localize in the same subcellular compartments, and proteins in the same subcellular compartment tend to interact with each other. The proteins encoded by genes that have persisted through deeper branches exhibit broader localization across multiple subcellular compartments, enhancing the likelihood of their integration into various protein or gene regulatory networks, thereby increasing functional diversity. These evolutionary patterns not only contribute to understanding the evolution of subcellular localization in proteins encoded by genes originating from different branches, but also provide insights into the evolution of protein-protein networks driven by the emergence of new genes.

Effect of Different Karyophilic Peptides on Physical Characteristics and In Vitro Transfection Efficiency of Chitosan-Plasmid Nanoparticles as Nonviral Gene Delivery Systems

A strategy to increase the transfection efficiency of chitosan-based nanoparticles for gene therapy is by adding nuclear localization signals through karyophilic peptides. Here, the effect of the length and sequence of these peptides and their interaction with different plasmids on the physical characteristics and biological functionality of nanoparticles is reported. The karyophilic peptides (P1 or P2) were used to assemble nanoparticles by complex coacervation with pEGFP-N1, pQBI25 or pSelect-Zeo-HSV1-tk plasmids, and chitosan. Size, polydispersity index, zeta potential, and morphology, as well as in vitro nucleus internalization and transfection capability of nanoparticles were determined. The P2 nanoparticles resulted smaller compared to the ones without peptides or P1 for the three plasmids. In general, the addition of either P1 or P2 did not have a significant impact on the polydispersity index and the zeta potential. P1 and P2 nanoparticles were localized in the nucleus after 30 min of exposure to HeLa cells. Nevertheless, the presence of P2 in pEGFP-N1 and pQBI25 nanoparticles raised their capability to transfect and express the green fluorescent protein. Thus, karyophilic peptides are an efficient tool for the optimization of nonviral vectors for gene delivery; however, the sequence and length of peptides have an impact on characteristics and functionality of nanoparticles.

Roles of Post-Translational Modifications of Transcription Factors Involved in Breast Cancer Hypoxia

BC is the most commonly diagnosed cancer and the second leading cause of cancer death among women worldwide. Cellular stress is a condition that leads to disrupted homeostasis by extrinsic and intrinsic factors. Among other stressors, hypoxia is a driving force for breast cancer (BC) progression and a general hallmark of solid tumors. Thus, intratumoral hypoxia is an important determinant of invasion, metastasis, treatment failure, prognosis, and patient mortality. Acquisition of the epithelial-mesenchymal transition (EMT) phenotype is also a consequence of tumor hypoxia. The cellular response to hypoxia is mainly regulated by the hypoxia signaling pathway, governed by hypoxia-inducible factors (HIFs), mainly HIF1α. HIFs are a family of transcription factors (TFs), which induce the expression of target genes involved in cell survival and proliferation, metabolic reprogramming, angiogenesis, resisting apoptosis, invasion, and metastasis. HIF1α cooperates with a large number of other TFs. In this review, we focused on the crosstalk and cooperation between HIF1α and other TFs involved in the cellular response to hypoxia in BC. We identified a cluster of TFs, proposed as the HIF1α-TF interactome, that orchestrates the transcription of target genes involved in hypoxia, due to their post-translational modifications (PTMs), including phosphorylation/dephosphorylation, ubiquitination/deubiquitination, SUMOylation, hydroxylation, acetylation, S-nitrosylation, and palmitoylation. PTMs of these HIF1α-related TFs drive their stability and activity, degradation and turnover, and the bidirectional translocation between the cytoplasm or plasma membrane and nucleus of BC cells, as well as the transcription/activation of proteins encoded by oncogenes or inactivation of tumor suppressor target genes. Consequently, PTMs of TFs in the HIF1α interactome are crucial regulatory mechanisms that drive the cellular response to oxygen deprivation in BC cells.

Structural basis for nuclear import of adeno-associated virus serotype 6 capsid protein

Adeno-associated viruses (AAVs) are the most extensively researched viral vectors for gene therapy globally. The AAV viral protein 1 (VP1) N-terminus controls the capsid's ability to translocate into the cell nucleus; however, the exact mechanism of this process is largely unknown. In this study, we sought to elucidate the precise interactions between AAV serotype 6 (AAV6), a promising vector for immune disorders, and host transport receptors responsible for vector nuclear localization. Focusing on the positively charged basic areas within the N-terminus of AAV6 VP1, we identified a 53-amino acid region that interacts with nuclear import receptors. We measured the binding affinities between this region and various nuclear import receptors, discovering a notably strong interaction with IMPα5 and IMPα7 in the low nanomolar range. We also elucidated the X-ray crystal structure of this region in complex with an importin alpha (IMPα) isoform, uncovering its binding as a bipartite nuclear localization signal (NLS). Furthermore, we show that using this bipartite NLS, AAV6 VP1 capsid protein can localize to the nucleus of mammalian cells in a manner dependent on the IMPα/IMPβ nuclear import pathway. This study provides detailed insights into the interaction between the AAV6 VP1 capsid protein and nuclear import receptors, deepening our knowledge of AAV nuclear import mechanisms and establishing a basis for the improvement of AAV6-based gene therapy vectors.IMPORTANCEAAVs, recognized as the most extensively researched viral vectors for gene therapy globally, offer significant advantages over alternatives due to their small size, non-pathogenic nature, and innate ability for tissue-specific targeting. AAVs are required to localize to the nucleus to perform their role as a gene therapy vector; however, the precise mechanisms that facilitate this process remain unknown. Despite sharing overt genomic similarities with AAV1 and AAV2, AAV6 is a unique serotype. It is currently recognized for its ability to effectively transduce hematopoietic cell lineages and, consequently, is considered promising for the treatment of immune disorders. Identifying the exact mechanisms that permit AAV6 to access the nucleus can open up new avenues for gene therapy vector engineering, which can ultimately lead to increased therapeutic benefits.

NEAT1 regulates BMSCs aging through disruption of FGF2 nuclear transport

BACKGROUND

The aging of bone marrow mesenchymal stem cells (BMSCs) impairs bone tissue regeneration, contributing to skeletal disorders. LncRNA NEAT1 is considered as a proliferative inhibitory role during cellular senescence, but the relevant mechanisms remain insufficient. This study aims to elucidate how NEAT1 regulates mitotic proteins during BMSCs aging.

METHODS

BMSCs were isolated from alveolar bone of human volunteers aged 26-33 (young) and 66-78 (aged). NEAT1 expression and distribution changes during aging process were observed using fluorescence in situ hybridization (FISH) in young (3 months) and aged (18 months) mice or human BMSCs. Subsequent RNA pulldown and proteomic analyses, along with single-cell analysis, immunofluorescence, RNA immunoprecipitation (RIP), and co-immunoprecipitation (Co-IP), were conducted to investigate that NEAT1 impairs the nuclear transport of mitotic FGF2 and contributes to BMSCs aging.

RESULTS

We reveal that NEAT1 undergoes significant upregulated and shifts from nucleus to cytoplasm in bone marrow and BMSCs during aging process. In which, the expression correlates with nuclear DNA content during karyokinesis, suggesting a link to mitogenic factor. Within NEAT1 knockdown, hallmarks of cellular aging, including senescence-associated secretory phenotype (SASP), p16, and p21, were significantly downregulated. RNA pulldown and proteomic analyses further identify NEAT1 involved in osteoblast differentiation, mitotic cell cycle, and ribosome biogenesis, highlighting its role in maintaining BMSCs differentiation and proliferation. Notably, as an essential growth factor of BMSCs, Fibroblast Growth Factor 2 (FGF2) directly abundant binds to NEAT1 and the sites enriched with nuclear localization motifs. Importantly, NEAT1 decreased the interaction between FGF2 and Karyopherin Subunit Beta 1 (KPNB1), influencing the nuclear transport of mitogenic FGF2.

CONCLUSIONS

Our findings position NEAT1 as a critical regulator of mitogenic protein networks that govern BMSC aging. Targeting NEAT1 might offer novel therapeutic strategies to rejuvenate aged BMSCs.

A framework for understanding and investigating polyphosphate-protein interactions

Many prokaryotic and eukaryotic cells store inorganic phosphate in the form of polymers called polyphosphate (polyP). There has been an explosion of interest in polyP over the past decade, in part due to newly suggested roles related to diverse aspects of human health. The physical interaction of polyP chains with specific proteins has been proposed to regulate cellular homeostasis and modulate signaling pathways in response to environmental changes. Recently, several studies have challenged existing models for how polyP interacts with its protein targets, while identifying new motifs that are capable of binding to polyP. In this review, we summarize these findings, delineate the functional implications for polyP-protein interactions at the molecular level, and define open questions that should be addressed to propel the field forward.

Multi-gene precision editing tool using CRISPR-Cas12a/Cpf1 system in Ogataea polymorpha

BACKGROUND

Ogataea polymorpha, a non-conventional methylotrophic yeast, has demonstrated significant potential for heterologous protein expression and the production of high-value chemicals and biopharmaceuticals. However, the lack of precise and efficient genome editing tools severely hinders the construction of cell factories. Although the CARISP-Cas9 system has been established in Ogataea polymorpha, the gene editing efficiency, especially for multiple genes edition, needs to be further improved.

RESULTS

In this study, we developed an efficient CRISPR-Cpf1-mediated genome editing system in O. polymorpha that exhibited high editing efficiency for single gene (98.1 ± 1.7%), duplex genes (93.9 ± 2.4%), and triplex genes (94.0 ± 6.0%). Additionally, by knocking out non-homologous end joining (NHEJ) related genes, homologous recombination (HR) efficiency was increased from less than 30% to 90 ~ 100%, significantly enhancing precise genome editing capabilities. The increased HR rates enabled over 90% integration efficiency of triplex genes, as well as over 90% deletion rates of large DNA fragments up to 20 kb. Furthermore, using this developed CRISPR-Cpf1 system, triple genes were precisely integrated into the genome by one-step, enabling lycopene production in O. polymorpha.

CONCLUSIONS

This novel multiplexed genome-editing tool mediated by CRISPR-Cpf1 can realize the deletion and integration of multiple genes, which holds great promise for accelerating engineering efforts on this non-conventional methylotrophic yeast for metabolic engineering and genomic evolution towards its application as an industrial cell factory.

Diverse genetic conflicts mediated by molecular mimicry and computational approaches to detect them

In genetic conflicts between intergenomic and selfish elements, driver and killer elements achieve biased survival, replication, or transmission over sensitive and targeted elements through a wide range of molecular mechanisms, including mimicry. Driving mechanisms manifest at all organismal levels, from the biased propagation of individual genes, as demonstrated by transposable elements, to the biased transmission of genomes, as illustrated by viruses, to the biased transmission of cell lineages, as in cancer. Targeted genomes are vulnerable to molecular mimicry through the conserved motifs they use for their own signaling and regulation. Mimicking these motifs enables an intergenomic or selfish element to control core target processes, and can occur at the sequence, structure, or functional level. Molecular mimicry was first appreciated as an important phenomenon more than twenty years ago. Modern genomics technologies, databases, and machine learning approaches offer tremendous potential to study the distribution of molecular mimicry across genetic conflicts in nature. Here, we explore the theoretical expectations for molecular mimicry between conflicting genomes, the trends in molecular mimicry mechanisms across known genetic conflicts, and outline how new examples can be gleaned from population genomic datasets. We discuss how mimics involving short sequence-based motifs or gene duplications can evolve convergently from new mutations. Whereas, processes that involve divergent domains or fully-folded structures occur among genomes by horizontal gene transfer. These trends are largely based on a small number of organisms and should be reevaluated in a general, phylogenetically independent framework. Currently, publicly available databases can be mined for genotypes driving non-Mendelian inheritance patterns, epistatic interactions, and convergent protein structures. A subset of these conflicting elements may be molecular mimics. We propose approaches for detecting genetic conflict and molecular mimicry from these datasets.

Parallel Proteomic and Transcriptomic Microenvironment Mapping (μMap) of Nuclear Condensates in Living Cells

Cellular activity is spatially organized across different organelles. While several structures are well-characterized, many organelles have unknown roles. Profiling biomolecular composition is key to understanding function but is difficult to achieve in the context of small, dynamic structures. Photoproximity labeling has emerged as a powerful tool for mapping these interaction networks, yet maximizing catalyst localization and reducing toxicity remains challenging in live cell applications. Here, we disclose a new intracellular photocatalyst with minimal cytotoxicity and off-target binding, and we utilize this catalyst for HaloTag-based microenvironment-mapping (μMap) to spatially catalog subnuclear condensates in living cells. We also specifically develop a novel RNA-focused workflow (μMap-seq) to enable parallel transcriptomic and proteomic profiling of these structures. After validating the accuracy of our approach, we generate a spatial map across the nucleolus, nuclear lamina, Cajal bodies, paraspeckles, and PML bodies. These results provide potential new insights into RNA metabolism and gene regulation while significantly expanding the μMap platform for improved live-cell proximity labeling in biological systems.

Less, but More: New Insights From Appendicularians on Chordate Fgf Evolution and the Divergence of Tunicate Lifestyles

The impact of gene loss on the diversification of taxa and the emergence of evolutionary innovations remains poorly understood. Here, our investigation on the evolution of the Fibroblast Growth Factors (FGFs) in appendicularian tunicates as a case study reveals a scenario of "less, but more" characterized by massive losses of all Fgf gene subfamilies, except for the Fgf9/16/20 and Fgf11/12/13/14, which in turn underwent two bursts of duplications. Through phylogenetic analysis, synteny conservation, and gene and protein structure, we reconstruct the history of appendicularian Fgf genes, highlighting their paracrine and intracellular functions. An exhaustive analysis of developmental Fgf expression in Oikopleura dioica allows us to identify four associated evolutionary patterns characterizing the "less, but more" conceptual framework: conservation of ancestral functions; function shuffling between paralogs linked to gene losses; innovation of new functions after the duplication bursts; and function extinctions linked to gene losses. Our findings allow us to formulate novel hypotheses about the impact of Fgf losses and duplications on the transition from an ancestral ascidian-like biphasic lifestyle to the fully free-living appendicularians. These hypotheses include massive co-options of Fgfs for the development of the oikoblast and the tail fin; recruitment of Fgf11/12/13/14s into the evolution of a new mouth, and their role modulating neuronal excitability; the evolutionary innovation of an anterior tail FGF signaling source upon the loss of retinoic acid signaling; and the potential link between the loss of Fgf7/10/22 and Fgf8/17/18 and the loss of drastic metamorphosis and tail absorption in appendicularians, in contrast to ascidians.

Evolution of antisense oligonucleotides: navigating nucleic acid chemistry and delivery challenges

INTRODUCTION

Antisense oligonucleotide (ASO) was established as a viable therapeutic option for genetic disorders. ASOs can target RNAs implicated in various diseases, including upregulated mRNA and pre-mRNA undergoing abnormal alternative splicing events. Therapeutic applications of ASOs have been proven with the Food and Drug Administration approval of several drugs in recent years. Earlier enzymatic stability and delivery remains a big challenge for ASOs. Introducing new chemical modifications and new formulations resolving the issues related to the nuclease stability and delivery of the ASOs. Excitingly, ASOs-based bioconjugates that target the hepatocyte have gained much attraction. Efforts are ongoing to increase the therapeutic application of the ASOs to the extrahepatic tissue as well.

AREA COVERED

We have briefly discussed the mechanism of ASOs, the development of new chemistries, and delivery strategies for ASO-based drug discovery and development. The discussion focuses more on the already approved ASOs and those in the clinical development stage.

EXPERT OPINION

To expand the clinical application of ASOs, continuous effort is required to develop precise delivery strategies for targeting extrahepatic tissue to minimize the off-target effects.

Importin subunit beta-1 mediates ERK5 nuclear translocation, and its inhibition synergizes with ERK5 kinase inhibitors in reducing cancer cell proliferation

The mitogen-activated protein kinase (MAPK) extracellular signal-regulated kinase 5 (ERK5) is emerging as a promising target in cancer. Indeed, alterations of the MEK5/ERK5 pathway are present in many types of cancer, including melanoma. One of the key events in MAPK signalling is MAPK nuclear translocation and its subsequent regulation of gene expression. Likewise, the effects of ERK5 in supporting cancer cell proliferation have been linked to its nuclear localization. Despite many processes regulating ERK5 nuclear translocation having been determined, the nuclear transporters involved have not yet been identified. Here, we investigated the role of importin subunit alpha (α importin) and importin subunit beta-1 (importin β1) in ERK5 nuclear shuttling to identify additional targets for cancer treatment. Either importin β1 knockdown or the α/β1 importin inhibitor ivermectin reduced the nuclear amount of overexpressed and endogenous ERK5 in HEK293T and A375 melanoma cells, respectively. These results were confirmed in single-molecule microscopy in HeLa cells. Moreover, immunofluorescence analysis showed that ivermectin impairs epidermal growth factor (EGF)-induced ERK5 nuclear shuttling in HeLa cells. Both co-immunoprecipitation experiments and proximity ligation assay provided evidence that ERK5 and importin β1 interact and that this interaction is further induced by EGF administration and prevented by ivermectin treatment. The combination of ivermectin and the ERK5 inhibitor AX15836 synergistically reduced cell viability and colony formation ability in A375 and HeLa cells and was more effective than single treatments in preventing the growth of A375 and HeLa spheroids. The increased reduction of cell viability upon the same combination was also observed in patient-derived metastatic melanoma cells. The combination of ivermectin and ERK5 inhibitors other than AX15836 provided similar effects on cell viability. The identification of importin β1 as the nuclear transporter of ERK5 may be exploited for additional ERK5-inhibiting strategies for cancer therapy.

The nuclear localization signal of CPSF6 governs post-nuclear import steps of HIV-1 infection

The early stages of HIV-1 infection include the trafficking of the viral core into the nucleus of infected cells. However, much remains to be understood about how HIV-1 accomplishes nuclear import and the consequences of the import pathways utilized on nuclear events. The host factor cleavage and polyadenylation specificity factor 6 (CPSF6) assists HIV-1 nuclear localization and post-entry integration targeting. Here, we used a CPSF6 truncation mutant lacking a functional nuclear localization signal (NLS), CPSF6-358, and appended heterologous NLSs to rescue nuclear localization. We show that some, but not all, NLSs drive CPSF6-358 into the nucleus. Interestingly, we found that some nuclear localized CPSF6-NLS chimeras supported inefficient HIV-1 infection. We found that HIV-1 still enters the nucleus in these cell lines but fails to traffic to speckle-associated domains (SPADs). Additionally, we show that HIV-1 fails to efficiently integrate in these cell lines. Collectively, our results demonstrate that the NLS of CPSF6 facilitates steps of HIV-1 infection subsequent to nuclear import and additionally identify the ability of canonical NLS sequences to influence cargo localization in the nucleus following nuclear import.

TSLP and TSLPr Expression and Localization in the Airways of COPD and Non-COPD Patients

Thymic stromal lymphopoietin (TSLP) is an alarmin cytokine activated by allergens, pathogens, and air pollutants. Recent studies suggest TSLP dysregulation in chronic inflammatory diseases. It was highlighted as a key player in the context of asthma-associated mucosal immunity. This study investigated the production and localization of TSLP and its receptors in airway epithelial cells and the related inflammatory response in chronic obstructive pulmonary disease (COPD) and non-COPD patients. TSLP transcripts and proteins were detected in epithelial cells but were not abundant at a steady state. The secretion of airway inflammatory mediators was altered in COPD in association with TSLP production. The cellular and molecular characterization of TSLP signaling may identify COPD patients that could benefit from anti-alarmin therapeutic approaches.

Sequence specificity of an essential nuclear localization sequence in Mcm3

Proteins with nuclear localization sequences (NLSs) are directed into the cell nucleus through interactions between the NLS and importin proteins. NLSs are generally short motifs rich in basic amino acids; however, identifying NLSs can be challenging due to the lack of a universally conserved sequence. In this study, we characterized the sequence specificity of an essential and conserved NLS in Mcm3, a subunit of the replicative DNA helicase. Through mutagenesis and AlphaFold 3 (AF3) modeling, we demonstrate that the precise positioning of basic residues within the NLS is critical for nuclear transport of Mcm3 through optimal interactions with importin. Disrupting these interactions impairs the nuclear import of Mcm3, resulting in defective chromatin loading of the MCM complex and poor cell growth. Our results provide a structure-guided framework for predicting and analyzing monopartite NLSs, which, despite lacking a single consensus sequence, retain key characteristics shared between the NLSs of Mcm3 and the SV40 large T antigen.

Endosomal Escape and Nuclear Localization: Critical Barriers for Therapeutic Nucleic Acids

Therapeutic nucleic acids (TNAs) including antisense oligonucleotides (ASOs) and small interfering RNA (siRNA) have emerged as promising treatment strategies for a wide variety of diseases, offering the potential to modulate gene expression with a high degree of specificity. These small, synthetic nucleic acid-like molecules provide unique advantages over traditional pharmacological agents, including the ability to target previously "undruggable" genes. Despite this promise, several biological barriers severely limit their clinical efficacy. Upon administration, TNAs primarily enter cells through endocytosis, becoming trapped inside membrane-bound vesicles known as endosomes. Studies estimate that only 1-2% of TNAs successfully escape endosomal compartments to reach the cytosol, and in some cases the nucleus, where they bind target mRNA and exert their therapeutic effect. Endosomal entrapment and inefficient nuclear localization are therefore critical bottlenecks in the therapeutic application of TNAs. This review explores the current understanding of TNA endosomal escape and nuclear transport along with strategies aimed at overcoming these challenges, including the use of endosomal escape agents, peptide-TNA conjugates, non-viral delivery vehicles, and nuclear localization signals. By improving both endosomal escape and nuclear localization, significant advances in TNA-based therapeutics can be realized, ultimately expanding their clinical utility.

Plugging synthetic DNA nanoparticles into the central dogma of life

Synthetic DNA nanotechnology has emerged as a powerful tool for creating precise nanoscale structures with diverse applications in biotechnology and materials science. Recently, it has evolved to include gene-encoded DNA nanoparticles, which have potentially unique advantages compared to alternative gene delivery platforms. In exciting new developments, we and others have shown how the long single strand within DNA origami nanoparticles, the scaffold strand, can be customized to encode protein-expressing genes and engineer nanoparticles that interface with the transcription-translation machinery for protein production. Remarkably, therefore, DNA nanoparticles - despite their complex three-dimensional shapes - can function as canonical genes. Characteristics such as potentially unlimited gene packing size and low immunogenicity make DNA-based platforms promising for a variety of gene therapy applications. In this review, we first outline various techniques for the isolation of the gene-encoded scaffold strand, a crucial precursor for building protein-expressing DNA nanoparticles. Next, we highlight how features such as sequence design, staple strand optimization, and overall architecture of gene-encoded DNA nanoparticles play a key role in the enhancement of protein expression. Finally, we discuss potential applications of these DNA origami structures to provide a comprehensive overview of the current state of gene-encoded DNA nanoparticles and motivate future directions.

FMR1 Disorders: Basics of Biology and Therapeutics in Development

Fragile X Syndrome (FXS) presents with a constellation of phenotypes, including trouble regulating emotion and aggressive behaviors, disordered sleep, intellectual impairments, and atypical physical development. Genetic study of the X chromosome revealed that substantial repeat expansion of the 5' end of the gene fragile X messenger ribonucleoprotein 1 (FMR1) promoted DNA methylation and, consequently, silenced expression of FMR1. Further analysis proved that shorter repeat expansions in FMR1 also manifested in disease at later stages in life. Treatment and therapy options do exist, but they only manage symptoms. Up to now, no cure for FMR1 disorders exists. In this review, we aim to provide an overview of FMR1 biology and the latest research focused on developing therapeutic interventions that can potentially prevent and/or reverse FXS.

Nuclear-Targeting Peptides for Cancer Therapy

Nucleus is the central regulator of cells that controls cell proliferation, metabolism, and cell cycle, and is considered the most important organelle in cells. The precision medicine that can achieve nuclear targeting has achieved good therapeutic effects in anti-tumor therapy. However, the presence of biological barriers such as cell membranes and nuclear membranes in cells limit the delivery of therapeutic agents to the nucleus. Therefore, developing effective nuclear-targeting drug delivery strategies is particularly important. Nuclear-targeting peptides are a class of functional peptides that can penetrate cell membranes and target the nucleus. They mainly recognize and bind to the nuclear transport molecules (such as Importin-α/β) and transport the therapeutic agents to the nucleus through nuclear pore complexes (NPC). This review summarizes the most recent developments of strategies for anti-tumor therapy utilizing nuclear-targeting peptides, which will ultimately contribute to the development of more effective nuclear-targeting strategies to achieve better anti-tumor outcomes.

The comprehensive SARS-CoV-2 'hijackome' knowledge base

The continuous evolution of SARS-CoV-2 has led to the emergence of several variants of concern (VOCs) that significantly affect global health. This study aims to investigate how these VOCs affect host cells at proteome level to better understand the mechanisms of disease. To achieve this, we first analyzed the (phospho)proteome changes of host cells infected with Alpha, Beta, Delta, and Omicron BA.1 and BA.5 variants over time frames extending from 1 to 36 h post infection. Our results revealed distinct temporal patterns of protein expression across the VOCs, with notable differences in the (phospho)proteome dynamics that suggest variant-specific adaptations. Specifically, we observed enhanced expression and activation of key components within crucial cellular pathways such as the RHO GTPase cycle, RNA splicing, and endoplasmic reticulum-associated degradation (ERAD)-related processes. We further utilized proximity biotinylation mass spectrometry (BioID-MS) to investigate how specific mutation of these VOCs influence viral-host protein interactions. Our comprehensive interactomics dataset uncovers distinct interaction profiles for each variant, illustrating how specific mutations can change viral protein functionality. Overall, our extensive analysis provides a detailed proteomic profile of host cells for each variant, offering valuable insights into how specific mutations may influence viral protein functionality and impact therapeutic target identification. These insights are crucial for the potential use and design of new antiviral substances, aiming to enhance the efficacy of treatments against evolving SARS-CoV-2 variants.

The Emerging Role of p21 in Diabetes and Related Metabolic Disorders

In the context of cell cycle inhibition, anti-proliferation, and the dysregulation observed in certain cancer pathologies, the protein p21 assumes a pivotal role. p21 links DNA damage responses to cellular processes such as apoptosis, senescence, and cell cycle arrest, primarily functioning as a regulator of the cell cycle. However, accumulating empirical evidence suggests that p21 is both directly and indirectly linked to a number of different metabolic processes. Intriguingly, recent investigations indicate that p21 significantly contributes to the pathogenesis of diabetes. In this review, we present a comprehensive evaluation of the scientific literature regarding the involvement of p21 in metabolic processes, diabetes etiology, pancreatic function, glucose homeostasis, and insulin resistance. Furthermore, we provide an encapsulated overview of therapies that target p21 to alleviate metabolic disorders. A deeper understanding of the complex interrelationship between p21 and diabetes holds promise for informing current and future therapeutic strategies to address this rapidly escalating health crisis.

Glycerol Kinase Drives Hepatic de novo Lipogenesis and Triglyceride Synthesis in Nonalcoholic Fatty Liver by Activating SREBP-1c Transcription, Upregulating DGAT1/2 Expression, and Promoting Glycerol Metabolism

Glycerol kinase (GK) participates in triglyceride (TG) synthesis by catalyzing glycerol metabolism. Whether GK contributes to nonalcoholic fatty liver (NAFL) is unclear. The expression of hepatic Gk is found to be increased in diet-induced and genetic mouse models of NAFL and is positively associated with hepatic SREBP-1c expression and TG levels. Cholesterol and fatty acids stimulate GK expression in hepatocytes. In HFD-induced NAFL mice, knockdown of hepatic Gk decreases expression of SREBP-1c and its target lipogenic genes as well as DGAT1/2, increases serum glycerol levels, decreases serum TG levels, and attenuates hepatic TG accumulation. Overexpression of GK in hepatocytes in mice or in culture produces opposite results. Mechanistic studies reveal that GK stimulates SREBP-1c transcription directly by binding to its gene promoter and indirectly by binding to SREBP-1c protein, thereby increasing lipogenic gene expression and de novo lipogenesis. Studies with truncated GK and mutant GKs indicate that GK induces SREBP-1c transcription independently of its enzyme activity. GK contributes to lipid homeostasis under physiological conditions by catalyzing glycerol metabolism rather than by regulating SREBP-1c transcription. Collectively, these results demonstrate that increased hepatic GK promotes de novo lipogenesis and TG synthesis in NAFL by stimulating SREBP-1c transcription and DGAT1/2 expression and catalyzing glycerol metabolism.

Beyond movement: expanding functional landscape of luteovirus movement proteins

Viruses explore the potential multifunctional capacity of the proteins encoded in their compact genome to establish infection. P4 of luteoviruses has emerged as one such multifunctional protein. Expressed from an open reading frame (ORF) nested within coat protein ORF, it displays diverse subcellular localizations and interactions, reflecting its complex role in virus infection. In this review we explore how P4, constrained by overlapping ORFs, has evolved multiple functional motifs. We analyze these motifs' conservation across different barley yellow dwarf virus (BYDV) species and related poleroviruses. We also discuss how viral proteins cooperate to facilitate movement and localization of the virus throughout infection. We provide insights into potential future research directions and suggest strategies for developing potential antiviral-resistant approaches.

Identification and functional characterization of the nuclear and nucleolar localization signals in the intrinsically disordered region of nucleomethylin

The nucleolar localization of proteins is regulated by specific signals directing their trafficking to nucleus and nucleolus. Here, we elucidate the mechanism underlying the nuclear and nucleolar localization of the nucleomethylin (NML) protein, focusing on its nuclear localization signals (NLSs) and nucleolar localization signal (NoLS). Using a combination of bioinformatic analysis and experimental validation, we identified two monopartite and one bipartite NLS motifs within NML. The combined presence of both monopartite NLSs significantly enhances nuclear localization of the protein, while specific basic amino acid clusters within the bipartite NLS are crucial for their functionality. We also reveal the functional role of the NLS-coupled NoLS motif in driving nucleolar localization of NML, which contains an arginine-rich motif essential for its function. The basic residues of the arginine-rich motif of NoLS of NML interacts with nucleophosmin 1 (NPM1), allowing the possible liquid-liquid phase separation and retention of NML in the nucleolus. Remarkably, the strong NoLS of NML can direct the nucleolar localization of a cytosolic protein, aldolase, emphasizing its potency. Overall, our findings provide insights into the combinatorial functioning of NLSs and NoLS in regulating the subcellular localization of NML, highlighting the intricate regulatory mechanisms governing its localization within the nucleus and nucleolus.

Circular RNA hsa_circ_0081343 modulates trophoblast autophagy through Rbm8a nuclear translocation

INTRODUCTION

Fetal growth restriction (FGR) is a kind of obstetric complication that seriously endangers fetal life. Recent studies reported significant reduction of hsa_circ_0081343 in human placenta developed in FGR and is involved in cell migration, invasion, and apoptosis of trophoblast by acting as microRNA sponges. Autophagy is required for invasion of trophoblast cells and for vascular remodeling during placentation. In this study, we aimed to explore the mechanistic link between hsa_circ_0081343 and autophagy.

METHODS

We investigated the interactions between hsa_circ_0081343 and RNA-binding proteins were studied by RNA pull-down assay, mass spectrometry and RNA immunoprecipitation assay. The mechanism of nuclear translocation of Rbm8a were assessed by reverse transcription-quantitative PCR, Western blot, immunofluorescence and Co-Immunoprecipitation. Western blot, immunofluorescence and transmission electron microscopy were performed to elucidate the mechanism underlying hsa_circ_0081343 and/or Rbm8a mediated regulation of autophagy.

RESULTS

hsa_circ_0081343 served as an RNA-binding protein (RBP) sponge. RNA binding motif protein 8A (Rbm8a) was directly bound to hsa_circ_0081343 in the cytoplasm, while knockdown of hsa_circ_0081343 facilitated Rbm8a localization in the nucleus. We also identified Rbm8a as a potential import cargo for Importin13 (Ipo13), which transported Rbm8a across the nuclear membrane into the nucleus. Ipo13 recognized Rbm8a via a functional nuclear localization signal (NLS). Furthermore, the mechanistic study revealed that hsa_circ_0081343-mediated nuclear translocation of Rbm8a activated trophoblast autophagy.

DISCUSSION

Our results suggest that hsa_circ_0081343 could bind to RBP and the interaction between hsa_circ_0081343 and Rbm8a participate in regulating autophagy. These findings offer novel molecular targets and insights for a potential therapeutic strategy against FGR.

Nucleic acid drugs: recent progress and future perspectives

High efficacy, selectivity and cellular targeting of therapeutic agents has been an active area of investigation for decades. Currently, most clinically approved therapeutics are small molecules or protein/antibody biologics. Targeted action of small molecule drugs remains a challenge in medicine. In addition, many diseases are considered 'undruggable' using standard biomacromolecules. Many of these challenges however, can be addressed using nucleic therapeutics. Nucleic acid drugs (NADs) are a new generation of gene-editing modalities characterized by their high efficiency and rapid development, which have become an active research topic in new drug development field. However, many factors, including their low stability, short half-life, high immunogenicity, tissue targeting, cellular uptake, and endosomal escape, hamper the delivery and clinical application of NADs. Scientists have used chemical modification techniques to improve the physicochemical properties of NADs. In contrast, modified NADs typically require carriers to enter target cells and reach specific intracellular locations. Multiple delivery approaches have been developed to effectively improve intracellular delivery and the in vivo bioavailability of NADs. Several NADs have entered the clinical trial recently, and some have been approved for therapeutic use in different fields. This review summarizes NADs development and evolution and introduces NADs classifications and general delivery strategies, highlighting their success in clinical applications. Additionally, this review discusses the limitations and potential future applications of NADs as gene therapy candidates.

Therapeutic Potential of Natural Compounds to Modulate WNT/β-Catenin Signaling in Cancer: Current State of Art and Challenges

Targeted therapies and immunotherapies have improved the clinical outcome of cancer patients; however, the efficacy of treatment remains frequently limited due to low predictability of response and development of drug resistance. Therefore, novel therapeutic strategies for various cancer types are needed. Current research emphasizes the potential therapeutic value of targeting WNT/β-catenin dependent signaling that is deregulated in various cancer types. Targeting the WNT/β-catenin signaling pathway with diverse synthetic and natural agents is the subject of a number of preclinical studies and clinical trials for cancer patients. The usage of nature-derived agents is attributed to their health benefits, reduced toxicity and side effects compared to synthetic agents. The review summarizes preclinical studies and ongoing clinical trials that aim to target components of the WNT/β-catenin pathway across a diverse spectrum of cancer types, highlighting their potential to improve cancer treatment.

Zfp260 choreographs the early stage osteo-lineage commitment of skeletal stem cells

The initial fine-tuning processes are crucial for successful bone regeneration, as they guide skeletal stem cells through progenitor differentiation toward osteo- or chondrogenic fate. While fate determination processes are well-documented, the mechanisms preceding progenitor commitment remain poorly understood. Here, we identified a transcription factor, Zfp260, as pivotal for stem cell maturation into progenitors and directing osteogenic differentiation. Zfp260 is markedly up-regulated as cells transition from stem to progenitor stages; its dysfunction causes lineage arrest at the progenitor stage, impairing bone repair. Zfp260 is required for maintaining chromatin accessibility and regulates Runx2 expression by forming super-enhancer complexes. Furthermore, the PKCα kinase phosphorylates Zfp260 at residues Y173, S182, and S197, which are essential for its functional activity. Mutations at these residues significantly impair its functionality. These findings position Zfp260 as a vital factor bridging stem cell activation with progenitor cell fate determination, unveiling a element fundamental to successful bone regeneration.