Licorice is an important medicinal herb worldwide, including three Chinese Pharmacopoeia species (Glycyrrhiza uralensis, G. inflata, G. glabra), with bioactive compounds crucial for disease treatment and industrial applications. However, the genetic mechanisms underlying the biosynthesis, diversification, and environmental adaptation of bioactive compounds in Glycyrrhiza species have long remained unclear. Herein, we assembled a gapless telomere-to-telomere (T2T) genome of G. uralensis with resolved telomeres and centromeres and three significantly improved high-quality chromosome-level Glycyrrhiza genomes, alongside a variation map of 188 wild accessions. Population analysis revealed evolutionary divergence among species, with selection signals linked to medicinal compound pathways. We identified 4CL5 as a key gene for stress response and compound synthesis. GWAS validation highlighted the GiPHL1-Gi4CL5 module's role in licochalcone A accumulation and enhanced stress adaptation in G. inflata. This study provides the first T2T Glycyrrhiza genome and insights into medicinal compound biosynthesis and environmental adaptation.
Immunosenescence, a major hallmark of systemic aging, refers to the progressive functional decline of the immune system. This decline not only compromises host defense and immunological memory but also fuels chronic inflammation and tissue degeneration (collectively known as inflammaging). While single-cell RNA sequencing (scRNA-seq) has revealed transcriptomic alterations associated with immune aging, analyses restricted to transcript abundance fail to capture deeper regulatory layers, such as transcript isoform diversity and the remodeling of immune receptor repertoires. To address this limitation, we present a human peripheral immune single-cell multi-omics atlas that integrates gene expression, transcript isoform diversity, and immune receptor repertoires. By combining single-cell full-length transcriptome sequencing (scCycloneSEQ), short-read scRNA-seq, and single-cell immune receptor sequencing (scTCR/BCR-seq), we systematically profiled peripheral blood mononuclear cells (PBMCs) from healthy donors aged 30–40 and 60–70 years. Our analyses uncovered extensive age-related remodeling of immune cell composition, functional states, and TCR/BCR diversity. Notably, we found that CD4+ effector memory T cells exhibited widespread differential isoform usage (DIU), 3′UTR length variation, and a marked reshaping of cytotoxic T lymphocyte (CTL) clonotypes—all of which were closely associated with aging-related inflammation and cellular senescence. This multi-omics atlas delineates key molecular features of immunosenescence and provides a high-resolution resource for deciphering the regulatory architecture underlying immune aging.
Multi-walled carbon nanotubes (MWCNTs) have emerged as promising candidates for bone tissue engineering due to their excellent biocompatibility, mechanical strength, and chemical stability. However, disparities often exist between their osteogenic performance in vitro and in vivo. The formation of protein corona on biomaterials is a key factor that may govern these biological outcomes. This study investigated how the distinct protein corona compositions in mouse serum (MS) and fetal bovine serum (FBS) modulate the immune recognition and osteogenic capacity of MWCNTs, thereby mimicking in vitro and in vivo environments, respectively. It was demonstrated that the MS-derived corona complexes, enriched with immunoreactive proteins such as complement 3, potently induced a pro-inflammatory M1 response via recognizable immune signals in both Raw264.7 cells and a mouse calvarial defect model. In contrast, FBS-derived corona complexes lacked murine-specific "alarm signals", thereby attenuating reactive oxygen species generation and polarizing macrophages toward M2 phenotype both in vitro and in vivo. Consequently, the MS-derived corona conferred no significant osteogenic effect, whereas the FBS-derived corona markedly enhanced osteogenic differentiation. We propose that the FBS corona acts as a physical barrier, preventing subsequent adsorption of host alarm signals onto MWCNTs, thereby suppressing immunogenicity and enhancing osteogenesis. These findings highlight a critical limitation of using FBS in conventional in vitro models for predicting in vivo immune responses, and underscore the decisive role of species-specific immune recognition in determining the osteogenic fate of biomaterials.
Sexual reproduction in plants is a tightly coordinated process that underpins biodiversity, drives speciation, and serves as a foundation for modern crop improvement. Here, we synthesize recent advances in elucidating the molecular mechanisms governing major reproductive events in flowering plants, including male and female gametogenesis, pollen-pistil communication, double fertilization, embryogenesis, and endosperm-mediated seed development. We also discuss the integration of asexual propagation through protoplast regeneration, highlighting its emerging importance in plant biotechnology. Together, these insights deepen our understanding of fundamental reproductive biology and open new opportunities for the rational design of hybrid breeding systems and stress-resilient crops, with broad implications for global food security under changing climatic conditions.
Patients with autoimmune diseases (AIDs) are at an increased risk of developing cancer; however, the immunometabolic programs that shape this comorbidity remain incompletely defined. We integrated targeted serum metabolomics with multiplex profiling of cytokines, chemokines, and immune checkpoint proteins in patients with five major AIDs-idiopathic inflammatory myopathies, rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome, and systemic sclerosis-with or without cancer. A total of 49 patients with AID and comorbid cancer (AID-CA), 47 patients with AID alone, and 15 healthy controls were enrolled. Compared with AID alone, AID-CA was associated with coordinated remodeling of amino acid and nucleotide metabolism, dominated by the alanine, aspartate, and glutamate pathways. Decreased L-glutamine and increased L-glutamic acid levels were consistently observed and remained significant after the false discovery rate correction. Immune profiling revealed modest but consistent differences, including higher levels of CXCL9 and Galectin-9 and lower levels of selected checkpoint molecules in AID-CA. The effects of major metabolites and immune mediators were directionally stable after adjusting for age, sex, treatment exposure, and autoimmune disease subtype. Integrative analyses revealed stronger associations between metabolites and immune mediators in AID-CA, centered on CXCL9 and Galectin-9, and linked to amino acid and pyrimidine metabolism. In ex vivo assays, perturbation of glutamine or arginine availability preferentially modulated the release of CXCL9 and Galectin-9 from peripheral blood mononuclear cells of patients with AID-CA. Together, these findings define an internally consistent immunometabolic pattern associated with cancer comorbidities in patients with AIDs. They nominated amino acid metabolism and CXCL9/Galectin-9-centered immune signaling as candidates for mechanistic investigation and biomarker development, while underscoring the need for validation in larger, longitudinal, and disease-specific cohorts.
Apoptotic vesicles (ApoVs) facilitate intercellular communication. Cardiac fibroblasts (CFbs) undergo apoptosis during myocardial ischemia-reperfusion (MI/R), but their ApoVs' role in cardiomyocyte survival is unknown. Here, CFbs-ApoVs were isolated from fibroblast conditioned medium (FCM). Transmission electron microscopy, nanoparticle tracking analysis, and protein blotting were used to characterize the properties of CFbs-ApoVs. Bioinformatics screening and experimental validation identified the molecular markers of CFbs-ApoVs. Enriched CFbs-ApoVs were explored in their effects and mechanisms on cardiomyocytes in vitro and in vivo. This study identified and characterized the apoptotic CFbs-derived ApoVs subtypes: CD22+-CFbs-ApoVs. The results showed that CD22+-CFbs-ApoVs were efficiently homed to cardiomyocytes. Mechanistically, miR-1246, which is enriched in CD22+-CFbs-ApoVs, effectively inhibits p53 protein expression and the translocation of p53 from the nucleus to mitochondria in MI/R-injured cardiomyocytes, rescues mitochondrial damage, and suppresses cardiomyocyte apoptosis. Overexpression of miR-1246 or inhibition of p53 enhanced the protective effect of CD22+-CFbs-ApoVs on injured cardiomyocytes. We found that CD22+-CFbs-ApoVs are effective endogenous cardioprotective vectors that can target cardiomyocytes for fusion, and we also revealed the dual inhibitory effect on p53 mediated by miR-1246. This study revealed a previously unidentified cell-to-cell communication mechanism of apoptotic CFbs that serves to promote cardiomyocyte survival during MI/R, and it also implies the potential use of ApoVs for combating MI/R injury.
Unconventional TCRαβ+ CD4−CD8− double negative T cells (DNT) can effectively impede the progression of leukemia, lymphoma, and solid tumors, highlighting their potential as a novel and effective cell therapy approach for cancer. However, the intrinsic mechanisms regulating DNT homeostasis and anti-tumor functions remain unclear. In this study, we discovered that DNT highly expressed IFITM1 (interferon-induced transmembrane protein 1) and further demonstrated that IFITM1 actively regulated the anti-tumor function of DNT both in vitro and in vivo. Furthermore, our investigation revealed that IFITM1+ DNT exhibited elevated expression of key molecules involved in immune cell-mediated anti-tumor responses, such as perforin, granzyme B, and NKG2D. Overexpression of IFITM1 promoted DNT anti-tumor activity. Notably, IFITM1 regulated mitophagy, which contributed to the improved mitochondrial function in DNT. Mechanistically, IFITM1 in the mitochondria of DNT interacts with the autophagosomal cargo protein p62/SQSTM1, recruiting more p62/SQSTM1 to the mitochondria, thereby promoting mitophagy. It is worth noting that IFITM1 is also highly expressed in activated human DNT (hDNT), and its regulatory effect on DNT mitophagy, homeostasis, and anti-tumor function has been validated. In conclusion, IFITM1 has emerged as a crucial player in enhancing DNT-mediated anti-tumor activity by regulating mitophagy and mitochondrial function. These findings suggested that upregulating IFITM1 expression in DNT may enhance mitophagy and promote DNT survival and cytotoxic functions, ultimately providing better control over cancer.
RNA N6-methyladenosine (m6A), as the most prevalent and abundant RNA modification on mRNAs, plays indispensable roles in biological processes and development by modulating the fate of target RNAs. However, whether other METTL proteins, besides dominant METTL3 and METTL14, participate in the intricate dynamic regulation of mRNA m6A remains elusive. Here, we reveal that METTL18 catalyzes the methylation of histidine within the YTHDF2 protein, which in turn facilitates the stability of m6A-modified RNAs. Mechanistically, METTL18 directly interacts with YTHDF2 and catalyzes the methylation of histidine at position 437 of YTHDF2, attenuating its binding to m6A-modified target RNAs, thereby safeguarding these RNAs from degradation. Our findings not only demonstrate the crucial roles of METTL family proteins but also deepen our understanding of the intricate regulatory dynamics of m6A modification.
Hypospadias is one of the most common birth defects in China and a key feature of differences in sex development (DSD), yet its genetic etiology remains largely unresolved. Current diagnostic approaches using DSD-targeted gene panels have a low rate of definitive diagnoses (5.5
Understanding how biodiversity arises and how organisms adapt to different environments is fundamental to evolutionary biology. Hybridization may play an essential role in generating genetic diversity and promoting adaptation. In this work, we analyzed the population structure, demographic history, and selective landscapes of East Asian domestic pigs using a whole-genome resequencing dataset of 1,092 samples from 43 breeds. Our results indicate that North and South pigs form two deeply divergent lineages that split approximately 17,797 years ago, with no extant wild boar population identified as the direct ancestor of South pigs. In contrast, Central and Southwest pigs originated from a North ancestral background (∼9,012 years ago) with introgression from South pigs before their divergence (∼6,284 years ago), which was likely driven by bidirectional migrations between ancient northern and southern human populations in China. The North ancestry under selection contributed to increased body weight, while the South ancestry enhanced environmental adaptation through pathways involved in UV-B response, stress tolerance, and extracellular matrix remodeling. This South-derived ancestry facilitated the geographic expansion of North pigs into broader ecological zones, which led to the establishment of the Central and Southwest pigs. Specifically, we demonstrate that North-South hybridization increases genetic diversity and produces a mosaic inheritance pattern. Moreover, hybridization and adaptive introgression contribute to novel phenotypic variation in domesticated animals, offering valuable insights for genetic improvement and selective breeding.
Engineered nanomaterials are frequently utilized as vectors for the targeted delivery of biomolecules such as DNA, RNA, proteins, and protein-nucleic acid complexes in mammalian cells, showing significant potential in medical applications. However, their use in plants remains limited. Little is known about the mechanisms of nanomaterial transport in plant cells and how their properties influence their internalization ability, which restricts their application in plant systems. In this review, we systematically summarize the translocation mechanism of nanomaterials within plant systems, and highlight how the size, shape, stiffness, and surface properties of nanomaterials affect their internalization in plants. Moreover, we discuss the types of cargoes and the transformation strategies employed in nanomaterial-mediated delivery. Finally, we highlight the key challenges and emerging opportunities associated with nanomaterial-based plant delivery systems, aiming to provide critical insights for advancing biomolecule delivery technologies in plant biotechnology.
Biomolecular condensates formed through phase separation have emerged as a central principle of cellular organization, enabling the dynamic regulation of gene expression, signaling, metabolism, and stress responses. While early conceptual advances in condensate biology have largely originated from animal and in vitro systems, plant cells present a unique set of biological and technical challenges, including rigid cell walls, turgor pressure, plastid autofluorescence, complex endomembrane organization, and acute environmental responsiveness. These distinctive features impede the direct transfer of existing methodologies and drive the development of heterogeneous experimental practices. In this community comment, we present a comprehensive methodological framework for studying biomolecular condensates in plants, spanning in silico prediction, in vitro reconstitution, molecular dynamics simulations, live-cell and super-resolution imaging, material property measurements, membrane-associated condensates, and synthetic condensate engineering. We highlight best practices, common pitfalls, and plant-specific considerations, emphasizing the need for orthogonal validation, quantitative interpretation, and physiological relevance. By consolidating current methodologies and articulating shared principles, this review aims to establish a foundation for rigorous, reproducible, and conceptually coherent research in condensate biology of plants and beyond, with emerging implications for crop genetic improvement and synthetic biology applications.
Rapid climate change poses risks to vital ecosystem services, thereby threatening human societies that depend on these services. But how are ecosystem services prioritized by various stakeholders, and how might these differential priorities affect the evaluation of climate change impacts on ecosystem-service multifunctionality (ESMF)? To address these questions, we defined ESMF as the joint supply of multiple services relative to stakeholder demand, and conducted a social survey to obtain quantitative measures of ecosystem service prioritization from diverse stakeholders, such as pastoralists and biodiversity conservation agencies. Integrating these stakeholder-specific weightings with biophysical data from a decade-long climate change experiment, we found that stakeholders differed in their priorities, leading to differences in their evaluation of ESMF responses to climate change. Specifically, while warming and altered precipitation led to a decline in ESMF for groups prioritizing biodiversity conservation, multifunctionality was maintained or even increased for pastoralists, whose priorities focused almost entirely on forage provision. Similarly, warming was predicted to negatively impact the ESMF prioritized by environmental protection and biodiversity conservation agencies. These negative impacts were consistently stronger under dry climate conditions than under wet conditions. This work deepens our understanding of how stakeholder priorities shape the evaluation of climate change impacts on ESMF. This knowledge is essential for encouraging the development of appropriate and sustainable management strategies for local ecosystem services under climate change.
Tumor-infiltrating CD8+ T cells undergo aberrant lipid accumulation in the tumor microenvironment (TME), which triggers ferroptosis, drives T cell dysfunction, and impairs anti-tumor activity. However, strategies to protect the effector functions of CD8+ T cells by preventing ferroptosis in vivo remain limited. Here, we report that menaquinone-4 (MK-4), a form of vitamin K2, serves as a potent ferroptosis inhibitor that preserves CD8+ T cell function within the TME and enhances anti-tumor activity. Specifically, we demonstrated that MK-4 acts as a potent anti-ferroptotic agent in CD8+ T cells, thereby restoring their effector cytotoxic potential. RNA sequencing (RNA-seq) analysis revealed that MK-4 reprograms the transcriptional landscape of CD8+ T cells by reversing RSL3-induced ferroptosis-related gene expression, restoring effector-associated gene expression, and mitigating dysfunction and exhaustion programs. In adoptive cell transfer models, MK-4 pretreatment effectively suppressed ferroptosis in CD8+ T cells, enhanced their effector functions, and inhibited tumor growth. Similarly, intravenous injection of MK-4 attenuated ferroptosis in endogenous CD8+ T cells and strengthened their anti-tumor capacity. Furthermore, the combination of MK-4 with anti-programmed death-1 (PD-1) antibody therapy elicits a synergistic anti-tumor effect. Collectively, our findings reveal that MK-4 preserves CD8+ T cell function by inhibiting ferroptosis, boosts anti-tumor immunity, thereby highlighting its potential as a therapeutic strategy for cancer treatment.
Metastatic disease remains the primary cause of cancer mortality, yet the identification of robust therapeutic targets is hampered by tumor heterogeneity and microenvironmental complexity. A key challenge lies in identifying epigenetic regulators that can simultaneously inhibit tumor progression and harness immunity. Here, we leverage single-cell transcriptomics from 120 liver cancer patients to identify E1A-like inhibitor of differentiation 1 (EID1) as the sole histone acetylation regulator upregulated in both tumor cells and effector lymphocytes within metastatic sites. Systemic Eid1 deletion markedly suppresses lung metastasis in melanoma, liver cancer, and breast cancer models. This protection is mediated dominantly by natural killer (NK) cells and type I/II interferons (IFNs), as evidenced by antibody-based cell depletion and cytokine neutralization. Eid1-deficient NK cells exhibit a hyperactivated state with robust proliferation, and their adoptive transfer confers superior metastatic suppression. Notably, Eid1 deficiency augments the accumulation of NK cells and dendritic cells (DCs) in lung metastases and induces a close spatial and transcriptional DC-NK interplay for metastatic defense. Mechanistically, loss of Eid1 upregulates formyl peptide receptor 1 (FPR1) and its ligand annexin A1 (ANXA1) on DCs and NK cells, enabling a FPR1-dependent DC-NK crosstalk that strengthens type I and II IFN responses against tumor dissemination. Conditional knockout demonstrated that intratumoral accumulation of NK cells and DCs is determined by cell-intrinsic Eid1. Critically, targeted Eid1 silencing delivered by nanoparticles significantly enhanced Fpr1 expression and NK activation, eventually suppressing tumor dissemination. Collectively, our study uncovers a previously unrecognized role of EID1 in promoting cancer metastasis by dampening the DC-NK joint immunosurveillance and establishes the therapeutic potential of EID1 inhibition in NK cell transfer and siRNA-based strategies.
Vascular smooth muscle cell (VSMC) migration is the key event in the pathogenesis of atherosclerosis (AS) and plaque instability. Trimethylamine-N-oxide (TMAO) induces VSMC migration to promote the progression of AS. However, the effects of the N6-methyladenosine (m6A) modification on this process remain unclear. Here, TMAO increased total m6A levels in human aortic smooth muscle cells (HASMCs) and decreased fat mass and obesity-associated protein (FTO) and YTH domain-containing family protein 2 (YTHDF2) protein expression. FTO or YTHDF2 overexpression significantly inhibited HASMC migration induced by TMAO. Mechanistically, the COL3A1 gene was shown to be critical for the regulation of HASMC migration by FTO or YTHDF2. Furthermore, methylated RNA immunoprecipitation and RNA stability assays demonstrated that FTO bound to the COL3A1 mRNA and altered its m6A modification, resulting in its decay. In vivo, VSMC-specific FTO or YTHDF2 deletion aggravated AS and plaque instability, whereas adeno-associated virus serotype 9 (AAV9)-mediated VSMC-specific YTHDF2 overexpression or COL3A1 knockdown exerted protective effects on AS and/or plaque instability. Notably, VSMC-specific FTO deletion promoted VSMC migration in atherosclerotic lesions in ApoE−/− AS model mice, whereas VSMC-specific YTHDF2 overexpression had the opposite effect. Overall, the in vitro and in vivo evidence highlights the critical role of the FTO/YTHDF2/COL3A1 axis in VSMC migration, AS, and plaque instability, suggesting that targeting the FTO/YTHDF2/COL3A1 axis in VSMCs may be a novel and promising therapeutic strategy for the treatment and prevention of AS and plaque instability.
