In the anthers of flowering plants, the innermost meiocytes and surrounding somatic cells (tapetum) are differentiated from the same precursor archesporial cells, and these cells acquire distinct cell identities after specification. However, the underlying mechanism regulating meiocyte identity is elusive. Here we demonstrate a conserved surveillance mechanism governed by Arabidopsis zinc-finger proteins C3H14 and C3H15, which redundantly regulate mRNA homoeostasis to ensure meiocyte identity. The meiocytes of Atc3h14 Atc3h15 display meiotic arrest accompanied by ectopic accumulation of mRNAs essential for archesporial cell differentiation and tapetum development. These meiocytes ultimately undergo reactive oxygen species bursts and programmed cell death in synchrony with the tapetum. Moreover, C3H14/C3H15 interacts with processing-body proteins and the CCR4-NOT deadenylase complex, and is required for eliminating unwanted transcripts. Consistently, CRISPR-Cas9-induced mutations in AtC3H14/15 paralogues in soybean and rice caused similar defects in meiocyte identity, indicating that the regulation of meiocyte identity by post-transcriptional RNA elimination is conserved in flowering plants.

Meiotic crossover (CO) exchanges genetic information between homologs, thereby promoting genetic diversity among offspring. COs are non-randomly distributed across chromosomes, tending to occur in euchromatin, but rarely in heterochromatin. In plants, H3 lysine 27 monomethylation (H3K27me1) is crucial for maintaining heterochromatin condensation and genome stability in somatic cells; however, its role in germline cells remains to be determined. Here, we demonstrate that the plant-specific H3K27 mono-methyltransferases ATXR5/6 (ARABIDOPSIS TRITHORAX-RELATED PROTEIN 5/6) play an important role in inhibiting CO formation in meiotic heterochromatin. In atxr5 atxr6, both ZMM-dependent Type I COs and ZMM-independent Type II COs are significantly increased. We further observed decondensation, decreased H3K27me1 signals, and specifically compromised non-CG methylation in atxr5 atxr6 meiotic heterochromatin. Unexpectedly, in contrast to their roles in somatic cells, where ATXR5/6 primarily regulate heterochromatin condensation and gene silencing without influencing DNA methylation, in meiocytes, ATXR5/6 mainly function in suppressing recombination and preserving heterochromatic DNA methylation without directly regulating gene expression. Moreover, loss of Type II CO regulator MMS AND UV SENSITIVE 81 (MUS81) leads to pericentromeric fragmentation and polyad formation during meiosis in the absence of ATXR5/6, indicating that MUS81 is critical for resolving atypical recombination intermediates in pericentromeric heterochromatin. Taken together, our results provide insights into the roles of ATXR5/6 in repressing meiotic recombination within heterochromatin by regulating chromosome compaction and modifications.

The reliance of clear cell renal cell carcinoma (ccRCC) on exogenous cholesterol import implies a metabolic susceptibility. This susceptibility represents a potential avenue that can be exploited as a novel therapeutic approach for ccRCC. Circular RNAs (circRNAs) are emerging regulators in cancer, yet their roles in ccRCC lipid metabolism and tumor microenvironment remodeling remain unclear. This study investigates the tumor-promoting role of circABCA1 in ccRCC cholesterol homeostasis and M2 macrophage polarization. The expression levels of circABCA1, IGF2BP3, SCARB1, autophagy-related proteins, and the IGF1R/PI3K/AKT/mTOR and ABCA1/ABCG1 pathways were measured using RT-qPCR and western blot. Untargeted metabolomics, RNA- sequencing, and MS2 RNA-pulldown were conducted to identify targets. Interaction analyses included RNA immunoprecipitation, RNA pull-down, and RNA fluorescence in situ hybridization (FISH) assays. Lipid raft measurements, cholesterol uptake/efflux assays, and lipophagy assessments were performed. A co-culture system between M2 macrophages and ccRCC cells was established. In vivo tumorigenesis and metastasis were evaluated using xenograft models and a hepatic metastasis model. Statistical analyses involved Student’s t-tests and ANOVA; significance set at P < 0.05. We identified a novel lipid metabolism-related circRNA, circABCA1, which was upregulated in ccRCC and positively correlated with tumor stage and distant metastasis. Functionally, circABCA1 enhanced the half-life of SCARB1 mRNA by forming a circABCA1-IGF2BP3-SCARB1 mRNA ternary complex, thereby increasing the expression of SCARB1 and consequent cholesterol uptake. Next, elevated cholesterol caused by circABCA1-SCARB1 axis-maintained lipid rafts, initiated IGF1R/PI3K/AKT/mTOR cascade, and protected lipid droplets from being destructed by lipophagy, leading to decreased cholesterol efflux. CircABCA1 facilitated the proliferation and migration of ccRCC in vitro and in vivo in a SCARB1 depended manner. Moreover, we uncovered that circABCA1 facilitated M2 macrophage polarization and subsequent pro-tumor effect by prompting cholesterol uptake of ccRCC from tumor microenvironment in a SCARB1-dependent manner. CircABCA1 plays a crucial role in promoting ccRCC progression by regulating cholesterol metabolism and facilitating M2 macrophage polarization, representing a potential therapeutic target for ccRCC treatment.

The soybean stem node is a key part of soybean growth and development, and its numbers play a crucial role in soybean yield formation. Traditional manual methods are labor-intensive and error-prone. The keypoint detection method is an ideal choice for stem node detection due to its high accuracy and wide applicability. In this study, a new deep learning method, You Only Look Once _Soybean Stalk Pose (YOLO_SSP) was proposed, which innovatively applied the Small_Effective Low-Level Aggregation Network (S_ELAN) module and fused it with a smaller detection head for detecting stem nodes in mature soybeans. After optimization and iteration, the model achieved 88.1% accuracy on the dataset. Subsequently, by ablating the model, it was found that different improvements were effective in increasing the accuracy of the model. In addition, when comparing the classic YOLO series of keypoint detection models, the results show that YOLO_SSP achieved up to 87.7% of APs, which was higher than YOLOv7-w6-pose, YOLOv7-tiny-pose, YOLOv3s-pose, YOLOv5n-pose, YOLOv5s-pose, YOLOv5m- pose, YOLOv6n-pose, YOLOv8n-pose, and YOLOv10b-pose, which were 2.5%, 12.8%, 5.3%, 3.8%, 3.5%, 3.5%, 5.1%, 5.1%, 5.0%, and 4.5% higher, respectively. Finally, the proposed model was applied to the unique dataset with 85.3% precision and 82.6% accuracy, and the visualization of the model’s detection results proved its applicability and universality. This study provides an effective strategy for soybean stem node detection and significantly improves the accuracy of detection.

Aflatoxin is a highly toxic substance found in peanuts, posing a serious threat to human health. To address this issue, an improved 1D-MCFViT model combining the Vision Transformer with multi-scale convolutional fusion is proposed to detect aflatoxin-contaminated peanuts under natural conditions. After data cleaning, indistinguishable samples in RGB images were obtained, and their spectral curves were extracted. Data generation was performed using autoencoder network and Gaussian resampling techniques, significantly enhancing the model's feature discrimination capability. This approach achieved 92.6 % accuracy and 94.4 % recall on the validation set, improving accuracy by 1.23 % over the 1D-ViT model. The performance of traditional machine learning and deep learning models before and after data generation was compared, demonstrating this method outperforms traditional machine learning models as well as mainstream deep learning models. This approach improves aflatoxin detection accuracy and provides a robust foundation for developing online detection devices.

Non-small-cell lung cancer (NSCLC) is a common and deadly cancer. IGF2BP3 has been determined as an oncogenic N6-methyladenosine modification "reader" in solid tumors. However, the role and mechanism of IGF2BP3 in NSCLC remains largely unknown. Here, we demonstrated that aberrant IGF2BP3 expression is associated with poor prognosis in NSCLC. IGF2BP3 deficiency significantly restrains cell proliferation and tumor growth in vitro and in vivo. Mechanistically, IGF2BP3 positively regulates S-Phase Kinase Associated Protein 2 (SKP2) expression. IGF2BP3 binds and stabilizes SKP2 mRNA in an m6A-dependent manner, with an elevated SKP2 expression. Further, we proved that USP10 acts as a novel deubiquitinase (DUB) of IGF2BP3 by screening a panel of 58 DUBs. USP10 increases IGF2BP3 expression by removing K48-linked polyubiquitination chains from IGF2BP3 and inhibiting its proteasome-mediated degradation.

A new disease commonly referred to as "glass post-larvae disease" (GPD) has emerged in many shrimp hatcheries in China since 2020. This highly infectious and lethal disease primarily affects 6 to 12-day-old post-larvae of Litopenaeus vannamei (L. vannamei). In hatchery environments, GPD spreads rapidly, often leading to a large-scale outbreak within 2-3 days from infection and can cause mortality rates as high as 90-100 %. The clinical signs of diseased post-larvae shrimp include low vitality, feeding cessation, empty digestive tract, white or colorless hepatopancreas and a translucent appearance. To identify the main pathogen responsible for GPD, pathogen isolation, pathogenicity tests and histopathological analysis were conducted on diseased post-larvae. A dominant strain, designated JM20210818, was isolated from diseased shrimp and identified as Vibrio parahaemolyticus by physiological and biochemical tests, as well as 16S rRNA and gyrB gene sequencing. JM20210818 did not carry the typical virulence genes pirAvp, pirBvp, tdh and trh. However, immersion challenge tests demonstrated that this strain could cause 100 % mortality in shrimp within 24 h at a concentration of 5.1 × 107 colony-forming units per milliliter (CFU/mL). Infected shrimp exhibited clinical signs consistent with GPD. Furthermore, gyrB sequence analysis confirmed that the dominant strain isolated from challenged shrimp was identical to JM20210818. Histopathological results revealed severe damage to the intestinal and hepatopancreatic tissues of shrimp infected with JM20210818. Antimicrobial-susceptibility results indicated that JM20210818 was resistant to several antibiotics, including ampicillin, cephalothin, tetracycline, amoxicillin, trimethoprim, amikacin and gentamicin. Whole-genome sequencing of JM20210818 (Illumina NovaSeq, ∼100 × coverage) assembled two circular chromosomes (5.903 Mb, 45.0 % GC) and three plasmids (p0818A-C), encoding 5396 CDS, 132 tRNAs and 37 rRNAs. A full complement of environmental-adaptation genes (σ/anti-σ factors, two-component systems, antioxidants) and complete Sec, Tat and T1-T4/VI secretion systems underscored its resilience and virulence potential. Bioinformatic screening identified 704 virulence genes and a broad array of antibiotic-resistance determinants-confirming its high pathogenicity and multidrug resistance. Transcriptomic results indicated that JM20210818 infection may induce shrimp pathology by affecting metabolic functions and regulating ferroptosis and PPAR signaling pathways. Together, these findings demonstrated that JM20210818 was not only a highly pathogenic Vibrio parahaemolyticus but also exhibited multi-drug resistance. It may further promote disease progression by disrupting shrimp metabolism and modulating ferroptosis and PPAR signaling pathways.

Precise genomic editing through the combination of CRISPR/Cas systems and recombinant adeno-associated virus (rAAV)-delivered homology directed repair (HDR) donor templates represents a powerful approach. However, the challenge of effectively suppressing leaky transcription from the rAAV vector, a phenomenon associated to cytotoxicity, persists. In this study, we demonstrated substantial promoter activities of various homology arms and inverted terminal repeats (ITR). To address this issue, we identified a novel rAAV variant, Y704T, which not only yields high-vector quantities but also effectively suppresses in cis mRNA transcription driven by a robust promoter. The Y704T variant maintains normal functionality in receptor interaction, intracellular trafficking, nuclear entry, uncoating, and second-strand synthesis, while specifically exhibiting defects in transcription. Importantly, this inhibitory effect is found to be independent of ITR, promoter types, and RNA polymerases. Mechanistic studies unveiled the involvement of Valosin Containing Protein (VCP/p97) in capsid-mediated transcription repression. Remarkably, the Y704T variant delivers HDR donor templates without compromising DNA replication ability and homologous recombination efficiency. In summary, our findings enhance the understanding of capsid-regulated transcription and introduce novel avenues for the application of the rAAV-CRISPR/Cas9 system in human gene therapy.

Heterochromatin is an organizational property of eukaryotic chromosomes, characterized by extensive DNA and histone modifications, that is associated with the silencing of transposable elements and repetitive sequences. Maintaining heterochromatin is crucial for ensuring genomic integrity and stability during the cell cycle. During meiosis, heterochromatin is important for homologous chromosome synapsis, recombination, and segregation, but our understanding of meiotic heterochromatin formation and condensation is limited. In this review, we focus on the dynamics and features of heterochromatin and how it condenses during meiosis in plants. We also discuss how meiotic heterochromatin influences the interaction and recombination of homologous chromosomes during prophase I.

Background Clear cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer with high aggressive phenotype and poor prognosis. Accumulating evidence suggests that circRNAs have been identified as pivotal mediators in cancers. However, the role of circRNAs in ccRCC progression remains elusive. Methods The differentially expressed circRNAs in 4 paired human ccRCC and adjacent noncancerous tissues ccRCC were screened using circRNA microarrays and the candidate target was selected based on circRNA expression level using weighted gene correlation network analysis (WGCNA) and the gene expression omnibus (GEO) database. CircPDHK1 expression in ccRCC and adjacent noncancerous tissues ( n = 148) were evaluated along with clinically relevant information. RT-qPCR, RNase R digestion, and actinomycin D (ActD) stability test were conducted to identify the characteristics of circPDHK1. The subcellular distribution of circPDHK1 was analyzed by subcellular fractionation assay and fluorescence in situ hybridization (FISH). Immunoprecipitation-mass spectrometry (IP-MS) and immunofluorescence (IF) were employed to evaluate the protein-coding ability of circPDHK1. ccRCC cells were transfected with siRNAs, plasmids or lentivirus approach, and cell proliferation, migration and invasion, as well as tumorigenesis and metastasis in nude mice were assessed to clarify the functional roles of circPDHK1 and its encoded peptide PDHK1-241aa. RNA-sequencing, western blot analysis, immunoprecipitation (IP) and chromatin immunoprecipitation (ChIP) assays were further employed to identify the underlying mechanisms regulated by PDHK1-241aa. Results CircPDHK1 was upregulated in ccRCC tissues and closely related to WHO/ISUP stage, T stage, distant metastasis, VHL mutation and Ki-67 levels. CircPDHK1 had a functional internal ribosome entry site (IRES) and encoded a novel peptide PDHK1-241aa. Functionally, we confirmed that PDHK1-241aa and not the circPDHK1 promoted the proliferation, migration and invasion of ccRCC. Mechanistically, circPDHK1 was activated by HIF-2A at the transcriptional level. PDHK1-241aa was upregulated and interacted with PPP1CA, causing the relocation of PPP1CA to the nucleus. This thereby inhibited AKT dephosphorylation and activated the AKT-mTOR signaling pathway. Conclusions Our data indicated that circPDHK1-encoded PDHK1-241aa promotes ccRCC progression by interacting with PPP1CA to inhibit AKT dephosphorylation. This study provides novel insights into the multiplicity of circRNAs and highlights the potential use of circPDHK1 or PDHK1-241aa as a therapeutic target for ccRCC.

This study aims to analyze the differential expression of METTL14 in pancreatic cancer (PC) tissues and adjacent normal tissues, and its correlation with clinical outcomes. According to the inclusion and exclusion criteria, a total of 80 patients diagnosed in our hospital from January 2021 to January 2023 were chosen as research subjects. RTQ-PCR has detected the mRNA level expression of METTL14 in cancer and para-cancerous tissues. Immunohistochemistry was used to detect the protein expression of METTL14 in cancer and para-cancerous tissues. To compare the relationship between METTL14 expression and clinicopathological parameters in different PC patients. Kaplan–Meier survival analysis of the relationship between METTL14 expression in PC tissues and patient survival prognosis. The Multifactor COX model evaluates factors affecting the prognosis of PC. The expression level of METTL14 mRNA in PC tissues was 5.51 ± 0.35 (kDa), and the positive rate of METTL14 protein expression in PC tissues of all patients was 73.75 (59/80). Tumor location (P = 0.012), tumor differentiation degree (P = 0.028), tumor AJCC stage (P = 0.000), and lymph node metastasis (P = 0.000) were significantly related to the positive rate of METTL14 protein expression in PC tissue. Follow-up results showed that among 80 patients, 63 died. The three-year survival rate of the METTL14 positive group was 13.56

This article is a Commentary on Xue et al. (2024), 244: 2326–2342.

Cardiovascular disease (CVD) is the leading cause of death in the world, with a high incidence and a youth-oriented tendency. RNA modification is ubiquitous and indispensable in cell, maintaining cell homeostasis and function by dynamically regulating gene expression. Accumulating evidence has revealed the role of aberrant gene expression in CVD caused by dysregulated RNA modification. In this review, we focus on nine common RNA modifications: N6-methyladenosine (m6A), N1-methyladenosine (m1A), 5-methylcytosine (m5C), N7-methylguanosine (m7G), N4-acetylcytosine (ac4C), pseudouridine (Ψ), uridylation, adenosine-to-inosine (A-to-I) RNA editing, and modifications of U34 on tRNA wobble. We summarize the key regulators of RNA modification and their effects on gene expression, such as RNA splicing, maturation, transport, stability, and translation. Then, based on the classification of CVD, the mechanisms by which the disease occurs and progresses through RNA modifications are discussed. Potential therapeutic strategies, such as gene therapy, are reviewed based on these mechanisms. Herein, some of the CVD (such as stroke and peripheral vascular disease) are not included due to the limited availability of literature. Finally, the prospective applications and challenges of RNA modification in CVD are discussed for the purpose of facilitating clinical translation. Moreover, we look forward to more studies exploring the mechanisms and roles of RNA modification in CVD in the future, as there are substantial uncultivated areas to be explored.

The status of hormone receptors (HR) at the molecular level is crucial for accurate diagnosis and effective treatment of breast cancer. Meanwhile, mammography is an effective screening method for detecting breast cancer, which significantly improve survival. However, diagnosing the molecular status of breast cancer involves a pathological biopsy, which can affect the accuracy of the diagnosis. To non-invasively diagnose the hormone receptor (HR) status of breast cancer and reduced manual annotation, we proposed a weakly supervised deep learning framework BSNet which detected breast cancer with HR status and benign tumors. BSNet was trained on 2321 multi-view mammography cases from female undergoing digital mammography for the general population at Harbin Medical University Cancer Hospital in Heilongjiang Province during the period 2017-2018 and was validated on the external cohort. The average AUCs of BSNet on the test set and the external validation set were 0.89 and 0.92, respectively. BSNet demonstrated excellent performance in non-invasive breast cancer diagnosis with HR status, using multiple mammography views without pixel annotation. Furthermore, we developed a web server (http://bsnet.edbc.org) for easy use. BSNet described high-dimensional mammography of breast cancer subtypes, which helped inform early management options.

BackgroundAlthough many biomarkers for lung adenocarcinoma (LUAD) have been identified, their specificity and sensitivity remain unsatisfactory. Endothelial lipase gene (LIPG) plays an important role in a variety of cancers, but its role in lung adenocarcinoma remains unclear. MethodsTCGA, GEO, K-M plotter, CIBERSORT, GSEA, HPA, and GDSC were used to analyze LIPG in LUAD. Data analysis was mainly achieved by R 4.0.3. ResultsThe expression of LIPG in LUAD tissues was higher than that in adjacent normal tissues, especially in women, patients aged >65 years, and those with lymph node metastasis. High expression predicted a poor prognosis. The results of enrichment analysis suggest that LIPG may exert profound effects on the development of LUAD through multiple stages of lipid metabolism and immune system regulation. In addition, LIPG expression was significantly correlated with the expression levels of multiple immune checkpoint genes and the abundance of multiple immune infiltrates, including the activated memory CD4 T cell, M1 macrophage, neutrophil, plasma cells, and T follicular helper (Tfh) cells in the LUAD microenvironment content. At the same time, patients with high LIPG expression respond well to a variety of antitumor drugs and have a low rate of drug resistance. ConclusionsLIPG is a prognostic marker and is associated with lipid metabolism and immune infiltration in LUAD.

Bone metastasis is one of the common complications of lung cancer and can lead to bone-related adverse events, such as pathological fractures, spinal cord defects, and nerve compression syndrome. As an effective medicinal component of Astragalus membranaceus, Astragalus polysaccharide (APS) has antitumor activity and alleviates osteoporosis to a certain extent. In this study, we explored the possible role and mechanism underlying APS inhibition of lung adenocarcinoma bone metastases by constructing a mouse model of lung adenocarcinoma bone metastases. First, we constructed osteoclast (OC) and osteoblast (OB) culture systems in vitro to confirm that APS affected the differentiation and function of OCs and OBs. Then, using the mouse bone metastasis model, microCT, and bone histopathology, we confirmed that APS inhibited osteolytic metastasis and tumor cell proliferation in mice, and the effect was mainly realized by inhibiting the CaSR/PTHrP signal pathway. The results showed that APS had a protective effect on lung adenocarcinoma bone metastases.

N6‑methyladenosine (m6A) RNA methylation is one of the most common post‑transcriptional modification mechanism in eukaryotes. m6A is involved in almost all stages of the mRNA life cycle, specifically regulating its stability, splicing, export and translation. Methyltransferase‑like 14 (METTL14) is a particularly important m6A methylation 'writer' that can recognize RNA substrates. METTL14 has been documented to improve the activity and catalytic efficiency of METTL3. However, as individual proteins they can also regulate different biological processes. Malignancies in the digestive system are some of the most common malignancies found in humans, which are typically associated with poor prognoses with limited clinical solutions. METTL14‑mediated methylation has been implicated in both the potentiation and inhibition of digestive system tumor growth, cell invasion and metastasis, in addition to drug resistance. In the present review, the research progress and regulatory mechanisms of METTL14‑mediated methylation in digestive system malignancies were summarized. In addition, future research directions and the potential for its clinical application were examined.

Non-small cell lung cancer (NSCLC) is the most prevalent type of cancer and the leading cause of cancer-related death. Chemotherapeutic resistance is a major obstacle in treating NSCLC patients. Here, we discovered that the E3 ligase Skp2 is overexpressed, accompanied by the downregulation of necroptosis-related regulator MLKL in human NSCLC tissues and cell lines. Knockdown of Skp2 inhibited viability, anchorage-independent growth, and in vivo tumor development of NSCLC cells. We also found that the Skp2 protein is negatively correlated with MLKL in NSCLC tissues. Moreover, Skp2 is increased and accompanied by an upregulation of MLKL ubiquitination and degradation in cisplatin-resistant NSCLC cells. Accordingly, inhibition of Skp2 partially restores MLKL and sensitizes NSCLC cells to cisplatin in vitro and in vivo. Mechanistically, Skp2 interacts and promotes ubiquitination-mediated degradation of MLKL in cisplatin-resistant NSCLC cells. Our results provide evidence of an Skp2-dependent mechanism regulating MLKL degradation and cisplatin resistance, suggesting that targeting Skp2-ubiquitinated MLKL degradation may overcome NSCLC chemoresistance.

Reciprocal exchanges of DNA between homologous chromosomes during meiosis, or crossovers (COs), shuffle genetic information in gametes and progeny. In many eukaryotes, the majority of COs (class I COs) are sensitive to a phenomenon called interference, which influences the occurrence of closely spaced double COs. Class I COs depend on a group of factors called ZMM (Zip, Msh, Mer) proteins including HEI10 (Human Enhancer of Invasion-10). However, how these proteins are recruited to class I CO sites is unclear. Here, we show that HEI10 forms foci on chromatin via a liquid–liquid phase separation (LLPS) mechanism that relies on residue Ser70. A HEI10 S70F allele results in LLPS failure and a defect in class I CO formation. We further used immunoprecipitation–mass spectrometry to identify RPA1a (Replication Protein A 1) as a HEI10 interacting protein. Surprisingly, we find that RPA1a also undergoes phase separation and its ubiquitination and degradation are directly regulated by HEI10. We also show that HEI10 is required for the condensation of other class I CO factors. Thus, our results provide mechanistic insight into how meiotic class I CO formation is controlled by HEI10 coupling LLPS and ubiquitination.