Structural basis of phosphorylation-independent nuclear import of CIRBP by TNPO3

Transportin 3 (TNPO3) is a nuclear import receptor known for its broad substrate specificity, often recognizing arginine-serine (SR/RS) repeat-rich nuclear localization signals (NLS) in SRSF proteins. While serine phosphorylation or glutamate presence has been associated with these NLSs, recent proteomic studies identified TNPO3 cargoes lacking SR/RS repeats. One such example is the cold-inducible RNA-binding protein (CIRBP), which contains a non-classical RSY-NLS. Using X-ray crystallography, here we investigate the TNPO3-CIRBP interaction and find that tyrosines within the RSY-NLS play a key role in binding, independent of phosphorylation. Surprisingly, serine and tyrosine phosphorylation in CIRBP's NLS inhibits TNPO3 binding, suggesting a regulatory mechanism for nuclear import. Our study reveals a non-conventional nuclear import mechanism mediated by TNPO3, which may extend to other known or yet undiscovered TNPO3 cargoes.

An antisense RNA regulates production of DnaA and affects sporulation in Bacillus subtilis

DnaA is the replication initiator and a transcription factor in virtually all bacteria. Although the synthesis and activity of DnaA are highly regulated, the mechanisms of regulation vary between organisms. We found that production of DnaA in Bacillus subtilis is regulated by an antisense RNA that overlaps with the 5' untranslated region upstream of the dnaA open reading frame. We initially observed this RNA in in vitro transcription experiments and found that its production was inhibited by DnaA. This RNA, now called ArrA for antisense RNA repressor of dnaA, is made in vivo. We identified the arrA promoter and made a mutation that greatly reduced (or eliminated) production of ArrA RNA in vitro and in vivo. In vivo, this arrA promoter mutation caused an increase in the amount of mRNA and protein from dnaA and dnaN, indicating that arrA expression normally inhibits expression of the dnaA-dnaN operon. The arrA mutation also caused a delay in sporulation that was alleviated by loss of sda, a sporulation-inhibitory gene that is directly activated by DnaA. arrA appears to be conserved in some members of the Bacillus genus, indicating that arrA has evolved in at least some endospore-forming bacteria to modulate production of DnaA and enable timely and robust sporulation.

Biochemical mapping reveals a conserved heme transport mechanism via CcmCD in System I bacterial cytochrome c biogenesis

Heme is a redox-active cofactor for essential processes across all domains of life. Heme's redox capabilities are responsible for its biological significance but also make it highly cytotoxic, requiring tight intracellular regulation. Thus, the mechanisms of heme trafficking are still not well understood. To address this, the bacterial cytochrome c biogenesis pathways are being developed into model systems to elucidate mechanisms of heme trafficking. These pathways function to attach heme to apocytochrome c, which requires the transport of heme from inside to outside of the cell. Here, we focus on the System I pathway (CcmABCDEFGH) which is proposed to function in two steps: CcmABCD transports heme across the membrane and attaches it to CcmE. HoloCcmE then transports heme to the holocytochrome c synthase, CcmFH, for attachment to apocytochrome c. To interrogate heme transport across the membrane, we focus on CcmCD, which can form holoCcmE independent of CcmAB, leading to the hypothesis that CcmCD is a heme transporter. A structure-function analysis via cysteine/heme crosslinking identified a heme acceptance domain and heme transport channel in CcmCD. Bioinformatic analysis and structural predictions across prokaryotic organisms determined that the heme acceptance domains are structurally variable, potentially to interact with diverse heme delivery proteins. In contrast, the CcmC transmembrane heme channel is structurally conserved, indicating a common mechanism for transmembrane heme transport. We provide direct biochemical evidence mapping the CcmCD heme channel and providing insights into general mechanisms of heme trafficking by other putative heme transporters.

IMPORTANCE

Heme is a biologically important cofactor for proteins involved with essential cellular functions, such as oxygen transport and energy production. Heme can also be toxic to cells and thus requires tight regulation and specific trafficking pathways. As a result, much effort has been devoted to understanding how this important, yet cytotoxic, molecule is transported. While several heme transporters/importers/exporters have been identified, the biochemical mechanisms of transport are not well understood, representing a major knowledge gap. Here, the bacterial cytochrome c biogenesis pathway, System I (CcmABCDEFGH), is used to elucidate the transmembrane transport of heme via CcmCD. We utilize a cysteine/heme crosslinking approach, which can trap endogenous heme in specific domains, to biochemically map the heme transport channel in CcmCD, demonstrating that CcmCD is a heme transporter. These results suggest a model for heme trafficking by other heme transporters in both prokaryotes and eukaryotes.

Solid phase transitions as a solution to the genome folding paradox

Ultra-long-range genomic contacts, which are key components of neuronal genome architecture1-3, constitute a biochemical enigma. This is because regulatory DNA elements make selective and stable contacts with DNA sequences located hundreds of kilobases away, instead of interacting with proximal sequences occupied by the exact same transcription factors1,4. This is exemplified in olfactory sensory neurons (OSNs), in which only a fraction of LHX2-, EBF1- and LDB1-bound sites interact with each other, converging into highly selective multi-chromosomal enhancer hubs5. To obtain biochemical insight into this process, here we assembled olfactory receptor (OR) enhancer hubs in vitro with recombinant proteins and enhancer DNA. Cell-free reconstitution of enhancer hubs revealed that OR enhancers form nucleoprotein condensates with unusual, solid-like characteristics. Assembly of these solid condensates is orchestrated by specific DNA motifs enriched in OR enhancers, which are likely to confer distinct homotypic properties on their resident LHX2-EBF1-LDB1 complexes. Single-molecule tracking and pulse-chase experiments in vivo confirmed that LHX2 and EBF1 assemble OR-transcription-competent condensates with solid properties in OSN nuclei, under physiological concentrations of protein. Thus, homophilic nucleoprotein interactions that are influenced by DNA sequence generate new types of biomolecular condensate, which might provide a generalizable explanation for the stability and specificity of long-range genomic contacts across cell types.

Characterizing differences in the muscle transcriptome between cattle with alternative LCORL-NCAPG haplotypes

BACKGROUND

The LCORL-NCAPG locus is a major quantitative trait locus (QTL) on bovine chromosome 6 (BTA6) that influences growth and carcass composition in cattle. To further understand the molecular mechanism responsible for the phenotypic changes associated with this locus, twenty-four Charolais-sired calves were selected for muscle transcriptome analysis based on alternative homozygous LCORL-NCAPG haplotypes (i.e., 12 "QQ" and 12 "qq", where "Q" is a haplotype harboring variation associated with increased growth). At 300 days of age, a biopsy of the longissimus dorsi muscle was collected from each animal for RNA sequencing.

RESULTS

Gene expression analysis identified 733 genes as differentially expressed between QQ and qq animals (q-value < 0.05). Notably, LCORL and genes known to be important regulators of growth such as IGF2 were upregulated in QQ individuals, while genes associated with adiposity such as FASN and LEP were downregulated, reflecting the increase in lean growth associated with this locus. Gene set enrichment analysis demonstrated QQ individuals had downregulation of pathways associated with adipogenesis, alongside upregulation of transcripts for cellular machinery essential for protein synthesis and energy metabolism, particularly ribosomal and mitochondrial components.

CONCLUSIONS

The differences in the muscle transcriptome between QQ and qq animals imply that muscle hypertrophy may be metabolically favored over accumulation of fat in animals with the QQ haplotype. Our findings also suggest this haplotype could be linked to a difference in LCORL expression that potentially influences the downstream transcriptional effects observed, though further research will be needed to confirm the molecular mechanisms underlying the associated changes in phenotype.

Molecular machineries shaping the mitochondrial inner membrane

Mitochondria display intricately shaped deep invaginations of the mitochondrial inner membrane (MIM) termed cristae. This peculiar membrane architecture is essential for diverse mitochondrial functions, such as oxidative phosphorylation or the biosynthesis of cellular building blocks. Conserved protein nano-machineries such as F1Fo-ATP synthase oligomers and the mitochondrial contact site and cristae organizing system (MICOS) act as adaptable protein-lipid scaffolds controlling MIM biogenesis and its dynamic remodelling. Signal-dependent rearrangements of cristae architecture and MIM fusion events are governed by the dynamin-like GTPase optic atrophy 1 (OPA1). Recent groundbreaking structural insights into these nano-machineries have considerably advanced our understanding of the functional architecture of mitochondria. In this Review, we discuss how the MIM-shaping machineries cooperate to control cristae and crista junction dynamics, including MIM fusion, in response to cellular signalling pathways. We also explore how mutations affecting MIM-shaping machineries compromise mitochondrial functions.

Emerging trends and hotspots of tRNA-derived small RNAs in tumours: a bibliometric analysis via VOSviewer and CiteSpace

INTRODUCTION

TRNA-derived small RNAs(tsRNAs) play an important role in many biological processes, and their dysregulation is closely related to the progression of cancer, but the research trend and future direction are not clear. This study aims to identify the leading contributors, collaboration networks, and emerging research trends in tsRNAs and their role in oncology, providing a more comprehensive and intuitive reference for researchers in this field.

MATERIALS AND METHODS

Related publications related to tsRNA in the field of oncology from 1990 to 2022 were collected from the Science Citation Index Expanded through the Web of Science Core Collection (WOSCC) database on 6 December 2022.

RESULTS

There were 2,108 publications related to tsRNAs in oncology. The articles came from 69 countries/regions, 2,218 institutions, 11,340 authors, and 200 journals, and included 9,530 keywords. The annual total number of papers and total global citation score increased steadily every year over the study period. Among the articles related to tsRNAs in oncology, the United States had the highest number of publications with 732 articles, and the United States, China, Japan, Canada, and South Korea had the highest number of collaborations. Seoul National University Sun and the journal Nucleic Acids Research had the most publications at 81 and 63 articles, respectively, and the keyword "tRF" was a hotspot.

CONCLUSION

This study provides an in-depth analysis of the research status and development trends of tsRNAs in the field of cancer from a bibliometric perspective. Offering possible guidance for researchers to explore hot topics and frontiers, select suitable journals, and partners in this field.

Appearance of transient heteromorphic large chromosome in glyphosate-resistant Amaranthus tuberculatus

Glyphosate resistance in crop weeds is commonly attributed to rapid evolution through the amplification of the target gene, EPSPS (5-enolpyruvylshikimate-3-phosphate synthase). This amplification typically occurs through mechanisms such as unequal recombination, segmental duplications within the target chromosome, or the formation of ring chromosomes and extrachromosomal circular (ecc) DNA elements containing EPSPS. However, structural abnormalities in chromosomes not directly associated with EPSPS amplification have not been documented in the glyphosate-resistant weed population. Here, we describe the presence of a large chromosome found exclusively in the glyphosate-resistant Amaranthus tuberculatus (waterhemp) population but absent in susceptible counterparts. This large chromosome (~ 6 μm) is approximately twice the size of normal chromosomes (~ 2-3 μm) and is present in both male and female euploid plants (2n = 32) in a heteromorphic state. It aroses through pericentromeric heterochromatin expansion and duplications of the 5S rDNA locus but notably lacks the EPSPS gene. The large chromosome pairs with its normal homolog but was not transmitted to progeny in controlled greenhouse matings, suggesting a fitness cost in the absence of glyphosate selection pressure. This large chromosome offers a potential resource for the investigation of chromosome evolution of adaptive traits for glyphosate resistance in A. tuberculatus.

Protein Arginine Methyltransferases from Regulatory Function to Clinical Implication in Central Nervous System

Arginine methylation, catalyzed by protein arginine methyltransferases (PRMTs), is a regulatory key mechanism involved in various cellular processes such as gene expression, RNA processing, DNA damage repair. Increasing evidence highlights the crucial role of PRMTs in human diseases, including cancer, cardiovascular and metabolic diseases. Here, this review focuses on the latest findings regarding PRMTs in the central nervous system (CNS), emphasizing their regulatory roles in neural stem cells, neurons, and glial cells. Additionally, we examine the connection between PRMTs dysregulation and neurological diseases affecting the CNS, including brain tumors, neurodegenerative diseases, and neurodevelopmental disorders. Therefore, this review aims to deepen our understanding of PRMTs-mediated arginine methylation in CNS and open avenues for developing novel therapeutic strategies for neurological diseases.

Hidden origami in Trypanosoma cruzi nuclei highlights its non-random 3D genomic organization

The protozoan Trypanosoma cruzi is the causative agent of Chagas disease and is known for its polycistronic transcription, with about 50% of its genome consisting of repetitive sequences, including coding (primarily multigenic families) and non-coding regions (such as ribosomal DNA, spliced leader [SL], and retroelements, etc). Here, we evaluated the genomic features associated with higher-order chromatin organization in T. cruzi (Brazil A4 strain) by extensive computational processing of high-throughput chromosome conformation capture (Hi-C). Through the mHi-C pipeline, designed to handle multimapping reads, we demonstrated that applying canonical Hi-C processing, which overlooks repetitive DNA sequences, results in a loss of DNA-DNA contacts, misidentifying them as chromatin-folding (CF) boundaries. Our analysis revealed that loci encoding multigenic families of virulence factors are enriched in chromatin loops and form shorter and tighter CF domains than the loci encoding core genes. We uncovered a non-random three-dimensional (3D) genomic organization in which nonprotein-coding RNA loci (transfer RNAs [tRNAs], small nuclear RNAs, and small nucleolar RNAs) and transcription termination sites are preferentially located at the boundaries of the CF domains. Our data indicate 3D clustering of tRNA loci, likely optimizing transcription by RNA polymerase III, and a complex interaction between spliced leader RNA and 18S rRNA loci, suggesting a link between RNA polymerase I and II machineries. Finally, we highlighted a group of genes encoding virulence factors that interact with SL-RNA loci, suggesting a potential regulatory role. Our findings provide insights into 3D genome organization in T. cruzi, contributing to the understanding of supranucleosomal-level chromatin organization and suggesting possible links between 3D architecture and gene expression.IMPORTANCEDespite the knowledge about the linear genome sequence and the identification of numerous virulence factors in the protozoan parasite Trypanosoma cruzi, there has been a limited understanding of how these genomic features are spatially organized within the nucleus and how this organization impacts gene regulation and pathogenicity. By providing a detailed analysis of the three-dimensional (3D) chromatin architecture in T. cruzi, our study contributed to narrowing this gap. We deciphered part of the origami structure hidden in the T. cruzi nucleus, showing the unidimensional genomic features are non-randomly 3D organized in the nuclear organelle. We uncovered the role of nonprotein-coding RNA loci (e.g., transfer RNAs, spliced leader RNA, and 18S RNA) in shaping genomic architecture, offering insights into an additional epigenetic layer that may influence gene expression.

Chaperone-mediated autophagy manipulates PGC1α stability and governs energy metabolism under thermal stress

Thermogenic proteins are down-regulated under thermal stress, including PGC1α· However, the molecular mechanisms are not fully understood. Here, we addressed that chaperone-mediated autophagy could regulate the stability of PGC1α under thermal stress. In mice, knockdown of Lamp2a, one of the two components of CMA, in BAT showed increased PGC1α protein and improved metabolic phenotypes. Combining the proteomics of brown adipose tissue (BAT), structure prediction, co-immunoprecipitation- mass spectrum and biochemical assays, we found that PARK7, a Parkinson's disease causative protein, could sense the temperature changes and interact with LAMP2A and HSC70, respectively, subsequently manipulate the activity of CMA. Knockout of Park7 specific in BAT promoted BAT whitening, leading to impaired insulin sensitivity and energy expenditure at thermoneutrality. Moreover, inhibiting the activity of CMA by knockdown of LAMP2A reversed the effects induced by Park7 ablation. These findings suggest CMA is required for BAT to sustain thermoneutrality-induced whitening through degradation of PGC1α.

HSC70 Promotes Breast Cancer Progression via PTEN Autophagic Degradation and PI3K/AKT/mTOR Activation

Heat shock cognate protein 70 (HSC70) functions as a molecular chaperone and plays a crucial role in the regulation of intracellular protein modifications that are involved in tumor autophagy. However, its expression and mechanism in breast cancer have not been studied. The expression of HSC70 was verified by TCGA database and breast cancer patient tissue. We established breast cancer cell models and mouse models using knockdown HSC70. The expression and mechanism of HSC70 in breast cancer were investigated by immunocoprecipitation, protein stability, RNA stability, flow cytometry and biogenic analysis. In this study, we found that HSC70 is highly expressed in breast cancer and that high HSC70 expression positive correlated with poor prognosis using TCGA database and patient tissue verification. Subsequent experimental verification demonstrated that HSC70 drives cell cycle progression and promotes proliferation in breast cancer. Further studies revealed that HSC70 significantly promoted the phosphorylation of PI3K, AKT and mTOR but did not affect the total protein levels. Additionally, the AKT agonist SC79 reversed the effects of HSC70 knockdown on proliferation and cell cycle progression of breast cancer cells. Mechanistically, HSC70 reduces the protein stability of PTEN but does not change its mRNA level, suggesting that HSC70 binds to PTEN and promotes its autophagic degradation. More importantly, in vivo experiments demonstrated that HSC70 knockdown results in slower tumor proliferation and growth. In conclusion, HSC70 can bind to PTEN and promote its autophagic degradation, thereby activating the PI3K/AKT/mTOR signaling pathway to promote cell cycle progression and proliferation in breast cancer. These findings suggest that HSC70 may be a feasible target for breast cancer treatment.

A modular mRNA vaccine platform encoding antigen-presenting capsid virus-like particles enhances the immunogenicity of the malaria antigen Pfs25

The COVID-19 pandemic has emphasized the potential of mRNA vaccines in fighting pandemics, owing to their rapid development, strong immunogenicity and adaptability. However, a drawback is their dose-limiting reactogenicity and inability to generate durable humoral immunity. Here we introduce a modular nucleotide vaccine platform combining the advantages of genetic and capsid virus-like-particle-based vaccines. This platform allows for the display of various antigens on different capsid virus-like particles, improving the magnitude, quality and longevity of the vaccine-induced immune responses. We applied this technology to enhance the immunogenicity of the Pfs25 antigen. Immunization with lipid-nanoparticle-formulated mRNA encoding Pfs25 capsid virus-like particles resulted in higher and potentially more durable anti-Pfs25 antibody responses, along with enhanced functional activity, compared with an mRNA vaccine encoding soluble Pfs25. By improving both humoral and cellular immune responses, this approach may reduce the dose and number of administrations required for effective protection. As a result, it can improve the feasibility of both DNA- and mRNA-based vaccines targeting pandemic and endemic infectious diseases.

Paediatric Cardiac Tumours: A National Population Study

Paediatric cardiac tumours are rare. The most common tumour is a rhabdomyoma, a benign tumour of the myocardium associated with Tuberous Sclerosis Complex (TSC), a rare genetic condition caused by constitutional pathogenic variants in either the TSC1 or TSC2 genes. Although benign, complications related to obstructed flow through the heart or intractable arrhythmias occur. A 23-year retrospective study of patients referred to the National Scottish Paediatric Cardiology service with evidence of a cardiac tumour. 51 patients identified; 12 prenatally, 8 live born. Of the 47 patients born alive, 44 (93.6%) patients had a benign cardiac tumour and 3 (6.4%) a malignant tumour. Rhabdomyomas were shown to be the most common tumour type in patients with TSC (p = 0.000861) and overall. 8/44 (18%) benign tumours had a documented arrhythmia, 50% requiring treatment with beta blockade. 7 patients with rhabdomyomas received an mTOR inhibitor, 6 were recorded as TSC 2 genotype. There was significant extra cardiac symptom burden for the TSC subtypes (p = 0.00105), particularly TSC2, related to renal and neurological complications. The natural history of rhabdomyomas is slow regression and if no significant mass or rhythm disturbances in early childhood, a positive cardiovascular prognosis. Identifying cases associated with TSC is important to counsel families regarding the longer-term implications related to morbidity and mortality particularly in TSC2 associated cases, which typically have a more severe phenotype. Targeted medical therapy is indicated and shown to be effective for the treatment of benign cardiac tumours causing significant rhythm or mass effect. mTOR inhibitors should be considered in the treatment of rhabdomyomas and beta blockade for haemangiomas.

Regulation of elevated expression of Mcl-1 in hepatocellular carcinoma - a review

Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors worldwide. Mcl-1 (myeloid cell leukemia-1) is highly expressed in HCC cells and plays a critical role in chemotherapy resistance and is a major contributor to chemotherapy failure in HCC. The purpose of this study is to review the recent research progress that explores the key factors in regulating Mcl-1 overexpression in HCC cells, contributing to chemotherapy resistance. The related studies from the past decade on agents targeting Mcl-1 to inhibit HCC were also reviewed to provide insights into overcoming chemotherapy resistance in HCC. Mcl-1 overexpression in HCC is mainly regulated by transcription factors (such as STAT3, p53), non-coding RNAs (such as miRNA, lncRNA), cell cycle proteins, mitochondrial dynamics, and the hypoxic microenvironment. Targeting Mcl-1, alongside multi-target combination therapies, may overcome HCC chemotherapy resistance and improve outcomes. Future research should focus on strategies addressing multiple pathways to minimize monotherapy resistance risks and offer enhanced treatment options for the betterment of human health.

METTL1-mediated m7G tRNA modification drives papillary thyroid cancer progression and metastasis by regulating the codon-specific translation of TNF-α

N7-methylguanosine (m7G) modification of transfer RNA (tRNA) is essential for the biological functions of tRNAs and has been found to play a regulatory role in a variety of human cancers. However, the biological function of METTL1-mediated m7G tRNA modification in papillary thyroid cancer (PTC) is unclear. Here, we found that METTL1 is significantly upregulated in PTC tissues compared to normal control tissues and is associated with poor PTC prognosis. Functional analysis confirmed that METTL1 promotes the proliferation and metastasis of PTC cells in a manner dependent on its tRNA methyltransferase activity. Mechanistically, METTL1 knockdown leads to a decrease in the abundance of certain m7G-modified tRNAs, which suppresses the m7G tRNA modification-mediated codon-specific translation of TNF-α. Furthermore, exogenous supplementation with TNF-α partially reversed the decrease in the proliferation and metastasis of PTC cells induced by METTL1 deletion. Positive correlations between METTL1, WDR4, and TNF-α expression, which affect the proliferation and metastasis of PTC, were confirmed via analysis of microarrays containing PTC tissues. These results demonstrate the oncogenic role of METTL1-mediated m7G tRNA modification in regulating codon-specific translation efficiency in PTC and suggest that targeting METTL1 may be a promising therapeutic approach for overcoming PTC progression by inhibiting PTC cell proliferation and metastasis.

Narciclasine enhances cisplatin-induced apoptotic cell death by inducing unfolded protein response-mediated regulation of NOXA and MCL1

BACKGROUND

Platinum-based chemotherapy is commonly used to treat non-small cell lung cancer (NSCLC); however, innate and acquired resistance is clinically seen in many patients. Hence, a combinatorial approach with novel therapeutic agents to overcome chemoresistance is a promising option for improving patient outcomes. We investigated the combinational anticancer efficacy of cisplatin and narciclasine in three-dimensional NSCLC tumor spheroids.

METHODS

To assess the efficacy of cisplatin and narciclasine, cell viability assays, live/dead cell staining, cell death enzyme-linked immunosorbent assay (ELISA), western blot analysis for proteins related to apoptosis, and in vivo xenograft experiments were performed. The synergistic effects of cisplatin and narciclasine were elucidated through transcriptomic analysis and subsequent validation of candidate molecules by regulating their expression. To clarify the underlying molecular mechanisms, the activation of unfolded protein responses and kinetics of a candidate protein were assessed.

RESULTS

Narciclasine inhibited viability of NSCLC tumor spheroids and augmented the sensitivity of cisplatin-resistant tumor spheroids to cisplatin by inducing apoptosis. After conducting bioinformatic analysis using RNA sequencing data and functional validation experiments, we identified NOXA as a key gene responsible for the enhanced apoptosis observed with the combination of cisplatin and narciclasine. This treatment dramatically increased NOXA while downregulating anti-apoptotic MCL1 levels. Silencing NOXA reversed the enhanced apoptosis and restored MCL1 levels, while MCL1 overexpression protected tumor spheroids from combination treatment-induced apoptosis. Interestingly, narciclasine alone and in combination with cisplatin induced unfolded protein response and inhibited general protein synthesis. Furthermore, the combination treatment increased NOXA expression through the IRE1α-JNK/p38 axis and the activation of p53. Cisplatin alone and in combination with narciclasine destabilized MCL1 via NOXA-mediated proteasomal degradation.

CONCLUSIONS

We identified a natural product, narciclasine, that synergizes with cisplatin. The combination of cisplatin and narciclasine induced NOXA expression, downregulated MCL1, and ultimately induced apoptosis in NSCLC tumor spheroids. Our findings suggest that narciclasine is a potential natural product for combination with cisplatin for treatment of NSCLC.

WDR62 affects the progression of ovarian cancer by regulating the cell cycle

BACKGROUND

Ovarian Cancer (OC) is a gynecological malignant tumor with an extremely high mortality rate, seriously endangering women's health. Due to its insidious clinical manifestations, most patients are diagnosed in the advanced stage of the disease. The currently clinically relied CA125 has limited specificity for the early diagnosis of ovarian cancer. Hence, identifying new promising biomarkers is crucial for the early screening, diagnosis, and treatment of ovarian cancer. Based on differential expression analysis, WGCNA and survival analysis, we identified a centromere-associated gene, WDR62, which is highly expressed in ovarian cancer and highly correlated with ovarian cancer, as well as the poor prognosis of ovarian cancer patients with high expression, suggesting that WDR62 may be a potential biomarker for ovarian cancer. Previous studies have shown that WDR62 is closely associated with the occurrence, development and prognosis of a variety of tumors. However, its role in ovarian cancer has not been studied in depth.

METHODS

Using combined TCGA and GTEx datasets from the UCSC database, along with WGCNA, and survival analysis, WDR62 was identified as a potential biomarker. GEPIA2 database, GEO database, qRT-PCR, and Western blot proved the expression of WDR62. Enrichment analysis, cell transfection, Western blots and CCK8 demonstrated the regulatory mechanism of WDR62, and the detailed mechanism of WDR62 involvement in the occurrence and development of ovarian cancer was predicted by interaction analysis and correlation analysis.

RESULTS

WDR62 was highly expressed in ovarian cancer cells compared to normal ovarian epithelial cells, both at the RNA and protein levels. Patients with high WDR62 expression had a poor survival prognosis. Upon WDR62 knockdown, the expression of cell cycle-related proteins CDK1 and C-Myc decreased in ovarian cancer cells, and the cell proliferative capacity was decreased. Based on bioinformatic analysis, it was hypothesized that WDR62 might mediate the JNK signaling pathway by interacting with MAPK8, thus affecting ovarian cancer progression through cell cycle regulation.

CONCLUSIONS

WDR62 is overexpressed in ovarian cancer and is closely related to the prognosis of ovarian cancer patients. WDR62 promotes ovarian cancer progression by regulating the cell cycle and may influence its development through interaction with MAPK8 to mediate the JNK signaling pathway. These findings suggest that WDR62 could be a potential target for the early screening, diagnosis, and treatment of ovarian cancer.

Epithelioid Hemangioendothelioma: Treatment Landscape and Innovations for an Ultra-Rare Sarcoma

OPINION STATEMENT

Epithelioid hemangioendothelioma (EHE) is an ultra-rare sarcoma with a paucity of data on best practices for management. Pathogenic translocations involving the YAP or TAZ genes lead to constitutive activation of TEAD and TEAD-associated pathways. As our understanding of the molecular drivers of EHE has advanced, investigational treatment strategies have shifted away from cytotoxic chemotherapy toward more targeted approaches. This review focuses on the historical context and evolving landscape of systemic therapies for patients with EHE. For newly diagnosed patients, we recommend consultation at a high-volume sarcoma center whenever possible. If the disease is localized and resectable, surgical excision by a sarcoma-focused surgical oncologist is preferred. When the disease is unresectable, we first assess for disease progression to determine whether active surveillance is appropriate. Some patients may experience indolent, asymptomatic disease for years-or even decades-without requiring intervention. In patients with progressive or symptomatic unresectable disease, systemic therapy is warranted. Setting realistic expectations about the goals of treatment is essential, as no current systemic therapies reliably reduce tumor burden. However, molecular profiling and ongoing correlative studies from clinical trials may soon identify more effective therapeutic targets. For this reason, we encourage referral to centers that routinely perform molecular profiling and offer clinical trials with eligibility criteria for EHE, even to be considered as a first-line approach. Outside of a clinical trial, cytotoxic chemotherapy remains the frontline standard of care for patients who require systemic treatment. Importantly, treatment decisions must incorporate patient preferences and recognition that symptomatic improvement alone can be a meaningful outcome for preserving quality of life.

The aryl hydrocarbon receptor: a new frontier in male reproductive system

BACKGROUND

The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor historically recognized for its role in the regulation of toxicity mediated by environmental chemicals. Recent research points to AhR's critical participation in male reproductive physiology, particularly in spermatogenesis, hormone signaling, and the maintenance of sperm quality. Both endogenous ligands (e.g., dietary and gut microbiota-derived metabolites) and exogenous pollutants (e.g., dioxins and benzo-α-pyrene) influence AhR-mediated pathways, making it a key link between environmental exposures and male fertility.

RESULTS

This review highlights AhR's influence on the male reproductive system, emphasizing the role of endogenous AhR ligands and AhR expression in the maturation and function of male reproductive organs. Environmental AhR agonists have been shown to induce oxidative stress, hormonal imbalance, and sperm DNA damage, which impact harmfully on the spermatogenesis process, which leads to reproductive abnormalities. Conversely, certain natural compounds such as resveratrol, curcumin, and lycopene appear to antagonize AhR activation and reduce its negative effects, thus offering potential protective benefits against male reproductive toxicity. Nevertheless, discrepancies persist regarding the exact interplay between AhR signaling and critical reproductive hormones such as testosterone and LH, and it remains unclear how transgenerational epigenetic changes triggered by AhR activation might affect long-term male fertility.

CONCLUSION

AhR is pivotal in male reproductive physiology, influencing spermatogenesis, sperm quality, and hormone regulation through its interactions with both endogenous and environmental ligands. Persistent pollutants such as dioxins and polycyclic aromatic hydrocarbons cause oxidative damage and hormonal disturbances via AhR, contributing to reduced sperm quality and fertility.

Fibroblasts in immune responses, inflammatory diseases and therapeutic implications

Once regarded as passive bystander cells of the tissue stroma, fibroblasts have emerged as active orchestrators of tissue homeostasis and disease. From regulating immunity and controlling tissue remodelling to governing cell growth and differentiation, fibroblasts assume myriad roles in guiding normal tissue development, maintenance and repair. By comparison, in chronic inflammatory diseases such as rheumatoid arthritis, fibroblasts recruit and sustain inflammatory leukocytes, become dominant producers of pro-inflammatory factors and catalyse tissue destruction. In other disease contexts, fibroblasts promote fibrosis and impair host control of cancer. Single-cell studies have uncovered striking transcriptional and functional heterogeneity exhibited by fibroblasts in both normal tissues and diseased tissues. In particular, advances in the understanding of fibroblast pathology in rheumatoid arthritis have shed light on pathogenic fibroblast states in other chronic diseases. The differentiation and activation of these fibroblast states is driven by diverse physical and chemical cues within the tissue microenvironment and by cell-intrinsic signalling and epigenetic mechanisms. These insights into fibroblast behaviour and regulation have illuminated therapeutic opportunities for the targeted deletion or modulation of pathogenic fibroblasts across many diseases.

Infection-relevant conditions dictate differential versus coordinate expression of Salmonella chaperones and cochaperones

Molecular chaperones are critical for protein homeostasis. In bacteria, chaperone trigger factor (TF) folds proteins co-translationally, and chaperone DnaK requires a J-domain cochaperone and nucleotide exchange factor GrpE to fold proteins largely post-translationally. However, when the pathogen Salmonella enterica serovar Typhimurium faces the infection-relevant condition of cytoplasmic Mg2+ starvation, DnaK reduces protein synthesis independently. This raises the possibility that bacteria differentially express chaperones and cochaperones. We now report that S. Typhimurium responds to cytoplasmic Mg2+ starvation by increasing mRNA amounts of dnaK while decreasing those of the TF-encoding gene tig and J-domain cochaperone genes dnaJ and djlA. This differential strategy requires the master regulator of Mg2+ homeostasis and virulence PhoP, which increases dnaK mRNA amounts by lowering the ATP concentration, thereby hindering proteolysis of the alternative sigma factor RpoH responsible for dnaK transcription. We also establish that DnaK exerts negative feedback on the RpoH protein and RpoH-dependent transcripts independently of J-domain cochaperones. Thus, bacteria express chaperones and cochaperones coordinately or differentially depending on the specific stress perturbing protein homeostasis.IMPORTANCEMolecular chaperones typically require cochaperones to fold proteins and to prevent protein aggregation, and the corresponding genes are thus coordinately expressed. We have now identified an infection-relevant stress condition in which the genes specifying chaperone DnaK and cochaperone DnaJ are differentially expressed despite belonging to the same operon. This differential strategy requires the master regulator of Mg2+ homeostasis and virulence in the pathogen Salmonella enterica serovar Typhimurium. Moreover, it likely reflects that Salmonella requires dnaK, but not J-domain cochaperone-encoding genes, for survival against cytoplasmic Mg2+ starvation and expresses genes only when needed. Thus, the specific condition impacting protein homeostasis determines the coordinate versus differential expression of molecular chaperones and cochaperones.

Why do histone monomethylation and dimethylation cause a significant difference in binding to LEDGF?

Lens epithelium-derived growth factor (LEDGF) is a chromatin-binding protein. It regulates gene transcription and is associated with acquired immunodeficiency syndrome and cancer. Its PWWP domain binds to histone H3 at K36 (H3K36). The binding affinity depends on H3K36 methylation. To investigate this dependency, we performed molecular dynamics simulations of the PWWP domain and histone fragments. We found that not only hydrophobic interaction but also electrostatic interaction is important. The binding is not maintained with nonmethylated and monomethylated H3K36 because the tips of these H3K36s form hydrogen bonds with water molecules, while dimethylated and trimethylated H3K36 form no such hydrogen bond, making this binding stable.

Systematic transcriptomics analysis of calorie restriction and rapamycin unveils their synergistic interaction in prolonging cellular lifespan

Aging is a multifaceted biological process marked by the decline in both mitotic and postmitotic cellular function, often central to the development of age-related diseases. In the pursuit of slowing or even reversing the aging process, a prominent strategy of significant interest is calorie restriction (CR), also known as dietary restriction, and the potential influence of a drug called rapamycin (RM). Both CR and RM have demonstrated the capacity to extend healthspan and lifespan across a diverse array of species, including yeast, worms, flies, and mice. Nevertheless, their individual and combined effects on mitotic and postmitotic cells, as well as their comparative analysis, remain areas that demand a thorough investigation. In this study, we employ RNA-sequencing methodologies to comprehensively analyze the impact of CR, RM, and their combination (CR + RM) on gene expression in yeast cells. Our analysis uncovers distinctive, overlapping, and even contrasting patterns of gene regulation, illuminating the unique and shared effects of CR and RM. Furthermore, the transcriptional synergistic interaction of CR + RM is validated in extending the lifespan of both yeast and human cells.

USP1 inhibits influenza A and B virus replication in MDCK cells by mediating RIG-I deubiquitination

The post-translational modification and stability regulation of RIG-I play critical roles in promoting IFN-I production and maintaining immune homeostasis. In this study, we found that ubiquitin-specific peptidase 1 (USP1) promotes RIG-I protein stability through deubiquitination, which in turn enhances antiviral immunity through the production of inflammatory cytokines, and inhibits the replication of influenza virus in MDCK cells. In contrast, USP1 knockdown inhibited the deubiquitination of RIG-I, decreased the RIG-I protein level, and significantly increased the influenza virus titer. Meanwhile, inhibition of USP1 expression did not have a significant effect on the proliferation of MDCK cells, suggesting that USP1 could be used as a target gene to establish a vaccine-producing MDCK cell line. The above results provide a more comprehensive understanding of the function of USP1 and the antiviral response mechanism, and provide a theoretical and methodological basis for the screening of target genes for the artificial establishment of high-yield MDCK cell lines for vaccine production.

Phenotypic plasticity of flowering time and plant height related traits in wheat

BACKGROUND

Climate changes pose challenges to crop production. However, the causes of phenotypic differences across environments remain unclear.

RESULTS

Here, heading date (HD), flowering date (FD), and plant height (PH) were measured along with four environmental factors (day length (DL), growing degree days (GDD), precipitation (PRCP), and photothermal ratio (PTR)) to investigate the genetic basis of phenotypic plasticity of these traits in 616 wheat accessions using genome-wide association studies. Regarding quantitative trait locus-by-environment interactions (QEIs), five known and three candidate genes for HD, six known and seven candidate genes for FD, and four known and eighteen candidate genes for PH were identified. For the genes associated with phenotypic plasticity, 10 genes exhibited responsiveness to alterations in diverse environmental conditions according to transcriptome data; haplotype effects of 33 genes were identified as significantly correlated with the changes in environmental factors; six candidate genes were identified as hub genes in the gene network, possibly influencing other genes and causing the phenotypic plasticity. And over-dominant effects can explain over 50% the genetic variance of phenotypic plasticity. More importantly, one FD/HD candidate gene (TraesCS4A01G180700) and two PH candidate genes (TraesCS5B01G054800 and TraesCS2A01G539400) partly explain the phenotypic plasticity for the FD/HD and PH traits, respectively. In addition, the potential utilization of these genes in wheat breeding was discussed.

CONCLUSIONS

This study elucidated the genetic basis of phenotypic differences caused by environments and provided a foundation for addressing the impact of climate change on crop production.

Study on the role of miR-10b-3p as SASP in exosomes of premature senescent hepatocytes induced by hexavalent chromium

The exact mechanisms through which chronic, low-concentration exposure to Cr(VI) facilitates the development of related pathological conditions remain to be fully elucidated. Senescence-associated secretory phenotype (SASP) exhibits a bidirectional regulatory function in biological processes. Consequently, it is essential to identify the formulation and functional characteristics of the SASP released by Cr(VI)-triggered senescent L02 hepatocytes (S-L02). In this study, exosomes were extracted from the conditioned media of both normal L02 cells and their senescent counterparts (Senescent L02, S-L02 cells). Among the miRNAs identified in the exosomes, miR-10b-3p was found to be the most abundantly expressed in the exosomes derived from S-L02 cells. As part of the SASP, miR-10b-3p was shown to suppress the proliferation of both L02 and S-L02 cells. Simultaneously, it promoted the growth, migration, and invasive capabilities of hepatocellular carcinoma (HCC) cells. The next mechanistic analysis showed that miR-10b-3p reduces the regulatory influence of the protein PHLPP2 on Akt by downregulating its target gene, PHLPP2. This suppression led to lower levels of p27, FOXO3a and p21, thereby enhancing the proliferation of HCC cells by relieving the negative regulatory mechanisms of the cell cycle. This research offers significant understanding into the oncogenic pathways induced by Cr(VI), and provides laboratory evidence for mechanistic studies targeting hepatic carcinoma associated with Cr(VI) exposure.

Phase behavior and dissociation kinetics of lamins in a polymer model of progeria

One of the key structural proteins in the eukaryotic cell nucleus is lamin. Lamins can assemble into a two-dimensional protein meshwork at the nuclear periphery, known as the nuclear lamina, which provides rigidity and shape to the nucleus. Mutations in lamin proteins that alter the structure of the nuclear lamina underlie laminopathic diseases, including Hutchinson-Gilford Progeria Syndrome (HGPS). Experiments have shown that, compared to healthy cells, lamin supramolecular structures (e.g., protofilaments) assemble into a thicker lamina in HGPS, where they form highly stable nematic microdomains at the nuclear periphery, reminiscent of liquid crystals. This significantly alters the morphological and mechanical properties of the nucleus. In this study, we investigate the aggregation of lamin fibrous structures and their dissociation kinetics from the nuclear periphery by modeling them as coarse-grained, rod-like polymer chains confined within a rigid spherical shell. Our model reproduces the formation of multidirectional nematic domains at the nuclear surface and the reduced lamin dissociation observed in HGPS nuclei by adjusting lamin concentration, lamin-lamin (head-tail), and lamin-shell association strengths. While nematic phase formation requires relatively strong lamin-shell affinity under any non-vanishing inter-lamin attraction, the thickness of the lamina layer is primarily controlled by the head-tail association strength in the model. Furthermore, the unbinding kinetics of lamin chains from the lamina exhibit a concentration-dependent facilitated dissociation, suppressed by strong intra-lamin interactions, reminiscent of diseased nuclei. Overall, our calculations reveal the physical mechanisms by which mutations affecting native lamin interactions and concentration could lead to an abnormal nuclear lamina in laminopathic diseases.

A high-fat diet suppresses growth hormone synthesis and secretion by influencing the Vit D receptor and Pit1

BACKGROUND

A long-term high-fat diet (HFD) leads to excessive lipid deposition, which may cause many diseases, including NAFLD, diabetes, and thyroid dysfunction. In addition, HFD leads to a decrease in serum growth hormone (GH) levels to further increase lipid deposition and obesity. However, the mechanism of such reduction of GH has not been fully elucidated.

METHODS

Male Sprague-Dawley rats were fed a regular diet (CD) or a high-fat diet (HFD) for 29 weeks. GH synthesis and secretion were evaluated in pituitary and blood samples, respectively. An in vitro model was constructed by treating cultured cells with palmitic acid (PA). Vit D receptor (VDR) plasmids (OE-VDR), paricalcitol and VDR knockdown virus (sh-VDR) were used to overexpress or depress the activation of VDR during PA treatment of GH3 cells. The GH content, lipid content, and relevant expression of different molecules were measured in pituitary and cell samples.

RESULTS

A HFD decreased the levels of circulating GH and the expression of Gh in the anterior pituitary gland tissues of rats. In vitro, PA treatment decreased Pit1 and Gh expression in cultured GH3 cells. VDR expression was reduced in the rat pituitary tissues under HFD conditions and in PA-treated GH3 cells. The overexpression and knockdown of VDR increased and decreased the expression of Pit1 and Gh, respectively. Paricalcitol antagonized the decrease in the expression of Pit1 and Gh caused by PA treatment.

CONCLUSIONS

HFD induced lipid deposition in the pituitary may cause GH deficiency, and VDR - Pit1 may be at least partially involved in the process.

Extracellular matrix stiffness in endometrial cancer: driving progression and modulating treatment sensitivity via the ROCK1/YAP1 axis

Endometrial cancer (EC) is among the most prevalent gynecological malignancies, with advanced or recurrent cases posing significant treatment challenges due to limited responses to conventional therapies. Growing evidence highlights the critical role of extracellular matrix (ECM) stiffness in driving tumor progression by shaping the tumor microenvironment. In this study, we demonstrate that ECM stiffness is significantly higher in EC tissues compared to normal endometrium, correlating with elevated expression of ROCK1, a mechanosensitive kinase. Using atomic force microscopy (AFM), we quantified ECM stiffness, while polyacrylamide gels with varying stiffness were employed to mimic ECM conditions in vitro. Bioinformatics analyses, immunofluorescence, Western blotting, and co-immunoprecipitation experiments revealed that ROCK1 modulates the phosphorylation of YAP1, promoting its nuclear localization and transcriptional activity, thereby driving aggressive tumor behaviors, including enhanced proliferation, migration, invasion, and reduced apoptosis. Pharmacological inhibition of ROCK1 with Y-27632 mitigated these effects, suppressing tumor growth, restoring apoptosis, and inducing cell cycle arrest. Treatment with Y-27632 improved sensitivity to chemotherapy and radiotherapy, and significantly enhanced macrophage-mediated phagocytosis, thereby boosting anti-tumor immune responses. In hormone-resistant EC cells, ROCK1 inhibition restored sensitivity to progesterone therapy. Notably, in vivo experiments in a xenograft mouse model confirmed the therapeutic potential of Y-27632, as combination therapy with progesterone showed superior tumor-suppressive effects compared to monotherapy. These findings underscore the dual role of ECM stiffness and ROCK1 in driving tumor progression and influencing treatment outcomes. By elucidating the relationship between ECM stiffness, ROCK1/YAP1 signaling, and treatment sensitivity, this study highlights the potential of targeting the ROCK1/YAP1 axis as a therapeutic strategy. ROCK1 serves as both a biomarker for prognosis and a target for improving personalized treatment approaches, offering new avenues to enhance clinical outcomes for EC patients.

Divergent DNA methylation dynamics in marsupial and eutherian embryos

Based on seminal work in placental species (eutherians)1-10, a paradigm of mammalian development has emerged wherein the genome-wide erasure of parental DNA methylation is required for embryogenesis. Whether such DNA methylation reprogramming is, in fact, conserved in other mammals is unknown. Here, to resolve this point, we generated base-resolution DNA methylation maps in gametes, embryos and adult tissues of a marsupial, the opossum Monodelphis domestica, revealing variations from the eutherian-derived model. The difference in DNA methylation level between oocytes and sperm is less pronounced than that in eutherians. Furthermore, unlike the genome of eutherians, that of the opossum remains hypermethylated during the cleavage stages. In the blastocyst, DNA demethylation is transient and modest in the epiblast. However, it is sustained in the trophectoderm, suggesting an evolutionarily conserved function for DNA hypomethylation in the mammalian placenta. Furthermore, unlike that in eutherians, the inactive X chromosome becomes globally DNA hypomethylated during embryogenesis. We identify gamete differentially methylated regions that exhibit distinct fates in the embryo, with some transient, and others retained and that represent candidate imprinted loci. We also reveal a possible mechanism for imprinted X inactivation, through maternal DNA methylation of the Xist-like noncoding RNA RSX11. We conclude that the evolutionarily divergent eutherians and marsupials use DNA demethylation differently during embryogenesis.

Drosophila melanogaster Toll-9 elicits antiviral immunity against Drosophila C virus

The Toll pathway plays a pivotal role in innate immune responses against pathogens. The evolutionarily conserved pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), play a crucial role in recognition of pathogen-associated molecular patterns (PAMPs). The Drosophila genome encodes nine Toll receptors that are orthologous to mammalian TLRs. While mammalian TLRs directly recognize PAMPs, most Drosophila Tolls recognize the proteolytically cleaved ligand Spätzle to activate downstream signaling cascades. In this study, we demonstrated that Toll-9 is crucial for antiviral immunity against Drosophila C virus (DCV), a natural pathogen of Drosophila. A transposable element insertion in the Toll-9 gene renders the flies more susceptible to DCV. The stable expression of Toll-9 in Drosophila S2 cells results in increased Dicer2 induction and reduced AKT phosphorylation, collectively establishing an antiviral state that inhibits DCV replication. Toll-9 localizes to endosomes, where it binds viral double-stranded RNA (dsRNA), highlighting its role in detecting viral replication intermediates. Together, these findings identify Toll-9 as a key player in antiviral immunity against DCV infection, acting through its ability to recognize dsRNA and drive Dicer2 expression, along with other AKT-mediated antiviral responses.

IMPORTANCE

Insects rely on innate immunity and RNA interference (RNAi) to combat viral infections. Our study underscores the pivotal role of Drosophila Toll-9 in antiviral immunity, aligning with findings in Bombyx mori, where Toll-9 activation upregulates the RNAi component Dicer2. We demonstrate that Drosophila Toll-9 functions as a pattern recognition receptor (PRR) for double-stranded RNA (dsRNA) during Drosophila C virus (DCV) infection, akin to mammalian Toll-like receptors (TLRs). Toll-9 activation during DCV infection leads to the upregulation of Dicer2 and Argonaute2 and dephosphorylation of AKT. This study also reveals that Toll-9 localizes in endosomal compartments where it interacts with dsRNA. These insights enhance our understanding of Drosophila innate immune mechanisms, reflecting the evolutionary conservation of immune responses across diverse species and providing impetus for further research into the conserved roles of TLRs across the animal kingdom.

PI3-kinase has multiple functions in asexual blood stages of Plasmodium falciparum

All symptoms of malaria are caused during the replication of the parasite Plasmodium falciparum in human red blood cells. The parasite digests the host cell cytoplasm in its food vacuole, a pathway of particular interest as drug target. The Vps34-type PI3-kinase in P. falciparum produces PI3-monophophate (PI3P) and has been linked to haemoglobin digestion, to resistance to the current first line antimalarial artemisinin and to biology of the apicoplast. Here we dissect the functions of PfPI3-kinase by inducible deletion of its gene using the loxP-DiCre system and find that PfPI3-kinase is essential for parasite survival. Mutant parasites accumulate undigested haemoglobin (Hb) confirming a defect in the pathway of Hb uptake and digestion, the most likely reason for parasite death. Some parasites are affected in apicoplast inheritance demonstrating that PI3P-dependent processes are important for apicoplast biology in P. falciparum. Finally, we discover that in PI3-kinase mutant parasites carrying a mutation conferring resistance to artemisinin, the lower amounts of PI3P correlate with lower levels of artemisinin resistance. We suggest that the reduced levels of PI3P in the PI3-kinase mutant dampen repair mechanisms like the autophagic processes normally associated with Kelch13 mutations, leading to a proteotoxic stress and to an increase in susceptibility to artemisinin.

Cancer-associated fibroblast-derived fibulin-5 promotes epithelial-mesenchymal transition in diffuse-type gastric cancer via cAMP response element-binding protein pathway, showing poor prognosis

Diffuse-type gastric cancer (DGC), characterized by poorly cohesive cells within fibrotic stroma, is associated with advanced disease and poor prognosis. Here, to identify distinct biomarkers for DGC compared with intestinal-type gastric cancer, we constructed a comprehensive large-scale signaling network using RNA-sequencing data from three genomic databases (The Cancer Genome Atlas, GSE62254 and GSE26253), developed a mathematical model and conducted simulation analyses. For validation, we used tissue microarray blocks of gastric cancers with immunohistochemical staining, single-cell RNA sequencing, primary cultures of cancer-associated fibroblasts (CAFs) and organoids, and a co-culture system involving CAFs and cancer cells. Signaling network analysis identified six differentially activated signaling components across the database, including BIRC5, TTK, NEK2, FHL1, NR2F1 and FBLN5. Among the differentially activated signaling components, high tumoral expression of fibulin-5 protein encoded by FBLN5 correlated with poor overall and disease-specific survival rates in patients with DGC, even after adjusting for the tumor, node, metastases (TNM) stage. Fibulin-5, derived from CAFs within DGC stroma, promoted organoid growth and epithelial-mesenchymal transition (EMT) in DGC cell lines via the cAMP response element-binding protein (CREB) pathway in a CAF co-culture system. FBLN5 knockdown in CAFs reduced the aggressive phenotype of co-cultured DGC cells, while CREB inhibitors reversed EMT. Furthermore, levels of secreted FBLN5 in patient blood samples correlated with its expression in primary tumors. In summary, fibulin-5 secreted by CAFs and interacted with DGC cells promotes EMT and is clinically associated with poor patient outcomes. These findings suggest fibulin-5 as a potential prognostic marker and therapeutic target in patients with DGC.

SV2B is a crucial factor for early larval development in the silkworm, Bombyx mori

Synaptic vesicle glycoprotein 2B (SV2B) gene plays a crucial role in neuromodulation and neurotransmission and is a key regulator of synaptotagmin trafficking. However, physiological functions of this gene in insects remain poorly understood. In this study, we investigated the function of the BmSV2B gene in growth and development of silkworms. Tissue expression profiling revealed that BmSV2B is highly expressed in head and midgut. A phylogenetic tree and sequence alignment demonstrated that this gene is highly conserved among lepidopteran insects. Knockout of BmSV2B using the clustered regularly interspaced small palindromic repeats (CRISPR) / CRISPR-associated nuclease 9 (Cas9) system resulted in smaller body size compared to the wild type (WT) strain. In the BmSV2B mutants, the levels of triacylglycerol were dramatically lower than that in WT. Furthermore, we found that deletion of BmSV2B extended the developmental time of larvae and led to early larval death. High-throughput RNA sequencing and quantitative real-time polymerase chain reaction analysis showed that the expression levels of juvenile hormone-degrading genes, digestive genes, 20-hydroxyecdysone -response genes and forkhead box O (FOXO) were significantly affected by the absence of BmSV2B. Taken together, BmSV2B is essential for early larval development in silkworms and could serve as a potential target for insecticides, offering a more effective approach to pest control management.

KDM6A Deficiency Induces Myeloid Bias and Promotes CMML-Like Disease Through JAK/STAT3 Activation by Repressing SOCS3

Chronic myelomonocytic leukemia (CMML) is a hematologic malignancy with a poor prognosis and limited targeted therapies. Lysine demethylase 6A (KDM6A), a H3K27 demethylase and key component of the COMPASS complex, is frequently mutated in hematologic malignancies, but its roles in embryonic hematopoiesis and tumor suppression in CMML remain unclear. Using zebrafish models with kdm6a mutants and integrative multi-omics analysis (ATAC-seq, RNA-seq, ChIP), we find that Kdm6a is a critical positive regulator of hematopoietic stem and progenitor cell (HSPC) emergence via Syk-related inflammatory signaling in a H3K27me3-dependent manner. We further find that Kdm6a haploinsufficiency in zebrafish leads to myeloid-biased hematopoiesis and a CMML-like disease, similar to CMML patients with reduced KDM6A expression. This KDM6A haploinsufficiency also significantly alters the chromatin landscape of genes associated with aging and cellular homeostasis in HSPCs. Mechanistically, KAM6A haploinsufficiency represses SOCS3 expression, thereby activating JAK/STAT3 signaling in HSPCs. Importantly, inhibitors targeting JAK or STAT3 phosphorylation alleviate myeloid expansion, providing a rationale for JAK/STAT pathway inhibition in CMML therapy. These findings enhance our understanding of CMML pathogenesis and propose new therapeutic avenues.

Effects of melatonin in polycystic ovary syndrome: is there Hippo pathway crosstalk?

OBJECTIVE

Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder among reproductive women, characterized by hyperandrogenism, oligo-ovulation and polycystic ovarian morphology. Incorporating complementary medicine alongside traditional lifestyle therapies for PCOS may offer additional benefits for affected women. Melatonin (MT), a hormone secreted by the pineal gland, has emerged as a potential treatment for regulating ovarian function in PCOS. However, the specific effects and underlying mechanisms of MT on PCOS need to be elucidated.

METHODS

This review consolidates evidence from randomized controlled trials, original research articles, systematic reviews, and meta-analyses regarding MT supplementation in PCOS, with a particular focus on its interaction with the Hippo pathway, to provide a comprehensive overview of current knowledge.

RESULTS

Current evidence suggests that MT plays a role in modulating PCOS through various mechanisms and is associated with the Hippo pathway. However, several uncertainties and key limitations in the existing literature must be addressed before these treatments can be integrated into standard clinical practice.

CLINICAL TRIAL NUMBER

Not applicable.

Novel small non-coding RNAs of Epstein-Barr virus upregulated upon lytic reactivation aid in viral genomic replication and virion production

Epstein-Barr virus (EBV) employs various strategies for long-term survival, including the expression of non-coding RNAs (ncRNAs). This study uncovers and characterizes two novel EBV-encoded ncRNAs, p7 and p8, which are upregulated during lytic reactivation and interact with both viral and host genomes. These ncRNAs bind to cellular RNA transcripts, significantly reducing ARMCX3 mRNA levels, while p8 also influences PTPN6 and RPL24 expressions. Although p7 does not directly bind to LMP1 RNA but both ncRNAs found to downregulate LMP1 expression. Furthermore, these ncRNAs interact with the OriLyt region of EBV genome, promoting viral DNA replication. Functional assays indicate that p7 and p8 enhance cell proliferation and inhibit apoptosis by modulating the p53 pathway and suppressing pro-apoptotic proteins. These findings highlight the role of p7 and p8 in supporting EBV persistence by regulating viral replication, cell survival, and immune evasion, making them promising targets for therapeutic strategies in EBV-related diseases.IMPORTANCEEpstein-Barr virus (EBV) employs diverse strategies for long-term persistence in the host, including the expression of viral non-coding RNAs (ncRNAs) that manipulate key cellular pathways to promote viral replication and immune evasion. This study identifies two novel EBV-encoded ncRNAs, p7 and p8, which are upregulated during lytic reactivation and interact with both viral and host genes to regulate viral DNA replication and promote host cellular survival. By modulating apoptotic and proliferative pathways, p7 and p8 facilitate viral reactivation while promoting host cell survival, highlighting their potential as critical regulators in EBV-driven oncogenesis. This discovery expands our understanding of EBV-host interactions, suggesting p7 and p8 as targets for novel therapeutic strategies in EBV-associated malignancies.

Trans-eQTL hotspots shape complex traits by modulating cellular states

Regulatory genetic variation shapes gene expression, providing an important mechanism connecting DNA variation and complex traits. The causal relationships between gene expression and complex traits remain poorly understood. Here, we integrated transcriptomes and 46 genetically complex growth traits in a large cross between two strains of the yeast Saccharomyces cerevisiae. We discovered thousands of genetic correlations between gene expression and growth, suggesting potential functional connections. Local regulatory variation was a minor source of these genetic correlations. Instead, genetic correlations tended to arise from multiple independent trans-acting regulatory loci. Trans-acting hotspots that affect the expression of numerous genes accounted for particularly large fractions of genetic growth variation and of genetic correlations between gene expression and growth. Genes with genetic correlations were enriched for similar biological processes across traits but with heterogeneous direction of effect. Our results reveal how trans-acting regulatory hotspots shape complex traits by altering cellular states.

Age-related impairment of intestinal inflammation resolution through an eicosanoid-immune-microbiota axis

Aging manifests a decline of immune function, induces microbiome dysbiosis, drives organ inflammation, and impedes the resolution of inflammation. However, the mechanisms underlying age-related intestinal inflammation remain poorly described. Here, we find that the resolution of T cell-initiated intestinal inflammation is impaired with aging. This impairment is mediated by disrupting the immune-microbiota interplay, controlled by intestinal eicosanoid metabolism. Pharmacologically inhibiting eicosanoid biosynthesis, blocking the prostaglandin E receptor subtype 4 (EP4), or genetically ablating EP4 diminishes age-related impairment of intestinal inflammation resolution. Mechanistically, mononuclear phagocyte-intrinsic eicosanoid-EP4 signaling impedes the resolution of intestinal inflammation through fostering gut microbial dysbiosis and, more importantly, interrupting segmented filamentous bacterial adhesion to the intestinal epithelium. Colonization with EP4-ablated mouse microbiota or segmented filamentous bacteria improves the resolution of intestinal inflammation. These findings reveal that eicosanoid-dependent immune-microbiota interactions impair inflammation resolution in the aged intestine, highlighting potential intervention strategies for improving age-related gut health.

Perinuclear mitochondrial clustering for mesenchymal-to-epithelial transition in pluripotency induction

Remodeled mitochondria are characteristic of pluripotent stem cells. However, a role for mitochondrial movement and distribution in pluripotency remains unknown. Here, we show that mitochondrial retrograde transport-mediated perinuclear clustering via dynein complex occurs at the early phase of pluripotency induction. Interestingly, this mitochondrial redistribution is regulated by Yamanaka factor OCT4 but not SOX2 or KLF4. This mitochondrial redistribution, which has effect on the efficiency of somatic cell reprogramming, also depends on DRP1-mediated mitochondrial fission. Importantly, perinuclear mitochondrial clustering is required for mesenchymal-to-epithelial transition (MET), an early step in reprogramming, during which β-catenin regulates the MET process. Furthermore, sufficient amount of β-catenin plays a key role in maintaining stabilization of E-CADHERIN. Taken together, these studies show that perinuclear mitochondrial clustering is an essential organellar step for MET process of pluripotency induction, which may shed light on the subcellular relationship between mitochondrial dynamics, pluripotency, and cellular morphology.

Structural insights into the ubiquitin-independent midnolin-proteasome pathway

The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.

Expression of insulinoma-associated protein 1 (INSM1) in gastric neuroendocrine and non-neuroendocrine neoplasms

AIMS

Insulinoma-associated protein 1 (INSM1) is a recently added nuclear marker for neuroendocrine differentiation. However, INSM1 expression in gastric neuroendocrine and non-neuroendocrine neoplasms has not been thoroughly investigated.

METHODS

We examined INSM1 expression in 72 gastric tumors, including 22 gastric neuroendocrine tumors and 50 gastric non-neuroendocrine neoplasms. Synaptophysin and chromogranin immunostaining were also performed for all cases.

RESULTS

For gastric neuroendocrine neoplasms, INSM1 immunostaining demonstrated excellent sensitivity (21/22, 95.5%), comparable to synaptophysin (22/22, 100.0%), but had lower specificity (32/50, 64.0%) compared with traditional neuroendocrine markers (synaptophysin (36/50, 72.0%) and chromogranin (42/50, 84.0%)). However, decreased expression of INSM1, measured by H-score, was frequently found among neuroendocrine carcinoma cases. Gastric non-neuroendocrine neoplasms frequently exhibited INSM1 positivity (18/50, 36.0%); however, in most cases (16/18, 88.9%), staining was focal (involving < 10% of tumor cells). Tumor histologic subtype and grade may be associated with INSM1 expression.

CONCLUSIONS

INSM1 nuclear positivity in gastric neoplasms should be interpreted with caution. INSM1 should not be used as a stand-alone marker for determining neuroendocrine differentiation in gastric tumors. Histologic evaluation with concurrent use of traditional neuroendocrine markers is warranted to accurately demonstrate neuroendocrine differentiation and minimize false positivity and false negativity.

Nuclear receptor PPARγ targets GPNMB to promote oligodendrocyte development and remyelination

Myelin injury occurs in brain ageing and in several neurological diseases. Failure of spontaneous remyelination is attributable to insufficient differentiation of oligodendrocyte precursor cells (OPCs) into mature myelin-forming oligodendrocytes in CNS demyelinated lesions. Emerging evidence suggests that peroxisome proliferator-activated receptor γ (PPARγ) is the master gatekeeper of CNS injury and repair and plays an important regulatory role in various neurodegenerative diseases. Although studies demonstrate positive effects of PPARγ in oligodendrocyte ontogeny in vitro, the cell-intrinsic role of PPARγ and the molecular mechanisms involved in the processes of OPC development and CNS remyelination in vivo are poorly understood. Here, we identify PPARγ as an enriched transcription factor in the dysfunctional OPCs accumulated in CNS demyelinated lesions. Its expression increases during OPC differentiation and myelination and is closely related to the process of CNS demyelination/remyelination. Administration of pharmacological agonists of PPARγ not only promotes OPC differentiation and CNS myelination, but also causes a significant increase in remyelination in both cuprizone- and lysophosphatidylcholine-induced demyelination models. In contrast, the attenuation of PPARγ function, either through the specific knockout of PPARγ in oligodendrocytes in vivo or through its inhibition in vitro, leads to decreased OPC maturation, hindered myelin generation and reduced therapeutic efficacy of PPARγ agonists. At a mechanistic level, PPARγ induces myelin repair by directly targeting glycoprotein non-metastatic melanoma protein B (GPNMB), a novel regulator that drives OPCs to differentiate into oligodendrocytes, promotes myelinogenesis in the developing CNS of postnatal mice and enhances remyelination in mice with lysophosphatidylcholine-induced demyelination. In conclusion, our evidence reveals that PPARγ is a positive regulator of endogenous OPC differentiation and CNS myelination/remyelination and suggests that PPARγ and/or its downstream sensor (GPNMB) might be a candidate pharmacological target for regenerative therapy in the CNS.

Towards a consensus atlas of human and mouse adipose tissue at single-cell resolution

Adipose tissue (AT) is a complex connective tissue with a high relative proportion of adipocytes, which are specialized cells with the ability to store lipids in large droplets. AT is found in multiple discrete depots throughout the body, where it serves as the primary repository for excess calories. In addition, AT has an important role in functions as diverse as insulation, immunity and regulation of metabolic homeostasis. The Human Cell Atlas Adipose Bionetwork was established to support the generation of single-cell atlases of human AT as well as the development of unified approaches and consensus for cell annotation. Here, we provide a first roadmap from this bionetwork, including our suggested cell annotations for humans and mice, with the aim of describing the state of the field and providing guidelines for the production, analysis, interpretation and presentation of AT single-cell data.

ncRNAs as Key Regulators in Gastric Cancer: From Molecular Subtyping to Therapeutic Targets

Gastric cancer (GC) poses a major global health challenge, underscoring the need for advanced diagnostic and therapeutic approaches. Non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), have emerged as pivotal regulators in GC, with their dysregulated expression driving key processes such as tumorigenesis, metastasis, immune evasion, and chemoresistance. The functional diversity of ncRNAs across different GC molecular subtypes highlights their potential as biomarkers for improved subtype classification and patient stratification. Beyond their diagnostic value, ncRNAs demonstrate critical regulatory functions in tumor biology, establishing these RNA molecules as promising targets for therapeutic development. Strategies based on RNA hold considerable promise for addressing critical challenges such as immune escape and drug resistance by modulating key signaling pathways. These approaches can enhance immune responses, reprogram the tumor microenvironment, and reverse resistance mechanisms that compromise treatment efficacy, thereby improving clinical outcomes. Although ncRNAs represent a promising frontier in GC precision medicine, further research is required to fully harness their clinical potential.

Competing dynamic gene regulatory networks involved in fibroblast reprogramming to hematopoietic progenitor cells

Direct reprogramming of somatic cells offers a potentially safer therapeutic approach to generate patient-specific hematopoietic cells. However, this strategy is limited by stochasticity of reprogramming. Investigating the gene regulatory networks involved during reprogramming would help generate functional cells in adequate numbers. To address this, we developed an inducible system to reprogram fibroblasts to hematopoietic progenitor cells by ectopically expressing the two transcription factors SCL and LMO2. Transcriptome and epigenome analysis at different stages of reprogramming revealed uniform silencing of fibroblast genes and upregulation of the hemogenic endothelial program. Integrated analysis suggested that the transcription factors FLI1, GATA1/2, and KLF14 are direct targets of SCL/LMO2, which subsequently induce the hematopoietic program. Single-cell RNA sequencing revealed conflicting and competing fate decisions at intermediate stages of reprogramming. Inhibiting signaling pathways associated with competing neuronal fate enhanced reprogramming efficiency. In conclusion, this study identifies early/intermediate reprogramming events and associated pathways that could be targeted to improve reprogramming efficiency.

Targeting vulnerabilities of aneuploid cells for cancer therapy

Aneuploidy is a common feature of cancer that drives tumor evolution, but it also creates cellular vulnerabilities that might be exploited therapeutically. Recent advances in genomic technologies and experimental models have uncovered diverse cellular consequences of aneuploidy, revealing dependencies on mitotic regulation, DNA replication and repair, proteostasis, metabolism, and immune interactions. Harnessing aneuploidy for precision oncology requires the combination of genomic, functional, and clinical studies that will enable translation of our improved understanding of aneuploidy to targeted therapies. In this review we discuss approaches to targeting both highly aneuploid cells and cells with specific common aneuploidies, summarize the biological underpinning of these aneuploidy-induced vulnerabilities, and explore their therapeutic implications.

Surfactin Activating KinB to Sense and Utilize Carbon Sources Against Cannibalism in Bacillus amyloliquefaciens

Bacillus species are ubiquitous microorganisms with broad applications. The lipopeptide surfactin serves as a signaling molecule to activate histidine kinases, subsequently activating the global regulatory protein Spo0A to modulate quorum sensing like cannibalism in response to specific environmental conditions such as carbon source limitation. Our previous studies revealed that deletion of the surfactin synthesis gene in Bacillus amyloliquefaciens resulted in rapid cell death during the logarithmic growth phase. In this study, by employing gene knockout strains involved in the surfactin signaling pathway, we found that B. amyloliquefaciens primarily employs histidine kinase KinB to perceive surfactin signals, enabling the utilization of environmental carbon sources. Surfactin signal transduction is not exclusively dependent on histidine kinases; cells utilize alternative pathways (e.g., cation-induced Spo0A activation) to regulate carbon source utilization. Adding glucose, NADH, and ATP all alleviated cell death in ΔsrfA cultures. Both the wild-type and ΔsrfA mutant produce polypeptide/protein-like autotoxins during growth, but ΔsrfA produced more toxins earlier. Carbon sources such as glucose inhibit autotoxin production, while surfactin initiates detoxifying against these toxins. The absence of Spo0A results in both the loss of autotoxin production and antitoxin capabilities, indicating that Spo0A regulates both toxin production and detoxification mechanisms. Collectively, we firstly reported that in B. amyloliquefaciens, cells utilize surfactin as a signaling molecule to activate KinB, which senses environmental carbon sources and thereby inhibits rather than promotes the production of autotoxins as seen in Bacillus subtilis. However, similar to B. subtilis, KinB activates Spo0A to combat autotoxins.

NF-κB-mediated developmental delay extends lifespan in Drosophila

Developmental time (or time to maturity) strongly correlates with an animal's maximum lifespan, with late-maturing individuals often living longer. However, the genetic mechanisms underlying this phenomenon remain largely unknown. This may be because most previously identified longevity genes regulate growth rate rather than developmental time. To address this gap, we genetically manipulated prothoracicotropic hormone (PTTH), the primary regulator of developmental timing in Drosophila, to explore the genetic link between developmental time and longevity. Loss of PTTH delays developmental timing without altering the growth rate. Intriguingly, PTTH mutants exhibit extended lifespan despite their larger body size. This lifespan extension depends on ecdysone signaling, as feeding 20-hydroxyecdysone to PTTH mutants reverses the effect. Mechanistically, loss of PTTH blunts age-dependent chronic inflammation, specifically in fly hepatocytes (oenocytes). Developmental transcriptomics reveal that NF-κB signaling activates during larva-to-adult transition, with PTTH inducing this signaling via ecdysone. Notably, time-restricted and oenocyte-specific silencing of Relish (an NF-κB homolog) at early 3rd instar larval stages significantly prolongs adult lifespan while delaying pupariation. Our study establishes an aging model that uncouples developmental time from growth rate, highlighting NF-κB signaling as a key developmental program in linking developmental time to adult lifespan.