iTRAQ-based quantitative proteomics reveals dysregulation of fibronectin 1 contributes to impaired endometrial decidualization in recurrent implantation failure

Recurrent implantation failure (RIF) poses challenges to successful embryo implantation. In this study, we utilized isobaric tags for relative and absolute quantification (iTRAQ) to profile endometrial protein abundance in RIF patients. Through functional and pathway analyses, ECM-related proteins including fibronectin 1 (FN1), collagen type I alpha 2 chain (COL1A2), and integrin beta-1 (ITGB1) were revealed to be associated with RIF. Correlation analysis identified TGF-β1 as an upstream regulator of FN1. Knockdown experiments showed TGF-β1 downregulation could inhibit FN1 expression to inhibit decidualization markers. Our findings suggest a mechanistic link between TGF-β1/FN1 axis dysregulation and impaired decidualization observed in RIF. SIGNIFICANCE: Our study addresses the pressing issue of RIF, a significant obstacle in assisted reproductive technology. By employing isobaric tags for relative and absolute quantification (iTRAQ), we comprehensively analyzed endometrial protein abundance in RIF patients. Through functional and pathway enrichment analyses, we identified dysregulation in extracellular matrix (ECM)-related proteins, including FN1, COL1A2, and ITGB1, shedding light on their potential roles in implantation failure. Additionally, our correlation analysis revealed TGF-β1 as an upstream regulator of FN1, suggesting a novel regulatory axis involved in decidualization. Knockdown experiments further demonstrated the impact of TGF-β1 and FN1 on decidualization markers. This study contributes to a better understanding of the molecular mechanisms underlying RIF.

Low-Intensity Pulsed Ultrasound Promotes Osteogenesis in Porous Titanium Alloys Through miR-1187/BMP4 Pathway

The repair of critical-sized bone defects remains a significant clinical challenge. Low-intensity pulsed ultrasound (LIPUS), in combination with porous titanium alloy (PTi) scaffolds, has emerged as a promising therapeutic strategy. However, its molecular mechanism remains unclear. This study aimed to investigate the role of bone morphogenetic protein 4 (BMP4) and microRNA-1187 (miR-1187) in LIPUS-mediated osteogenesis in PTi scaffolds. In vitro, the expression of BMP4 and miR-1187 in MC3T3-E1 cells following LIPUS stimulation was assessed using quantitative real-time PCR (RT-qPCR), western blotting, ELISA, alkaline phosphatase (ALP) activity assay, and staining techniques. A luciferase reporter assay confirmed BMP4 as a direct target of miR-1187. Functional studies demonstrated that BMP4 overexpression and miR-1187 inhibition promoted osteoblast differentiation, whereas BMP4 knockdown and miR-1187 overexpression suppressed osteogenesis. In vivo, a BMP4 knockdown rat model was established by si-BMP4 injection into mandibular defects and evaluated new bone formation using micro-CT and histological analyses. LIPUS stimulation significantly upregulated BMP4 expression, promoted new bone formation in PTi scaffolds, and partially rescued the inhibitory effects of BMP4 silencing. These findings establish BMP4 as a key regulator in LIPUS-enhanced osteogenesis via miR-1187 suppression. This mechanistic insight supports the combined use of LIPUS and PTi scaffolds for bone defect repair and highlights BMP4 as a potential therapeutic target to further enhance bone regeneration in LIPUS-stimulated scaffold therapies.

Palmitoylation prevents B7-H4 lysosomal degradation sustaining tumor immune evasion

B7-H4 functions as an immune checkpoint in the tumor microenvironment (TME). However, the post-translational modification (PTM) of B7-H4 and its translational potential in cancer remains incompletely understood. We find that ZDHHC3, a zinc finger DHHC-type palmitoyltransferase, palmitoylates B7-H4 at Cys130 in breast cancer cells, preventing its lysosomal degradation and sustaining B7-H4-mediated immunosuppression. Knockdown of ZDHHC3 in tumors results in robust anti-tumor immunity and reduces tumor progression in murine models. Moreover, abemaciclib, a CDK4/6 inhibitor, primes lysosome activation and promotes lysosomal degradation of B7-H4 independently of the tumor cell cycle. Treatment with abemaciclib results in T cell activation and mitigates B7-H4-mediated immune suppression via inducing B7-H4 degradation in preclinical tumor models. Thus, B7-H4 palmitoylation is an important PTM controlling B7-H4 protein stability and abemaciclib may be repurposed to promote B7-H4 degradation, thereby treating patients with B7-H4 expressing tumors.

Super-Enhancer-Driven LncRNA UNC5B-AS1 Inhibits Inflammatory Phenotypic Transition in Pulmonary Artery Smooth Muscle Cells via Lactylation

BACKGROUND

The phenotypic transition of pulmonary artery smooth muscle cells (PASMCs) is a central pathological alteration in pulmonary artery remodeling, contributing to pulmonary hypertension. Super-enhancers (SEs), characterized by histone modifications and the binding of coactivators, drive the expression of prominent genes that define cellular identity. However, the specific role of SEs, particularly SE-driven long noncoding RNAs, in hypoxia-induced phenotypic plasticity of PASMCs remains unclear.

METHODS

In this study, the long noncoding RNA UNC5B antisense RNA 1 (UNC5B-AS1) regulated by SEs was screened in hypoxic PASMCs using RNA sequencing and H3K27ac (histone 3 lysine 27 acetylation) chromatin immunoprecipitation sequencing. Overexpression or knockdown of UNC5B-AS1 in vitro was performed to elucidate its role in pulmonary hypertension pathogenesis. A serotype 5 adenovirus-associated virus carrying a conserved functional fragment of UNC5B-AS1 was used to treat pulmonary hypertension in vivo.

RESULTS

We identified UNC5B-AS1 as an SE-driven long noncoding RNA transcriptionally activated by the transcription factor FOXP3 (forkhead box protein P3), which regulates phenotypic transition in PASMCs. Notably, we demonstrated that UNC5B-AS1 interacts with key glycolytic enzymes in the cytoplasm and likely serves as a molecular scaffold for LRPPRC (leucine-rich PPR motif-containing protein) and oxidative respiratory chain complex IV in mitochondria. Consequently, the deficiency of UNC5B-AS1 in PASMCs promotes the lactylation of promoter regions within inflammatory genes, including those of IL (interleukin)-1β, IL-6, and TNF-α (tumor necrosis factor-α), under hypoxic conditions, ultimately leading to inflammatory phenotypic transition of PASMCs.

CONCLUSIONS

Our findings identify SE-driven UNC5B-AS1 as a novel regulatory factor in the hypoxia-induced phenotypic transition of PASMCs and suggest that overexpression of UNC5B-AS1 may represent a promising therapeutic strategy for pulmonary hypertension.

MEIS1: From functional versatility to post-transcriptional/translational regulation

Myeloid ecotropic virus insertion site 1 (MEIS1) is a transcription factor involved in a myriad of functions such as hematopoiesis, cardiac regeneration, cell cycle progression, and limb and organ development. Its functional versatility extends beyond developmental biology, as aberrant MEIS1 expression has been implicated in various pathological contexts like carcinogenesis, cardiomyopathies, and neurodegenerative disorders. Recent advances in the field have uncovered novel layers of MEIS1 regulation, focusing on post-transcriptional and translational mechanisms, which collectively fine-tune its activity, stability, and subcellular localization. These include chromatin remodeling, epigenetic modifications in the enhancer and promoter regions, and protein modifications like phosphorylation and ubiquitination. The sophisticated regulation of MEIS1 including its interplay with non-coding RNAs (ncRNAs), either being an upstream or downstream of ncRNAs, equally represents an important regulatory mechanism orchestrating MEIS1 expression and function. This review explores the multifaceted roles of MEIS1, emphasizing its dynamic regulatory networks and their implications in physiological and pathological conditions. It also provides forward-thinking guidance on the utilization of MEIS1 in targeted therapies across various clinical settings, highlighting its potential as a key regulatory factor in disease modulation and therapeutic innovation.

Guizhi Fuling decoction protects against bone destruction via suppressing exosomal ERK1 in multiple myeloma

BACKGROUND

Myeloma-related bone disease (MBD) is a common complication of multiple myeloma (MM) that deteriorates patients' quality of life and affects overall survival. Modulating the interaction between myeloma cells and the bone marrow microenvironment may offer therapeutic potential. While certain natural medicines may regulate bone homeostasis by directly targeting osteoclasts or osteoblasts, few studies have explored the effects of intervening in myeloma cells on osteoclasts, particularly through the role of exosomes.

PURPOSE

To investigate the inhibitory effect of Guizhi Fuling Decoction (GZFL) on bone lesions formation induced by exosomes secreted by myeloma cells and provide evidence to support the clinical application of GZFL in treating MBD.

METHODS

TRAP staining and Von Kossa staining were used to evaluate the inhibition of GZFL on RANKL-induced osteoclastogenesis in vitro. Micro-CT and bone histomorphometric analyses were performed to identify the protective effect of GZFL on bone destruction in vivo. RNA immunoprecipitation (RIP), RNA-seq, and UHPLC-MS/MS were conducted to investigate the MBD targets of GZFL. A clinical trial was carried out to evaluate the efficacy of GZFL capsules in the treatment of MBD.

RESULTS

The main bioactive components of GZFL, paeoniflorin, quercitrin and kaempferol, could target ERK1 and downregulate its expression in MM exosomes. In vitro, GZFL treatment inhibited the promoting effect of MM exosomes on osteoclast (OC) formation, bone resorption, and activated ERK1 expression. In vivo, GZFL prolonged survival rate, inhibited the exacerbation of bone lesions caused by MM exosomes and RANKL-induced ERK1 activation in mice model. Clinical data showed that GZFL capsule combined with bortezomib (Bortezomib) and dexamethasone (PD) significantly reduced the numeric rating scale, as well as the expression levels of ERK and RANKL in bone marrow. ERK1 levels exhibited a positive correlation with both the number of bone lesions and RANKL levels. Higher ERK1 expression indicated a worse prognosis.

CONCLUSION

GZFL inhibited MBD progression by reducing MM-derived exosomal ERK1, thereby suppressing RANKL-induced ERK1 activation and the downstream OC formation. GZFL combined with PD regimen had good clinical efficacy and safety in the treatment of MBD.

The roles of enhancer, especially super-enhancer-driven genes in tumor metabolism and immunity

Abnormal metabolism is a characteristic of malignant tumors. Numerous factors play roles in the regulation of tumor metabolism. As epigenetic regulators, enhancers, especially the super-enhancers (SEs), serve as platforms for transcription factors that regulate the expression of metabolism-related enzymes or transporters at the gene level. In this study, we review the effects of enhancer/ SE-driven genes on tumor metabolism and immunity. Enhancers/SEs play regulatory roles in glucose metabolism (glycolysis, gluconeogenesis, tricarboxylic acid (TCA) cycle, pyruvate, and pentose phosphate pathway, lipid metabolism (cholesterol, fatty acid, phosphatide, and sphingolipid), and amino acid metabolism (glutamine, tryptophan, arginine, and cystine). By regulating tumor metabolism, enhancers and SEs can reprogram tumor microenvironment, especially the status of various immune cells. Therefore, interfering enhancers/SEs that regulate the tumor metabolism is likely to enhance the effectiveness of immunotherapy.

The combination of BET and METTL3 inhibitors elicits synergistic antitumor effects in ovarian cancer cells via reducing SP1 and BCL-2 expression

Ovarian cancer (OC) remains a major health threat to woman despite treatment advances. New therapeutic strategies are demanded to persistently explored. In this study, we found that inhibitors of bromodomain and extra-Terminal domain (BET) and methyltransferase-like 3 (METTL3) exerted synergistic proliferative inhibition in different OC cell lines. In vitro synergism was translated into in vivo antitumor activity through the combination of BET inhibitor HJP-178 and METTL3 inhibitor STM2457. Mechanistically, this combination mainly enhanced apoptosis rather than affecting cell cycle arrest. Furthermore, it was revealed that HJP-178 decreased the transcription of Specificity protein 1 (SP1) while STM2457 lowered the N6-methyladenosine (m6A) levels of SP1 mRNA. Consequently, their combination synergistically reduces SP1 RNA and protein levels through both transcriptional and post-transcriptional modifications. Further exploration demonstrated that inhibiting SP1 directly downregulates the anti-apoptotic protein B-cell lymphoma-2 (BCL-2), activating the caspase-mediated apoptotic pathway and triggering programmed cell death. Importantly, SP1 overexpression significantly reducing the apoptosis induction and proliferation inhibition induced by the combination. Similarly, BCL-2 overexpression mimicked the effects of increased SP1. These results demonstrate the critical roles of SP1 and BCL-2 in the synergistic antitumor activity between BET and METTL3 inhibitors. Collectively, our findings broaden the potential applications of both drug types and present a promising therapeutic approach for OC, warranting further investigation in clinical settings.

Interplay and cooperation between GLI2 and master transcription factors promote progression of esophageal squamous cell carcinoma

The establishment of gene expression programs that drive cell identity is governed by tightly regulated transcription factors (TFs) that engage in auto- and cross-regulation in a feedforward manner, forming core regulatory circuitries (CRCs). Here, we identify and validate an important interconnected CRC formed by three master TFs-GLI2, TP63, and RUNX1-in esophageal squamous cell carcinoma (ESCC). Furthermore, master TFs co-bind to their own and each other's super-enhancers, forming an interconnected auto-regulatory loop. Mechanistically, these master TFs occupy the majority of ESCC super-enhancers and cooperatively orchestrate the ESCC transcription program. Functionally, GLI2, a master TF, is essential for ESCC viability, migration, invasion, and the growth of xenograft tumors. Moreover, the overexpression of GLI2 is significantly associated with shorter overall survival of patients with ESCC. Downstream, this CRC apparatus coordinately regulates gene expression networks in ESCC, controlling important cancer-promoting pathways, including Hedgehog, glycolysis, and epidermal growth factor receptor signaling pathways. Together, these findings offer significant mechanistic insights into the transcriptional dysregulation in ESCC and recognize GLI2 as a potential therapeutic target and prognostic marker for ESCC. More importantly, CRC-downstream genes and signaling pathways may contain potential therapeutic targets for this malignancy.

Deciphering the role of liquid-liquid phase separation in sarcoma: Implications for pathogenesis and treatment

Liquid-liquid phase separation (LLPS) is a significant reversible and dynamic process in organisms. Cells form droplets that are distinct from membrane-bound cell organelles by phase separation to keep biochemical processes in order. Nevertheless, the pathological state of LLPS contributes to the progression of a variety of tumor-related pathogenic issues. Sarcoma is one kind of highly malignant tumor characterized by aggressive metastatic potential and resistance to conventional therapeutic agents. Despite the significant clinical relevance, research on phase separation in sarcomas currently faces several major challenges. These include the limited availability of sarcoma samples, insufficient attention from the research community, and the complex genetic heterogeneity of sarcomas. Recently, emerging evidence have elaborated the specific effects and pathways of phase separation on different sarcoma subtypes, including the effect of sarcoma fusion proteins and other physicochemical factors on phase separation. This review aims to summarize the multiple roles of phase separation in sarcoma and novel molecular inhibitors that target phase separation. These insights will broaden the understanding of the mechanisms concerning sarcoma and offer new perspectives for future therapeutic strategies.

Unraveling the Role of the Wnt Pathway in Hepatocellular Carcinoma: From Molecular Mechanisms to Therapeutic Implications

Hepatocellular carcinoma (HCC) is one of the deadliest malignant tumors in the world, and its incidence and mortality have increased year by year. HCC research has increasingly focused on understanding its pathogenesis and developing treatments.The Wnt signaling pathway, a complex and evolutionarily conserved signal transduction system, has been extensively studied in the genesis and treatment of several malignant tumors. Recent investigations suggest that the pathogenesis of HCC may be significantly influenced by dysregulated Wnt/β-catenin signaling. This article aimed to examine the pathway that controls Wnt signaling in HCC and its mechanisms. In addition, we highlighted the role of this pathway in HCC etiology and targeted treatment.

Leveraging a disulfidptosis-based signature to characterize heterogeneity and optimize treatment in multiple myeloma

Background

Disulfidptosis is an emerging type of programmed cell death related to ROS accumulation and aberrant disulfide bond formation. Multiple myeloma (MM) is the second most prevalent hematologic malignancy characterized by a high synthesis rate of disulfide bond-rich proteins and chronic oxidative stress. However, the relationship between disulfidptosis and MM is still unclear.

Methods

Using the non-negative matrix factorization and lasso algorithm, we constructed the disulfidptosis-associated subtypes and the prognostic model on the GEO dataset. We further explored genetic mutation mapping, protein-protein interactions, functional enrichment, drug sensitivity, drug prediction, and immune infiltration analysis among subtypes and risk subgroups. To improve the clinical benefits, we combined risk scores and clinical metrics to build a nomogram. Finally, in vitro experiments examined the expression patterns of disulfidptosis-related genes (DRGs) in MM.

Results

By cluster analysis, we obtained three subtypes with C2 having a worse prognosis than C3. Consistently, C2 exhibited significantly lower sensitivity to doxorubicin and lenalidomide, as well as a higher propensity for T-cell depletion and a non-responsive state to immunotherapy. Similarly, in the subsequent prognostic model, the high-scoring group had a worse prognosis and a higher probability of T-cell dysfunction, immunotherapy resistance, and cancer cell self-renewal. DRGs and risk genes were widely mutated in cancers. Subtypes and risk subgroups differed in ROS metabolism and the p53 signaling pathway. We further identified eight genes differentially expressed in risk subgroups as drug targets against MM. Then 27 drugs targeting the high-risk group were predicted. Based on the DRGs and risk genes, we constructed the miRNA and TF regulatory networks. The nomogram of combined ISS, age, and risk score showed good predictive performance. qRT-PCR of cell lines and clinical specimens provided further support for prognostic modeling.

Conclusion

Our research reveals the prognostic value of disulfidptosis in MM and provides new perspectives for identifying heterogeneity and therapeutic targets.

Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis

Super-enhancers (SEs) are expansive cis-regulatory elements known for amplifying oncogene expression across various cancers. However, their role in cervical cancer (CC), a remarkable global malignancy affecting women, remains underexplored. Here we applied integrated epigenomic and transcriptomic profiling to delineate the distinct SE landscape in CC by analyzing paired tumor and normal tissues. Our study identifies a tumor-specific SE at the EFNA1 locus that drives EFNA1 expression in CC. Mechanically, the EFNA1-SE region contains consensus sequences for the transcription factor FOSL2, whose knockdown markedly suppressed luciferase activity and diminished H3K27ac enrichment within the SE region. Functional analyses further underlined EFNA1's oncogenic role in CC, linking its overexpression to poor patient outcomes. EFNA1 knockdown strikingly reduced CC cell proliferation, migration, and tumor growth. Moreover, EFNA1 cis-interacted with its receptor EphA2, leading to decreased EphA2 tyrosine phosphorylation and subsequent activation of the Src/AKT/STAT3 forward signaling pathway. Inhibition of this pathway with specific inhibitors substantially attenuated the tumorigenic capacity of EFNA1-overexpressing CC cells in both in vitro and in vivo models. Collectively, our study unveils the critical role of SEs in promoting tumor progression through the FOSL2-EFNA1-EphA2-Src/AKT/STAT3 axis, providing new prognostic and therapeutic avenues for CC patients.

Biologically targeted discovery-replication scan identifies G×G interaction in relation to risk of Barrett's esophagus and esophageal adenocarcinoma

Inherited genetics represents an important contributor to risk of esophageal adenocarcinoma (EAC), and its precursor Barrett's esophagus (BE). Genome-wide association studies have identified ∼30 susceptibility variants for BE/EAC, yet genetic interactions remain unexamined. To address challenges in large-scale G×G scans, we combined knowledge-guided filtering and machine learning approaches, focusing on genes with (1) known/plausible links to BE/EAC pathogenesis (n = 493) or (2) prior evidence of biological interactions (n = 4,196). Approximately 75 × 106 SNP×SNP interactions were screened via hierarchical group lasso (glinternet) using BEACON GWAS data. The top ∼2,000 interactions retained in each scan were prioritized using p values from single logistic models. Identical scans were repeated among males only (78%), with two independent GWAS datasets used for replication. In overall and male-specific primary replications, 11 of 187 and 20 of 191 interactions satisfied p < 0.05, respectively. The strongest evidence for secondary replication was for rs17744726×rs3217992 among males, with consistent directionality across all cohorts (Pmeta = 2.19 × 10-8); rs3217992 "T" was associated with reduced risk only in individuals homozygous for rs17744726 "G." Rs3217992 maps to the CDKN2B 3' UTR and reportedly disrupts microRNA-mediated repression. Rs17744726 maps to an intronic enhancer region in BLK. Through in silico prioritization and experimental validation, we identified a nearby proxy variant (rs4841556) as a functional modulator of enhancer activity. Enhancer-gene mapping and eQTLs implicated BLK and FAM167A as targets. The first systematic G×G investigation in BE/EAC, this study uncovers differential risk associations for CDKN2B variation by BLK genotype, suggesting novel biological dependency between two risk loci encoding key mediators of tumor suppression and inflammation.

Extracellular vesicles in multiple myeloma: pathogenesis and therapeutic application

Multiple myeloma (MM), characterised by the clonal proliferation of plasma cells in the bone marrow, is the second most common haematological malignancy worldwide. Although there is now an impressive artillery of therapeutics to tackle this condition, resistance remains a prevalent issue. The bone marrow microenvironment performs a crucial role in supporting MM pathogenesis and promoting the development of therapeutic resistance. Extracellular vesicles (EVs), small vesicles that carry bioactive molecules, are a key component of cell-to-cell communication within the bone marrow microenvironment. In this review, we summarise the contribution of EVs to disease progression and anticancer treatment resistance and discuss the potential therapeutic applications of EVs in MM.

The MLL3/GRHL2 complex regulates malignant transformation and anti-tumor immunity in squamous cancer

Upper aerodigestive squamous cell carcinoma (UASCC) presents significant challenges in clinical management due to its aggressive nature. Here, we elucidate the role of MLL3 mutations as early, clonal genomic events in UASCC tumorigenesis, highlighting their role as foundational drivers of cancer development. Utilizing CRISPR-edited, cross-species organoid modeling, we demonstrate that loss of MLL3 contributes to early squamous neoplastic evolution. Furthermore, we identify an MLL3/GRHL2 protein complex that regulates the UASCC epigenome, particularly impacting immune response pathways. Notably, a novel MLL3/GRHL2-IRF1 axis promotes the expression of Th1 chemokines, enhancing anti-tumor immunity by facilitating T cell infiltration into the tumor microenvironment. Consequently, MLL3 regulates the in vivo efficacy of immune checkpoint blockade (ICB) therapy, corroborated by the strong association between MLL3 expression and human patients' clinical response to ICB therapy. Our work underscores the significance of MLL3 in UASCC pathogenesis and highlights the interplay between MLL3/GRHL2 and immune response pathways as potential therapeutic targets for UASCC treatment.

A human model to deconvolve genotype-phenotype causations in lung squamous cell carcinoma

Tractable, patient-relevant models are needed to investigate cancer progression and heterogeneity. Here, we report an alternative in vitro model of lung squamous cell carcinoma (LUSC) using primary human bronchial epithelial cells (hBECs) from three healthy donors. The co-operation of ubiquitous alterations (TP53 and CDKN2A loss) and components of commonly deregulated pathways including squamous differentiation (SOX2), PI3K signalling (PTEN) and the oxidative stress response (KEAP1) is investigated by generating hBECs harbouring cumulative alterations. Our analyses confirms that SOX2-overexpression initiates early preinvasive LUSC stages, and co-operation with the oxidative stress response and PI3K pathways to drive more aggressive phenotypes, with expansion of cells expressing LUSC biomarkers and invasive properties. This cooperation is consistent with the classical LUSC subtype. Importantly, we connect pathway dysregulation with gene expression changes associated with cell-intrinsic processes and immunomodulation. Our approach constitutes a powerful system to model LUSC and unravel genotype-phenotype causations of clinical relevance.

Self-Oxygenating PROTAC Microneedle for Spatiotemporally-Confined Protein Degradation and Enhanced Glioblastoma Therapy

Glioblastoma (GBM) is the most aggressive subtype of primary brain tumors, which marginally respond to standard chemotherapy due to the blood-brain barrier (BBB) and the low tumor specificity of the therapeutics. Herein, a double-layered microneedle (MN) patch is rationally engineered by integrating acid and light dual-activatable PROteolysis TArgeting Chimera (PROTAC) nanoparticles and self-oxygenating BSA-MnO2 (BM) nanoparticles for GBM treatment. The MN is administrated at the tumor site to locally deliver the PROTAC prodrug and BM nanoparticles. The PROTAC nanoparticles are rapidly released from the outer layer of the MN and specifically activated in the acidic intracellular environment of tumor cells. Subsequently, near-infrared light activates the photosensitizer to produce singlet oxygen (1O2) through photodynamic therapy (PDT), thereby triggering spatiotemporally-tunable degradation of bromodomain and extraterminal protein 4 (BRD4). The BM nanoparticles, in the inner layer of the MN, serve as an oxygen supply station, and counteracts tumor hypoxia by converting hydrogen peroxide (H2O2) into oxygen (O2), thus promoting PDT and PROTAC activation. This PROTAC prodrug-integrated MN significantly inhibits tumor growth in both subcutaneous and orthotopic GBM tumor models. This study describes the first spatiotemporally-tunable protein degradation strategy for highly efficient GBM therapy, potentially advancing precise therapy of other kinds of refractory brain tumors.

Multi-omics profiling reveals key factors involved in Ewing sarcoma metastasis

Ewing sarcoma (EWS) is the second most common bone tumor affecting children and young adults, with dismal outcomes for patients with metastasis at diagnosis. Mechanisms leading to metastasis remain poorly understood. To deepen our knowledge on EWS progression, we have profiled tumors and metastases from a spontaneous metastasis mouse model using a multi-omics approach. Combining transcriptomics, proteomics, and methylomics analyses, we identified signaling cascades and candidate genes enriched in metastases that could be modulating aggressiveness in EWS. Phenotypical validation of two of these candidates, cyclic AMP-responsive element-binding protein 1 (CREB1) and lipoxygenase homology domain-containing protein 1 (LOXHD1), showed an association with migration and clonogenic abilities. Moreover, previously described CREB1 downstream targets were present amongst the metastatic-enriched results. Combining the different omics datasets, we identified FYVE, RhoGEF, and PH domain-containing protein 4 (FGD4) as a CREB1 target interconnecting the different EWS biological layers (RNA, protein and methylation status) and whose high expression is associated with worse clinical outcome. Further studies will provide insight into EWS metastasis mechanisms and ultimately improve survival rates for EWS patients.

circEgg inhibits BmCPV infection by regulating the transition between H3K9me3 and H3K9ac

Our previous study demonstrated that the expression level of circRNA circEgg, which is encoded by histone-lysine N-methyltransferase eggless (BmEgg), is responsive to Bombyx mori cytoplasmic polyhedrosis virus (BmCPV) infection in the silkworm. However, the precise relationship between BmCPV infection and circEgg remains unclear. In this study, we observed that the expression level of circEgg in both the midguts and cultured BmN cells significantly increased after BmCPV infection, while the expression of its host gene, BmEgg, exhibited an opposite trend. Transient expression experiments revealed that circEgg acts to inhibit BmCPV infection. Additionally, Western blot analyses indicated that BmCPV infection leads to a downregulation of histone 3 lysine 9 trimethylation (H3K9me3) and an upregulation of histone 3 lysine 9 acetylation (H3K9ac). Notably, the levels of H3K9ac and H3K9me3 were found to be positively and negatively correlated with circEgg expression, respectively, suggesting that circEgg may regulate the transition between H3K9me3 and H3K9ac. Mechanistically, we discovered that circEgg inhibits BmCPV infection by enhancing the H3K9ac level through the circEgg-bmo-miR-3391-5p-histone deacetylase Rpd3 network, while simultaneously reducing the H3K9me3 level via the circEgg-encoded protein circEgg-P122. Collectively, these findings indicate that circEgg plays a crucial role in inhibiting BmCPV infection by modulating the balance between H3K9me3 and H3K9ac.

Targeting aldehyde dehydrogenase ALDH3A1 increases ferroptosis vulnerability in squamous cancer

Ferroptosis is a unique modality of regulated cell death induced by excessive lipid peroxidation, playing a crucial role in tumor suppression and providing potential therapeutic strategy for cancer treatment. Here, we find that aldehyde dehydrogenase-ALDH3A1 tightly links to ferroptosis in squamous cell carcinomas (SCCs). Functional assays demonstrate the enzymatic activity-dependent regulation of ALDH3A1 in protecting SCC cells against ferroptosis through catalyzing aldehydes and mitigating lipid peroxidation. Furthermore, a specific covalent inhibitor of ALDH3A1-EN40 significantly enhances the ferroptosis sensitivity induced by the ferroptosis inducer. The combination of EN40 and a ferroptosis inducer exhibits a synergistic effect, effectively inhibiting the proliferation of SCC cells/organoids and suppressing tumor growth both in vitro and in vivo. On mechanism, high expression of ALDH3A1 is transcriptionally governed by TP63, which binds to super-enhancer of ALDH3A1. Collectively, our findings reveal a yet-unrecognized function of ALDH3A1 exploited by SCC cells to evade ferroptosis, and targeting ALDH3A1 may enhance the effect of ferroptosis-induced therapy in SCCs.

Functional characterization of a novel protein-coding circular RNA, circRNA_1193, from the mAAP gene in silkworm and its role in antiviral defense against BmCPV

A novel circular RNA, circRNA_1193, which originates from the membrane alanyl aminopeptidase-like gene in silkworms, was explored for its potential function and regulatory mechanism. We validated the presence of circRNA_1193 in Bombyx mori cytoplasmic polyhedrosis virus (BmCPV)-infected silkworm ovary cell line (BmN) cells through a combination of reverse transcription polymerase chain reaction, Northern blotting, and in situ hybridization. CircRNA_1193 exhibited tissue-specific expression, being highly enriched in the midgut and Malpighian tubules, and displayed a specific response to BmCPV infection, but not to Bombyx mori nucleopolyhedrovirus or lipopolysaccharide. Functional analyses revealed that the overexpression of circRNA_1193 suppressed BmCPV replication, whereas its knockdown increased viral replication. Bioinformatic analyses revealed potential internal ribosome entry sites, m6A methylation sites, and open reading frames (ORFs) within circRNA_1193, suggesting its potential coding capacity. We confirmed the translation of the ORF by constructing a DsRed reporter vector and demonstrating DsRed expression in transfected cells. Furthermore, a mutation of the start codon within circRNA_1193 abolished its antiviral activity, highlighting the crucial role of the translated protein, which is 35 kDa and is designated as VSP35. Furthermore, our data suggest that the formation of circRNA_1193 relies on reverse complementary flanking sequences. These findings unveil a novel protein-coding circular RNA in silkworms that plays a critical role in antiviral defense.

IMPORTANCE

This study identified a novel circular RNA, circRNA_1193, in the silkworm Bombyx mori, and revealed its critical role in antiviral defense against Bombyx mori cytoplasmic polyhedrosis virus (BmCPV). We demonstrated that circRNA_1193 exhibits tissue-specific expression, is upregulated in response to BmCPV infection, and possesses antiviral activity. Importantly, we show that circRNA_1193 encodes the viral protein VSP35, which is essential for its antiviral function. These findings provide new insights into the complex regulatory mechanisms of circular RNAs in antiviral immunity and underscore the potential of circular RNAs as therapeutic targets in viral diseases. The identification of a protein-coding circular RNA with antiviral activity in B. mori has broader implications for understanding the evolution and diversity of host defense mechanisms against viruses.

Cell-cycle dependent DNA repair and replication unifies patterns of chromosome instability

Chromosomal instability (CIN) is pervasive in human tumours and often leads to structural or numerical chromosomal aberrations. Somatic structural variants (SVs) are intimately related to copy number alterations but the two types of variant are often studied independently. Additionally, despite numerous studies on detecting various SV patterns, there are still no general quantitative models of SV generation. To address this issue, we develop a computational cell-cycle model for the generation of SVs from end-joining repair and replication after double-strand break formation. Our model provides quantitative information on the relationship between breakage fusion bridge cycle, chromothripsis, seismic amplification, and extra-chromosomal circular DNA. Given whole-genome sequencing data, the model also allows us to infer important parameters in SV generation with Bayesian inference. Our quantitative framework unifies disparate genomic patterns resulted from CIN, provides a null mutational model for SV, and reveals deeper insights into the impact of genome rearrangement on tumour evolution.

CONNECTING THE DOTS: EPIGENETIC REGULATION OF EXTRACHROMOSOMAL AND INHERITED DNA AMPLIFICATIONS

DNA amplification has intrigued scientists for decades. Since its discovery, significant progress has been made in understanding the mechanisms promoting DNA amplification and their associated function(s). While DNA copy gains were once thought to be regulated purely by stochastic processes, recent findings have revealed the important role of epigenetic modifications in driving these amplifications and their integration into the genome. Furthermore, advances in genomic technology have enabled detailed characterization of these genomic events in terms of size, structure, formation, and regulation. This review highlights how our understanding of DNA amplifications has evolved over time, tracing its trajectory from initial discovery to the contemporary landscape. We describe how recent discoveries have started to uncover how these genomic events occur by controlled biological processes rather than stochastic mechanisms, presenting opportunities for therapeutic modulation.

Therapeutic insights into epidermal growth factor receptor/reactive oxygen species proto-oncogene 1-receptor co-mutated non-small cell lung cancer: Crizotinib as a promising option

This letter provides a review of the report by Peng et al on a unique case of non-small cell lung cancer (NSCLC), specifically lung adenocarcinoma, featuring reactive oxygen species proto-oncogene 1-receptor (ROS1) co-mutation. The case involves a 64-year-old patient who exhibited both epidermal growth factor receptor (EGFR) L858R mutation and ROS1 rearrangement, achieving significant disease stabilization following treatment with crizotinib. This rare EGFR/ROS1 co-mutation poses distinct challenges for clinical management and highlights the necessity of personalized treatment strategies. While third-generation EGFR tyrosine kinase inhibitors (TKIs), such as osimertinib, are commonly regarded as first-line therapies, recent studies indicate that crizotinib may offer superior disease control in certain EGFR-mutant patients, particularly those who exhibit poor responses to EGFR TKIs. The case also examines the influence of tumor cell genetic heterogeneity on treatment response, underscoring the importance of evaluating tumor characteristics. In patients with EGFR/ROS1 co-mutation, gefitinib is generally effective as a first-line treatment; however, its efficacy can be limited, whereas crizotinib has demonstrated improved disease control. Future research should focus on identifying optimal treatment strategies for patients with EGFR/ROS1 co-mutation to enhance patient outcomes. In conclusion, this case report not only illustrates the effectiveness of crizotinib in managing patients with EGFR/ROS1 co-mutation but also underscores the importance of personalized treatment approaches, offering valuable insights for improving clinical outcomes in NSCLC patients with complex genetic profiles.

Ferrostatin-1 inhibits tracheal basal cell ferroptosis to facilitate the rapid epithelization of 3D-printed tissue-engineered tracheas

BACKGROUND

Tracheal replacement is a promising approach for treating tracheal defects that are caused by conditions such as stenosis, trauma, or tumors. However, slow postoperative epithelial regeneration often leads to complications, such as infection and granulation tissue formation. Ferroptosis, which is an iron-dependent form of regulated cell death, limits the proliferation of tracheal basal cells (TBCs), which are essential for the epithelialization of tissue-engineered tracheas (TETs). This study explored the potential of ferrostatin-1 (FER-1), which is a ferroptosis inhibitor, to increase TBC proliferation and accelerate the epithelialization of 3D-printed TETs.

METHODS

TBCs were isolated from rabbit bronchial mucosal tissues and cultured in vitro. Ferroptosis was induced in TBCs at passage 2, as shown by increased reactive oxygen species (ROS) levels, Fe2⁺ accumulation, decreased ATP contents, and mitochondrial damage. TBCs were treated with FER-1 (1 μM) for 48 h to inhibit ferroptosis. The effects on ROS levels, Fe2⁺ levels, ATP contents, and mitochondrial morphology were measured. For in vivo experiments, FER-1-treated TBCs were seeded onto 3D-printed polycaprolactone (PCL) scaffolds, which were implanted into rabbits with tracheal injury. Epithelial regeneration and granulation tissue formation were evaluated 6 months after surgery.

RESULTS

FER-1 treatment significantly reduced ferroptosis marker levels in vitro; that is, FER-1 treatment decreased ROS and Fe2⁺ accumulation, ameliorated mitochondrial structures, and increased ATP levels. TBC proliferation and viability were increased after ferroptosis inhibition. In vivo, the group that received 3D-printed scaffolds seeded with TBCs exhibited accelerated TET epithelialization and reduced granulation tissue formation compared with the control groups. These results suggest that inhibiting ferroptosis with FER-1 improves TBC function, leading to more efficient tracheal repair.

CONCLUSIONS

Ferrostatin-1 effectively inhibits ferroptosis in tracheal basal cells, promoting their viability and proliferation. This results in faster epithelialization of tissue-engineered tracheas, offering a promising strategy for improving tracheal reconstruction outcomes and reducing complications such as infection and granulation tissue formation. Future studies are needed to further investigate the molecular mechanisms underlying ferroptosis in TBCs and its potential clinical applications.

Functional combinatorial precision medicine for predicting and optimizing soft tissue sarcoma treatments

Soft tissue sarcomas (STS) are rare, heterogeneous tumors with poor survival outcomes, primarily due to reliance on cytotoxic chemotherapy and lack of targeted therapies. Given the uniquely individualized nature of STS, we hypothesized that the ex vivo drug sensitivity platform, quadratic phenotypic optimization platform (QPOP), can predict treatment response and enhance combination therapy design for STS. Using QPOP, we screened 45 primary STS patient samples, and showed improved or concordant patient outcomes that are attributable to QPOP predictions. From a panel of approved and investigational agents, QPOP identified AZD5153 (BET inhibitor) and pazopanib (multi-kinase blocker) as the most effective combination with superior efficacy compared to standard regimens. Validation in a panel of established patient lines and in vivo models supported its synergistic interaction, accompanied by repressed oncogenic MYC and related pathways. These findings provide preliminary clinical evidence for QPOP to predict STS treatment outcomes and guide the development of novel therapeutic strategies for STS patients.

The synergistic antitumour effect of Carrimycin combined with 5-fluorouracil on colorectal cancer

5-Fluorouracil (5-FU)-based chemotherapy often leads to drug resistance and adverse reactions in individuals with colorectal cancer (CRC). Carrimycin (CAM), a drug with notable antitumour effects across various tumour types, including hepatocellular carcinoma, glioblastoma, and small-cell lung carcinoma, offers an alternative owing to its limited side effects. Combination therapy is a common strategy to mitigate the negative effects of 5-FU and enhance its therapeutic efficacy. This study aimed to investigate the potential synergistic antitumour effects of CAM and 5-FU on HCT-15 and HT-29 CRC cell lines. Using computational analysis, we identified and quantified the synergistic effects of CAM and 5-FU. The combination therapy significantly outperformed 5-FU alone in inhibiting cell proliferation, colony formation, cell cycle progression, and migration. Additionally, it markedly increased the levels of reactive oxygen species and induced DNA damage. Furthermore, RNA-seq analysis revealed that the JNK and p38 MAPK signalling pathways were activated by this combination. In addition, the synergistic effects of the combination therapy were validated in a mouse subcutaneous tumour graft model. In conclusion, CAM enhances the sensitivity of CRC cells to 5-FU both in vitro and in vivo, suggesting its potential as a promising candidate for combination cancer therapy.

Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies

Transcriptional dysregulation is a hallmark of cancer initiation and progression, driven by genetic and epigenetic alterations. Enhancer reprogramming has emerged as a pivotal driver of carcinogenesis, with cancer cells often relying on aberrant transcriptional programs. The advent of high-throughput sequencing technologies has provided critical insights into enhancer reprogramming events and their role in malignancy. While targeting enhancers presents a promising therapeutic strategy, significant challenges remain. These include the off-target effects of enhancer-targeting technologies, the complexity and redundancy of enhancer networks, and the dynamic nature of enhancer reprogramming, which may contribute to therapeutic resistance. This review comprehensively encapsulates the structural attributes of enhancers, delineates the mechanisms underlying their dysregulation in malignant transformation, and evaluates the therapeutic opportunities and limitations associated with targeting enhancers in cancer.

IRF1 is a core transcriptional regulatory circuitry member promoting AML progression by regulating lipid metabolism

BACKGROUND

Acute myeloid leukemia (AML) is a prevalent malignancy of the hematologic system. Despite advancements in therapeutic approaches, significant heterogeneity and therapeutic resistance pose substantial challenges to treatment. Tumors driven by core transcription factors through super-enhancers can establish core transcriptional regulatory circuits (CRCs) that modulate oncogene expression programs. Identifying CRC is crucial for understanding disease-related transcriptional regulation. This study sought to predict and establish a CRC model for AML, identify genes critical for AML survival and explore their regulatory mechanisms in AML progression.

METHODS

The dbCoRC tool was used for predictive analysis of H3K27ac ChIP-seq data from 11 AML samples to construct and validate the CRC model in AML patients. To elucidate the functional role of the CRC member IRF1, we utilized short hairpin RNA (shRNA) to knock down IRF1 in AML cells. RNA-seq, CUT&Tag and lipidomics technologies were subsequently used to investigate the regulatory roles and downstream mechanisms of IRF1 in AML.

RESULTS

This study established a core transcriptional regulatory circuit consisting of IRF1, ELF1, ETV6, RUNX2, and MEF2D, which formed an interconnected autoregulatory loop. Further investigations revealed up-regulated expression of IRF1 in AML patients, which was associated with poor prognosis. Inhibition of IRF1 expression resulted in decreased AML cell proliferation and induced apoptosis, indicating its essential role in the survival of AML cells. Additionally, this study revealed that IRF1 directly regulates the transcription of key genes such as FASN, SCD, and SREBF1 for lipid synthesis, thereby affecting lipid metabolism in AML cells.

CONCLUSION

In summary, this study identified IRF1 as a novel core transcription factor involved in AML pathogenesis. IRF1 collaborates with ELF1, ETV6, RUNX2, and MEF2D to form a core transcriptional regulatory circuit that promotes AML progression. Furthermore, we demonstrated that IRF1 directly regulates the expression of key genes involved in lipid metabolism, influencing the synthesis of diverse lipid molecules crucial for AML survival.

Insights into Extrachromosomal DNA in Cancer: Biogenesis, Methodologies, Functions, and Therapeutic Potential

Originating from, but independent of, linear chromosomes, extrachromosomal DNA (ecDNA) exists in a more active state of transcription and autonomous replication. It plays a crucial role in the development of malignancies and therapy resistance. Since its discovery in eukaryotic cells more than half a century ago, the biological characteristics and functions of ecDNA have remained unclear due to limitations in detection methods. However, recent advancements in research tools have transformed ecDNA research. It is believed that ecDNA exhibits greater activity in the abnormal amplification of oncogenes, thereby driving cancer progression through their overexpression. Notably, compared to linear DNA, ecDNA can also function as a genomic element with regulatory roles, including both trans- and cis-acting functions. Its critical roles in tumorigenesis, evolution, progression, and drug resistance in malignant tumors are increasingly recognized. This review provides a comprehensive summary of the evolutionary context of ecDNA and highlights significant progress in understanding its biological functions and potential applications as a therapeutic target in malignant tumors.

Identifying Lipid Metabolism-Related Therapeutic Targets and Diagnostic Markers for Lung Adenocarcinoma by Mendelian Randomization and Machine Learning Analysis

BACKGROUND

Lipid metabolic disorders are emerging as a recognized influencing factors of lung adenocarcinoma (LUAD). This study aims to investigate the influence of lipid metabolism-related genes (LMRGs) on the diagnosis and treatment of LUAD and to identify significant biomarkers.

METHODS

DESeq2 and robust rank aggregation (RRA) analyses were employed to determine the differential expression of LMRGs from TCGA-LUAD and five GEO datasets. Mendelian randomization (MR) was conducted utilizing protein quantitative trait loci (pQTLs) in the deCODE, prot-a, and UKB-PPP Study to estimate causal relationships between plasma proteins and LUAD within the ieu-a-984, ieu-a-965, and FinnGen R10 cohorts as potential drug targets of LUAD. Subsequently, an optimal machine learning model for diagnosing LUAD was established by comparing four models: support vector machine, random forest (RF), glmBoost, and eXtreme Gradient Boosting. Finally, the diagnostic performance of five plasma proteins was validated through nomogram analysis, calibration curve assessment, decision curve analysis (DCA), independent internal and external datasets.

RESULT

A total of five biomarkers were identified from 1034 LMRGs via MR and differential expression analysis. TNFRSF21 exhibited a positive association with LUAD risk; conversely, BCHE, FABP4, LPL, and PLBD1 demonstrated negative correlations with this risk. The RF machine learning model was determined to be the optimal model for diagnosing LUAD using these five plasma proteins. Ultimately, nomogram construction, calibration curve analysis, DCA, as well as independent internal and external dataset validation confirmed that these biomarkers exhibit excellent diagnostic performance.

CONCLUSIONS

BCHE, FABP4, LPL, PLBD1, and TNFRSF21 represent potential novel reliable diagnostic markers as well as therapeutic targets for LUAD.

Is there direct photoentrainment in the goldfish liver? Wavelength-dependent regulation of clock genes and investigation of the opsin 7 family

Widespread direct photoentrainment in zebrafish peripheral tissues is linked to diverse non-visual opsins. To explore whether this broadly distributed photosensitivity is specific to zebrafish or is a general teleost feature, we investigated hepatic photosynchronization in goldfish. First, we focused on the opsin 7 family (OPN7, a key peripheral novel opsin in zebrafish), investigating its presence in the goldfish liver. Subsequently, we studied whether light can directly entrain the goldfish liver and retina clocks. Silico analysis revealed seven OPN7 paralogs from four gene families, suggesting expansion through whole-genome and tandem duplications. The paralogs of families OPN7a, OPN7b, and OPN7d were mainly localized in neural tissues, while OPN7c paralogs were more abundant in peripheral tissues-including the liver-suggesting divergent roles. Light (independently of the wavelength employed) directly induced the per2a clock gene in the retina both in vivo and in vitro, confirming expected photoentrainment. However, in the liver, photoinduction of per1a and cry1a only occurred in vivo, not in vitro. These results suggest an indirect light-entrainment mechanism of the goldfish hepatic clock, possibly mediated by other oscillators or photosensitive organs. Our findings challenge the assumption of widespread direct photosensitivity in the peripheral tissues of teleosts. Further research is needed to understand the role of tissue-specific photoentrainment and non-visual opsins in diverse teleost species.

Core transcriptional regulatory circuitry molecule ZNF217 promotes AML cell proliferation by up-regulating MYB

Leukemia is characterized by multiple rearrangements of signal transduction genes and overexpression of nonmutated genes, such as transcription factors (TFs) genes. Super-enhancers (SEs) are prevalent in human cancers and are associated with the accumulation of numerous core TFs. SEs drive the expression of core TF genes by delivering robust transcriptional activation signals. Additionally, core TFs sustain the stability and activity of SEs through mutual auto-regulation loops, creating a positive feedback loop known as the Core Transcriptional Regulation Circuit (CRC). Using ChIP-seq data, we identified the involvement of the SE-related gene ZNF217 in acute myeloid leukemia (AML), in which its functional role and underlying mechanism remain unclear. We demonstrated that ZNF217, ELF1, MEF2D, RUNX2, and FOXP1 are likely integral components of the AML CRC through various experimental techniques, including CUT&Tag, short hairpin RNA (shRNA) transduction, and Luciferase reporter assays. Notably, ZNF217 was determined to be indispensable for the proliferation and viability of AML cells both in vitro and in vivo. Subsequent analysis of RNA-seq and CUT&Tag results identified MYB as a key direct target of ZNF217. Overall, our research highlights ZNF217 as a critical oncogene in AML and offers new insights into the transcriptional regulatory mechanisms at play in AML.

LINC00673 binds with leptin to regulate osteogenic function in periodontal ligament stem cells

BACKGROUND

The aim of this study is to investigate whether LINC00673 and leptin are associated with osteogenesis of periodontal ligament stem cells in the microenvironment of advanced glycation end products.

METHODS

LINC00673 expression was detected in PDLSCs by qRT-PCR performed during osteogenic differentiation. By using alkaline phosphatase and Alizarin red S staining, we were able to confirm the role of LINC00673 in regulating osteogenesis in PDLSCs. Assays were performed on nude mice to test bone regeneration in the dorsal region to investigate MiR-188-3p's binding to LINC00673 and leptin (LEP). Western blot was used to detect osteoblast markers (COL1, ALP and RUNX2).

RESULTS

As predicted, miR-188-3p interacts with LINC00673 directly, and miR-188-3p overexpression increases osteogenic differentiation. However, overexpression of LINC00673 reversed this effect, suggesting that LINC00673 functions as a competing endogenous RNA for miR-188-3p. A regulatory network formed by LINC00673 and miR-188-3p regulates the expression of LEP, a gene that inhibits the canonical Wnt pathway, reducing bone formation in PDLSCs.

CONCLUSIONS

PDLSCs differentiate osteogenically as a result of a regulatory network between lncRNA and miRNA (microRNA), which may serve as a therapeutic target for diabetes-related periodontitis.

Mapping chromatin remodelling in glioblastoma identifies epigenetic regulation of key molecular pathways and novel druggable targets

BACKGROUND

Glioblastoma is the most common and aggressive malignant brain tumour in the adult population and its prognosis is dismal. The heterogeneous nature of the tumour, to which epigenetic dysregulation significantly contributes, is among the main therapeutic challenges of the disease.

RESULTS

We have leveraged SYNGN, an experimental pipeline enabling the syngeneic comparison of glioblastoma stem cells and expanded potential stem cell (EPSC)-derived neural stem cells to identify regulatory features driven by chromatin remodelling specifically in glioblastoma stem cells.

CONCLUSIONS

We show epigenetic regulation of the expression of genes and related signalling pathways contributing to glioblastoma development. We also identify novel epigenetically regulated druggable target genes on a patient-specific level, including SMOX and GABBR2.

Deciphering the generation of heterogeneity in esophageal squamous cell carcinoma metastasis via single-cell multiomics analysis

BACKGROUND

Chromatin accessibility plays a crucial role in mediating transcriptional dysregulation and heterogeneity in Esophageal Squamous Cell Carcinoma (ESCC). Examining the chromatin accessibility of ESCC at single-cell level is imperative to understand how it activates oncogenes and contributes to the onset and metastasis of ESCC.

METHODS

We performed single-cell assay for transposase-accessible chromatin sequencing (scATAC-seq) on cancerous and adjacent noncancerous tissues from four ESCC patients who were pathological staged as T1a, T2b, T3b, or T4a, to investigate whether regulatory elements are pivotal in instigating cellular heterogeneity during ESCC metastasis. In conjunction, we integrated these data with 55 scRNA-seq datasets, ChIP-seq or CUT&Tag sequencing data, Hi-C sequencing data, bulk RNA-seq data, and bulk ATAC-seq data from ESCC cell lines to dissect the mechanisms underlying the heterogeneity of ESCC and tumor microenvironment (TME).

RESULTS

Our study identified enhancer-specific activation within epithelial cells orchestrated by the three-dimensional structure of chromatin that regulates SERPINH1 transcription, and promotes the epithelial-mesenchymal transition (EMT) and metastasis of ESCC. Additionally, chromatin element activation facilitated the expression of TNFSF4 in CD8 + exhausted T cells, thereby activating Tregs. Furthermore, we observed that chromatin accessibility promoted the differentiation of tumor-associated macrophages (TAMs) and cancer associated fibroblasts (CAFs).

CONCLUSIONS

In summary, utilizing multiomics analyses, we have revealed chromatin accessibility maps and illuminated the intricate molecular mechanisms that underlie cellular heterogeneity during ESCC metastasis, offering valuable insights to further advance research on tumor progression and deterioration.

Leveraging AI to automate detection and quantification of extrachromosomal DNA to decode drug responses

Introduction

Traditional drug discovery efforts primarily target rapid, reversible protein-mediated adaptations to counteract cancer cell resistance. However, cancer cells also utilize DNA-based strategies, often perceived as slow, irreversible changes like point mutations or drug-resistant clone selection. Extrachromosomal DNA (ecDNA), in contrast, represents a rapid, reversible, and predictable DNA alteration critical for cancer's adaptive response.

Methods

In this study, we developed a novel post-processing pipeline for automated detection and quantification of ecDNA in metaphase Fluorescence in situ Hybridization (FISH) images, leveraging the Microscopy Image Analyzer (MIA) tool. This pipeline is tailored to monitor ecDNA dynamics during drug treatment.

Results

Our approach effectively quantified ecDNA changes, providing a robust framework for analyzing the adaptive responses of cancer cells under therapeutic pressure.

Discussion

The pipeline not only serves as a valuable resource for automating ecDNA detection in metaphase FISH images but also highlights the role of ecDNA in facilitating swift and reversible adaptation to epigenetic remodeling agents such as JQ1.

The role of exosomal non-coding RNAs in the breast cancer tumor microenvironment

The leading form of cancer affecting females globally is breast cancer, characterized by an unregulated growth of cells within the breast. Therefore, examining breast tissue is crucial in accurately identifying and treating this disease. Exosomes are very small enclosures bounded by a layer of cells and produced by a variety of cells present in the cancerous tissue surroundings. They play a crucial role in several biological functions in cancerous tumors. These exosomes carry non-coding RNAs (ncRNAs) and are discharged into the TME, where they are instrumental in the development and advancement of tumors. Additionally, the ncRNAs enclosed in exosomes act as significant mediators of communication within cells. Consequently, there is limited comprehension regarding the precise roles and targets of exosomal RNA in regulation, as research in this area is still in its preliminary phases. This piece provides a comprehensive overview of the latest studies on exosomes, delving into their impact on the behavior of cancer cells and immune cells. Moreover, it presents a compilation of the diverse forms of non-coding RNA molecules found in exosomes released by both cancerous and supportive cells, including circular RNAs, microRNAs, and long non-coding RNAs. Current research has proven the noteworthy influence that non-coding RNA molecules have on the progression, proliferation, drug resistance, and immune responses of breast cancer cells.

Epithelial stem cells from human small bronchi offer a potential for therapy of idiopathic pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a fibrosing interstitial pneumonia with restrictive ventilation. Recently, the structural and functional defects of small airways have received attention in the early pathogenesis of IPF. This study aimed to elucidate the characteristics of small airway epithelial dysfunction in patients with IPF and explore novel therapeutic interventions to impede IPF progression by targeting the dysfunctional small airways.

METHODS

Airway trees spanning the proximal-distal axis were harvested from control lungs and explanted lungs with end-stage IPF undergoing transplant. Qualified basal cells (BCs, p63/Krt5/ITGA6/NGFR) were expanded, and their cellular functions, feasibility, safety and efficacy for transplantation therapy in IPF were validated with experiments in vitro and mouse model. Single-cell RNA-sequencing was employed to elucidate the underlying mechanisms governing the BCs based therapy. Based upon these evidences, three patients with advanced IPF and small airway dysfunction received autologous-BCs transplantation. Post-transplantation assessments included lung function, exercise capacity and high resolution computed tomography (HRCT) scans were analyzed to quantify the clinical benefits conferred by the BCs transplantation.

FINDINGS

An overall landscape of senescent phenotype in airway epithelial cells and airway stem/progenitor cells along the proximal-distal axis of the airway tree in IPF were outlined. In contrast to the cells situated in distal airways, BCs located in small bronchi in IPF displayed a non-senescent phenotype, with comparable proliferative, differentiative capabilities, and similar transcriptomic profiles to normal controls. In a mouse model of pulmonary fibrosis, BCs exhibited promising protective efficacy and safety for transplantation therapy. Autologous BCs transplantation in three advanced IPF patients with small airway dysfunction yielded significant clinical improvements in pulmonary function, particularly evidence in lung volume and small airway function.

INTERPRETATION

Epithelia of small bronchi in IPF contain functional and expandable basal stem cells, which exert therapeutic benefits via bronchoscopic implantation. Our findings offer a potential for IPF treatment by targeting small airways.

FUNDING

National Natural Science Foundation of China (82430001, 81930001, and 81900059), Shanghai Shenkang Hospital Development Center (SHDC2020CR3063B), Department of Science and Technology of Shandong Province (2024HWYQ-058).

Downregulation of LncRNA CCAT1 Enhances Chemosensitivity in Cisplatin-Resistant Gastric Cancer Cells

Chemotherapy is an effective treatment for gastric cancer. However, many patients develop resistance to chemotherapeutic agents during clinical treatment. LncRNA CCAT1 has recently been shown to influence cellular resistance to specific chemotherapeutic drugs, but its role in gastric cancer remains underexplored. This study aims to investigate the role of LncRNA CCAT1 in cisplatin resistance in gastric cancer cells and its potential underlying mechanisms. Gastric cancer cell lines with acquired resistance were established. The expression of CCAT1 was assessed in both cisplatin-sensitive and cisplatin-resistant AGS cell lines. CCAT1 expression was knocked down in AGS/DDP cells, and the changes in IC50 values were measured using the Cell Counting Kit-8 (CCK-8) assay. Apoptosis in gastric cancer cells was evaluated by flow cytometry. Additionally, Western blotting was employed to measure the expression levels of PI3K/AKT/mTOR signaling pathway proteins and apoptosis-related proteins in both interference and control groups. RT-qPCR results indicated that CCAT1 expression was significantly elevated in cisplatin-resistant gastric cancer cells compared to non-resistant cells. Similarly, CCK-8 assay results demonstrated that knocking down CCAT1 in resistant cells increased their sensitivity to cisplatin treatment. Flow cytometry and Western blot results further confirmed that silencing CCAT1 promoted apoptosis in these cells. Additionally, the expression of PI3K/AKT/mTOR signaling pathway proteins was higher in resistant cells compared to their sensitive counterparts, and silencing CCAT1 in AGS/DDP cells resulted in reduced expression of these proteins. In conclusion, the above studies demonstrated that LncRNA CCAT1 induced cisplatin resistance in gastric cancer cells.

Mood variation under dual regulation of circadian clock and light

The intricate relationship between circadian rhythms and mood is well-established. Disturbances in circadian rhythms and sleep often precede the development of mood disorders, such as major depressive disorder (MDD), bipolar disorder (BD), and seasonal affective disorder (SAD). Two primary factors, intrinsic circadian clocks and light, drive the natural fluctuations in mood throughout the day, mirroring the patterns of sleepiness and wakefulness. Nearly all organisms possess intrinsic circadian clocks that coordinate daily rhythms, with light serving as the primary environmental cue to synchronize these internal timekeepers with the 24-hour cycle. Additionally, light directly influences mood states. Disruptions to circadian rhythms, such as those caused by jet lag, shift work, or reduced daylight hours, can trigger or exacerbate mood symptoms. The complex and often subtle connections between circadian disruptions and mood dysregulation suggest that focusing solely on individual clock genes is insufficient to fully understand their etiology and progression. Instead, mood instability may arise from systemic misalignments between external cycles and the internal synchronization of circadian clocks. Here, we synthesize past research on the independent contributions of circadian clocks and light to mood regulation, drawing particularly on insights from animal studies that illuminate fundamental mechanisms relevant to human health.

Signaling pathways and targeted therapies in Ewing sarcoma

Ewing sarcoma, the second most prevalent malignant bone tumor with potential occurrence in soft tissues, exhibits a high level of aggressiveness, primarily afflicting children and adolescents. It is characterized by fusion proteins arising from chromosomal translocations. The fusion proteins induce aberrations in multiple signaling pathways and molecules, constituting a key event in oncogenic transformation. While diagnostic and therapeutic modalities have advanced in recent decades and multimodal treatments, including surgery, radiotherapy, and chemotherapy, have significantly improved survival of patients with localized tumors, patients with metastatic tumors continue to face poor prognoses. There persists a pressing need for novel alternative treatments, yet the translation of our understanding of Ewing sarcoma pathogenesis into improved clinical outcomes remains a critical challenge. Here, we provide a comprehensive review of Ewing sarcoma, including fusion proteins, various signaling pathways, pivotal pathogenetic molecules implicated in its development, and associated targeted therapies and immunotherapies. We summarize past endeavors, current advancements, and deliberate on limitations and future research directions. It is envisaged that this review will furnish novel insights into prospective treatment avenues for Ewing sarcoma.

Combined replacement of lnc-MEG3 and miR-155 elicit tumor suppression in multiple myeloma

AIMS

To investigate the biological impact of simultaneous overexpression of lncRNA MEG3 and miR-155, termed a "double hit," on multiple myeloma (MM) cells compared to individual biomarker substitution.

MATERIALS AND METHODS

Human MM cells were transfected with MEG3-overexpressed plasmids and miR-155 mimics. Cell cytotoxicity, apoptosis, and gene expression were evaluated in transfected cells and clinical samples.

RESULTS

MEG3 and miR-155 were significantly downregulated in MM patients, with lower expression levels correlating with advanced disease stages and poorer survival. Dual overexpression induced potent cytotoxic effects in MM cells.

CONCLUSION

MEG3 and miR-155 are potential tumor suppressors in MM. Simultaneous overexpression of both biomarkers could represent a novel therapeutic strategy, and their levels could serve as diagnostic and prognostic markers.

Targeting BRD4 ameliorates experimental emphysema by disrupting super-enhancer in polarized alveolar macrophage

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a progressive chronic lung disease characterized by chronic airway inflammation and emphysema. Macrophage polarization plays an important role in COPD pathogenesis by secreting inflammatory mediators. Bromodomain-containing protein 4 (BRD4), an epigenetic reader that specifically binds to histones, plays a crucial role in inflammatory diseases by regulating macrophage polarization. Herein, we attempted to examine the hypothesis that modulating alveolar macrophage polarization via BRD4 inhibitors might has a potential for COPD treatment.

METHODS

We firstly analyzed BRD4 expression and its correlation with clinical parameters and macrophage polarization markers in sputum transcriptomes from 94 COPD patients and 36 healthy individuals. In vivo, BRD4 inhibitor JQ1 and degrader ARV-825 were intraperitoneally administrated into emphysema mice to assess their effects on lung emphysema and inflammation. In vitro, RNA-seq and CUT&Tag assay of BRD4 and H3K27ac were applied for elucidating how BRD4 regulates macrophage polarization.

RESULTS

We found an increased expression of BRD4 in the induced sputum from patients with COPD and unveiled a strong correlation between BRD4 expression and clinical parameters as well as macrophage polarization. Subsequently, BRD4 inhibitor JQ1 and degrader ARV-825 significantly mitigated emphysema and airway inflammation along with better protection of lung function in mice. BRD4 inhibition also suppressed both M1 and M2 alveolar macrophage polarization. The CUT&Tag assay of BRD4 and H3K27ac, revealed that BRD4 inhibition disrupted the super-enhancers (SEs) of IRF4 (a crucial transcription factor for M2 macrophage), and subsequently affected the expression of matrix metalloproteinase 12 (MMP12) which is vital for emphysema development.

CONCLUSION

This study suggested that downregulation of BRD4 might suppress airway inflammation and emphysema through disrupting the SEs of IRF4 and alveolar macrophages polarization, which might be a potential target of therapeutic intervention in COPD. A diagram of the mechanism by which BRD4 mediated super-enhancer of IRF4 in M2 AMs. Graphic illustration showed targeting BRD4 in M2 polarized AMs lead to the downregulation of MMP12 expression, resulting in the amelioration of experimental emphysema by disrupting the super-enhancer of IRF4.

The Relationship Between Differential Expression of Non-coding RNAs (TP53TG1, LINC00342, MALAT1, DNM3OS, miR-126-3p, miR-200a-3p, miR-18a-5p) and Protein-Coding Genes (PTEN, FOXO3) and Risk of Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a rapidly progressive interstitial lung disease of unknown pathogenesis with no effective treatment currently available. Given the regulatory roles of lncRNAs (TP53TG1, LINC00342, H19, MALAT1, DNM3OS, MEG3), miRNAs (miR-218-5p, miR-126-3p, miR-200a-3p, miR-18a-5p, miR-29a-3p), and their target protein-coding genes (PTEN, TGFB2, FOXO3, KEAP1) in the TGF-β/SMAD3, Wnt/β-catenin, focal adhesion, and PI3K/AKT signaling pathways, we investigated the expression levels of selected genes in peripheral blood mononuclear cells (PBMCs) and lung tissue from patients with IPF. Lung tissue and blood samples were collected from 33 newly diagnosed, treatment-naive patients and 70 healthy controls. Gene expression levels were analyzed by RT-qPCR. TaqMan assays and TaqMan MicroRNA assay were employed to quantify the expression of target lncRNAs, mRNAs, and miRNAs. Our study identified significant differential expression in PBMCs from IPF patients compared to healthy controls, including lncRNAs MALAT1 (Fold Change = 3.809, P = 0.0001), TP53TG1 (Fold Change = 0.4261, P = 0.0021), and LINC00342 (Fold Change = 1.837, P = 0.0448); miRNAs miR-126-3p (Fold Change = 0.102, P = 0.0028), miR-200a-3p (Fold Change = 0.442, P = 0.0055), and miR-18a-5p (Fold Change = 0.154, P = 0.0034); and mRNAs FOXO3 (Fold Change = 4.604, P = 0.0032) and PTEN (Fold Change = 2.22, P = 0.0011). In lung tissue from IPF patients, significant expression changes were observed in TP53TG1 (Fold Change = 0.2091, P = 0.0305) and DNM3OS (Fold Change = 4.759, P = 0.05). Combined analysis of PBMCs expression levels for TP53TG1, MALAT1, miRNA miR-126-3p, and PTEN distinguished IPF patients from healthy controls with an AUC = 0.971, sensitivity = 0.80, and specificity = 0.955 (P = 6 × 10-8). These findings suggest a potential involvement of the identified ncRNAs and mRNAs in IPF pathogenesis. However, additional functional validation studies are needed to elucidate the precise molecular mechanisms by which these lncRNAs, miRNAs, and their targets contribute to PF.

Genomic and transcriptomic insights into vitamin A-induced thermogenesis and gene reuse as a cold adaptation strategy in wild boars

Wild boars inhabit diverse climates, including frigid regions like Siberia, but their migration history and cold adaptation mechanisms into high latitudes remain poorly understood. We constructed the most comprehensive wild boar whole-genome variant dataset to date, comprising 124 samples from tropical to frigid zones, among which 47 Russian, 8 South Chinese and 3 Vietnamese wild boars were newly supplemented. We also gathered 75 high-quality RNA-seq datasets from 10 tissues of 6 wild boars from Russia and 6 from southern China. Demographic analysis revealed the appearance of Russian wild boars in Far East of Asia (RUA) and Europe (RUE) after the last glacial maximum till ~ 10 thousand years ago. Recent gene flow (<100 years) from RUA to RUE reflects human-mediated introductions. Cold-region wild boars exhibit strong selection signatures indicative of genetic adaptation to cold climates. Further pathway and transcriptomic analyses reveal a novel cold resistance mechanism centered on enhanced vitamin A metabolism and catalysis, involving the reuse of UGT2B31 and rhythm regulation by ANGPTL8, RLN3 and ZBTB20. This may compensate for the pig's lack of brown fat/UCP1 thermogenesis. These findings provide new insights into the molecular basis of cold adaptation and improve our understanding of Eurasian wild boar migration history.

Exosomal lncRNAs as diagnostic and therapeutic targets in multiple myeloma

Multiple Myeloma (MM) is the second most common malignancy of the hematopoietic system, accounting for approximately 10% of all hematological malignancies, and currently, there is no complete cure. Existing research indicates that exosomal long non-coding RNAs (lncRNAs) play a crucial regulatory role in the initiation and progression of tumors, involving various interactions such as lncRNA-miRNA, lncRNA-mRNA, and lncRNA-RNA binding proteins (RBP). Despite the significant clinical application potential of exosomal lncRNAs, research in this area still faces challenges due to their low abundance and technical limitations. To our knowledge, this review is the first to comprehensively integrate and elucidate the three mechanisms of action of exosomal lncRNAs in MM, and to propose potential therapeutic targets and clinical cases based on these mechanisms. We highlight the latest advancements in the potential of exosomal lncRNAs as biomarkers and therapeutic targets, offering not only a comprehensive analysis of the role of exosomal lncRNAs in MM but also new perspectives and methods for future clinical diagnosis and treatment of multiple myeloma.

Exploring Hepatocellular Carcinoma Pathogenesis: The Influence of Genetic Polymorphisms

Hepatocellular carcinoma (HCC) is influenced by several factors, among which genetic polymorphisms play a key role. Polymorphisms in various genes affect key pathways involved in HCC development, including metabolism, expression of inflammatory cytokines, cell proliferation, and apoptosis regulation. These polymorphisms induce differential effects on susceptibility to HCC, disease progression, and treatment outcomes. Understanding the effect of genetic variations on HCC pathogenesis is essential to elucidate underlying mechanisms and identify potential therapeutic targets. This review explores the diverse roles of genetic polymorphisms in HCC, providing insights into the complex interplay between genetic factors and disease development.

Super-Enhancer-Driven IRF2BP2 is Activated by Master Transcription Factors and Sustains T-ALL Cell Growth and Survival

Super enhancers (SEs) are large clusters of transcriptional enhancers driving the expression of genes crucial for defining cell identity. In cancer, tumor-specific SEs activate key oncogenes, leading to tumorigenesis. Identifying SE-driven oncogenes in tumors and understanding their functional mechanisms is of significant importance. In this study, a previously unreported SE region is identified in T-cell acute lymphoblastic leukemia (T-ALL) patient samples and cell lines. This SE activates the expression of interferon regulatory factor 2 binding protein 2 (IRF2BP2) and is regulated by T-ALL master transcription factors (TFs) such as ETS transcription factor ERG (ERG), E74 like ETS transcription factor 1 (ELF1), and ETS proto-oncogene 1, transcription factor (ETS1). Hematopoietic system-specific IRF2BP2 conditional knockout mice is generated and showed that IRF2BP2 has minimal impact on normal T cell development. However, in vitro and in vivo experiments demonstrated that IRF2BP2 is crucial for T-ALL cell growth and survival. Loss of IRF2BP2 affects the MYC and E2F pathways in T-ALL cells. Cleavage under targets and tagmentation (CUT&Tag) assays and immunoprecipitation revealed that IRF2BP2 cooperates with the master TFs of T-ALL cells, targeting the enhancer of the T-ALL susceptibility gene recombination activating 1 (RAG1) and modulating its expression. These findings provide new insights into the regulatory network within T-ALL cells, identifying potential new targets for therapeutic intervention.