Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

Identification of USP39 as a prognostic and predictive biomarker for determining the response to immunotherapy in pancreatic cancer

Ubiquitin-Specific Protease 39 (USP39) has been implicated in numerous malignancies, however, its pathogenic mechanisms and impact on the tumor immune microenvironment (TIME) remain incompletely characterized. Based on The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) databases, we investigated the diagnostic and prognostic values of USP39 across various cancer types. Additionally, we examined the correlation between USP39 expression and immune-related gene signature, immune cell infiltration pattern, tumor microsatellite instability (MSI), and tumor mutation burden (TMB). This study specifically focused on exploring the clinical relevance and molecular functions of USP39 in pancreatic adenocarcinoma (PAAD), with particularly emphasis on its role in shaping the TIME and modulating responses to immunotherapy. The results demonstrated that evaluated USP39 expression significantly correlated with advanced tumor stage and unfavorable clinical outcomes across multiple cancer types, most notably in PAAD. Functional enrichment analysis indicated that USP39 potentially promotes tumor progression through multiple oncogenic signaling cascades. In vitro experimental validation confirmed that USP39 knockdown inhibited migration and proliferation of pancreatic cancer cells while inducing apoptosis. Additionally, we identified significant positive correlations between USP39 expression and immune checkpoint molecules, particularly prominent in PAAD. Furthermore, we observed associations between USP39 expression and TMB in 16 cancer types and MSI in 11 cancer types, suggesting that heightened USP39 expression may enhance responsiveness to immunotherapeutic interventions. Collectively, our findings establish USP39 as a valuable immune-related biomarker with both diagnostic and prognostic utility across multiple cancer types, especially PAAD, underscoring its potential as a promising therapeutic target for cancer immunotherapy. Clinical trial number Not applicable.

Exploring Integrin α5β1 as a Potential Therapeutic Target for Pulmonary Arterial Hypertension: Insights From Comprehensive Multicenter Preclinical Studies

BACKGROUND

Pulmonary arterial hypertension (PAH) is characterized by obliterative vascular remodeling of the small pulmonary arteries (PAs) and progressive increase in pulmonary vascular resistance leading to right ventricular failure. Although several drugs are approved for the treatment of PAH, mortality rates remain high. Accumulating evidence supports a pathological function of integrins in vessel remodeling, which are gaining renewed interest as drug targets. However, their role in PAH remains largely unexplored.

METHODS

The expression of the RGD (arginylglycylaspartic acid)-binding integrin α5β1 was assessed in PAs, PA smooth muscle cells, and PA endothelial cells from patients with PAH and controls using NanoString, immunoblotting, and Mesoscale Discovery assays. RNA sequencing was conducted to identify gene networks regulated by α5β1 inhibition in PAH PA smooth muscle cells. The therapeutic efficacy of α5β1 inhibition was evaluated using a novel small molecule inhibitor and selective neutralizing antibodies in Sugen/hypoxia and monocrotaline rat models, with validation by an external contract research organization. Comparisons were made against standard-of-care therapies (ie, macitentan, tadalafil) and sotatercept and efficacy was assessed using echocardiographic, hemodynamic, and histological assessments. Ex vivo studies using human precision-cut lung slices were performed to further assess the effects of α5β1 inhibition on pulmonary vascular remodeling.

RESULTS

We found that the arginine-glycine-aspartate RGD-binding integrin α5β1 is upregulated in PA endothelial cells and PA smooth muscle cells from patients with PAH and remodeled PAs from animal models. Blockade of the integrin α5β1 or depletion of the α5 subunit downregulated FOXM1 (forkhead box protein M1)-regulated gene networks, resulting in mitotic defects and inhibition of the pro-proliferative and apoptosis-resistant phenotype of PAH cells. We demonstrated that α5β1 integrin blockade safely attenuates pulmonary vascular remodeling and improves hemodynamics and right ventricular function and matched or exceeded the efficacy of standard of care and sotatercept in multiple preclinical models. Ex vivo studies further validated its potential in reversing advanced remodeling in human precision-cut lung slices.

CONCLUSIONS

These findings establish α5β1 integrin as a pivotal driver of PAH pathology and we propose its inhibition as a novel, safe, and effective therapeutic strategy for PAH.

Ginsenoside Rh2 in combination with IFNγ potentiated the anti-cancer effect by enhancing interferon signaling response in colorectal cancer cells

Interferon gamma (IFNγ) can amplify immune cell-mediated anti-tumor immunity, as well as directly kill cancer cells. Ginsenoside Rh2 (Rh2), a bioactive compound in traditional Chinese medicine, exhibits anti-cancer effects such as inhibiting proliferation and metastasis. Our earlier research found that Rh2 combined with IFNγ enhanced CXCL10 secretion in cancer cells. Here, we explored whether Rh2 and IFNγ exerted more potent anti-cancer activity in vitro and in vivo, along with its mechanisms and clinical value. Our data showed that Rh2 in combination with IFNγ resulted in a remarkably increased cytotoxicity in colorectal cancer cells including HT29, LoVo and T84 cell lines. Consistently, intratumoral injection with Rh2 plus IFNγ further restricted the HT29 tumor growth in vivo, and importantly, it was demonstrated to be safe for mice. Meanwhile, the combo treatment activated the stimulator of interferon genes (STING) pathway in cancer cells, promoting the transcription of downstream type I interferon. RNA sequencing revealed a dramatically transcriptional alteration in cancer cells with combo treatment and indicated that Rh2 further augmented the activation of interferon signaling pathway, compared with the IFNγ alone. Inhibition of janus kinase (JAK) by ruxolitinib could significantly rescue the cell death-triggered by the combo treatment. Then, a gene set named Rh2+IFNγ signature genes (RISG) was defined, which contained top 20 significantly upregulated genes from the combo treatment. Patients who exhibited a favorable response to the immunotherapy had a higher expression of RISG in tumor compared with those who did not respond. And the high expression of RISG was correlated with better clinical outcome in patients with colorectal cancer (CRC) and skin cutaneous melanoma (SKCM). Herein, the combination of Rh2 with IFNγ served as a promising strategy for cancer treatment, and its-derived RISG gene set also exhibited potential value in predicting clinical outcome. Schematic diagram of the anti-cancer effect of Rh2 combined with IFNγ. The schematic diagram illustrated that ginsenoside Rh2 in combination with IFNγ robustly activated the interferon signals in cancer cells, ultimately leading a significant cell death of cancer cells. ISGs, interferon-stimulated genes. Created with BioRender.com.

Oncogenic properties of wild-type DNA repair gene FANCA in breast cancer

FANCA is one of the 23 genes whose deficiencies lead to defective DNA interstrand crosslink repair and cancer-prone Fanconi anemia disease. Beyond its functions in DNA repair and tumor suppression, we report that high FANCA expression is strongly associated with breast cancer development. Overexpression of WT-FANCA significantly promotes breast cancer cell proliferation and tumor growth both in vitro and in vivo, while FANCA deficiency severely compromises the proliferation of breast cancer cells, but not non-tumorigenic breast epithelial cells. Heterozygous knockout of FANCA in breast cancer mouse models is sufficient to cause significant reduction of breast tumor growth in vivo. Furthermore, we have shown that high FANCA expression in breast cancer correlates with promoter hypomethylation in a TET-dependent manner, and TET inhibition recapitulates the proliferation defects caused by FANCA deficiency. Our study identifies the oncogenic properties of WT-FANCA and shows that FANCA is a promising target for breast cancer intervention.

TFE3 fusion oncoprotein condensates drive transcriptional reprogramming and cancer progression in translocation renal cell carcinoma

Translocation renal cell carcinoma (tRCC) presents a significant clinical challenge due to its aggressiveness and limited treatment options. It is primarily driven by fusion oncoproteins (FOs), yet their role in oncogenesis is not fully understood. Here, we investigate TFE3 fusions in tRCC, focusing on NONO::TFE3 and SFPQ::TFE3. We demonstrate that TFE3 FOs form liquid-like condensates with increased transcriptional activity, localizing to TFE3 target genes and promoting cell proliferation and migration. The coiled-coil domains (CCDs) of NONO and SFPQ are essential for condensate formation, prolonging TFE3 FOs' chromatin binding time and enhancing transcription. Compared with wild-type TFE3, TFE3 FOs bind to new chromatin regions, alter chromatin accessibility, and form new enhancers and super-enhancers at pro-growth gene loci. Disruption of condensate formation via CCD modification abolishes these genome-wide changes. Altogether, our integrated analyses underscore the critical functions of TFE3 FO condensates in driving tumor cell growth, providing key insights for future therapeutic strategies.

DNA methylation signature of a lifestyle-based resilience index for cognitive health

Cognitive resilience (CR) contributes to the variability in risk for developing and progressing in Alzheimer's disease (AD) among individuals. Beyond genetics, recent studies highlight the critical role of lifestyle factors in enhancing CR and delaying cognitive decline. DNA methylation (DNAm), an epigenetic mechanism influenced by both genetic and environmental factors, including CR-related lifestyle factors, offers a promising pathway for understanding the biology of CR. We studied DNAm changes associated with the Resilience Index (RI), a composite measure of lifestyle factors, using blood samples from the Healthy Brain Initiative (HBI) cohort. After corrections for multiple comparisons, our analysis identified 19 CpGs and 24 differentially methylated regions significantly associated with the RI, adjusting for covariates age, sex, APOE ε4, and immune cell composition. The RI-associated methylation changes are significantly enriched in pathways related to lipid metabolism, synaptic plasticity, and neuroinflammation, and highlight the connection between cardiovascular health and cognitive function. By identifying RI-associated DNAm, our study provided an alternative approach to discovering future targets and treatment strategies for AD, complementary to the traditional approach of identifying disease-associated variants directly. Furthermore, we developed a Methylation-based Resilience Score (MRS) that successfully predicted future cognitive decline in an external dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI), even after accounting for age, sex, APOE ε4, years of education, baseline diagnosis, and baseline MMSE score. Our findings are particularly relevant for a better understanding of epigenetic architecture underlying cognitive resilience. Importantly, the significant association between baseline MRS and future cognitive decline demonstrated that DNAm could be a predictive marker for AD, laying the foundation for future studies on personalized AD prevention.

Maternal age is associated with apoptotic gene abundance patterns in blastocoel fluid-conditioned media from euploid embryos: a pilot study

PURPOSE

This retrospective study measured global gene abundance using RNASeq of blastocoel fluid-conditioned media from euploid ICSI-generated embryos to identify genes and signaling pathways associated with maternal age.

METHODS

Blastocoel fluid-conditioned media was obtained following trophectoderm biopsy of ICSI-generated day-5 blastocysts. Media for RNASeq were from 24 euploid blastocysts (9 from patients aged 35 or older). Transcriptome analysis identified differentially expressed genes when comparing media from patients of advanced maternal age to those younger than 35. Further gene abundance analysis on genes and pathways identified from the RNASeq analysis was conducted with another group of media samples using RT-qPCR.

RESULTS

Twenty-five protein encoding genes identified in the RNASeq study were differentially expressed when comparing blastocoel fluid-conditioned media associated with patients of advanced maternal age to media associated with patients under the age of 35. Genes encoding the proteins SHARPIN and BCL2L12 showed a statistically significant increase (p < 0.05) in abundance in patients of advanced maternal age. Abundance analysis using RT-qPCR in additional media samples revealed elevated SHARPIN abundance in media associated with successful implantation in patients under 35 alongside a decrease in CASP8 abundance. This abundance pattern was the opposite in media associated with successful implantation in patients of advanced maternal age.

CONCLUSIONS

This study uncovered differential apoptotic gene abundance associated with maternal age by assessing blastocoel fluid-conditioned media from euploid blastocysts. These unique abundance patterns may provide insight into the regulation of apoptosis in embryos from women of advanced maternal age, and how this signaling pathway may impact implantation outcomes.

DNA damage response deficiency enhances neuroblastoma progression and sensitivity to combination PARP and ATR inhibition

Sequencing of neuroblastoma (NB) tumors has revealed genetic alterations in genes involved in DNA damage response (DDR) pathways. However, roles for specific alterations of DDR genes in pediatric solid tumors remain poorly understood. To address this, mutations in the DDR pathway including Brca2, Atm, and Palb2 were incorporated into an established zebrafish MYCN transgenic model (Tg(dbh:EGFP-MYCN)). These mutations enhance NB formation and metastasis and result in upregulation of cell-cycle checkpoint and DNA damage repair signatures, revealing molecular vulnerabilities in DDR-deficient NB. DDR gene knockdown in zebrafish and human NB cells increases sensitivity to the poly(ADP-ribose) polymerase (PARP) inhibitor olaparib, and this effect is enhanced by inhibition of the ataxia telangiectasia and rad3-related (ATR) kinase. This work provides in vivo evidence demonstrating that alterations in certain DDR-pathway genes promote aggressive NB and supports combination PARP + ATR inhibitor therapy for NB patients with tumors harboring specific genetic alterations in DDR.

Deletion of splicing factor Cdc5 in Toxoplasma disrupts transcriptome integrity, induces abortive bradyzoite formation, and prevents acute infection in mice

Toxoplasma gondii, an apicomplexan parasite, has over 75% of its genes containing introns; however, the role of RNA splicing in regulating gene expression remains unclear. Here, we demonstrate that the pre-mRNA splicing factor Cdc5 is part of a large spliceosomal complex essential for maintaining the transcriptome integrity in Toxoplasma. TgCdc5 depletion results in splicing inhibition with widespread changes in gene expression affecting several parasite processes, including the lytic cycle, DNA replication and repair, and protein folding and degradation. Consequently, non-cystogenic RH TgCdc5-depleted parasites begin spontaneously differentiating from tachyzoites to slow-growing bradyzoites, evidenced by the differential expression of key developmental regulators; however, these early-stage bradyzoites are unable to survive, likely due to a deficiency in functional proteins necessary for their growth and maintenance. Furthermore, consistent with our in vitro findings, we demonstrate that TgCdc5 is essential for parasite survival in mice, as its depletion provides complete protection against acute infection. Interestingly, this attenuated growth mutant resulting from TgCdc5 depletion elicits a robust immune response that fully protects mice from future infections and offers partial protection during pregnancy. Overall, this study highlights the indispensable role of the splicing factor Cdc5 in preserving transcriptional homeostasis in the intron-rich genome of Toxoplasma.

Antagonistic roles for MITF and TFE3 in melanoma plasticity

Melanoma cells can switch from a melanocytic and proliferative state to a mesenchymal and invasive state and back again. This plasticity drives intratumoral heterogeneity, progression, and therapeutic resistance. Microphthalmia-associated transcription factor (MITF) promotes the melanocytic/proliferative phenotype, but factors that drive the mesenchymal/invasive phenotype and the mechanisms that effect the switch between cell states are unclear. Here, we identify the MITF paralog, TFE3, and the non-canonical mTORC1 pathway as regulators of the mesenchymal state. We show that TFE3 expression drives the metastatic phenotype in melanoma cell lines and tumors. Deletion of TFE3 in MITF-low melanoma cell lines suppresses their ability to migrate and metastasize. Further, MITF suppresses the mesenchymal phenotype by directly or indirectly activating expression of FNIP1, FNIP2, and FLCN, which encode components of the non-canonical mTORC1 pathway, thereby promoting cytoplasmic retention and lysosome-mediated degradation of TFE3. These findings highlight a molecular pathway controlling melanoma plasticity and invasiveness.

Modulation of the cell cycle and inhibition of histone deacetylases by small molecules increase recombinant adeno-associated virus productivity across different HEK293 cell lines

Recombinant adeno-associated viruses (rAAV) are one of the most popular gene therapy vectors. To date, low-product yields are limiting a broader clinical application. To identify targets for improving productivity, two human embryonic kidney cell lines (HEK293) with varying productive profiles were transiently transfected for rAAV2 production and transcriptomes were compared at 18 h after transfection. As expected, high-producing cell lines exhibited elevated levels of plasmid-derived viral gene expression. Gene set enrichment analysis indicated that these cells demonstrated increased transcriptional activity and upregulation of mRNA-processing mechanisms. Furthermore, transcriptomic analysis suggested increased transcription of histone-coding genes and a modulated cell cycle under the influence of viral gene expression, with differences being more prominent in the high-producer cell line. Aiming to increase rAAV yield, cyclin-dependent kinases and histone deacetylases were targeted by treatment with the small molecule inhibitors Flavopiridol and M344, respectively. Without compromising biological activity, Flavopiridol increased rAAV titer by 2-fold, and M344 increased it up to 8-fold in a cell line-independent manner, while also enhancing the percentage of filled capsids. A DoE-based approach also revealed the potential for combining both molecules to enhance rAAV production, exhibiting an additive effect across three different HEK293 derivatives. Consequently, novel functions of M344 and Flavopiridol as enhancers of rAAV production were unraveled, which can be employed to enhance the accessibility of in vivo gene therapy applications.

Identification of novel biomarkers and prognostic model for neuroblastoma using Mendelian randomization and transcriptomic analysis

BACKGROUND

Neuroblastoma (NB) is the most common extracranial malignant tumor in children, presenting significant challenges in prognosis and treatment stratification. This study aims to identify novel biomarkers for NB and develop a prognostic model using comprehensive analytical methods, including Mendelian randomization (MR) analysis.

METHODS

Utilizing bioinformatics and Mendelian randomization methods, we explored biomarkers associated with neuroblastoma at the mRNA level. We used chip expression data from the GEO database to screen for differentially expressed genes (DEGs) and conducted two-sample MR analysis using expression quantitative trait loci (eQTL) and neuroblastoma data from the IEU database to identify co-expressed genes through colocalization. A relevant prognostic model was constructed using lasso regression based on the co-expressed genes. Furthermore, we confirmed the correlation between high-risk and low-risk groups with the tumor microenvironment and immune cell infiltration. Subsequently, we evaluated the relationship between risk scores and sensitivity to immunotherapy and anti-tumor drugs.

RESULTS

Differential analysis identified 485 downregulated and 349 upregulated genes that play important roles in NB. MR analysis identified 4 significant co-expressed genes associated with NB: CAV2, CTSK, LXN, and NDRG2. GO and KEGG enrichment analyses revealed that these genes are involved in crucial biological processes and pathways. A prognostic model based on these four genes was constructed, and its independence as a prognostic factor was confirmed. NB patients were divided into two different risk score groups, with survival analysis indicating that the high-risk group had poorer overall survival, lower immune infiltration, and poorer immune therapy response. In contrast, the low-risk group showed potential efficacy in immunotherapy and higher sensitivity to anti-tumor drugs.

CONCLUSION

Our findings provide new insights into the molecular basis of NB, identifying four novel biomarkers and developing a risk scoring model based on four co-expressed genes. This model has the potential to become an effective tool for predicting prognosis and guiding treatment in NB patients.

Mitochondrial hyperactivity and reactive oxygen species drive innate immunity to the yellow fever virus-17D live-attenuated vaccine

The yellow fever virus 17D (YFV-17D) live attenuated vaccine is considered one of the most successful vaccines ever generated associated with high antiviral immunity, yet the signaling mechanisms that drive the response in infected cells are not understood. Here, we provide a molecular understanding of how metabolic stress and innate immune responses are linked to drive type I IFN expression in response to YFV-17D infection. Comparison of YFV-17D replication with its parental virus, YFV-Asibi, and a related dengue virus revealed that IFN expression requires RIG-I-like Receptor signaling through MAVS, as expected. However, YFV-17D uniquely induces mitochondrial respiration and major metabolic perturbations, including hyperactivation of electron transport to fuel ATP synthase. Mitochondrial hyperactivity generates reactive oxygen species (ROS) including peroxynitrite, blocking of which abrogated MAVS oligomerization and IFN expression in non-immune cells without reducing YFV-17D replication. Scavenging ROS in YFV-17D-infected human dendritic cells increased cell viability yet globally prevented expression of IFN signaling pathways. Thus, adaptation of YFV-17D for high growth imparts mitochondrial hyperactivity to meet energy demands, resulting in generation of ROS as the critical messengers that convert a blunted IFN response into maximal activation of innate immunity essential for vaccine effectiveness.

Therapeutic targeting of the p300/CBP bromodomain enhances the efficacy of immune checkpoint blockade therapy

Blockade of immune checkpoints, such as programmed death-ligand 1 (PD-L1), has shown promise in cancer treatment; however, clinical response remains limited in many cancer types. Our previous research demonstrated that p300/CBP mediates the acetylation of the PD-L1 promoter, regulating PD-L1 expression. In this study, we further investigated the role of the p300/CBP bromodomain in regulating PD-L1 expression using CCS1477, a selective bromodomain inhibitor developed by our team. We found that the p300/CBP bromodomain is essential for H3K27 acetylation at PD-L1 enhancers. Inhibiting this modification significantly reduced enhancer activity and PD-L1 transcription, including exosomal PD-L1, which has been implicated as key contributors to resistance against PD-L1 blockade therapy in various cancers. Furthermore, CCS1477 treatment resulted in a marked reduction of myeloid-derived suppressor cells (MDSCs) in the tumor microenvironment (TME) by inhibiting key cytokines such as IL6, CSF1, and CSF2, which are crucial for MDSC differentiation and recruitment. By reducing PD-L1 expression and modulating the immunosuppressive TME, CCS1477 creates a more favorable environment for tumor-infiltrating lymphocytes, significantly enhancing the efficacy of immune checkpoint blockade (ICB) therapy. Notably, these effects were observed in both prostate cancer and melanoma models, underscoring the broad therapeutic potential of p300/CBP bromodomain inhibition in improving ICB outcomes.

Transcriptome-wide analysis of differential expression in perturbation atlases

Single-cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are noisy, and many effects may go undetected. Here we introduce transcriptome-wide analysis of differential expression (TRADE)-a statistical model for the distribution of true differential expression effects that accounts for estimation error appropriately. TRADE estimates the 'transcriptome-wide impact', which quantifies the total effect of a perturbation across the transcriptome. Analyzing several large Perturb-seq datasets, we show that many transcriptional effects remain undetected in standard analyses but emerge in aggregate using TRADE. A typical gene perturbation affects an estimated 45 genes, whereas a typical essential gene affects over 500. We find moderate consistency of perturbation effects across cell types, identify perturbations where transcriptional responses vary qualitatively across dosage levels and clarify the relationship between genetic and transcriptomic correlations across neuropsychiatric disorders.

Integrated multiomics analysis identifies potential biomarkers and therapeutic targets for autophagy associated AKI to CKD transition

This study explored the relationship between acute kidney injury (AKI) and chronic kidney disease (CKD), focusing on autophagy-related genes and their immune infiltration during the transition from AKI to CKD. We performed weighted correlation network analysis (WGCNA) using two microarray datasets (GSE139061 and GSE66494) in the GEO database and identified autophagy signatures by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and GSEA enrichment analysis. Machine learning algorithms such as LASSO, random forest, and XGBoost were used to construct the diagnostic model, and the diagnostic performance of GSE30718 (AKI) and GSE37171 (CKD) was used as validation cohorts to evaluate its diagnostic performance. The study identified 14 autophagy candidate genes, among which ATP6V1C1 and COPA were identified as key biomarkers that were able to effectively distinguish between AKI and CKD. Immune cell infiltration and GSEA analysis revealed immune dysregulation in AKI, and these genes were associated with inflammation and immune pathways. Single-cell analysis showed that ATP6V1C1 and COPA were specifically expressed in AKI and CKD, which may be related to renal fibrosis. In addition, drug prediction and molecular docking analysis proposed SZ(+)-(S)-202-791 and PDE4 inhibitor 16 as potential therapeutic agents. In summary, this study provides new insights into the relationship between AKI and CKD and lays a foundation for the development of new treatment strategies.

Integrated bioinformatic analysis of immune infiltration and disulfidptosis related gene subgroups in type A aortic dissection

Type A aortic dissection (TAAD) is a lethal cardiovascular disease characterized by the separation of the layers within the aortic wall. The underlying pathological mechanisms of TAAD requires further elucidation to develop effective prevention and pharmacological treatment strategies. Inflammation plays a crucial role in TAAD pathogenesis. Disulfidptosis, an emerging type of cell death, may shed light on disease mechanisms. This study investigates the role of disulfidptosis-related genes in immune infiltration in TAAD. TAAD gene expression datasets were obtained from the Gene Expression Omnibus (GEO) database. Immune cell infiltration analysis assessed immune cell dysregulation in TAAD. Differentially expressed genes (DEGs) between TAAD samples and controls were identified and intersected with known disulfidptosis-related gene sets to obtain relevant DEGs. Hub genes were identified using machine learning algorithms. A diagnostic model was constructed using Least Absolute Shrinkage and Selection Operator (LASSO) regression on 25 TAAD samples. Consensus clustering classified TAAD samples based on disulfidptosis-related gene expression. Functional enrichment analyses, including Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses, elucidated associated biological processes and pathways. A total of 13,316 DEGs were identified, among which 11 disulfidptosis-related genes were screened: INF2, CD2AP, PDLIM1, ACTN4, MYH10, MYH9, FLNA, FLNB, TLN1, MYL6, ACTB, CAPZB, DSTN, and IQGAP1. Most of these genes exhibited lower expression levels in TAAD samples, except CAPZB, and were correlated with immune cell infiltration. Cluster-specific DEGs were found in one cluster, involving several immune response processes. Co-clustering analysis based on disulfidptosis-related genes classified TAAD samples into two clusters, with higher gene expression levels observed in cluster C2 compared to cluster C1. Three key hub genes were identified, and potential therapeutic mechanisms for TAAD were explored. Immuno-infiltration results revealed significant differences in immune profiles, with higher immunological scores and more extensive immune infiltration in TAAD. Disulfidptosis occurs in TAAD and is associated with immune cell infiltration and metabolic activity, influencing immune cell function and responses. These findings suggest that disulfidptosis may promote TAAD progression through the induction of immune responses and metabolic activities. This research provides new insights into the pathogenesis and identifies potential therapeutic targets for TAAD.

NR2F2 and its contribution to lymph node metastasis in oral squamous cell carcinoma

OBJECTIVES

To investigate the role of cancer stem cells (CSCs) in lymph node metastasis (LNM) of oral squamous cell carcinoma (OSCC), focusing on the expression and biological significance of nuclear receptor subfamily 2 group F member 2 (NR2F2).

METHODS

Single-cell RNA sequencing data from OSCC patients were analyzed using the CytoTRACE algorithm to assess stemness. Gene set scores were calculated with the irGSEA and GSVA R packages. GO and KEGG analyses identified enriched pathways. NR2F2 and CD44 expression in OSCC and lymph nodes (LNs) were validated via immunohistochemistry and immunofluorescence. NR2F2/Nr2f2 overexpression and knockdown cell lines were established, with stemness markers confirmed by Western blot. Functional assays evaluated stemness, proliferation, migration, and invasion capabilities of OSCC cells. In vivo experiments evaluated the ability of NR2F2 to promote tumor growth and metastasis. Bulk RNA sequencing and drug sensitivity analyses explored NR2F2-related mechanisms and drug responses.

RESULTS

CSCs in OSCC were divided into five subgroups, with NR2F2 identified as the key gene in CSC4, the subgroup with the highest stemness, and found to be overexpressed in metastatic LNs. Immunohistochemistry showed NR2F2 overexpression in OSCC, associated with LNM. Immunofluorescence confirmed co-expression of NR2F2 and CD44 in metastatic OSCC and LNs. Overexpression of NR2F2 enhanced stemness, proliferation, and migration of OSCC cells. In vivo experiments showed that NR2F2 promoted the growth and LNM of OSCC. Bulk RNA sequencing revealed that NR2F2 is involved in multiple pathways and plays a role in LNM. Trametinib was identified as a sensitive drug.

CONCLUSION

NR2F2 is associated with the maintenance of tumor stemness and may influence LNM in OSCC by promoting tumor cell proliferation and migration.

The role of cytokine licensing in shaping the therapeutic potential of wharton's jelly MSCs: metabolic shift towards immunomodulation at the expense of differentiation

BACKGROUND

Cytokine licensing with pro-inflammatory molecules, such as tumour necrosis factor-alpha (TNF-α) and interferon-gamma (IFN-γ), has emerged as a promising strategy to enhance the therapeutic potential of multipotent mesenchymal stromal cells (MSCs). While licensing has demonstrated benefits for immunomodulation, its effects on other key MSC functions, including differentiation and paracrine activity, remain incompletely explored. In this study, we evaluated the transcriptomic, metabolomic, and functional changes induced by short-term TNF-α/IFN-γ priming of Wharton's jelly-derived MSCs (WJ-MSCs).

METHODS

WJ-MSCs were expanded and exposed to TNF-α and IFN-γ (10 ng/ml each) for 24 h. Transcriptomic analysis was performed using RNA sequencing to identify differentially expressed genes related to immune modulation and lineage commitment. Metabolomic profiling was conducted using high-resolution mass spectrometry to assess changes in metabolic pathways. Functional assays evaluated the effects of cytokine priming on induced differentiation and growth factor secretion.

RESULTS

Cytokine licensing induced notable alterations in gene expression, upregulating pathways linked to immune response, inflammation, and cytokine signalling. However, short-term cytokine treatment significantly attenuated the osteogenic and adipogenic differentiation of MSCs, as evidenced by the reduced expression of RUNX2, ALP, CEBPA, and PPARG. The priming had a negligible effect on EGF, FGF-2, HGF, LIF, and SCF secretion. The production of VEGF-A and VEGF-C was elevated, although the levels remained low. Metabolomic analysis revealed enhanced kynurenine pathway activity, indicative of increased tryptophan catabolism, accompanied by elevated levels of fatty acids and polyamines.

CONCLUSIONS

Our findings demonstrate that TNF-α/IFN-γ priming reprograms WJ-MSCs by enhancing their immunomodulatory capacity at the expense of differentiation potential. These results highlight the need for tailored strategies to optimize MSC functionality for specific clinical applications.

Vitamin C promotes epidermal proliferation by promoting DNA demethylation of proliferation-related genes in human epidermal equivalents

Keratinocyte differentiation is highly regulated to produce the stratified structure of the epidermis and must be balanced with cell proliferation. Our prior studies revealed that hairless mice that cannot synthesize vitamin C (VC) exhibit epidermal atrophy. VC is a cofactor for the DNA demethylation (TET) enzyme, but the role of VC in DNA demethylation during keratinocyte differentiation remains unclear. In this study, we evaluated the role of VC in epigenetic regulation of epidermal proliferation and differentiation in a human epidermal equivalent model. Our findings demonstrated that intracellular VC uptake increased epidermal thickness, cell proliferation, and global levels of 5-hydroxymethylcytosine (5-hmC) DNA. Notably, these effects of VC were attenuated by an inhibitor of the TET enzyme. DNA microarray and whole-genome bisulfite sequencing (WGBS) analyses revealed that twelve genes related to cell proliferation were significantly upregulated by VC. Further, hypomethylated DNA regions associated with these genes were revealed in the presence of VC. Collectively, our findings provide insight into how VC increases epidermal thickness by promoting keratinocyte proliferation via the DNA demethylation of proliferation-related genes. VC is a promising molecule that can be used as developing treatment for epidermal thinning, including in aging.

Etoposide-induced protein 2.4 homolog promotes argininosuccinate synthase 1 and cancer cell survival upon arginine deprivation

BACKGROUND

Arginine auxotrophy has been reported in a subset of cancers with inherently defective de novo arginine synthesis. However, the use of arginine deprivation therapy seems to be unequally effective, partially owing to the resistance acquired by cancer cells. Study of underlying factors involved in this response thus becomes of utmost importance. Meanwhile, the function of etoposide-induced 2.4 homolog (EI24) in cancer metabolism, and specifically in arginine metabolism, remains unknown.

METHODS

EI24 was overexpressed in cancer cells using a doxycycline-inducible system or adenovirus transduction, while siRNA was used to knockdown EI24. Amino acid(s) deprivation medium was exploited with a cell viability assay to check the reliance of cancer cell survival on arginine. Protein expression and activation were examined through western blot and co-immunoprecipitation blot. Furthermore, global and specific protein translation were assessed through the SUnSET assay and polysome fractionation analysis. Gene expression and arginine level were downloaded from public cancer datasets for in silico validation including gene set enrichment and survival analysis to objectively evaluate the association between EI24 and arginine metabolism.

RESULTS

EI24 promoted cancer survival under arginine starvation. Mechanistically, EI24 replenished translation of argininosuccinate synthase 1 (ASS1) by inducing the inactive S-nitrosylated form of phosphatase and tensin homolog (PTEN), leading to release of the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) axis. This tumor-promoting action of EI24 could be found in multiple ASS1-deficient cancer cells regardless of p53 status. Furthermore, expression of EI24 was linked to enrichment of arginine metabolism pathway as well as poor survival of patients with cancer across various cancer types, suggesting its role in cancer resistance to arginine deprivation.

CONCLUSIONS

This study is the first to report the role of EI24 in promoting cancer survival via translational regulation of the metabolic enzyme ASS1, thus paving a route for further investigation into the link between EI24 and cancer metabolism.

Targeted inhibition of WIP1 and histone H3K27 demethylase activity synergistically suppresses neuroblastoma growth

High-risk neuroblastoma frequently exhibits segmental gain of chromosome 17q, including the locus of PPM1D, which encodes the phosphatase WIP1, a regulator of p53 activity, DNA repair, and apoptosis. High expression of PPM1D is correlated to poor prognosis, and genetic or pharmacologic inhibition of WIP1 suppresses neuroblastoma growth. Here, we show that combining drugs that target WIP1 and H3K27 demethylation induces synergistic cytotoxicity in neuroblastoma. We screened 527 different compounds together with inhibitors of WIP1 and identified a strong cytotoxic synergism between the WIP1 inhibitor SL-176 and GSK-J4, a specific inhibitor of the H3K27 demethylase JMJD3. Viability assays in neuroblastoma cell lines and treatment of tumor spheroids confirmed the synergistic effect of combining SL-176 with GSK-J4. Immunoblot experiments demonstrated a marked effect on WIP1 downstream targets and apoptosis markers, while qPCR showed a synergistic upregulation of p53 downstream targets PUMA and p21. RNA sequencing revealed a vast number of differentially expressed genes, suggesting a pervasive effect of this drug combination on transcription, with enrichment of pathways involved in DNA damage response. Finally, this drug combination was confirmed to reduce tumor growth in zebrafish xenograft experiments. In conclusion, the combination of the WIP1 inhibitor SL-176 and the epigenetic modifier GSK-J4 induces synergistic cytotoxicity in neuroblastoma cells by potentiating p53 downstream effects.

LPCAT3 regulates the immune infiltration and prognosis of ccRCC patients by mediating ferroptosis and endoplasmic reticulum stress

BACKGROUND

Clear cell renal cell carcinoma (ccRCC) accounts for 70% of renal cell carcinoma (RCC) cases. Although surgery remains the mainstay treatment, renal injury and high metastasis rates after nephrectomy dramatically reduce patient quality of life. Drugs that stimulate the immune system by targeting checkpoint pathways improve overall survival in patients with RCC. Here, we investigated the applicability of lysophosphatidylcholine acyltransferase 3 (LPCAT3) as a target for immunotherapy.

METHODS

In the present study, high LPCAT3 expression in ccRCC was identified using The Cancer Genome Atlas (TCGA) data and validated in two external cohorts from the Gene Expression Omnibus (GEO) database. qRT-PCR was performed to identify the mRNA level of LPCAT3 in tumors and adjacent normal tissues. And immunohistochemistry was used to evaluate the protein level of LPCAT3 between two groups of samples. Furthermore, gene set enrichment analysis was performed to explore the biological processes and pathways related to LPCAT3 expression. Key gene expression and correlation analyses were performed to determine the crosstalk among LPCAT3 expression, ferroptosis, and endoplasmic reticulum stress (ERS). Subsequently, CIBERSORT was used to analyze the immune infiltration status of patients with high and low LPCAT3 expression.

RESULTS

TCGA and GEO data revealed that LPCAT3 expression in ccRCC tumor tissues was higher than that in adjacent normal tissues; moreover, patients with high LPCAT3 expression had better survival outcomes. qRT-PCR and immunohistochemistry verified the high LPCAT3 expression in tumor tissue. Pathways related to ferroptosis and ERS were upregulated in patients with high LPCAT3 expression. Univariate and multivariate regression analyses revealed that low LPCAT3 levels represent an independent risk factor for ccRCC. LPCAT3 expression was positively correlated with M2 macrophage infiltration levels but negatively correlated with the memory B cell, CD8+ T cell, follicular helper T cell, regulatory T cell, activated natural killer cell, and activated memory CD4+ T cell infiltration levels.

CONCLUSIONS

LPCAT3was identified as a ccRCC biomarker and may regulate immune infiltration and prognosis in ccRCC by mediating ferroptosis and ERS. Thus, it has potential for exploitation as a prognostic and immune therapeutic target for patients with ccRCC.

Molecular structure of VEGFA polysaccharide protein and its regulation of monocyte infiltration and oxidative stress after myocardial infarction

The pathogenesis of myocardial infarction (MI) is complex, involving multiple biomarkers and cell signaling pathways. The aim of this study was to elucidate the molecular structure of VEGFA dioglycan protein and explore how it regulates monocyte infiltration and oxidative stress response after myocardial infarction, so as to provide a new molecular target for the treatment of myocardial infarction. Differential expression analysis and enrichment analysis were performed to investigate the composition and characteristics of immune cells in myocardial infarction. The regulatory network was constructed by network analysis, and in vitro experiments were carried out by BMDM isolation culture. Animal experiments were conducted in mouse models, and data were verified and statistically analyzed by combining immunohistochemical staining, real-time PCR, Western blot and enzyme-linked immunosorbent assay (ELISA). Genome-wide association studies (GWAS) and single-cell data successfully identified key immune-related genes and analyzed differentially expressed mRNA and its characteristics in myocardial infarction. The immune microenvironment of myocardial infarction was investigated, the differentially expressed circRNA and miRNA were characterized, and the circrNa-mirNA-mrna regulatory network was constructed. The characteristics of differentially expressed proteins in myocardial infarction and the changes of mRNA during oxidative stress were identified and compared. By analyzing the changes in chromatin accessibility, the regulatory network between oxidative stress and myocardial infarction in immune cells was constructed, and the expression and co-localization of oxidative stress in myocardial infarction were verified.

Urolithin A alleviates radiation pneumonitis by activating PINK1/PRKN-mediated Mitophagy

BACKGROUND

Radiation pneumonitis (RP) is a common and severe complication of radiotherapy, whose pathogenesis involves complex inflammatory responses and cellular damage. Despite its clinical significance, effective treatments remain limited. This study investigates the role of radiation-induced PINK1/PRKN-mediated mitophagy and type I interferon responses in RP and evaluates the therapeutic potential of Urolithin A (UA) in regulating inflammation through mitophagy activation.

METHODS

We established RP mouse models (20 Gy thoracic irradiation) and radiation-induced BEAS-2B cell models (6 Gy). We systematically investigated mitochondrial damage, mtRNA release, RIG-I/MDA5-MAVS pathway activation, and PINK1/PRKN-mediated mitophagy changes. Moreover, the effects of UA and the mitophagy inhibitor Mdivi-1 on inflammation and lung injury were analyzed.

RESULTS

Radiation significantly caused mitochondrial damage in lung tissues, inducing mtRNA release and RIG-I/MDA5-MAVS-mediated type I interferon response. PINK1/PRKN-mediated mitophagy was significantly enhanced, clearing damaged mitochondria and reducing cytosolic mtRNA release, thereby suppressing inflammation. Pharmacological activation of mitophagy with UA markedly improved lung pathology, reduced inflammatory cytokine levels, and inhibited excessive activation of the RIG-I/MDA5-MAVS pathway. Conversely, the knockdown of PINK1 or PRKN weakened the protective effects of UA. Both in vitro and in vivo, UA reduced radiation-induced inflammation and improved lung tissue structure and function through mitophagy.

CONCLUSIONS

Radiation-induced mtRNA release activates the RIG-I/MDA5-MAVS-mediated type I interferon response, driving inflammation in RP. PINK1/PRKN-mediated mitophagy significantly alleviates inflammation by reducing cytosolic mtRNA release. As a mitophagy inducer, UA demonstrates therapeutic potential for RP, providing a new direction for the development of anti-inflammatory strategies.

SIRT1-based therapy targets a gene program involved in mitochondrial turnover in a model of retinal neurodegeneration

Neurodegenerative diseases of the eye such as optic neuritis (ON) are hallmarked by retinal ganglion cell (RGC) loss and optic nerve degeneration leading to irreversible blindness. Therapeutic interventions enhancing expression or activity of SIRT1, an NAD+-dependent deacetylase, support, at least in part, survival of RGCs in the face of injury. Herein, we used mice with experimental autoimmune encephalomyelitis (EAE) which recapitulates axonal and neuronal damages characteristic of ON to identify gene regulatory networks affected by constitutive ubiquitous Sirt1 expression in SIRT1 knock-in mice and wild-type mice upon targeted adeno-associated virus (AAV)-mediated SIRT1 expression in RGCs. RNA seq data analysis showed that the most upregulated genes in EAE mouse retinas include those involved in inflammation, immune response, apoptosis, and mitochondrial turnover. The latter includes genes regulating mitophagy (e.g., Atg4), mitochondrial transport (e.g., Ipo- 6, Xpo- 6), and mitochondrial localization (e.g., Chrna4, Scn9a). The constitutive or RGC-targeted SIRT1 overexpression in EAE mice upregulated the expression of non-mitochondrial genes such as Ecel1 and downregulated the expression of mitophagy genes (e.g., Atg2b, Arifip1) which were upregulated by EAE alone. Thus, SIRT1 induces neuroprotection by, at least in part, balancing mitochondrial biogenesis and mitophagy and/or enhancing mitochondrial self-repair to preserve the bioenergetic capacity of RGCs.

Rituximab-Chidamide combination chemotherapy enhances autophagy to overcome drug resistance in diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is a challenging malignancy, particularly when resistance to standard therapies such as Rituximab develops. This study investigates the combined therapeutic effects of Rituximab and Chidamide on DLBCL, focusing on drug resistance mechanisms and autophagy regulation. Using high-throughput proteomics and transcriptomic analyses, key proteins and signaling pathways were identified. BTG1 emerged as a signature gene, while autophagy-related genes such as BECN1, ATG5, HSPA8, PTEN, and MAPK8 were highlighted as pivotal players. In vitro experiments using Rituximab-sensitive and -resistant DLBCL cell lines (Raji and Raji-4RH) demonstrated that Chidamide significantly inhibited cell proliferation in a dose- and time-dependent manner, induced G0/G1 phase arrest, and enhanced autophagy. Mechanistically, Chidamide upregulated histone acetylation and autophagy-related proteins while reducing p62 levels, synergistically promoting autophagy with Rituximab. In vivo mouse models confirmed the combined treatment's efficacy in suppressing tumor growth. These findings suggest that the BTG1/BECN1/ATG5 signaling axis plays a critical role in enhancing autophagy and reversing Rituximab resistance. The combination of Chidamide and Rituximab presents a promising therapeutic strategy, offering new insights into overcoming drug resistance in DLBCL.

Oral exposure to nanoplastics and food allergy in mice fed a normal or high-fat diet

The global prevalence of food allergies, particularly IgE-mediated responses, is increasing at an alarming rate. This trend is likely driven by environmental factors such as nanoplastics (NPs) ingestion and the westernization of dietary and lifestyle habits. This study examines the impact of polystyrene nanoplastics (PS-NPs) on ovalbumin (OVA)-induced food allergies in mice subjected to either a normal diet (ND) or a high-fat diet (HFD). BALB/c mice were stratified into eight groups based on dietary regimen, NP exposure, and OVA sensitization. Food allergy was induced via OVA administration, and multiple physiological and immunological parameters were evaluated, including body weight, intestinal permeability, cytokine profiles, gut microbiota composition, and small intestinal gene expression. Mice in the HFD + OVA + NP group exhibited significant increases in intestinal permeability, diarrhea severity, and serum OVA-specific IgE levels compared to other groups. Flow cytometric analysis revealed an expansion of innate lymphoid cells (ILC2 and ILC1) within the lamina propria of the small intestine. Shotgun metagenomic sequencing demonstrated gut microbiota dysbiosis, characterized by a reduction in beneficial bacterial populations in the HFD + OVA + NP cohort. Weighted Gene Co-Expression Network Analysis (WGCNA) identified a negative correlation between NPs exposure or OVA sensitization and the expression of Slc1a1, Slc5a8, and Mep1a, while a positive correlation was observed with Aa467197 expression. These findings indicate that oral exposure to PS-NPs exacerbates OVA-induced food allergies, particularly in the context of an HFD, through mechanisms involving increased intestinal permeability, gut microbial dysbiosis, and gene expression modulation. This study highlights the potential health hazards posed by environmental microplastic contamination and its possible contribution to the escalating incidence of food allergies.

Pooled tagging and hydrophobic targeting of endogenous proteins for unbiased mapping of unfolded protein responses

To achieve system-level insights into proteome organization, regulation, and function, we developed an approach to generate complex cell pools with endogenously tagged proteins amenable to high-throughput visualization and perturbation. Pooled imaging coupled to in situ barcode sequencing identified the subcellular localization of each HaloTag-tagged protein, and subsequent ligand-induced misfolding of the library followed by single-cell RNA sequencing revealed responses to spatially restricted protein misfolding. These datasets characterized protein quality control responses in previously uninterrogated cellular compartments, and cross-compartment analyses revealed mutually exclusive rather than collaborative responses, whereby the heat shock response (HSR) is induced in some compartments and repressed in others where autophagy genes are induced. We further assign protein quality control functions to previously uncharacterized genes based on shared transcriptional responses to protein misfolding across cellular compartments. Altogether, we present an efficient method for large-scale studies of proteome dynamics, function, and homeostasis.

Dnmt3a overexpression disrupts skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces metabolic elasticity

Mammalian aging is reportedly driven by the loss of epigenetic information; however, its impact on skeletal muscle aging remains unclear. This study shows that aging mouse skeletal muscle exhibits increased DNA methylation, and overexpression of DNA methyltransferase 3a (Dnmt3a) induces an aging-like phenotype. Muscle-specific Dnmt3a overexpression leads to an increase in central nucleus-positive myofibers, predominantly in fast-twitch fibers, a shift toward slow-twitch fibers, elevated inflammatory and senescence markers, mitochondrial OXPHOS complex I reduction, and decreased basal autophagy. Dnmt3a overexpression resulted in reduced muscle mass and strength and impaired endurance exercise capacity with age, accompanied by an enhanced inflammatory signature. In addition, Dnmt3a overexpression reduced not only sensitivity to starvation-induced muscle atrophy but also the restorability from muscle atrophy. These findings suggest that increased DNA methylation disrupts skeletal muscle homeostasis, promotes an aging-like phenotype, and reduces muscle metabolic elasticity.

MYC-Targeting PROTACs Lead to Bimodal Degradation and N-Terminal Truncation

MYC is a master regulatory transcription factor whose sustained dysregulation promotes the initiation and maintenance of numerous cancers. While MYC is a regarded as a potenial therapeutic target in cancer, its intrinsically disordered structure has proven to be a formidable barrier toward the development of highly effective small molecule inhibitors. We rationalized that proteolysis targeting chimeras (PROTACs), which might accomplish the targeted degradation of MYC, would achieve more potent cell killing in MYC-driven cancer cells than reversible inhibitors. PROTACs are bifunctional small molecules designed to produce a ternary complex between a target protein and an E3 ligase leading the target's ubiquitination and degradation by the 26S proteasome. We generated PROTAC MTP3 based on modifications of the previously reported MYC-targeting compound KJ-Pyr-9. We found that MTP3 depletes endogenous full-length MYC proteins and uniquely induces increasing levels of a functional, N-terminally truncated MYC species, tMYC. Furthermore, MTP3 perturbs cellular MYC levels in favor of a tMYC-dominated state whose gene regulatory landscape is not significantly altered compared to that of wild type MYC. Moreover, although it lacks ∼10 kDa of MYC's N-terminal transactivation domain, tMYC is sufficient to maintain an oncogenic proliferative state. Our results highlight the complexities of proximity-inducing compounds against highly regulated and conformationally dynamic protein targets such as MYC and indicate that PROTACs can induce alternative outcomes beyond target protein degradation.

A direct effect of the hematocrit on blood glucose: Evidence from hypoxia- and erythropoietin-treated mice

Blood glucose is lower in mountain dwellers living under low partial oxygen pressure. We show that obese mice maintained under hypoxia exhibit a delayed but distinct decrease in blood glucose with improved insulin sensitivity, which is independent of changes in body weight. This effect of hypoxia is mediated by erythropoiesis and is a direct result of the rising hematocrit, which could be due to erythrocytes acting as carriers of glucose units in the blood. Glucose lowering by the red cell mass is evidenced by a prompt decrease in glycemia in mice receiving a blood transfusion. Furthermore, life under hypoxia as well as treatment with erythropoietin reduce glycemia also in mice expressing the erythropoietin receptor exclusively in hematopoietic cells, which contrasts with previous assumptions attributing metabolic actions of erythropoietin to direct action on nonhematopoietic tissues. Our results provide a rationale for associations between hematocrit and blood glucose in humans under anti-anemic therapy, polycythemia, smoking, and high-altitude exposure.

Effects of In Vitro Hemolysis and Repeated Freeze-Thaw Cycles in Protein Abundance Quantification Using the SomaScan and Olink Assays

SomaScan and Olink are affinity-based platforms that aim to estimate the relative abundance of thousands of human proteins with a broad range of endogenous concentrations. In this study, we investigated the effects of in vitro hemolysis and repeated freeze-thaw cycles in protein abundance quantification across 10,776 (11 K SomaScan) and 1472 (Olink Explore 1536) analytes, respectively. Using SomaScan, we found two distinct groups, each one consisting of 4% of all aptamers, affected by either hemolysis or freeze-thaw cycles. Using Olink, we found 6% of analytes affected by freeze-thaw cycles and nearly half of all measured probes significantly impacted by hemolysis. Moreover, we observed that Olink probes affected by hemolysis target proteins with a larger number of annotated protein-protein interactions. We found that Olink probes affected by hemolysis were significantly associated with the erythrocyte proteome, whereas SomaScan probes were not. Given the extent of the observed nuisance effects, we propose that unbiased, quantitative methods of evaluating hemolysis, such as the hemolysis index successfully implemented in many clinical laboratories, should be adopted in proteomics studies. We provide detailed results for each SomaScan and Olink probe in the form of extensive Supporting Information files to be used as resources for the growing user communities of both platforms.

Construction of a prognostic model and identification of key genes in liver hepatocellular carcinoma based on multi-omics data

Liver hepatocellular carcinoma (LIHC) strongly contributes to global cancer mortality, highlighting the need for a deeper understanding of its molecular mechanisms to enhance patient prognosis and treatment approaches. We aimed to investigate the differential expression of immunogenic cell death-related genes (ICDRGs) and cellular senescence-related genes (CSRGs) in LIHC and their effects on patient prognosis. We combined the GSE25097, GSE46408, and GSE121248 datasets by eliminating batch effects and standardizing the data. After processing, 16 genes were identified as ICDR&CSR differentially expressed genes (ICDR&CSRDEGs), including UBE2T, HJURP, PTTG1, CENPA, and FOXM1. Gene set enrichment analysis indicated a strong enrichment of these genes in pre-Notch expression and processing. Gene set variation analysis revealed 20 pathways with significant differences between the LIHC and control groups. Mutation analysis identified TP53 as the most commonly mutated gene in LIHC samples. A prognostic risk model integrating 12 ICDR&CSRDEGs was developed, showing high precision at 1 year but diminished accuracy at 2 and 3 years. Our constructed prognostic risk model provides valuable insights for predicting patient outcomes and may guide future therapeutic interventions targeting these specific genes. Further research is needed to explore the mechanistic roles of these genes in LIHC progression and treatment response.

COL1A1-positive endothelial cells promote gastric cancer progression via the ANGPTL4-SDC4 axis driven by endothelial-to-mesenchymal transition

Gastric cancer (GC) is an aggressive and heterogeneous disease with poor survival outcomes. The progression of GC involves complex, multi-step processes. Endothelial cells (ECs) play a crucial role in tumor angiogenesis, proliferation, invasion, and metastasis, particularly through the process of endothelial-to-mesenchymal transition (EndoMT). However, the specific role and mechanisms of EndoMT in gastric cancer remain unclear. Based on 6 GC single-cell RNA-sequencing (scRNA-seq) cohorts (samples = 97), we established an EndoMT-related gene signature, termed EdMTS. Leveraging this gene signature, ssGSEA was applied to calculate sample scores across multiple bulk RNA-seq datasets, which include information on immunotherapy, metastasis, GC progression, and survival. Moreover, we applied the Monocle2 method to calculate cell pseudotime and used CellChat to analyze interactions between malignant and EC cells. We verified the molecular mechanism by multiple immunofluorescence and cell function experiments. Findings In this study, we established a single-cell atlas of ECs in GC and identified a subpopulation of COL1A1+ ECs that play a critical role in tumor progression and metastasis. These COL1A1+ ECs were significantly associated with worse clinical outcomes in GC patients. Further analysis revealed that COL1A1+ ECs originated from lymphatic ECs and underwent EndoMT through the upregulation of CEBPB, driving tumor invasiveness. Moreover, COL1A1+ ECs interacted with malignant cells via ANGPTL4-SDC4 axis, enhancing invasion and migration. These findings provide a deeper understanding of the role of COL1A1+ ECs in GC progression and highlight potential therapeutic targets for disrupting the EndoMT process in these cells to provide a benefit for GC patients.

Discovery of Chemical Tools for Polysorbate-Degradative Enzyme Control in the Biopharmaceutical Upstream Process via Multi-Omic Profiling of Host Cell Clones

Host cell proteins are process-related impurities in biotherapeutics and can potentially pose risks to patient safety and product quality. Specifically, certain host cell-derived enzymes, including lipases, can degrade the formulation excipient polysorbate (PS) in biopharmaceutical formulations, affecting drug product stability in liquid formulations. We leveraged multiomics approaches, including transcriptomics, proteomics, and activity-based protein profiling (ABPP), to identify mechanisms that regulate PS-degradative enzyme (PSDE) abundance and to develop strategies for their control. Comparative multiomics analysis of two monoclonal antibody (mAb)-producing host cell clones revealed differential lipase profiles at the mRNA, protein, and enzyme activity levels and associated increased lipase activity with upregulated lipid catabolic pathways such as the fatty acid beta oxidation pathway. Further, for the first time in the literature, we identified peroxisome proliferator-activated receptor γ (PPARγ) as a key regulator of PSDEs in manufacturing Chinese Hamster Ovary (CHO) cells. Downregulation of the PPARγ pathway with its antagonists resulted in a selective reduction of PSDE levels and improved PS stability without compromising mAb productivity or quality. This study highlights the potential of PPARγ modulators as chemical tools for PSDE control at the gene regulation level, offering significant implications for biopharmaceutical process development and control.

Prognosis stratification of patients with breast cancer based on disulfidptosis and ferroptosis

Disulfidptosis and ferroptosis, recently identified patterns of programmed cell death, play pivotal roles in the progression of breast cancer. This study aimed to explore the potential of disulfidptosis and ferroptosis in the prognostic stratification of Breast Cancer. Correlation analysis, Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithm, univariate and multivariate Cox regression analyses were performed to identify the core long non-coding RNAs associated with disulfidptosis and ferroptosis. A risk signature and a prognostic nomogram were constructed based on these findings. Additionally, investigations concerning functional pathways, mutation landscapes, immune infiltration, and drug sensitivity were conducted in different risk stratification groups. Machine learning analyses revealed a risk signature comprising seven long non-coding RNAs closely associated with disulfidptosis and ferroptosis. Validated in two datasets, breast cancer patients with high-risk scores exhibited a poorer prognosis. The prognostic nomogram, integrating the risk signature with age and TNM stage, demonstrated a favorable predictive capability for survival outcomes. Furthermore, the high-risk group showed a higher tumor mutation burden compared to the low-risk group, which was also characterized by immune suppression and sensitivity to cisplatin, lapatinib and olaparib. Our study highlights the crucial role of disulfidptosis and ferroptosis in guiding clinical decision-making for patients with breast cancer, which also characterizes the intricate landscape of breast cancer and deepens our understanding of tumor heterogeneity.

Pharmaceutical inhibition of the Chk2 kinase mitigates cone photoreceptor degeneration in an iPSC model of Bardet-Biedl syndrome

Bardet-Biedl syndrome (BBS) is a syndromic ciliopathy leading to progressive blindness starting in childhood, but the mechanism of photoreceptor degeneration remains unclear. The basal body of the photoreceptor primary cilium originates from the centrosome's mother centriole, and BBS-related proteins form a complex at basal body. Centrosomes also organize microtubules of the mitotic spindle. We show here that photoreceptors from Bbs10 -/- mouse pups present a DNA damage response (DDR) that becomes persistent and localizes to the basal body. In patient-derived induced pluripotent stem cells (iPSCs) carrying BBS10 mutations, BBS retinal progenitor cells (RPCs) present a DDR that correlates with activation of the mitotic spindle checkpoint. Pharmaceutical inhibition of the Chk2 kinase in BBS RPCs mitigates cell death and genomic instability and restores the phospho-proteome. Drug treatment of BBS retinal organoids improves tissue organization, cone survival, and outer segment maturation, thus opening a possible therapeutic avenue to delay photoreceptor degeneration in BBS.

Regulatory mechanism and prognostic value of sex hormone pathways connected with metabolism and immune signaling in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) represents a major subtype of kidney cancer with variable prognosis. A comprehensive understanding of sex hormone-related pathways could potentially refine the prediction of patient outcomes in ccRCC. Patients from TCGA-KIRC (n = 528) and GSE22541 (n = 40) cohorts were analyzed. Sex-hormone-associated pathways were manually collected and calculated with the activated score, then subtypes were identified. Differential gene expression, pathway enrichment, and tumor-infiltrating immunocytes were assessed. A prognostic signature was developed using Cox analysis and LASSO regression. Immunohistochemistry (IHC) was performed to validate the protein level of key model gene in ccRCC tissues. Three distinct subtypes (C1, C2, C3) based on sex hormone pathway activation were discovered. C1 showed the most favorable prognosis (P = 0.00029). 1,094 genes were upregulated in C1 and 197 in C3. 20 risk-associated and 172 protective genes for ccRCC prognosis were identified. LASSO regression narrowed down to 33 genes for the sex-hormone-related-gene (SHAG) prognostic model. In the TCGA-KIRC cohort, the high-SHAG score group had a worse prognosis with an HR of 3.26 (95% CI: 2.334-4.555, P < 0.001). Validation in the GSE22541 cohort corroborated these findings. The nomogram incorporating the SHAG model demonstrated robust predictive accuracy higher than 0.75. IHC validation confirmed that ARHGEF17 protein levels were higher in early-stage ccRCC (stage I-II) compared to advanced-stage (stage III) tumors, supporting its prognostic relevance. The SHAG signature serves as a promising prognostic tool for ccRCC, providing insights into the role of sex hormone-related pathways in tumor progression. Further experimental and clinical validation is warranted to explore its potential in personalized therapy.

Cell-specific mitochondrial response in progressive supranuclear palsy

Progressive supranuclear palsy (PSP) is a main form of idiopathic tauopathy characterized neuropathologically by subcortical neurofibrillary tangles in neurons, oligodendroglial coiled bodies, and tufted astrocytes, which follow sequential distribution in the human brain. Mitochondrial dysfunction is thought to be a contributor to many neurodegenerative diseases, but its role in PSP at the cellular level remains incompletely understood. To address this, we performed cell-specific morphometric analysis of mitochondrial markers in post-mortem tissues from motor cortex of PSP patients and non-diseased controls (n = 5 each) followed by single-nuclear transcriptomics (n = 3 each) to identify changes in genes that regulate mitochondrial function. We treated iCell astrocytes with PSP brain homogenates and isolated viable astrocytes from multiple regions of PSP-affected brains. We found that PSP is characterized by significant mitochondrial changes in neurons and astrocytes at the immunohistochemical level, particularly in complex I, with distinct transcriptomic responses across cell types. Glial cells exhibited upregulation of pathways associated with mitochondrial function. In contrast, excitatory and inhibitory neurons showed downregulation in these pathways, indicating impaired mitochondrial function. Astrocytes derived from different human brain regions express varied levels of GFAP and EAAT1 immunoreactivity. Astrocytic tau pathology in cell culture derived from postmortem PSP brains mirrors that seen in corresponding brain tissue histology. Tau pathology in human astrocyte cell culture is associated with clumps of mitochondria potentially associated with impairment in their neuron supportive function. Our results underscore selective complex I damage and cell-type specific patterns that differentiate PSP from other neurodegenerative diseases.

Endothelial-driven TGFβ signaling supports lung interstitial macrophage development from monocytes

Lung interstitial macrophages (IMs) are monocyte-derived parenchymal macrophages whose tissue-supportive functions remain unclear. Despite progress in understanding lung IM diversity and transcriptional regulation, the signals driving their development from monocytes and their functional specification remain unknown. Here, we found that lung endothelial cell-derived Tgfβ1 triggered a core Tgfβ receptor-dependent IM signature in mouse bone marrow-derived monocytes. Myeloid-specific impairment of Tgfβ receptor signaling severely disrupted monocyte-to-IM development, leading to the accumulation of perivascular immature monocytes, reduced IM numbers, and a loss of IM-intrinsic identity, a phenomenon similarly observed in the absence of endothelial-specific Tgfβ1. Mice lacking the Tgfβ receptor in monocytes and IMs exhibited altered monocyte and IM niche occupancy and hallmarks of aging including impaired immunoregulation, hyperinflation, and fibrosis. Our work identifies a Tgfβ signaling-dependent endothelial-IM axis that shapes IM development and sustains lung integrity, providing foundations for IM-targeted interventions in aging and chronic inflammation.

YBX1 promotes 5-Fluorouracil resistance in gastric cancer via m5C-dependent ATG9A mRNA stabilization through autophagy

5-Fluorouracil (5-FU) is a first-line chemotherapeutic agent for advanced gastric cancer (GC). However, its clinical efficacy is often undermined by the development of chemoresistance. Aberrant activation of oncogenic pathways, including autophagy, has been implicated in 5-FU resistance. Epigenetic modifications, such as 5-methylcytosine (m5C), are also recognized to modulate autophagy and contribute to chemoresistance, though the underlying molecular mechanisms remain poorly understood. In this study, we discovered that YBX1, an m5C reader protein, was significantly upregulated in 5-FU-resistant GC cell lines and patient tissues. Both in vitro and in vivo experiments demonstrated that YBX1 promoted autophagy in GC cells, thereby enhancing 5-FU resistance. Mechanistically, the transcription factor MAZ was found to bind to the YBX1 promoter, driving its transcriptional upregulation. YBX1, in turn, stabilized ATG9A mRNA via NSUN2-mediated m5C modification, thereby enhancing autophagic activity and conferring chemoresistance. Clinically, elevated YBX1 expression correlated with poor prognosis in patients with advanced GC undergoing 5-FU-based chemotherapy. These findings establish YBX1 as a key regulator of autophagy and 5-FU resistance in GC and highlight its potential as a novel therapeutic target for overcoming 5-FU resistance.

Critical roles of chronic BCR signaling in the differentiation of anergic B cells into age-associated B cells in aging and autoimmunity

Age-associated B cells (ABCs) with autoreactive properties accumulate with age and expand prematurely in autoimmune diseases. However, the mechanisms behind ABC generation and maintenance remain poorly understood. We show that continuous B cell receptor (BCR) signaling is essential for ABC development from anergic B cells in aged and autoimmune mice. ABCs exhibit constitutive BCR activation, with surface BCRs being internalized. Notably, anergic B cells, but not nonautoreactive B cells, contributed to ABC formation in these models. Anergic B cells also showed a greater propensity for in vitro differentiation into ABCs, which was inhibited by the expression of the transcription factor Nr4a1. Bruton's tyrosine kinase (Btk), a key BCR signaling component, was constitutively activated in ABCs from aged and autoimmune mice as well as patients with lupus. Inhibiting Btk reduced ABC numbers and ameliorated the pathogenicity of lupus mice. Our findings reveal critical mechanisms underlying ABC development and offer previously unrecognized therapeutic insights for autoimmune diseases.

Berberine inhibits metastasis of ovarian cancer by blocking lipid metabolism, alleviating aging of adipose tissue and increasing tumor infiltrating immune cells

Extensive peritoneal metastasis and malignant ascites continue to pose substantial challenges in achieving favorable treatment outcomes for ovarian cancer. Berberine (BBR), an active component of numerous traditional Chinese herbs, has demonstrated potent anti - tumor effects across various malignancies, including ovarian cancer. In this study, we comprehensively evaluated the impact of BBR on the growth and metastasis of ovarian cancer both in vitro and in vivo. RNA - sequencing was employed to elucidate the underlying mechanisms. Specifically, we investigated lipid metabolism and mitochondrial function in ovarian cancer cells and mice, comparing BBR - treated and untreated groups. Additionally, CIBERSORT analysis and immunohistochemical (IHC) staining were utilized to confirm BBR's ability to enhance the infiltration of tumor-infiltrating immune cells into adipose tissue and improve the inflammatory tumor microenvironment. Our findings indicate that BBR significantly inhibits the growth and metastasis of ovarian cancer in vitro and in vivo. The effects can be attributed to two key processes. Firstly, BBR suppresses the lipid metabolism by downregulating lipid uptake related receptor CD36, lipid metabolic enzyme and mitochondrial function. Secondly, BBR alleviates the aging of adipose tissue and adipose derived stem cells (ADSCs), thereby decreasing the secretion of senescence-associated secretory phenotype (SASP). These ultimately lead to the increasing the improvement of tumor infiltrating immune cells, such as CD4⁺ helper T cells (CD3⁺CD4⁺) and cytotoxic T lymphocytes (CD3⁺CD8⁺), and inflammation in ovarian cancer tissue. Collectively, these findings suggested a potential therapeutic effect of BBR in the treatment of advanced ovarian cancer, particularly cases complicated by peritoneal metastasis and malignant ascites.

Purinosomes as a therapeutic target in hepatocellular carcinoma: insights and opportunities

The formation of purinosomes, dynamic complexes involved in de novo purine biosynthesis, has been recognized as a critical process for cell growth. Although their upregulation in cancer cells suggests their potential as a therapeutic target, the specific role of purinosomes in hepatocellular carcinoma (HCC) remains uncertain. The purinosome score was found to have prognostic value. Enrichment analyses indicated a connection between purinosome-related genes and cell cycle regulation. Moreover, our research has demonstrated a correlation between the upregulation of genes associated with purinosomes and the enhanced formation of purinosomes in Huh-7 cells. Pyrimethamine has been identified as a promising therapeutic option for targeting purinosome to exert anti-cancer effects. Furthermore, the purinosome score exhibited an positive relationship with the response to immunotherapy. It may guide the stratification of liver cancer patients and screen for populations that may benefit from immunotherapy. This study examines the prognostic and predictive value of purinosome in liver cancer, suggesting that targeting purinosome formation with pyrimethamine or immunotherapy could benefit patients with high purinosome scores.

A fatty acid metabolism-related gene signature can predict poor prognosis in glioma

Gliomas, arising from supportive glial cells in the central nervous system, present significant challenges in oncology due to their varying aggressiveness and poor prognosis, particularly in high-grade forms. Understanding the molecular pathways involved in glioma progression is essential for developing effective treatment strategies. This study aimed to develop a fatty acid metabolism (FAM)-related gene signature to better predict poor prognosis in glioma patients, thereby facilitating more targeted therapeutic approaches. We employed the Least Absolute Shrinkage and Selection Operator regression analysis to identify a gene signature associated with FAM from The Cancer Genome Atlas and Chinese Glioma Genome Atlas RNA-seq datasets. Survival analyses, including Kaplan-Meier and Cox regression analyses, were conducted to assess the prognostic value of the identified genes. A total of seven FAM-related genes were associated with survival outcomes in isocitrate dehydrogenase-1 wild-type glioblastoma. The constructed gene signature effectively stratified patients into high-risk and low-risk groups, with high-risk patients demonstrating significantly poorer survival. PTGR1 emerged as the core gene, closely linked to malignant progression and poor prognosis. The FAM-related gene signature developed in this study provides a reliable tool for predicting poor outcomes in glioma patients. PTGR1, identified as a pivotal gene within this signature, may serve as a potential target for future therapeutic interventions, offering promising avenues for enhancing patient survival.

A CDKN2B-Associated Immune Prognostic Model for Predicting Immune Cell Infiltration and Prognosis in Esophageal Carcinoma

Objective

Studies have indicated that cyclin dependent protein kinase inhibitor 2B (CDKN2B) deletion is one of the most common changes in esophageal cancer (EC) which affects its progression and prognosis. This study explored the association between CDKN2B deletion, immunophenotype, and the prognosis of EC.

Methods

We investigated CDKN2B status and RNA expression, identified differentially expressed immune-associated genes between wild-type CDKN2B (CDKN2BWT) and deleted CDKN2B (CDKN2Bdeletion) in Cancer Genome Atlas (TCGA) EC samples. We also a constructed an immune prognostic model (IPM) based on these genes. Thereafter, the effects of IPM on the immune microenvironment of EC were analyzed. Finally, we established a nomogram by integrating the IPM and other clinical factors.

Results

CDKN2B deletion leads to downregulation of the immune response in EC. A total of 136 immune-associated genes were identified based on the CDKN2B deletion status, and three genes with remarkable potential as individual targets were selected for model construction. An IPM was developed and validated, it showed good performance in differentiating patients with a low or high risk of poor prognosis, and its predictive ability was independent of traditional clinical features. High-risk patients with EC had increased T follicular helper cells (Tfh) and M0 macrophages, and lower infiltration levels of resting CD4 memory T cells resting, and naive B cells. The nomogram developed for clinical application showed good predictive performance.

Conclusions

Our results suggested that CDKN2B deletion was associated with the survival and immune microenvironment in EC. IPM is not only an effective indicator of the immune response and prognosis, but also suggest potential targets for immunotherapy in patients with EC.

CellSP: Module discovery and visualization for subcellular spatial transcriptomics data

Spatial transcriptomics has enabled the study of mRNA distributions within cells, a key aspect of cellular function. However, there is a dearth of tools that can identify and interpret functionally relevant spatial patterns of subcellular transcript distribution. To address this, we present CellSP, a computational framework for identifying, visualizing, and characterizing consistent subcellular spatial patterns of mRNA. CellSP introduces the concept of "gene-cell modules", which are gene sets with coordinated subcellular transcript distributions in many cells. It provides intuitive visualizations of the captured patterns and offers functional insights into each discovered module. We demonstrate that CellSP reliably identifies functionally significant modules across diverse tissues and technologies. We use the tool to discover subcellular spatial phenomena related to myelination, axonogenesis and synapse formation in the mouse brain. We find immune response-related modules that change between kidney cancer and healthy samples, and myelination-related modules specific to mouse models of Alzheimer's Disease.

PRC1 as an independent adverse prognostic factor in Wilms tumor via integrated bioinformatics and experimental validation

Wilms Tumor (WT), a prevalent pediatric renal malignancy, exhibits marked heterogeneity and variable clinical outcomes. Epithelial-mesenchymal transition (EMT), a biological process enabling epithelial cells to acquire mesenchymal traits associated with enhanced migratory and invasive capacities, plays a crucial role in cancer progression. Protein Regulator of Cytokinesis 1 (PRC1) is a critical protein in cell division, whose overexpression is linked to poor prognosis in various cancers. This study investigates the role of PRC1 as a key prognostic factor in WT and explore the mechanism through comprehensive bioinformatic and experimental approaches. Through bulk RNA-seq data from the TARGET database, we identified PRC1 as significantly up-regulated in WT and associated with poor overall survival. Functional enrichment analyses (GO, KEGG, GSEA) demonstrated PRC1's involvement in cell division, chromatin dynamics, and activation of oncogenic pathways including Wnt/β-catenin, PI3K/AKT/mTOR, and Hedgehog signaling. Immunological analysis showed that elevated PRC1 expression correlates with diminished immune cell activity, particularly in NK cells, suggesting potential immune evasion mechanisms. Single-cell RNA-seq analysis (GSE200256) confirmed PRC1's elevated expression in anaplastic Wilms tumor (AWT) compared to favorable Wilms tumor (FWT), and highlighted its involvement in intercellular communication and metastasis via the EMT process. Genomic analyses identified copy number variations (CNVs) and downregulated PRC1-targeting microRNAs as drivers of its overexpression. In vitro, PRC1 knockdown in WIT-49 cells significantly impaired migratory capacity, invasive potential, EMT progression, and glycolytic metabolism. These findings collectively position PRC1 as a promising therapeutic target and prognostic biomarker in WT.

Circular RMST cooperates with lineage-driving transcription factors to govern neuroendocrine transdifferentiation

Circular RNA (circRNA) is a class of noncoding RNA with regulatory potentials. Its role in the transdifferentiation of prostate and lung adenocarcinoma into neuroendocrine prostate cancer (NEPC) and small cell lung cancer (SCLC) remains unexplored. Here, we identified circRMST as an exceptionally abundant circRNA predominantly expressed in NEPC and SCLC, with strong conservation between humans and mice. Functional studies using shRNA, siRNA, CRISPR-Cas13, and Cas9 consistently demonstrate that circRMST is essential for tumor growth and the expression of ASCL1, a master regulator of neuroendocrine fate. Genetic knockout of Rmst in NEPC genetic engineered mouse models prevents neuroendocrine transdifferentiation, maintaining tumors in an adenocarcinoma state. Mechanistically, circRMST physically interacts with lineage transcription factors NKX2-1 and SOX2. Loss of circRMST induces NKX2-1 protein degradation through autophagy-lysosomal pathway and alters the genomic binding of SOX2, collectively leading to the loss of ASCL1 transcription.