p53 exerts anticancer effects by regulating enhancer formation and activity

The abnormality of the p53 tumor suppressor is crucial in lung cancer development,because p53 regulates target gene promoters to combat cancer.Recent studies have shown extensive p53 binding to enhancer elements.However,whether p53 exerts a tumor suppressor role by shaping the enhancer landscape remains poorly understood.In the current study,we employed several functional genomics approaches to assess the enhancer activity at p53 binding sites throughout the genome based on our established TP53 knockout(KO)human bronchial epithelial cells(BEAS-2B).A total of 943 active regular enhancers and 370 super-enhancers(SEs)disappeared upon the deletion of p53,indicating that p53 modulates the activity of hundreds of enhancer elements.We found that one p53-dependent SE,located on chromosome 9 and designated as KLF4-SE,regulated the expression of the Krüppel-like factor 4(KLF4)gene.Furthermore,the deletion of p53 significantly decreased the KLF4-SE enhancer activity and the KLF4 expression,but increased colony formation ability in the nitrosamines 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone-induced cell transformation model.Subsequently,in TP53 KO cells,the overexpression of KLF4 partially reversed the increased clonogenic capacity caused by p53 deficiency.Consistently,KLF4 expression also decreased in lung cancer tissues and cell lines.It appeared that overexpression of KLF4 significantly suppressed the proliferation and migration of lung cancer cells.Collectively,our results suggest that the regulation of enhancer formation and activity by p53 is an integral component of the p53 tumor suppressor function.Therefore,our findings offer some novel insights into the regulation mechanism of p53 in lung oncogenesis and introduce a new strategy for screening therapeutic targets.

Identification of cell surface markers for acute myeloid leukemia prognosis based on multi-model analysis

Given the extremely high inter-patient heterogeneity of acute myeloid leukemia(AML),the identification of biomarkers for prognostic assessment and therapeutic guidance is critical.Cell surface markers(CSMs)have been shown to play an important role in AML leukemogenesis and progression.In the current study,we evaluated the prognostic potential of all human CSMs in 130 AML patients from The Cancer Genome Atlas(TCGA)based on differential gene expression analysis and univariable Cox proportional hazards regression analysis.By using multi-model analysis,including Adaptive LASSO regression,LASSO regression,and Elastic Net,we constructed a 9-CSMs prognostic model for risk stratification of the AML patients.The predictive value of the 9-CSMs risk score was further validated at the transcriptome and proteome levels.Multivariable Cox regression analysis showed that the risk score was an independent prognostic factor for the AML patients.The AML patients with high 9-CSMs risk scores had a shorter overall and event-free survival time than those with low scores.Notably,single-cell RNA-sequencing analysis indicated that patients with high 9-CSMs risk scores exhibited chemotherapy resistance.Furthermore,PI3K inhibitors were identified as potential treatments for these high-risk patients.In conclusion,we constructed a 9-CSMs prognostic model that served as an independent prognostic factor for the survival of AML patients and held the potential for guiding drug therapy.

A Novel ATM Antisense Transcript ATM-AS Positively Regulates ATM Expression in Normal and Breast Cancer Cells

Objective:The ataxia telangiectasia mutated(ATM)gene is a master regulator in cellular DNA damage response.The dysregulation of ATM expression is frequent in breast cancer,and is known to be involved in the carcinogenesis and prognosis of cancer.However,the underlying mechanism remains unclear.The bioinformatic analysis predicted a potential antisense transcript ATM-antisense(AS)from the opposite strand of the ATM gene.The purpose of this study was to identify ATM-AS and investigate the possible effect of ATM-AS on the ATM gene regulation.Methods:Single strand-specific RT-PCR was performed to verify the predicted antisense transcript ATM-AS within the ATM gene locus.qRT-PCR and Western blotting were used to detect the expression levels of ATM-AS and ATM in normal and breast cancer cell lines as well as in tissue samples.Luciferase reporter gene assays,biological mass spectrometry,ChIP-qPCR and RIP were used to explore the function of ATM-AS in regulating the ATM expression.Immunofluorescence and host-cell reactivation(HCR)assay were performed to evaluate the biological significance of ATM-AS in ATM-mediated DNA damage repair.Breast cancer tissue samples were used for evaluating the correlation of the ATM-AS level with the ATM expression as well as prognosis of the patients.Results:The ATM-AS significantly upregulated the ATM gene activity by recruiting KAT5 histone acetyltransferase to the gene promoter.The reduced ATM-AS level led to the abnormal downregulation of ATM expression,and impaired the ATM-mediated DNA damage repair in normal breast cells in vitro.The ATM-AS level was positively correlated with the ATM expression in the examined breast cancer tissue samples,and the patient prognosis.Conclusion:The present study demonstrated that ATM-AS,an antisense transcript located within the ATM gene body,is an essential positive regulator of ATM expression,and functions by mediating the binding of KAT5 to the ATM promoter.These findings uncover the novel mechanism underlying the dysregulation of the ATM gene in breast cancer,and enrich our understanding of how an antisense transcript regulates its host gene.

GSDMD protects intestinal epithelial cells against bacterial infections through its N-terminal activity affecting intestinal immune homeostasis

The intestinal mucosal barrier serves as a vital guardian of the gut health,maintaining a delicate equilibrium between gut microbiota and host immune homeostasis.Gasdermin D(GSDMD),a key executioner of pyroptosis downstream of the inflammasome,has been found to play intricate roles in modulating colitis by influencing intestinal macrophages and regulating mucus secretion from goblet cells.However,the exact nature of the regulatory function of GSDMD in maintaining intestinal immune homeostasis and defending against pathogens remains to be elucidated.In the current study,by using the Citrobacter rodentium infection model,we found that GSDMD played a key role in the defense against intestinal Citrobacter rodentium infection,with high expression levels in intestinal epithelial and lamina propria myeloid cells.Our results showed that GSDMD acted specifically in intestinal epithelial cells to combat the infection,independently of its effects on antimicrobial peptides or mucin secretion.Instead,the resistance was mediated by the N-terminal fragment of GSDMD,highlighting its importance in intestinal immunity.However,the specific mechanism underlying the N-terminal activity of GSDMD in protecting against intestinal bacterial infections requires future investigation.

Ferroptosis:Iron-mediated cell death linked to disease pathogenesis

Ferroptosis is a pattern of iron-mediated regulatory cell death characterized by oxidative damage.The molecular regulatory mechanisms are related to iron metabolism,lipid peroxidation,and glutathione metabolism.Additionally,some immunological signaling pathways,such as the cyclic GMP-AMP synthase-stimulator of the interferon gene axis,the Janus kinase-signal transducer and activator of transcription 1 axis,and the transforming growth factor beta 1-Smad3 axis,may also participate in the regulation of ferroptosis.Studies have shown that ferroptosis is significantly associated with many diseases such as cancer,neurodegenerative diseases,inflammatory diseases,and autoimmune diseases.Considering the pivotal role of ferroptosis-regulating signaling in the pathogenesis of diverse diseases,the development of ferroptosis inducers or inhibitors may have significant clinical potential for the treatment of aforementioned conditions.

Unlocking the novel activation mechanism of human IL-18

Interleukin(IL)-18,a member of the IL-1 family,is commonly known as an interferon-γinducer and is expressed in both hematopoietic and non-hematopoietic cells,such as intestinal epithelial cells,keratinocytes,and endothelial cells.In the immune system,the mature IL-18 plays a critical role in eliminating tumors and infectious agents by activating NK cells and T-lymphocytes,and by synergizing with other cytokines like IL-12 and IL-1βto induce inflammation[1-2].

Construction and evaluation of a polygenic hazard score for prognostic assessment in localized gastric cancer

To investigate whether genetic variants may provide additional prognostic value to improve the existing clinical staging system for gastric cancer(GC),we performed two genome-wide association studies(GWASs)of GC survival in the Jiangsu(N=1049)and Shanghai(N=1405)cohorts.By using a TCGA dataset,we validated genetic markers identified from a meta-analysis of these two Chinese cohorts to determine GC survival-associated loci.Then,we constructed a weighted polygenic hazard score(PHS)and developed a nomogram in combination with clinical variables.We also evaluated prognostic accuracy with the time-dependent receiver operating characteristic(ROC)curve,net reclassification improvement(NRI)and integrated discrimination improvement(IDI).We identified a single nucleotide polymorphism(SNP)of rs1618332 at 15q15.1 that was associated with the survival of GC patients with a P value of 4.12×10^(-8),and we also found additional 25 SNPs having consistent associations among these two Chinese cohort and TCGA cohort.The PHS derived from these 26 SNPs(PHS-26)was an independent prognostic factor for GC survival(all P<0.001).The 5-year AUC of PHS-26 was 0.68,0.66 and 0.67 for Jiangsu,Shanghai and their pooled cohorts,respectively,which increased to 0.80,0.82 and 0.81,correspondingly,after being integrated into a nomogram together with variables of the clinical model.The PHS-26 could improve the NRIs by 16.20%,4.90%and 8.70%,respectively,and the IDIs by 11.90%,8.00%and 9.70%,respectively.The 26-SNP based PHS could substantially improve the accuracy of prognostic assessment and might facilitate precision medicine for GC patients.

Galectin-14 promotes hepatocellular carcinoma tumor growth via enhancing heparan sulfate proteoglycan modification

Hepatocellular carcinoma(HCC)is a highly heterogeneous malignancy and lacks effective treatment.Bulk-sequencing of different gene transcripts by comparing HCC tissues and adjacent normal tissues provides some clues for investigating the mechanisms or identifying potential targets for tumor progression.However,genes that are exclusively expressed in a subpopulation of HCC may not be enriched or detected through such a screening.In the current study,we performed a single cell-clone-based screening and identified galectin-14 as an essential molecule in the regulation of tumor growth.The aberrant expression of galectin-14 was significantly associated with a poor overall survival of liver cancer patients with database analysis.Knocking down galectin-14 inhibited the proliferation of tumor growth,whereas overexpressing galectin-14 promoted tumor growth in vivo.Non-targeted metabolomics analysis indicated that knocking down galectin-14 decreased glycometabolism;specifically that glycoside synthesis was significantly changed.Further study found that galectin-14 promoted the expression of cell surface heparan sulfate proteoglycans(HSPGs)that functioned as co-receptors,thereby increasing the responsiveness of HCC cells to growth factors,such as epidermal growth factor and transforming growth factor-alpha.In conclusion,the current study identifies a novel HCC-specific molecule galectin-14,which increases the expression of cell surface HSPGs and the uptake of growth factors to promote HCC cell proliferation.

Improving antibody affinity through in vitro mutagenesis in complementarity determining regions

High-affinity antibodies are widely used in diagnostics and for the treatment of human diseases.However,most antibodies are isolated from semi-synthetic libraries by phage display and do not possess in vivo affinity maturation,which is triggered by antigen immunization.It is therefore necessary to engineer the affinity of these antibodies by way of in vitro assaying.In this study,we optimized the affinity of two human monoclonal antibodies which were isolated by phage display in a previous related study.For the 42A1 antibody,which targets the liver cancer antigen glypican-3,the variant T57H in the second complementarity-determining region of the heavy chain(CDR-H2)exhibited a 2.6-fold improvement in affinity,as well as enhanced cell-binding activity.For the I4A3 antibody to severe acute respiratory syndrome coronavirus 2,beneficial single mutations in CDR-H2 and CDR-H3 were randomly combined to select the best synergistic mutations.Among these,the mutation S53P-S98T improved binding affinity(about 3.7 fold)and the neutralizing activity(about 12 fold)compared to the parent antibody.Taken together,single mutations of key residues in antibody CDRs were enough to increase binding affinity with improved antibody functions.The mutagenic combination of key residues in different CDRs creates additive enhancements.Therefore,this study provides a safe and effective in vitro strategy for optimizing antibody affinity.

Cytosolic TGM2 promotes malignant progression in gastric cancer by suppressing the TRIM21-mediated ubiquitination/degradation of STAT1 in a GTP binding-dependent modality

Background:Previous studies have revealed the critical role of transglutaminase 2(TGM2)as a potential therapeutic target in cancers,but the oncogenic roles and underlying mechanisms of TGM2 in gastric cancer(GC)are not fully understood.In this study,we examined the role and potential mechanism of TGM2 in GC.Methods:Western blotting,immunohistochemistry,CCK8,colony formation and transwell assays were used to measure TGM2 expression in the GC cells and tissues and to examine the in vitro role of TGM2 in GC.Xenograft and in vivo metastasis experiments were performed to examine the in vivo role of TGM2 in GC.Gene set enrichment analysis,quantitative PCR and western blotting were conducted to screen for potential TGM2 targets involved in GC.Gain/loss-offunction and rescue experiments were conducted to detect the biological roles of STAT1 in GC cells in the context of TGM2.Co-immunoprecipitation,mass spectrometry,quantitative PCR and western blotting were conducted to identify STAT1-interacting proteins and elucidate their regulatory mechanisms.Mutations in TGM2 and two molecules(ZM39923 and A23187)were used to identify the enzymatic activity of TGM2 involved in the malignant progression of GC and elucidate the underlying mechanism.Results:In this study,we demonstrated elevated TGM2 expression in the GC tissues,which closely related to pathological grade,and predicted poor survival in patients with GC.TGM2 overexpression or knockdown promoted(and inhibited)cell proliferation,migration,and invasion,which were reversed by STAT1 knockdown or overexpression.Further studies showed that TGM2 promoted GC progression by inhibiting STAT1 ubiquitination/degradation.Then,tripartite motif-containing protein 21(TRIM21)was identified as a ubiquitin E3 ligase of STAT1 in GC.TGM2 maintained STAT1 stability by facilitating the dissociation of TRIM21 and STAT1 with GTP-binding enzymatic activity.A23187 abolished the role of TGM2 in STAT1 and reversed the pro-tumor role of TGM2 in vitro and in vivo.Conclusions:This study revealed a critical role and regulatory mechanism of TGM2 on STAT1 in GC and highlighted the potential of TGM2 as a therapeutic target,which elucidates the development of medicine or strategies by regulating the GTP-binding activity of TGM2 in GC.

Inhibition of MYC suppresses programmed cell death ligand-1 expression and enhances immunotherapy in triple-negative breast cancer

Background:Cancer immunotherapy has emerged as a promising strategy against triple-negative breast cancer(TNBC).One of the immunosuppressive pathways involves programmed cell death-1(PD-1)and programmed cell death ligand-1(PD-L1),but many patients derived little benefit from PD-1/PD-L1 checkpoint blockades treatment.Prior research has shown that MYC,a master transcription amplifier highly expressed in TNBC cells,can regulate the tumor immune microenvironment and constrain the efficacy of immunotherapy.This study aims to investigate the regulatory relationship between MYC and PD-L1,and whether a cyclin-dependent kinase(CDK)inhibitor that inhibits MYC expression in combination with anti-PD-L1 antibodies can enhance the response to immunotherapy.Methods:Public databases and TNBC tissue microarrays were used to study the correlation between MYC and PD-L1.The expression of MYC and PD-L1 in TNBCs was examined by quantitative real-time polymerase chain reaction and Western blotting.A patient-derived tumor xenograft(PDTX)model was used to evaluate the influence of a CDK7 inhibitor THZ1 on PD-L1 expression.Cell proliferation and migration were detected by 5-ethynyl-2′-deoxyuridine(EdU)cell proliferation and cell migration assays.Tumor xenograft models were established for in vivo verification.Results:A high MYC expression level was associated with a poor prognosis and could alter the proportion of tumor-infiltrating immune cells(TIICs).The positive correlation between MYC and PD-L1 was confirmed by immunostaining samples from 165 TNBC patients.Suppression of MYC in TNBC caused a reduction in the levels of both PD-L1 messenger RNA and protein.In addition,antitumor immune response was enhanced in the TNBC cancer xenograft mouse model with suppression of MYC by CDK7 inhibitor THZ1.Conclusions:The combined therapy of CDK7 inhibitor THZ1 and anti-PD-L1 antibody appeared to have a synergistic effect,which might offer new insight for enhancing immunotherapy in TNBC.

N6-methyladenosine modification of CENPF mRNA facilitates gastric cancer metastasis via regulating FAK nuclear export

Background:N6-methyladenosine(m^(6)A)modification is the most common modification that occurs in eukaryotes.Although substantial effort has been made in the prevention and treatment of gastric cancer(GC)in recent years,the prognosis of GC patients remains unsatisfactory.The regulatory mechanism between m^(6)A modification and GC development needs to be elucidated.In this study,we examined m^(6)A modification and the downstream mechanism in GC.Methods:Dot blotting assays,The Cancer Genome Atlas analysis,and quantitative real‑time PCR(qRT-PCR)were used to measure the m^(6)A levels in GC tissues.Methylated RNA-immunoprecipitation sequencing and RNA sequencingwere performed to identify the targets ofm^(6)Amodification.Western blotting,Transwell,wound healing,and angiogenesis assays were conducted to examine the role of centromere protein F(CENPF)in GC in vitro.Xenograft,immunohistochemistry,and in vivo metastasis experiments were conducted to examine the role of CENPF in GC in vivo.Methylated RNA-immunoprecipitation-qPCR,RNA immunoprecipitation-qPCR and RNA pulldown assays were used to verify the m^(6)A modification sites of CENPF.Gain/loss-of-function and rescue experiments were conducted to determine the relationship between CENPF and the mitogen-activated protein kinase(MAPK)signaling pathway in GC cells.Coimmunoprecipitation,mass spectrometry,qRT-PCR,and immunofluorescence assays were performed to explore the proteins that interact with CENPF and elucidate the regulatory mechanisms between them.Results:CENPF was upregulated in GC and facilitated the metastasis of GC both in vitro and in vivo.Mechanistically,increasedm^(6)A modification of CENPF was mediated by methyltransferase 3,and this modified molecule could be recognized by heterogeneous nuclear ribonucleoprotein A2/B1(HNRNPA2B1),thereby promoting its mRNA stability.In addition,the metastatic phenotype of CENPF was dependent on the MAPK signaling pathway.Furthermore,CENPF could bind to FAK and promote its localization in the cytoplasm.Moreover,we discovered that high expression of CENPF was related to lymphatic invasion and overall survival in GC patients.Conclusions:Our findings revealed that increased m^(6)A modification of CENPF facilitates the metastasis and angiogenesis of GC through the CENPF/FAK/MAPK and epithelial-mesenchymal transition axis.CENPF expression was correlated with the clinical features of GC patients;therefore,CENPF may serve as a prognostic marker of GC.

Relationship of sleep duration and annual changes in sleep duration with the incidence of gastrointestinal cancers:a prospective cohort study

Background:Prospective analyses have yet to identify a consistent relationship between sleep duration and the incidence of gastrointestinal(GI)cancers.The effect of changes in sleep duration on GI cancer incidence has scarcely been studied.Therefore,we aimed to examine the association between baseline sleep duration and annual changes in sleep duration and GI cancer risk in a large population-based cohort study.Methods:A total of 123,495 participants with baseline information and 83,511 participants with annual changes in sleep duration information were prospectively observed from 2006 to 2015 for cancer incidence.Cox proportional-hazards models were used to calculate hazard ratios(HRs)and their confidence intervals(CIs)for GI cancers according to sleep duration and annual changes in sleep duration.Results:In baseline sleep duration analyses,short sleep duration(≤5 h)was significantly associated with a lower risk of GI cancer in females(HR:0.31,95%CI:0.10-0.90),and a linear relationship between baseline sleep duration and GI cancer was observed(P=0.010),especially in males and in the>50-year-old group.In the annual changes in sleep duration analyses,with stable category(0 to-15 min/year)as the control group,decreased sleep duration(≤-15 min/year)was significantly associated with the development of GI cancer(HR:1.29;95%CI:1.04-1.61),especially in the>50-year-old group(HR:1.32;95%CI:1.01-1.71),and increased sleep duration(>0 min/year)was significantly associated with GI cancer in females(HR:2.89;95%CI:1.14-7.30).Conclusions:Both sleep duration and annual changes in sleep duration were associated with the incidence of GI cancer.

Conserved immuno-collagenic subtypes predict response to immune checkpoint blockade

Background:Immune checkpoint blockade(ICB)has revolutionized the treatment of various cancer types.Despite significant preclinical advancements in understanding mechanisms,identifying the molecular basis and predictive biomarkers for clinical ICB responses remains challenging.Recent evidence,both preclinical and clinical,underscores the pivotal role of the extracellular matrix(ECM)in modulating immune cell infiltration and behaviors.This study aimed to create an innovative classifier that leverages ECM characteristics to enhance the effectiveness of ICB therapy.Methods:We analyzed transcriptomic collagen activity and immune signatures in 649 patients with cancer undergoing ICB therapy.This analysis led to the identification of three distinct immuno-collagenic subtypes predictive of ICB responses.We validated these subtypes using the transcriptome data from 9,363 cancer patients from The Cancer Genome Atlas(TCGA)dataset and 1,084 inhouse samples.Additionally,novel therapeutic targets were identified based on these established immuno-collagenic subtypes.Results:Our categorization divided tumors into three subtypes:“soft&hot”(low collagen activity and high immune infiltration),“armored&cold”(high collagen activity and low immune infiltration),and“quiescent”(low collagen activity and immune infiltration).Notably,“soft&hot”tumors exhibited the most robust response to ICB therapy across various cancer types.Mechanistically,inhibiting collagen augmented the response to ICB in preclinical models.Furthermore,these subtypes demonstrated associations with immune activity and prognostic predictive potential across multiple cancer types.Additionally,an unbiased approach identified B7 homolog 3(B7-H3),an available drug target,as strongly expressed in“armored&cold”tumors,relating with poor prognosis.Conclusion:This study introduces histopathology-based universal immunocollagenic subtypes capable of predicting ICB responses across diverse cancer types.These findings offer insights that could contribute to tailoring personalized immunotherapeutic strategies for patients with cancer.