EP300 mutation is associated with tumor mutation burden and promotes antitumor immunity in bladder cancer patients

Contemporary Molecular Markers for Predicting Systemic Treatment Response in Urothelial Bladder Cancer: A Narrative Review

The search for dependable molecular biomarkers to enhance routine clinical practice is a compelling challenge across all oncology fields. Urothelial bladder carcinoma, known for its significant heterogeneity, presents difficulties in predicting responses to systemic therapies and outcomes post-radical cystectomy. Recent advancements in molecular cancer biology offer promising avenues to understand the disease's biology and identify emerging predictive biomarkers. Stratifying patients based on their recurrence risk post-curative treatment or predicting the efficacy of conventional and targeted therapies could catalyze personalized treatment selection and disease surveillance. Despite progress, reliable molecular biomarkers to forecast responses to systemic agents, in neoadjuvant, adjuvant, or palliative treatment settings, are still lacking, underscoring an urgent unmet need. This review aims to delve into the utilization of current and emerging molecular signatures across various stages of urothelial bladder carcinoma to predict responses to systemic therapy.

FAT4 Mutation is Related to Tumor Mutation Burden and Favorable Prognosis in Gastric Cancer

Objective

This study aimed to investigate the frequently mutated genes in Gastric Cancer (GC), assess their association with Tumor Mutation Burden (TMB) and the patients' survival, and identify the potential biomarkers for tailored therapy.

Methods

Simple somatic mutation data of GC were collected from the TCGA and ICGC databases. The high-frequency mutated genes were identified from both datasets. The samples were initially dichotomized into wild-type and mutation groups based on the status of overlapping genes. TMB difference between the two groups was evaluated by the Mann-Whitney U-test. Survival difference between the two groups was compared by the Kaplan-Meier method with a log-rank test. The prognostic value of the target gene was assessed by the Cox proportional hazards model. The signaling pathways involved in FAT4 mutation were identified by Gene Set Enrichment Analysis (GSEA). The fractions of different tumor-infiltrating immune cells were calculated by the CIBERSORT algorithm.

Results

21 overlapping genes with frequent mutation were identified in both datasets. Mutation of these genes was significantly associated with higher TMB (P<0.05) in GC. The survival of the FAT4 mutation group was superior to the wild-type group. FAT4 mutation was also identified as an independent favorable prognostic factor for the GC patients. GSEA indicated that FAT4 mutation activated the signaling pathways involved in energy metabolism. Finally, CD4 memory-activated T cells, follicular helper T cells, and gamma delta T cells were significantly more enriched, while naïve B cells and regulatory T cells (Tregs) were significantly less enriched in the FAT4 mutation group (P<0.05).

Conclusion

FAT4 mutation is relevant to TMB and favorable prognosis in GC, which may become a useful biomarker for immunotherapy of GC patients.

The potent potential of MFAP2 in prognosis and immunotherapy of triple-negative breast cancer

BACKGROUNDS

Microfibril-associated protein 2 (MFAP2) is a protein presenting in the extracellular matrix that governs the activity of microfibrils through its interaction with fibrillin. While the involvement of MFAP2 in metabolic disorders has been documented, its expression and prognostic significance in triple-negative breast cancer (TNBC) remain unexplored.

METHODS

We acquired datasets pertaining to breast cancer (BC) from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases. Next, a Venn diagram was used to identify the differentially expressed genes (DEGs). The DEGs were used to perform Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), protein-protein interaction (PPI), immune and survival analysis. The expressions of MFAP2, PD-1 and PD-L1 were examined by immunohistochemistry and western blot and their relationship with clinical pathological parameters were analyzed by clinical specimen samples from patients with TNBC. Tumor Immune Estimation Resource (TIMER, https://cistrome.shinyapps.io/timer/ ) was adopted to calculate the immune infiltration level of TNBC. The link between gene expression and tumor mutational burden (TMB) was described using Spearman's correlation analysis.

RESULTS

We identified 66 differentially expressed genes (DEGs) that were up-regulated. Among these DEGs, MFAP2 was found to be overexpressed in TNBC and was associated with a lower probability of survival. This finding was confirmed through the use of immunohistochemistry and western blot techniques. Additionally, MFAP2 was found to be related to various pathological parameters in TNBC patients. Mechanistically, gene set enrichment analysis (GSEA) revealed that MFAP2 primarily influenced cellular biological behavior in terms of epithelial mesenchymal transition, glycolysis, and apical junction. Notably, MFAP2 expression was positively correlated with the abundance of macrophages, while a negative correlation was observed with the abundance of B cells, CD4 + T cells, CD8 + T cells, neutrophils and dendritic cells through immune analysis. Furthermore, it was observed that MFAP2 displayed a negative correlation not only with tumor mutational burden (TMB), a recognized biomarker for PD-1/PD-L1 immunotherapy, but also with PD-L1 in samples of TNBC.

CONCLUSION

MFAP2 may be an important prognostic biomarker for TNBC, as well as a viable target for immunotherapy in this disease.

Identification and validation of neutrophils-related subtypes and prognosis model in triple negative breast cancer

BACKGROUND

Neutrophils are considered to be crucial players in the initiation and progression of cancer. However, the complex relationship between neutrophils and cancer prognosis remains elusive, mainly due to the significant plasticity and diversity exhibited by these immune cells.

METHODS

As part of our thorough investigation, we examined 38 Neutrophils-Related Genes (NRGs) and the associated copy number variations (CNV), somatic mutations, and gene expression patterns in relation to triple negative breast cancer (TNBC). The interactions between these genes, their biological roles, and their possible prognostic significance were then examined. With the NRGs as our basis, we applied Lasso and Cox regression analyses to create a predictive model for overall survival (OS). Furthermore, TNBC tissue and a public database were used to assess changes in MYO1D expression (MYO1D is characterized as a member of the myosin-I family, a group of motor proteins based on actin), its connection to neutrophil infiltration, and the clinical importance of MYO1D in TNBC.

RESULTS

Four neutrophil-related genes were included in the development of a prognostic model based on neutrophils. The model was further shown to be an independent predicted factor for overall survival by multivariate Cox regression analysis. According to this study, neutrophil subtype B as well as gene subtype B, were associated with activated cancer immunity and poor prognosis of TNBC patients. Furthermore, considering that poor OS was linked to increased MYO1D expression, MYO1D was increased in TNBC tissues and associated with neutrophil infiltration. In vitro experiments also confirmed that MYO1D facilitates breast cancer invasion and metastasis.

CONCLUSION

Based on the degree of gene expression linked to neutrophils, a unique prognostic model was created. MYO1D could be a potential prognostic biomarker in TNBC patients and also a prospective target for therapy.

Comprehensive analysis of scRNA-seq and bulk RNA-seq reveal the characteristics of disulfidptosis and a prognostic signature in BLCA

Disulfidptosis is a newly discovered mode of cell death. However, its biological mechanism in bladder cancer (BLCA) is still uncharacterized. In this investigation, we firstly examined the expression and mutation of disulfidptosis-related genes (DRGs) in BLCA. Two disulfidptosis phenotypes associated with DRGs expression patterns and immune cell infiltration were built. A disulfidptosis risk score signature was constructed based on ten differentially expressed genes (DEGs) between the disulfidptosis subtypes, which allowed patients to be stratified into high- and low-risk groups. We further confirmed that the disulfidptosis risk score signature has great power to predict prognosis, immune cell infiltration, and immunotherapy efficacy in BLCA. Additionally, we analyzed the differences in therapeutic sensitivities between high- and low-risk groups concerning targeted inhibitor therapy and immunotherapy. Analysis of single-cell RNA sequencing was conducted of the ten hub DRGs. Of the ten genes, we found that DUSP2 and SLCO1B3 were differentially expressed in BLCA tissues and adjacent normal tissues, and were markedly associated with patients' prognosis. Functional experiments revealed that overexpression of DUSP2 or knockdown of SLCO1B3 significantly inhibited cell proliferation, migration, and invasion in BLCA cells. In all, we present a fresh disulfidptosis-related prognostic signature, which has a remarkable capacity to characterize the immunological landscape and prognosis of BLCA patients.

Exploring the genetic factors behind the discrepancy in resistance to bovine tuberculosis between African zebu cattle and European taurine cattle

Caused by the pathogenic agent Mycobacterium bovis, bovine tuberculosis (bTB) is a major concern in cattle breeding due to both its zoonotic potential and economic impact. Greater resistance to this disease has been reported in certain African zebu breeds compared to European taurine breeds. However the genetic basis for the lower susceptibility to bTB infection observed in zebu cattle remains poorly explored. This study was conducted on whole genome sequencing data of three bTB infection-resistant African zebu breeds and two bTB infection-susceptible taurine breeds to decipher the genetic background. A set of four selection signature statistics based on linkage disequilibrium, site frequency spectrum, and population differentiation were used on SNPs whereas between population variance based VST and t-test were used on CNVs. As a complement, genes from previous literature reported as candidate genes for bTB resistance were also inspected to identify genetic variations. Interestingly, the resulting nine candidate genes had deleterious missense variants (SHC3, IFNGR1, TLR2, TLR6, IL1A, LRRK2, EP300 and IRAK4) or a CNV difference (CD48) segregating between the groups. The genes found in the study play a role in immune pathways activated during Mycobacterium infection, contributing to the proliferation of immune cells and the granuloma formation, ultimately modulating the outcome of the infectious event. In particular, a deleterious variant in the LRRK2 gene, whose deficiency has been linked to improved prognosis upon tuberculosis infection, was found in the bTB infection-resistant zebu breeds. Therefore, these genes constitute credible candidates in explaining the discrepancy in Mycobacterium bovis infection susceptibility among different breed.

Discovery of an EP300 Inhibitor using Structure-based Virtual Screening and Bioactivity Evaluation

BACKGROUND

EP300 (E1A binding protein p300) played a significant role in serial diseases such as cancer, neurodegenerative disease. Therefore, it became a significant target.

METHODS

Targeting EP300 discovery of a novel drug to alleviate these diseases. In this paper, 17 candidate compounds were obtained using a structure-based virtual screening approach, 4449-0460, with an IC50 of 5.89 ± 2.08 uM, which was identified by the EP300 bioactivity test. 4449-0460 consisted of three rings. The middle benzene ring connected the 5-ethylideneimidazolidine-2,4-dione group and the 3-F-Phenylmethoxy group.

RESULTS

Furthermore, the interaction mechanism between 4449-0460 and EP300 was explored by combining molecular dynamics (MD) simulations and binding free energy calculation methods.

CONCLUSION

The binding free energy of EP300 with 4449-0460 was -10.93 kcal/mol, and mainly came from the nonpolar energy term (ΔGnonpolar). Pro1074, Phe1075, Val1079, Leu1084, and Val1138 were the key residues in EP300/4449-0460 binding with more -1 kcal/mol energy contribution. 4449-0460 was a promising inhibitor targeting EP300, which had implications for the development of drugs for EP300-related diseases.

Histone lactylation regulates cancer progression by reshaping the tumor microenvironment

As a major product of glycolysis and a vital signaling molecule, many studies have reported the key role of lactate in tumor progression and cell fate determination. Lactylation is a newly discovered post-translational modification induced by lactate. On the one hand, lactylation introduced a new era of lactate metabolism in the tumor microenvironment (TME), and on the other hand, it provided a key breakthrough point for elucidation of the interaction between tumor metabolic reprogramming and epigenetic modification. Studies have shown that the lactylation of tumor cells, tumor stem cells and tumor-infiltrating immune cells in TME can participate in the development of cancer through downstream transcriptional regulation, and is a potential and promising tumor treatment target. This review summarized the discovery and effects of lactylation, as well as recent research on histone lactylation regulating cancer progression through reshaping TME. We also focused on new strategies to enhance anti-tumor effects via targeting lactylation. Finally, we discussed the limitations of existing studies and proposed new perspectives for future research in order to further explore lactylation targets. It may provide a new way and direction to improve tumor prognosis.

Construction and validation of a cuproptosis-related lncRNA prognosis signature in bladder carcinoma

BACKGROUND

Bladder cancer (BLCA) is a prevalent urological tumor with high morbidity and mortality. However, BLCA treatment remains challenging due to a lack of effective biomarkers. Long non-coding RNAs (lncRNAs), as active participants in tumor progression are involved in multiple biological regulatory mechanisms, and cuproptosis-related genes participate in the development of cancer. It is important to discover cuproptosis- related lncRNAs for BLCA diagnosis and treatment.

METHODS

A predictive signature was constructed based on least absolute shrinkage and selection operator regression (LASSO) and Cox regression analyses of the 9 cuproptosis-related lncRNAs. Samples were divided into high-risk group and low-risk group based on their median risk scores to explore their prognosis.

RESULTS

This signature is well predictive, as evidenced by the receiver operating characteristic curves (ROC curves) and K-M curves. Based on the nomogram, we were able to visually forecast the survival rates of patients with BLCA at 1-, 3-, and 5-year, and the calibration plots displayed that the actual results were well matched with the predicted 1-, 3-, and 5-year survival rates. Furthermore, BLCA patients in the high-risk group had a higher Tumor Immune Dysfunction and Exclusion (TIDE) score and lower TMB. Finally, we investigated the response of antitumor drugs for BLCA patients in different risk groups, and a statistically significant difference was observed in the sensitivity of those drugs between low- and the high-risk groups.

CONCLUSION

According to the 9 cuproptosis-related lncRNAs, we constructed a signature which can be served as a promising prognostic biomarker for BLCA patients.

Emerging glyco-risk prediction model to forecast response to immune checkpoint inhibitors in colorectal cancer

BACKGROUND

Aberrant glycosylation is one of the most common post-translational modifications leading to heterogeneity in colorectal cancer (CRC). This study aims to construct a risk prediction model based on glycosyltransferase to forecast the response to immune checkpoint inhibitors in CRC patients.

METHODS

Based on the TCGA dataset and glycosyltransferase genes, the NMF algorithm and WGCNA were used to identify molecular subtypes and co-expressed genes, respectively. Lasso and multivariate COX regression were used to identify prognostic glycosyltransferase genes and construct a glyco-risk prediction model in CRC patients. Univariate and multivariate Cox regression, Kaplan-Meier, and ROC curves were applied to further verify the prognostic performance of the model in CRC patients in the training and validation sets. We compared the responsiveness of immunotherapy and chemotherapy between the two groups. In vitro experiments and clinical specimens verified the specific function of the key glycosyltransferase genes in CRC.

RESULTS

The CRC cohort was divided into two subtypes with prominent differences in survival based on the well-robust seven-gene glyco-risk prediction model (composed of ALG1L2, HAS1, PYGL, COLGALT2, B3GNT4, POFUT2, and GALNT7). The nomograms based on the risk model could predict the prognosis of CRC patients independently of other clinicopathologic characteristics. Our prediction model showed a better overall prediction performance than other models. Compared with the low-risk group, the high-risk CRC patients showed a lower immune infiltration state, but a higher TMB and a lower response to anti-PD-1, anti-PD-L1, and anti-CTLA-4 therapy. Clinical specimen validation showed an obvious difference in the expression of seven glycosyltransferase genes between the low- and high-risk groups. Significant reduction in POFUT2 expression in high-risk groups was associated with reduced N-glycans production.

CONCLUSION

Our study constructed a robust glyco-risk prediction model that could provide direction for immunotherapy and chemotherapy in CRC patients, which could help clinicians make personalized treatment decisions.

Molecular targets of spermidine: implications for cancer suppression

Spermidine is a ubiquitous, natural polyamine with geroprotective features. Supplementation of spermidine extends the lifespan of yeast, worms, flies, and mice, and dietary spermidine intake correlates with reduced human mortality. However, the crucial role of polyamines in cell proliferation has also implicated polyamine metabolism in neoplastic diseases, such as cancer. While depleting intracellular polyamine biosynthesis halts tumor growth in mouse models, lifelong external spermidine administration in mice does not increase cancer incidence. In contrast, a series of recent findings points to anti-neoplastic properties of spermidine administration in the context of immunotherapy. Various molecular mechanisms for the anti-aging and anti-cancer properties have been proposed, including the promotion of autophagy, enhanced translational control, and augmented mitochondrial function. For instance, spermidine allosterically activates mitochondrial trifunctional protein (MTP), a bipartite protein complex that mediates three of the four steps of mitochondrial fatty acid (β-oxidation. Through this action, spermidine supplementation is able to restore MTP-mediated mitochondrial respiratory capacity in naïve CD8⁺ T cells to juvenile levels and thereby improves T cell activation in aged mice. Here, we put this finding into the context of the previously described molecular target space of spermidine.

JARID2 and EZH2, The Eminent Epigenetic Drivers In Human Cancer

Cancer has become a prominent cause of death, accounting for approximately 10 million death worldwide as per the World Health Organization reports 2020. Epigenetics deal with the alterations of heritable phenotypes, except for DNA alterations. Currently, we are trying to comprehend the role of utmost significant epigenetic genes involved in the burgeoning of human cancer. A sundry of studies reported the Enhancer of Zeste Homologue2 (EZH2) as a prime catalytic subunit of Polycomb Repressive Complex2, which is involved in several pivotal activities, including embryogenesis. In addition, EZH2 has detrimental effects leading to the onset and metastasis of several cancers. Jumonji AT Rich Interacting Domain2 (JARID2), an undebated crucial nuclear factor, has strong coordination with the PRC2 family. In this review, we discuss various epigenetic entities, primarily focusing on the possible role and mechanism of EZH2 and the significant contribution of JARID2 in human cancers.

Implication of KDM6A in bladder cancer

Background: Bladder cancer is a common urogenital malignancy characterized by frequent genetic alterations. Histone demethylase gene KDM6A is commonly mutated in bladder cancer. Aim: To review the characteristics of KDM6A and its mutation consequences, and to introduce a potential KDM6A-targeted treatment. Methods: We conducted a comprehensive literature search using two electronic databases, MEDLINE and Cochrane Library, to retrieve topic-related articles from July 2013 to July 2022 using keywords 'KDM6A', 'bladder cancer', 'UTX', 'treatment' and 'mutation'. Five reviewers independently screened literature search results and abstracted data from included studies. Descriptive analysis was conducted and 30 articles were retained. Main Results: A total of 30 articles were retrieved. Experimental and clinical data were collected and grouped by theme. Therapeutic strategies are depicted and organized by tables for a better understanding. Conclusion: This review demonstrates that KDM6A has crucial implications in bladder cancer pathogenesis and treatment.

The role of lysine-specific demethylase 6A (KDM6A) in tumorigenesis and its therapeutic potentials in cancer therapy

Histone demethylation is a key post-translational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Lysine specific demethylase 6A (KDM6A, also known as UTX) is an Fe²⁺- and α-ketoglutarate- dependent oxidase which belongs to KDM6 Jumonji histone demethylase subfamily, and it can remove mono-, di- and tri-methyl groups from methylated lysine 27 of histone H3 (H3K27me1/2/3). Mounting studies indicate that KDM6A is responsible for driving multiple human diseases, particularly cancers and pharmacological inhibition of KDM6A is an effective strategy to treat varieties of KDM6A-amplified cancers in cellulo and in vivo. Although there are several reviews on the roles of KDM6 subfamily in cancer development and therapy, all of them only simply introduce the roles of KDM6A in cancer without systematically summarizing the specific mechanisms of KDM6A in tumorigenesis, which greatly limits the advances on the understanding of roles KDM6A in varieties of cancers, discovering targeting selective KDM6A inhibitors, and exploring the adaptive profiles of KDM6A antagonists. Herein, we present the structure and functions of KDM6A, simply outline the functions of KDM6A in homeostasis and non-cancer diseases, summarize the role of KDM6A and its distinct target genes/ligand proteins in development of varieties of cancers, systematically classify KDM6A inhibitors, sum up the difficulties encountered in the research of KDM6A and the discovery of related drugs, and provide the corresponding solutions, which will contribute to understanding the roles of KDM6A in carcinogenesis and advancing the progression of KDM6A as a drug target in cancer therapy.

A novel cuproptosis-related lncRNAs signature predicts prognostic and immune of bladder urothelial carcinoma

Bladder Urothelial Carcinoma (BLCA) remains the most common urinary system tumor, and its prognosis is poor. Cuproptosis is a recently discovered novel cell death involved in the development of tumor cells. However, the use of cuproptosis to predict the prognosis and immunity of Bladder Urothelial Carcinoma remains largely unclear, and this study was designed to verify cuproptosis-related long non-coding RNAs (lncRNAs) to estimate the prognosis and immunity of Bladder Urothelial Carcinoma. In our study, we first defined the expression of cuproptosis-related genes (CRGs) in BLCA, and 10 CRGs were up- or downregulated. We then constructed a co-expression network of cuproptosis-related mRNA and long non-coding RNAs using RNA sequence data from The Cancer Genome Atlas Bladder Urothelial Carcinoma (TCGA-BLCA), clinical features and mutation data from BLCA patients to obtain long non-coding RNAs by Pearson analysis. Afterward, univariate and multivariate COX analysis identified 21 long non-coding RNAs as independent prognostic factors and used these long non-coding RNAs to construct a prognostic model. Then, survival analysis, principal component analysis (PCA), immunoassay, and comparison of tumor mutation frequencies were performed to verify the accuracy of the constructed model, and GO and KEGG functional enrichment analysis was used to verify further whether cuproptosis-related long non-coding RNAs were associated with biological pathways. The results showed that the model constructed with cuproptosis-related long non-coding RNAs could effectively evaluate the prognosis of BLCA, and these long non-coding RNAs were involved in numerous biological pathways. Finally, we performed immune infiltration, immune checkpoint and drug sensitivity analyses on four genes (TTN, ARID1A, KDM6A, RB1) that were highly mutated in the high-risk group to evaluate the immune association of risk genes with BLCA. In conclusion, the cuproptosis-related lncRNA markers constructed in this study have evaluation value for prognosis and immunity in BLCA, which can provide a certain reference for the treatment and immunity of BLCA.

Effects of the Acetyltransferase p300 on Tumour Regulation from the Novel Perspective of Posttranslational Protein Modification

p300 acts as a transcription coactivator and an acetyltransferase that plays an important role in tumourigenesis and progression. In previous studies, it has been confirmed that p300 is an important regulator in regulating the evolution of malignant tumours and it also has extensive functions. From the perspective of non-posttranslational modification, it has been proven that p300 can participate in regulating many pathophysiological processes, such as activating oncogene transcription, promoting tumour cell growth, inducing apoptosis, regulating immune function and affecting embryo development. In recent years, p300 has been found to act as an acetyltransferase that catalyses a variety of protein modification types, such as acetylation, propanylation, butyylation, 2-hydroxyisobutyration, and lactylation. Under the catalysis of this acetyltransferase, it plays its crucial tumourigenic driving role in many malignant tumours. Therefore, the function of p300 acetyltransferase has gradually become a research hotspot. From a posttranslational modification perspective, p300 is involved in the activation of multiple transcription factors and additional processes that promote malignant biological behaviours, such as tumour cell proliferation, migration, and invasion, as well as tumour cell apoptosis, drug resistance, and metabolism. Inhibitors of p300 have been developed and are expected to become novel anticancer drugs for several malignancies. We review the characteristics of the p300 protein and its functional role in tumour from the posttranslational modification perspective, as well as the current status of p300-related inhibitor research, with a view to gaining a comprehensive understanding of p300.

Experimental analysis of bladder cancer-associated mutations in EP300 identifies EP300-R1627W as a driver mutation

BACKGROUND

Bladder cancer (BCa) is the most common malignant tumor of the urinary system, with transitional cell carcinoma (TCC) being the predominant type. EP300 encodes a lysine acetyltransferase that regulates a large subset of genes by acetylating histones and non-histone proteins. We previously identified several bladder cancer-associated mutations in EP300 using high-throughput sequencing; however, the functional consequences of these mutations remain unclear.

METHODS

Bladder cancer cells T24 and TCC-SUP were infected with shEP300 lentiviruses to generate stable EP300 knockdown cell lines. The expression levels of EP300, p16 and p21 were detected by real-time PCR and western blots. The transcriptional activity of p16 and p21 were detected by dual luciferase assay. Cell proliferation assay, flow cytometric analyses of cell cycle, invasion assay and xenograft tumor model were used to measure the effect of EP300-R1627W mutation in bladder cancer. Immunoprecipitation was used to explore the relationship between EP300-R1627W mutation and p53. Structural analysis was used to detect the structure of EP300-R1627W protein compared to EP300-wt protein.

RESULTS

we screened the mutations of EP300 and found that the EP300-R1627W mutation significantly impairs EP300 transactivation activity. Notably, we demonstrated that the R1627W mutation impairs EP300 acetyltransferase activity, potentially by interfering with substrate binding. Finally, we show that EP300-R1627W is more aggressive in growth and invasion in vitro and in vivo compared to cells expressing EP300-wt. We also found that the EP300-R1627W mutation occurs frequently in seven different types of cancers.

CONCLUSION

In summary, our work defines a driver role of EP300-R1627W in bladder cancer development and progression.

The role of histone methylase and demethylase in antitumor immunity: A new direction for immunotherapy

Epigenetic modifications may alter the proliferation and differentiation of normal cells, leading to malignant transformation. They can also affect normal stimulation, activation, and abnormal function of immune cells in the tissue microenvironment. Histone methylation, coordinated by histone methylase and histone demethylase to stabilize transcription levels in the promoter area, is one of the most common types of epigenetic alteration, which gained increasing interest. It can modify gene transcription through chromatin structure and affect cell fate, at the transcriptome or protein level. According to recent research, histone methylation modification can regulate tumor and immune cells affecting anti-tumor immune response. Consequently, it is critical to have a thorough grasp of the role of methylation function in cancer treatment. In this review, we discussed recent data on the mechanisms of histone methylation on factors associated with immune resistance of tumor cells and regulation of immune cell function.

Investigation of prognostic biomarkers in patients with urothelial carcinoma treated with platinum-based regimens

BACKGROUND

Bladder cancer (BC) is a heterogeneous malignancy with dismal outcome.

PATIENTS AND METHODS

Mutations in genes, altered or linked to platinum sensitivity in BC, were examined in 66 patients' tumors along with tumor infiltrating lymphocytes (TILs) density and MMR, PD-L1 and CD8 protein expression, as well as basal and luminal subtypes, defined by protein expression of markers, including CK5/6 and GATA3 or CK20, respectively.

RESULTS

41 tumors harbored mutations, mainly in TP53 (38%), ARID1A (17%) and the DNA damage response and repair (DDR) genes ERCC2 (17%) and BRCA2 (15%). Mutations in other DDR relevant genes were also present. Age showed unfavorable prognosis for overall survival (HR=1.07, P = 0.026); no benefit was seen for patients with TP53, ARID1A, ERCC2 or BRCA2 mutations or mutations in 1 or more DDR genes. PD-L1 status positively correlated with stromal (rho=0.46, P < 0.001) and intratumoral (rho=0.53, P < 0.001) CD8 expression or TILs (rho=0.29, P = 0.018); none associated with overall survival (OS). A statistically significant difference was observed between PD-L1 status and immunohistochemistry (IHC)‑based subtypes, with tumors classified as luminal (GATA3+ and/or CK20+ and CK5/6-) showing lower PD-L1 expression relative to basal (CK5/6+ and GATA3- and/or CK20-) (median value 0 vs. 2.5, P = 0.029). Concerning OS, no statistically significant difference was seen among patients with basal or luminal tumors.

CONCLUSION

No association was seen herein between DDR mutations, TILs, PD-L1, CD8 expression or IHC-based subtypes and patient survival; these observations warrant validation within a larger cohort.

Identification and validation of novel biomarkers affecting bladder cancer immunotherapy via machine learning and its association with M2 macrophages

BACKGROUND

Immunotherapy has shown promising results in bladder cancer therapy options.

METHODS

Analysis of open-access data was conducted using the R software. Open-access data were obtained from The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and IMvigor210 databases. Immunofluorescence and co-culture systems were utilized to validate the effect of PTHLH on M2 macrophage polarization.

RESULTS

Here, through the combined (TCGA, GSE128959, GSE13507, and GSE83586) and IMvigor210 cohorts, we comprehensively investigated the biological and immune microenvironment differences in patients with diverse immunotherapy responses. Meanwhile, we found that M2 macrophage could affect bladder cancer immunotherapy sensibility. Moreover, based on the machine learning algorithm (LASSO logistics regression), PTHLH, BHMT2, and NGFR were identified, which all have good prediction abilities for patient immunotherapy. Then, a logistics regression model was established based on PTHLH, BHMT2, and NGFR, and each patient was assigned a logistics score. Subsequently, we investigated the difference in patients with high low logistics scores, including biological enrichment, immune microenvironment, and genomic characteristics. Meanwhile, data from the Human Protein Atlas database indicated a higher protein level of PTHLH in bladder cancer tissue. Immunofluorescence indicated that the knockdown of PTHLH in bladder cancer cells can significantly inhibit the M2 polarization of co-culture M0 macrophages.

CONCLUSIONS

Our study investigated the difference between bladder cancer immunotherapy responders and non-responders. Meanwhile, the PTHLH was identified as a novel biomarker for bladder cancer immunotherapy.

Identification of bromodomain-containing proteins prognostic value and expression significance based on a genomic landscape analysis of ovarian serous cystadenocarcinoma

Background

Ovarian serous cystadenocarcinoma (OSC), a common gynecologic tumor, is characterized by high mortality worldwide. Bromodomain (BRD)-containing proteins are a series of evolutionarily conserved proteins that bind to acetylated Lys residues of histones to regulate the transcription of multiple genes. The ectopic expression of BRDs is often observed in multiple cancer types, but the role of BRDs in OSC is still unclear.

Methods

We performed the differential expression, GO enrichment, GSEA, immune infiltration, risk model, subtype classification, stemness feature, DNA alteration, and epigenetic modification analysis for these BRDs based on multiple public databases.

Results

Most BRDs were dysregulated in OSC tissues compared to normal ovary tissues. These BRDs were positively correlated with each other in OSC patients. Gene alteration and epigenetic modification were significant for the dysregulation of BRDs in OSC patients. GO enrichment suggested that BRDs played key roles in histone acetylation, viral carcinogenesis, and transcription coactivator activity. Two molecular subtypes were classified by BRDs for OSC, which were significantly correlated with stemness features, m6A methylation, ferroptosis, drug sensitivity, and immune infiltration. The risk model constructed by LASSO regression with BRDs performed moderately well in prognostic predictions for OSC patients. Moreover, BRPF1 plays a significant role in these BRDs for the development and progression of OSC patients.

Conclusion

BRDs are potential targets and biomarkers for OSC patients, especially BRPF1.

Identification of necroptosis-related subtypes and prognosis model in triple negative breast cancer

Background

Necroptosis is considered to be a new form of programmed necrotic cell death, which is associated with metastasis, progression and prognosis of various types of tumors. However, the potential role of necroptosis-related genes (NRGs) in the triple negative breast cancer (TNBC) is unclear.

Methods

We extracted the gene expression and relevant clinicopathological data of TNBC from The Cancer Genome Atlas (TCGA) databases and the Gene Expression Omnibus (GEO) databases. We analyzed the expression, somatic mutation, and copy number variation (CNV) of 67 NRGs in TNBC, and then observed their interaction, biological functions, and prognosis value. By performing Lasso and COX regression analysis, a NRGs-related risk model for predicting overall survival (OS) was constructed and its predictive capabilities were verified. Finally, the relationship between risk_score and immune cell infiltration, tumor microenvironment (TME), immune checkpoint, and tumor mutation burden (TMB), cancer stem cell (CSC) index, and drug sensitivity were analyzed.

Results

A total 67 NRGs were identified in our analysis. A small number of genes (23.81%) detected somatic mutation, most genes appeared to have a high frequency of CNV, and there was a close interaction between them. These genes were remarkably enriched in immune-related process. A seven-gene risk_score was generated, containing TPSG1, KRT6A, GPR19, EIF4EBP1, TLE1, SLC4A7, ESPN. The low-risk group has a better OS, higher immune score, TMB and CSC index, and lower IC50 value of common therapeutic agents in TNBC. To improve clinical practicability, we added age, stage_T and stage_N to the risk_score and construct a more comprehensive nomogram for predicting OS. It was verified that nomogram had good predictive capability, the AUC values for 1-, 3-, and 5-year OS were 0.847, 0.908, and 0.942.

Conclusion

Our research identified the significant impact of NRGs on immunity and prognosis in TNBC. These findings were expected to provide a new strategy for personalize the treatment of TNBC and improve its clinical benefit.

Prognostic Value of MUC16 Mutation and Its Correlation with Immunity in Hepatocellular Carcinoma Patients

Objective

Identifying gene mutation signatures will enable a better understanding for the occurrence, development, and prognosis of hepatocellular carcinoma (HCC) and provide some potential biomarkers for clinical practice. This study investigated the mutated genes in HCC patients and assessed their relationship with tumor mutation burden (TMB) and prognosis.

Methods

The somatic mutation annotation format (MAF) document, mRNA expression matrix, and clinical information of HCC patients were obtained from the International Cancer Genome Consortium (ICGC) and the Cancer Genome Atlas (TCGA) database. The differences of TMB between the mutant type and the wild-type genes were detected using the Mann–Whitney U test. The link of gene mutations with prognosis was explored by the Kaplan–Meier analysis. The proportion of 22 immune cells' composition was measured using CIBERSORT algorithm.

Results

The two databases screened 16 common mutated genes, which included TP53, TTN, LRP1B, ZFHX4, MUC16, OBSCN, CSMD3, FLG, CSMD1, SYNE1, SPTA1, USH2A, KMT2C, PCLO, HMCN1, and FAT3. After a series of analysis, MUC16 mutation was found to be highly correlated with TMB and was regarded as an independent factor predicting HCC. Furthermore, gene set enrichment analysis (GSEA) indicated that the MUC16 mutation was significantly involved in HCC cell metabolism.

Conclusions

MUC16 mutation seems to be a valuable potential biomarker for HCC development and its overall survival.

The potential value of cuprotosis (copper-induced cell death) in the therapy of clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) accounts for 75% of the total incidence of renal cancer, and every year the number of morbidity and mortality increases, posing a serious threat to public health. The current main treatment methods for kidney cancer include drug-targeted therapy and immunotherapy. Although there are many treatment options for kidney cancer, they all have limitations, including drug resistance, unsatisfied long-term benefits, and adverse effects. Therefore, it is crucial to identify more effective therapeutic targets. As a newly discovered mechanism of cell death, copper-induced cell death (cuprotosis) is closely related to changes in cell metabolism, particularly in copper metabolism. Current studies have shown that the key signaling pathway of cuprotosis, the FDX1 (Ferredoxin 1)-LIAS (Lipoic Acid Synthetase) axis, plays an important role in the regulation of cellular oxidative stress, which can directly affect cell survival via inducing or promoting cancer cell death. Therefore, we speculated that this regulatory cell death mechanism might serve as a potential therapeutic target for the clinical treatment of renal cancer. To test this, we first performed a pan-cancer analysis based on cuprotosis-related genomic and transcriptomic levels to reveal the expression of cuprotosis in cancer. Next, GSVA-clustering analysis was performed with data from the Cancer Genome Atlas (TCGA) cohort, and the cohort was divided into three clusters according to the gene enrichment levels of cuprotosis marker genes. In addition, we analyzed the potential of using cuprotosis in clinical treatment from multiple perspectives, including chemotherapeutic drug susceptibility test, immune target inhibition treatment responsiveness, and histone modification. Combining the results of multi-omics analysis, we focused on the feasibility of this novel regulatory cell death mechanism in ccRCC treatment and further constructed a prognostic model. Finally, we verified our results by integrating the patient's gene expression information and radiomics information. Our study provides new insights into the development and clinical application of targeting cuprotosis pathway.

Downregulation of PTCD1 in Bladder Urothelial Carcinoma Predicts Poor Prognosis and Levels of Immune Infiltration

Pentatricopeptide repeat domain 1 (PTCD1) was reported to regulate mitochondrial metabolism and oxidative phosphorylation. However, the effect and mechanism of PTCD1 in the development of bladder urothelial carcinoma (BLCA) remain unclear. The databases from The Cancer Genome Atlas (TCGA) and Human Protein Atlas (HPA) were used to analyze the expression changes, clinical features, and prognostic values of PTCD1. A nomogram was built to predict the prognostic outcomes of BLCA cases. The potential genes interacting with PTCD1 were explored by Weighted Gene Coexpression Network Analysis (WGCNA). The estimation of associations between PTCD1 and tumor mutations, tumor immunities, and m6A methylations was performed. The study found that the gradual decrease of PTCD1 expression was observed with the increase of stage and grade. Low PTCD1 expression was greatly correlated with higher pathological stage, N stage, and poor prognosis in TCGA cohorts; interestingly, low-grade BLCA cases all exhibited high expression of PTCD1. HPA database analysis implied that the expression of PTCD1 protein in BLCA was lower than that in normal bladder tissue, and the protein expression of PTCD1 in high-grade BLCA was lower than that in low-grade BLCA. Multivariate Cox regression analysis indicated that PTCD1 may serve as an independent factor influencing prognosis of BLCA. Mechanistically, PTCD1 played a regulatory role in BLCA progression through multiple tumor-related pathways containing PI3K-Akt signaling, ECM-receptor interaction, oxidative phosphorylation, and extracellular matrix organization. WGCNA reported that PTCD1 had a strong positive correlation with POLR2J, ZNHT1, ATP5MF, PDAP1, BUD31, and COPS6. Besides, the mRNA expression of PTCD1 was negatively associated with immune cells' infiltrations, immune functions, and checkpoints, especially with some m6A methylation regulators in BLCA. In sum, downregulation of PTCD1 expression may be involved in the development of BLCA and remarkably correlated with poor prognosis. Meantime, it showed an influence in immune cell infiltration and may serve as an agreeable prognostic indicator in BLCA.

Therapeutic significance of ARID1A mutation in bladder cancer

Bladder cancer (BC) develops from the tissues of the urinary bladder and is responsible for nearly 200,000 deaths annually. This review aims to integrate knowledge of recently discovered functions of the chromatin remodelling tumour suppressor protein ARID1A in bladder urothelial carcinoma with a focus on highlighting potential new avenues for the development of personalised therapies for ARID1A mutant bladder tumours. ARID1A is a component of the SWI/SNF chromatin remodelling complex and functions to control many important biological processes such as transcriptional regulation, DNA damage repair (DDR), cell cycle control, regulation of the tumour microenvironment and anti-cancer immunity. ARID1A mutation is emerging as a truncal driver mutation that underlies the development of a sub-set of urothelial carcinomas, in cooperation with other driver mutations, to cause dysregulation of a number of key cellular processes. These processes represent tumour drivers but also represent potentially attractive therapeutic targets.

Identification of potential druggable targets of cell cycle with small-molecule inhibitors in oral squamous cell carcinoma

Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumors worldwide and there are few crucial regulators and druggable targets for early diagnosis. Therefore, the identification of biomarkers for the early diagnosis and druggable targets of OSCC is imminent. In this study, we integrated gene set enrichment analysis, differential gene expression analysis based on the negative binomial distribution, weighted correlation network analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes into analyzing the OSCC cohort downloaded from The Cancer Genome Atlas, and found that cell cycle and related biologic processes are significantly enriched. Then, we constructed the core gene network of OSCC, which showed the connection of encode human Cyclin-A2 protein, encode RAD51-associated protein 1, encode human centromere-associated protein E (CENPE), encode humans centromere protein I (CENPI) and encode polo-like kinase 1 (PLK1) to several cell cycle-related genes. Survival analysis further showed that low expression of these genes was associated with a better prognosis. Furthermore, we utilized a high-throughput virtual screening to find new CENPE and PLK1 inhibitors, and one of the CENPE inhibitor DB04517 suppressed the proliferation of OSCC cells by cell cycle arrest of cell cycle. Taken together, these candidate regulators could serve as the candidate diagnostic and prognostic biomarkers for OSCC, and specific suppression of these genes may be a potential approach to prevent and treat OSCC with the candidate inhibitors.

Machine Learning Identifies Pan-Cancer Landscape of Nrf2 Oxidative Stress Response Pathway-Related Genes

BACKGROUND

Oxidative stress produced a large amount of reactive oxygen species (ROS), which played a pivotal role in balanced ability and determining cell fate. The activated Nrf2 signaling pathway that responds to the excessive ROS regulated the expressions of antiapoptotic proteins, antioxidative enzymes, drug transporters, and detoxifying factors.

METHODS

The Nrf2 signaling pathway-related genes that had a direct relationship with Nrf2, including ATF4, BACH1, CREBBP, CUL3, EIF2AK3, EP300, FOS, FOSL1, GSK3B, JUN, KEAP1, MAF, MAFF, MAFG, MAFK, MAPK1, MAPK3, MAPK7, MAPK8, MAPK9, PIK3CA, PRRT2, and RIT1, were selected to do a systematic pan-cancer analysis. The relationship of Nrf2 signaling pathway-related gene expressions with tumor mutation burden, microsatellite status, clinical characteristics, immune system, cancer stemness index, and drug sensitivity was calculated by the Spearson correlation analysis across 11,057 subjects representing 33 cancer types. The prognosis models in lung squamous carcinoma, breast cancer, and stomach cancer were constructed with the Cox multivariate regression analysis and least absolute shrinkage and selection operator (Lasso) regression.

RESULTS

Many Nrf2 signaling pathway-related genes were differently expressed between tumor and normal tissues. PIK3CA showed high mutation rate in pan-cancer. The expressions of Nrf2 signaling pathway-related genes were significantly related to tumor mutation burden, copy number variant, microsatellite instability score, survival rate, pathological stage, immune phenotype, immune score, immune cell, cancer stemness index, and drug sensitivity. The prognosis models were significantly associated with survival rate in lung squamous carcinoma, breast cancer, and stomach cancer; and the prognosis model-based riskscore was significantly associated with clinicopathological characteristics of each cancer.

CONCLUSIONS

The study provided a comprehensive pan-cancer landscape of Nrf2 pathway-related genes. Based on the same Nrf2 pathway-related genes, the different prognosis models were constructed for different types of cancers.

Identification of Prognostic Biomarkers for Bladder Cancer Based on DNA Methylation Profile

Background: DNA methylation is an important epigenetic modification, which plays an important role in regulating gene expression at the transcriptional level. In tumor research, it has been found that the change of DNA methylation leads to the abnormality of gene structure and function, which can provide early warning for tumorigenesis. Our study aims to explore the relationship between the occurrence and development of tumor and the level of DNA methylation. Moreover, this study will provide a set of prognostic biomarkers, which can more accurately predict the survival and health of patients after treatment.

Methods: Datasets of bladder cancer patients and control samples were collected from TCGA database, differential analysis was employed to obtain genes with differential DNA methylation levels between tumor samples and normal samples. Then the protein-protein interaction network was constructed, and the potential tumor markers were further obtained by extracting Hub genes from subnet. Cox proportional hazard regression model and survival analysis were used to construct the prognostic model and screen out the prognostic markers of bladder cancer, so as to provide reference for tumor prognosis monitoring and improvement of treatment plan.

Results: In this study, we found that DNA methylation was indeed related with the occurrence of bladder cancer. Genes with differential DNA methylation could serve as potential biomarkers for bladder cancer. Through univariate and multivariate Cox proportional hazard regression analysis, we concluded that FASLG and PRKCZ can be used as prognostic biomarkers for bladder cancer. Patients can be classified into high or low risk group by using this two-gene prognostic model. By detecting the methylation status of these genes, we can evaluate the survival of patients.

Conclusion: The analysis in our study indicates that the methylation status of tumor-related genes can be used as prognostic biomarkers of bladder cancer.

A comprehensive multi-omics analysis reveals molecular features associated with cancer via RNA cross-talks in the Notch signaling pathway

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Many Notch genes are identified as cancer-associated genes with an important role in tumorigenesis.

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Dynamic expression patterns are associated with the Notch activity that are largely regulated by multiple ncRNAs.

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Cross-talks among diverse RNAs are crucial in cancers via ceRNA network.

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The Notch pathway shows a robust prognostic ability via integrating multi-omics features as well as their targets.

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The Notch pathway is also correlated with immune infiltration and maybe available cancer treatment drug targets.

The Notch signaling has an important role in multiple cellular processes and is related to carcinogenic process. To understand the potential molecular features of the crucial Notch pathway, a comprehensive multi-omics analysis is performed to explore its contributions in cancer, mainly including analysis of somatic mutation landscape, pan-cancer expression, ncRNA regulation and potential prognostic power. The screened 22 Notch core genes are relative stable in DNA variation. Dynamic expression patterns are associated with the Notch activity, which are mainly regulated by multiple ncRNAs via interactions of ncRNA:mRNA and ceRNA networks. The Notch pathway shows a potential prognostic ability through integrating multi-omics features as well as their targets, and it is correlated with immune infiltration and maybe available drug targets, implying the potential role in individualized treatment. Collectively, all of these findings contribute to exploring crucial role of the key pathway in cancer pathophysiology and gaining mechanistic insights into cross-talks among RNAs and biological pathways, which indicates the possible application of the well-conserved Notch signaling pathway in precision medicine.

USH2A Mutation is Associated With Tumor Mutation Burden and Antitumor Immunity in Patients With Colon Adenocarcinoma

Colon adenocarcinoma (COAD) is one of the diseases with the highest morbidity and mortality in the world. At present, immunotherapy has become a valuable method for the treatment of COAD. Tumor mutational burden (TMB) is considered to be the most common biomarker for predicting immunotherapy. According to reports, the mutation rate of COAD ranks third. However, whether these gene mutations are related to TMB and immune response is still unknown. Here, COAD somatic mutation data were downloaded from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) databases. Bioinformatics methods were used to study the relationships among gene mutations, COAD survival prognosis, and tumor immune response. A total of 22 of the top 40 mutations in TCGA and ICGC databases were the same. Among them, the USH2A mutation was associated with high TMB and poor clinical prognosis. According to Gene Set Enrichment Analysis (GSEA) and the CIBERSORT algorithm, we determined that the USH2A mutation upregulates signaling pathways involved in the immune system and the antitumor immune response. In cases with a USH2A mutation, the immune score and MSI score of TCGA samples increased, the expression of immune checkpoint genes decreased significantly, and the TIDE score decreased significantly. Dependent on the presence or absence of a USH2A mutation, TCGA COAD samples were analyzed for differentially expressed genes, 522 of which were identified. Using a univariate Cox analysis and LASSO COX analysis of these differential genes, a prediction model was established, which established significant differences in the infiltration of immune cells, immune checkpoint gene expression, immune score, MSI score, TMB, and TIDE in patients in high- and low-risk groups. In conclusion, mutation of USH2A is frequent in COAD and is related to an increase in TMB and the antitumor immunity. The differential genes screened by USH2A mutation allowed the construction of a risk model for predicting the survival and prognosis of cancer patients, in addition to providing new ideas for COAD immunotherapy.

Bioinformatic Analysis of Immune Significance of RYR2 Mutation in Breast Cancer

BACKGROUND

Currently, immunotherapy is widely used for breast cancer (BC) patients, and tumor mutation burden (TMB) is regarded as a valuable independent predictor of response to immunotherapy. However, specific gene mutations and their relationship with TMB and tumor-infiltrating immune cells in BC are not fully understood.

METHODS

Comprehensive bioinformatic analyses were performed using data from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets. Survival curves were analyzed via Kaplan-Meier analysis. Univariate and multivariate Cox regression analyses were used for prognosis analysis. Gene set enrichment analysis (GSEA) was performed to explore regulatory mechanisms and functions. The CIBERSORT algorithm was used to calculate the tumor-infiltrating immune cell fractions.

RESULTS

We analyzed somatic mutation data of BC from TCGA and ICGC datasets and found that 19 frequently mutated genes were reported in both cohorts, namely, SPTA1, TTN, MUC17, MAP3K1, CDH1, FAT3, SYNE1, FLG, HMCN1, RYR2 (ryanodine receptor 2), GATA3, MUC4, PIK3CA, KMT2C, TP53, PTEN, ZFHX4, MUC16, and USH2A. Among them, we observed that RYR2 mutation was significantly associated with higher TMB and better clinical prognosis. Moreover, GSEA revealed that RYR2 mutation-enriched signaling pathways were related to immune-associated pathways. Furthermore, based on the CIBERSORT algorithm, we found that RYR2 mutation enhanced the antitumor immune response by enriching CD8+ T cells, activated memory CD4+ T cells, and M1 macrophages.

CONCLUSION

RYR2 is frequently mutated in BC, and its mutation is related to increased TMB and promotes antitumor immunity; thus, RYR2 may serve as a valuable biomarker to predict the immune response.

Pan-Cancer Analysis Reveals That E1A Binding Protein p300 Mutations Increase Genome Instability and Antitumor Immunity

E1A binding protein p300 (EP300) is mutated in diverse cancers. Nevertheless, a systematic investigation into the associations of EP300 mutations with genome instability and antitumor immunity in pan-cancer remains lacking. Using the datasets from The Cancer Genome Atlas, we analyzed the correlations between EP300 mutations and genome instability and antitumor immune response in 11 cancer types. Compared to EP300-wild-type cancers, EP300-mutated cancers had significantly higher tumor mutation burden (TMB) in 10 cancer types. EP300-mutated cancers harbored a much higher fraction of microsatellite instable cancers in the colon and gastric cancers. EP300 was co-mutated with genes involved in DNA damage repair pathways in multiple cancers. Furthermore, compared to EP300-wild-type cancers, EP300-mutated cancers had significantly higher immune cytolytic activity scores and ratios of immune-stimulatory over immune-inhibitory signatures in diverse cancers. Also, EP300-mutated cancers showed significantly higher programmed death-ligand 1 (PD-L1) expression levels than EP300-wild-type cancers. The increased TMB, antitumor immune activity, and PD-L1 expression indicated a favorable response to immune checkpoint inhibitors (ICIs) in EP300-mutated cancers, as evident in three cancer cohorts treated with ICIs. Thus, the EP300 mutation could be a predictive biomarker for the response to immunotherapy.

Nivolumab-associated DRESS in a genetic susceptible individual

The use of immune checkpoint inhibitors (ICIs) is rising exponentially in numerous cancers, but immune-related adverse events can occur. We report a rare case of high-grade drug reaction with eosinophilia and systemic symptoms (DRESS) syndrome developed stepwise in a patient with gastric cancer after nivolumab treatment. Subclinical myocarditis was sensitively detected by cardiovascular magnetic resonance 3 weeks after initiating nivolumab. Eruption, eosinophilia, and interstitial pneumonitis occurred 1 week later. Corticosteroids were started and his condition improved. Four months later, when he was still on steroids tapering off, acute kidney injury and sequential herpes zoster virus activation developed. Severe acute tubulointerstitial nephritis (ATN) with an intense infiltration of lymphocytes was observed on renal biopsy. In blood, a substantial shift to Th2 response, an increase of Th17 cells, and strikingly enriched granzyme B⁺ and perforin⁺ CD8⁺ T cells were detected at ATN onset. Serum interleukin (IL)-5, IL-17, interferon gamma, and IL-6 levels were consistently elevated. Further molecular profiling identified a DRESS risk allele human leukocyte antigen (HLA)-A*31:01 in this patient. His ATN responded favorably to a high dose of corticosteroids. In parallel, complete antitumor response was observed during the clinical course of DRESS. This is the first ever case report of nivolumab-associated DRESS syndrome with exploration of the mechanisms from the histopathological, cellular and molecular aspects. Nivolumab-induced DRESS may result from type IV hypersensitivity-related 'off-target effect' and PD-1 block-mediated 'on-target effect'. HLA risk alleles may constitute the genetic susceptible basis. HLA typing assay has the potential to screen susceptible individuals to avoid ICI-induced DRESS.

Molecular markers of systemic therapy response in urothelial carcinoma

Identification of reliable molecular biomarkers that can complement clinical practice represents a fascinating challenge in any cancer field. Urothelial carcinoma is a very heterogeneous disease and responses to systemic therapies, and outcomes after radical cystectomy are difficult to predict. Advances in molecular biology such as next generation sequencing and whole genome or transcriptomic analysis provide promising platforms to achieve a full understanding of the biology behind the disease and can identify emerging predictive biomarkers. Moreover, the ability to categorize patients' risk of recurrence after curative treatment, or even predict benefit from a conventional or targeted therapies, represents a compelling challenge that may reshape both selection for tailored treatment and disease monitoring. Progress has been made but currently no molecular biomarkers are used in the clinical setting to predict response to systemic agents in either neoadjuvant or adjuvant settings highlighting a relevant unmet need. Here, we aim to present the emerging role of molecular biomarkers in predicting response to systemic agents in urothelial carcinoma.

Identification of Notch signaling pathway gene mutations as a prognostic biomarker for bladder cancer

Purpose: The authors aimed to identify Notch signaling pathway gene mutations as a prognostic biomarker for bladder cancer. Methods: First, critical Notch signaling pathway genes were screened using The Cancer Genome Atlas and validation sets. Second, immune infiltration, protein-protein interaction network, Kyoto Encyclopedia of Genes and Genomes and Gene Set Enrichment Analysis analyses were performed. Finally, potential immunotherapy drug targets were screened using T-cell receptors, B-cell receptors and CERES scores for bladder cancer. Results: The NOTCH7 gene was identified, with a significant difference in immune infiltration level between mutant and wild type in bladder cancer, mainly related to T cells. NOTCH7 was an immunotherapy prognostic factor, and IRF1 and B2M were the potential drug targets for NOTCH7 mutation in bladder cancer. Conclusion: NOTCH7 gene mutation can be used as an immunotherapy biomarker for bladder cancer.

Prognostic Implications of Immune-Related Gene Pairs Signatures in Bladder Cancer

Compelling evidence indicates that immune function is correlated with the prognosis of bladder cancer (BC). Here, we aimed to develop a clinically translatable immune-related gene pairs (IRGPs) prognostic signature to estimate the overall survival (OS) of bladder cancer. From the 251 prognostic-related IRGPs, 37 prognostic-related IRGPs were identified using LASSO regression. We identified IRGPs with the potential to be prognostic markers. The established risk scores divided BC patients into high and low risk score groups, and the survival analysis showed that risk score was related to OS in the TCGA-training set (p < 0.001; HR = 7.5 [5.3, 10]). ROC curve analysis showed that the AUC for the 1-year, 3-year, and 5-year follow-up was 0.820, 0.883, and 0.879, respectively. The model was verified in the TCGA-testing set and external dataset GSE13507. Multivariate analysis showed that risk score was an independent prognostic predictor in patients with BC. In addition, significant differences were found in gene mutations, copy number variations, and gene expression levels in patients with BC between the high and low risk score groups. Gene set enrichment analysis showed that, in the high-risk score group, multiple immune-related pathways were inhibited, and multiple mesenchymal phenotype-related pathways were activated. Immune infiltration analysis revealed that immune cells associated with poor prognosis of BC were upregulated in the high-risk score group, whereas immune cells associated with a better prognosis of BC were downregulated in the high-risk score group. Other immunoregulatory genes were also differentially expressed between high and low risk score groups. A 37 IRGPs-based risk score signature is presented in this study. This signature can efficiently classify BC patients into high and low risk score groups. This signature can be exploited to select high-risk BC patients for more targeted treatment.

Genomic complexity is associated with epigenetic regulator mutations and poor prognosis in diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common type of lymphoma with high mutation burdens but a low response rate to immune checkpoint inhibitors. In this study, we performed targeted next-generation sequencing and fluorescent multiplex immunohistochemistry, and investigated the clinical significance and immunological effect of mutation numbers in 424 DLBCL patients treated with standard immunochemotherapy. We found that KMT2D and TP53 nonsynonymous mutations (MUT) were significantly associated with increased nonsynonymous mutation numbers, and that high mutation numbers (MUT^high) were associated with significantly poorer clinical outcome in germinal center B-cell-like DLBCL with wild-type TP53. To understand the underlying mechanisms, we identified a gene-expression profiling signature and the association of MUT^high with decreased T cells in DLBCL patients with wild-type TP53. On the other hand, in overall cohort, MUT^high was associated with lower PD-1 expression in T cells and PD-L1 expression in macrophages, suggesting a positive role of MUT^high in immune responses. Analysis in a whole-exome sequencing dataset of 304 patients deposited by Chapuy et al. validated the correlation of MUT-KMT2D with genomic complexity and the significantly poorer survival associated with higher numbers of genomic single nucleotide variants in activated B-cell-like DLBCL with wild-type TP53. Together, these results suggest that KMT2D inactivation or epigenetic dysregulation has a role in driving DLBCL genomic instability, and that genomic complexity has adverse impact on clinical outcome in DLBCL patients with wild-type TP53 treated with standard immunochemotherapy. The oncoimmune data in this study have important implications for biomarker and therapeutic studies in DLBCL.

Integrative analysis of immune molecular subtypes and microenvironment characteristics of bladder cancer

The emergence of immunotherapy has provided an option of treatment methods for bladder cancer (BC). However, the beneficiaries of immunotherapy are still limited to small‐scale patients, and immunotherapy‐related adverse events often occur. It is a major challenge for clinical work to study the immune subtypes of BC and the molecular mechanism of immune escape, and identify the immune responders accurately. Here, we explore the immune molecular subtypes of bladder cancer and potential escape mechanisms. First, we screened the expression profiles of 303 differentially expressed immune‐related genes in BC patients from the Cancer Genome Atlas (TCGA) database, and successfully identified 4 molecular subtypes of BC. By comparing the clinical characteristics, immune cells infiltration, the expression of checkpoint genes, human leukocyte antigen (HLA) genes, and gene mutation status of different subtypes, we identified different clinical and immunological characteristics of 4 subtypes. Among 4 subtypes, Cluster 2 met the general characteristics of immunotherapy responders and responded well to immunotherapy, while Cluster 4 had the highest expression of immune characteristics, and is similar to the immune environment of normal bladder tissue. Then, the weighted gene co‐expression network analysis (WGCNA) of immune‐related genes revealed that brown module was positively correlated with subtypes. Pathway enrichment analysis explored the major pathways associated with subtypes, which are also associated with immune escape mechanisms. Moreover, the decision tree model, which was constructed by the principle of random forest screening factors, was also validated in internal validation set and external validation set from the Gene Expression Omnibus (GEO) cohort (GSE133624), and could achieve accurate subtypes prediction for BC patients with high‐throughput sequencing. Taken together, we explored the immune molecular subtypes and their mechanisms of BC, and these results may provide guidance for the development of new BC immunotherapy strategies.

Insights of fibroblast growth factor receptor 3 aberrations in pan-cancer and their roles in potential clinical treatment

Fibroblast growth factor receptor 3 (FGFR3) alters frequently across various cancer types and is a common therapeutic target in bladder urothelial carcinoma (BLCA) with FGFR3 variants. Although emerging evidence supports the role of FGFR3 in individual cancer types, no pan-cancer analysis is available. In this work, we used the open comprehensive datasets, covering a total of 10,953 patients with 10,967 samples across 32 TCGA cancer types, to identify the full alteration spectrum of FGFR3. FGFR3 abnormal expression, methylation patterns, alteration frequency, mutation location distribution, functional impact, and prognostic implications differed greatly from cancer to cancer. The overall alteration frequency of FGFR3 was relatively low in all cancers. Targetable mutations were mainly detected in BLCA, and S249C, Y373C, G370C, and R248C were hotspot mutations that could be targeted by an FDA approved erdafitinib. Genetic fusions were mainly observed in glioma, followed by BLCA. FGFR3-TACC3 was the most common fusion type which was proposed as novel therapeutic targets in glioma and was targetable with erdafitinib in BLCA. Lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC) were two lung cancer subtypes, FGFR3 fusion and hotspot mutation like S249C were observed more commonly in LUSC but not in LUAD. DNA methylation was correlated with the expression of FGFR3 and its downstream genes in some tumors. FGFG3 abnormal expression and alterations exhibited clinical correlations with patient prognosis in several tumors. This work exhibited the full alteration spectrum of FGFR3 and indicated several new clues for their application as potential therapeutic targets and prognostic indicators.

LRP1B mutation: a novel independent prognostic factor and a predictive tumor mutation burden in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most common malignancies globally and the second leading cause of cancer-related death. Low-density lipoprotein (LDL) receptor-related protein 1B (LRP1B) is one of the commonly mutated genes in HCC, but its role in HCC remains unclear. In this study, we analyzed the role of LRP1B mutation in HCC. The bioinformatics results show that LRP1B had a frequency of mutation in HCC patients, and LRP1B mutation was associated with a higher tumor mutation burden (TMB), and survival analysis proved that the prognosis of HCC patients with LRP1B mutation was poor. Univariate and multivariate COX regression analysis indicated that LRP1B mutation was an independent risk factor in evaluating HCC patients' prognosis. Correlation analysis showed that LRP1B mutation status was associated with the infiltration of 2 types of immune cells and higher expression of immune checkpoint gene human endogenous retrovirus-H long terminal repeat-associating protein 2 (HHLA2) in HCC patients. In summary, the results show that LRP1B mutation is associated with the higher TMB and poor prognosis of patients with HCC, and it was an independent risk factor for clinical outcomes of HCC patients. LRP1B gene mutations can serve as predictors in HCC patients with higher TMB and higher expression of HHLA2. The results of this study will be beneficial to future studies on targeted therapy and immunotherapy for HCC.

ARID1 proteins: from transcriptional and post-translational regulation to carcinogenesis and potential therapeutics

The ARID1 proteins are mutually exclusive subunits of the BRG1/BRM-associated factor (BAF) complexes that play an important role in chromatin remodeling and regulate many fundamental cell functions. The role of ARID1s is well defined as a tumor-suppressive. The cancer cells evolve different mechanisms to downregulate ARID1s and inactivate their functions. ARID1s are frequently mutated in human cancer. The recent findings of ARID1A/B downregulation at transcriptional and translational levels along with their low levels in human cancers indicate the significance of regulatory mechanisms of ARID1s in cancers. In this review, we present the current knowledge on the regulation and alterations of ARID1 protein expression in human cancers and indicate the importance of regulators of ARID1s as a prognostic marker and in potential therapeutic strategies.

Tumor Mutation Burden and Immune Invasion Characteristics in Triple Negative Breast Cancer: Genome High-Throughput Data Analysis

In recent years, the emergence of immunotherapy has provided a new perspective for the treatment and management of triple-negative breast cancer (TNBC). However, the relationship between tumor mutation burden (TMB) and immune infiltration and the prognosis of TNBC remains unclear. In this study, to explore the immunogenicity of TNBC, we divided patients with TNBC into high and low TMB groups based on the somatic mutation data of TNBC in The Cancer Genome Atlas (TCGA), and screened out genes with mutation rate ≥10. Then, Kaplan-Meier survival analysis revealed that the 5-year survival rate of the high TMB group was much higher than that of the low TMB group and the two groups also showed differences in immune cell infiltration. Further exploration found that the FAT3 gene, which displays significant difference and a higher mutation rate between the two groups, is not only significantly related to the prognosis of TNBC patients but also exhibits difference in immune cell infiltration between the wild group and the mutant group of the FAT3 gene. The results of gene set enrichment analysis and drug sensitivity analysis further support the importance of the FAT3 gene in TNBC. This study reveals the characteristics of TMB and immune cell infiltration in triple-negative breast cancer and their relationship with prognosis, to provide new biomarkers and potential treatment options for the future treatment of TNBC. The FAT3 gene, as a risk predictor gene of TNBC, is considered a potential biological target and may provide new insight for the treatment of TNBC.

Identification of Tumor Mutation Burden and Immune Infiltrates in Hepatocellular Carcinoma Based on Multi-Omics Analysis

We aimed to explore the tumor mutational burden (TMB) and immune infiltration in HCC and investigate new biomarkers for immunotherapy. Transcriptome and gene mutation data were downloaded from the GDC portal, including 374 HCC samples and 50 matched normal samples. Furthermore, we divided the samples into high and low TMB groups, and analyzed the differential genes between them with GO, KEGG, and GSEA. Cibersort was used to assess the immune cell infiltration in the samples. Finally, univariate and multivariate Cox regression analyses were performed to identify differential genes related to TMB and immune infiltration, and a risk prediction model was constructed. We found 10 frequently mutated genes, including TP53, TTN, CTNNB1, MUC16, ALB, PCLO, MUC, APOB, RYR2, and ABCA. Pathway analysis indicated that these TMB-related differential genes were mainly enriched in PI3K-AKT. Cibersort analysis showed that memory B cells (p = 0.02), CD8+ T cells (p = 0.09), CD4+ memory activated T cells (p = 0.07), and neutrophils (p = 0.06) demonstrated a difference in immune infiltration between high and low TMB groups. On multivariate analysis, GABRA3 (p = 0.05), CECR7 (p < 0.001), TRIM16 (p = 0.003), and IL7R (p = 0.04) were associated with TMB and immune infiltration. The risk prediction model had an area under the curve (AUC) of 0.69, suggesting that patients with low risk had better survival outcomes. Our study demonstrated for the first time that CECR7, GABRA3, IL7R, and TRIM16L were associated with TMB and promoted antitumor immunity in HCC.

Oncostatin M expression and TP53 mutation status regulate tumor-infiltration of immune cells and survival outcomes in cholangiocarcinoma

In this study, we used bioinformatics tools to analyze transcriptome data from cholangiocarcinoma (CCA) patients in multiple datasets (Sun Yat-sen University, TCGA and GSE32225 cohorts) to identify mechanisms that regulate tumor infiltration by immune cells and survival outcomes. We identified 96 differentially expressed genes (DEGs), including 13 upregulated and 83 downregulated genes, in CCA tissues as regulatory T cells were significantly higher and the proportions of activated natural killer cells and monocytes were significantly lower in CCA tissues than the precancerous tissues. The survival outcomes of CCA patients were associated with the TP53 gene mutation status, levels of Oncostatin M (OSM) expression, and the proportions of tumor-infiltrating immune cell types, including dendritic cells, monocytes, and T follicular helper cells. Functional enrichment analysis of the DEGs in the high OSM-expressing CCA tissues showed that pathways related to tumor progression and immune response were significantly upregulated. Our study demonstrates that OSM expression and TP53 mutation status regulate the tumor infiltration by immune cells and survival outcomes in CCA. OSM is thus a potential prognostic biomarker and therapeutic target in cholangiocarcinoma.

Circular RNAs and Bladder Cancer

Bladder cancer (BC) is the most common urinary system malignancy and is a serious threat to human health. Circular RNAs (circRNAs) are members of a newly defined class of noncoding RNAs (ncRNAs) that can regulate gene expression at the transcriptional or posttranscriptional level. Studies have shown that circRNAs are related to the clinicopathological characteristics, prognosis, and chemosensitivity of BC, and basic research has further confirmed that changes in the expression of circRNAs in BC are closely related to various tumor biological functions. CircRNAs promote tumor development by interacting with miRNAs to regulate transcription factors and both classical and nonclassical tumor signaling pathways. The nonclassical signaling pathways are related to cell cycle progression, epithelial–mesenchymal transition (EMT), extracellular matrix maintenance, and tumor stem cell maintenance. In this article, the relationships between circRNAs and the clinical characteristics of BC are reviewed, and the molecular mechanisms by which circRNAs promote tumor development are explored.

ATM Mutations Benefit Bladder Cancer Patients Treated With Immune Checkpoint Inhibitors by Acting on the Tumor Immune Microenvironment

Immune checkpoint inhibitors (ICIs) have shown promising results in bladder cancer (BC). However, only some patients respond to ICIs. DNA repair defects (DDR) play an important role in the therapeutic response of bladder cancer. Therefore, we aimed to elucidate the association between ICIs in bladder cancer and ataxia telangiectasia mutated (ATM), a core component of the DNA repair system. From a collected immunotherapy cohort (n = 210) and The Cancer Genome Atlas (TCGA)-Bladder cancer cohort, which were both retrieved from publicly available resources, we performed a series of analyses to evaluate the prognostic value and potential mechanism of ATM in bladder cancer immunotherapy. We found that ATM-mutant (ATM-MT) bladder cancer patients derived greater benefit from ICIs [overall survival (OS), hazard ratio (HR) = 0.28, [95% confidence interval (CI), 0.16 to 0.51], P = 0.007] and showed a higher mutation load (P < 0.05) and immunogenicity (P < 0.05) than ATM-wild-type (ATM-WT) patients. The immune inflammatory response to antigenic stimulation, the regulation of the IFN pathway and the macrophage activation pathway were significantly enriched in the ATM-MT group (NES > 1, P < 0.05), while insulin-like growth factor receptor signaling pathways and vasculogenesis were significantly downregulated (NES < −1, P < 0.05). ATM mutation significantly upregulated the number of DNA damage repair pathway gene mutations (P < 0.05). ATM mutations resulted in increased bladder cancer sensitivity to 29 drugs (P < 0.05), including cisplatin and BMS-536924, an IGF-1R inhibitor. Our results demonstrate the importance of ATM as a prognostic signature in bladder cancer and reveal that ATM may impact the effects of ICIs by acting on the tumor immune microenvironment.