Constructing a disulfidptosis-related prognostic signature of hepatocellular carcinoma based on single-cell sequencing and weighted co-expression network analysis.

Hepatocellular carcinoma (HCC) ranks as the second leading cause of cancer-related deaths globally. Disulfidptosis is a newly identified form of regulated cell death that is induced by glucose starvation. However, the clinical prognostic characteristics of disulfidptosis-associated genes in HCC remain poorly understood. We conducted an analysis of the single-cell datasets GSE149614 and performed weighted co-expression network analysis (WGCNA) on the Cancer Genome Atlas (TCGA) datasets to identify the genes related to disulfidptosis. A prognostic model was constructed using univariate COX and Lasso regression. Survival analysis, immune microenvironment analysis, and mutation analysis were performed. Additionally, a nomogram associated with disulfidptosis-related signature was constructed to identify the prognosis of HCC patients. Patients with HCC in the TCGA and GSE14520 datasets were categorized using a disulfidptosis-related model, revealing significant differences in survival times between the high- and low-disulfidptosis groups. High-disulfidptosis patients exhibited increased expression of immune checkpoint-related genes, implying that immunotherapy and certain chemotherapies may be beneficial for them. Meanwhile, the ROC and decision curves analysis (DCA) indicated that the nomogram has satisfying prognostic efficacy. Moreover, the experimental results of GATM in this prognostic model indicated that GATM is low expressed in HCC tissues, and GATM knockdown promotes the proliferation and migration of HCC cells. By analyzing single-cell and bulk multi-omics sequencing data, we developed a prognostic signature related to disulfidptosis and explored the relationship between high- and low-disulfidptosis groups in HCC. This study offers a novel reference for gaining a deeper understanding of the role of disulfidptosis in HCC.

Identification and functional activity of Nik related kinase (NRK) in benign hyperplastic prostate.

OBJECTIVE: Benign prostatic hyperplasia (BPH) is common in elder men. The current study aims to identify differentially expressed genes (DEGs) in hyperplastic prostate and to explore the role of Nik related kinase (NRK) in BPH. METHODS: Four datasets including three bulk and one single cell RNA-seq (scRNA-seq) were obtained to perform integrated bioinformatics. Cell clusters and specific metabolism pathways were analyzed. The localization, expression and functional activity of NRK was investigated via RT-PCR, western-blot, immunohistochemical staining, flow cytometry, wound healing assay, transwell assay and CCK-8 assay. RESULTS: A total of 17 DEGs were identified by merging three bulk RNA-seq datasets. The findings of integrated single-cell analysis showed that NRK remarkably upregulated in fibroblasts and SM cells of hyperplasia prostate. Meanwhile, NRK was upregulated in BPH samples and localized almost in stroma. The expression level of NRK was significantly correlated with IPSS and Qmax of BPH patients. Silencing of NRK inhibited stromal cell proliferation, migration, fibrosis and EMT process, promoted apoptosis and induced cell cycle arrest, while overexpression of NRK in prostate epithelial cells showed opposite results. Meanwhile, induced fibrosis and EMT process were rescued by knockdown of NRK. Furthermore, expression level of NRK was positively correlated with that of α-SMA, collagen-I and N-cadherin, negatively correlated with that of E-cadherin. CONCLUSION: Our novel data identified NRK was upregulated in hyperplastic prostate and associated with prostatic stromal cell proliferation, apoptosis, cell cycle, migration, fibrosis and EMT process. NRK may play important roles in the development of BPH and may be a promising therapeutic target for BPH/LUTS.

The deubiquitinating enzyme USP19 facilitates hepatocellular carcinoma progression through stabilizing YAP.

Hippo pathway plays a crucial role in the progression of hepatocellular carcinoma (HCC), and yes-associated protein (YAP) is one of the major factors of the Hippo pathway. However, the mechanism of abnormal YAP activation in HCC has not been well elucidated. Here, we screened a Deubiquitinating enzymes' (DUB) siRNA library targeting DUBs, and identified Ubiquitin Specific Peptidase 19 (USP19) as a specific deubiquitinating enzyme of YAP in HCC, which could stabilize YAP at K76 and K90 sites via removing the K48- and K11-linked ubiquitin chains. USP19 knockdown decreased the expression of YAP protein and its target gene (CTGF, CYR61, ANKRD1) expression. Through substantial in vivo and in vitro experiments, we prove that USP19 facilities the proliferation and migration of HCC. More importantly, we found that USP19 was upregulated in HCC tissues and associated with poor prognosis. In general, our research revealed a novel post-translational mechanism between USP19 and YAP in HCC, suggesting that USP19 may be a pivotal therapeutic target for HCC treatment.

Molecular pathogenesis: Connections between viral hepatitis-induced and non-alcoholic steatohepatitis-induced hepatocellular carcinoma.

Hepatocellular carcinoma(HCC) is the sixth most common cancer in the world and is usually caused by viral hepatitis (HBV and HCV), alcoholic, and non-alcoholic fatty liver disease(NAFLD). Viral hepatitis accounts for 80% of HCC cases worldwide. In addition, With the increasing incidence of metabolic diseases, NAFLD is now the most common liver disease and a major risk factor for HCC in most developed countries. This review mainly described the specificity and similarity between the pathogenesis of viral hepatitis(HBV and HCV)-induced HCC and NAFLD-induced HCC. In general, viral hepatitis promotes HCC development mainly through specific encoded viral proteins. HBV can also exert its tumor-promoting mechanism by integrating into the host chromosome, while HCV cannot. Viral hepatitis-related HCC and NASH-related HCC differ in terms of genetic factors, and epigenetic modifications (DNA methylation, histone modifications, and microRNA effects). In addition, both of them can lead to HCC progression through abnormal lipid metabolism, persistent inflammatory response, immune and intestinal microbiome dysregulation.

Research Progress on Long Noncoding RNAs and N6-Methyladenosine in Hepatocellular Carcinoma.

N6-methyladenosine (m6A) is an epigenetic modification that widely exists in long noncoding RNAs (lncRNAs) and is involved in the regulation of oncogenes or tumor suppressor genes that form complex enzymes to affect the occurrence of tumors. The abnormal modification of m6A methylation can alter the overall m6A level and thus contribute to the malignant biological behaviors of hepatocellular carcinoma (HCC). LncRNAs related to m6A methylation are involved in lipogenesis, the proliferation, migration and invasion of HCC cells, the stemness of tumor cells and sorafenib resistance. In this review, we systematically elaborated the occurrence mechanism of lncRNA and m6A methylation modification in HCC and the effect of m6A methylation modification of lncRNA on the occurrence of HCC, suggesting that the combination of m6A methylation modification and lncRNA will be more meaningful as molecular markers or prognostic markers. It is helpful to provide further ideas for exploring the pathogenesis of HCC and identifying new targets for HCC treatment and diagnosis and achieve precise individual treatment of liver cancer.

The initial expression alterations occurring to transcription factors during the formation of breast cancer: Evidence from bioinformatics.

BACKGROUND: Breast cancer (BC) is the leading malignancy among women worldwide. AIM: This work aimed to present a comprehensively bioinformatic analysis of gene expression profiles and to identify the hub genes during BC tumorigenesis, providing potential biomarkers and targets for the diagnosis and therapy of BC. MATERIALS & METHODS: In this study, multiple public databases, bioinformatics approaches, and online analytical tools were employed and the real-time reverse transcription polymerase chain reaction was implemented. RESULTS: First, we identified 10, 107, and 3869 differentially expressed genes (DEGs) from three gene expression datasets (GSE9574, GSE15852, and GSE42568, covering normal, para-cancerous, and BC samples, respectively), and investigated different biological functions and pathways involved. Then, we screened out 8, 16, and 29 module genes from these DEGs, respectively. Next, 10 candidate genes were determined through expression and survival analyses. We noted that seven candidate genes JUN, FOS, FOSB, EGR1, ZFP36, CFD, and PPARG were downregulated in BC compared to normal tissues and lower expressed in aggressive types of BC (basal, HER2+ , and luminal B), TP53 mutation group, younger patients, higher stage BC, and lymph node metastasis BC, while CD27, PSMB9, and SELL were upregulated. The present study discovered that the expression levels of these candidate genes were correlated with the infiltration of immune cells (CD8+ T cell, macrophage, natural killer [NK] cell, and cancer-associated fibroblast) in BC, as well as biomarkers of immune cells and immune checkpoints. We also revealed that promoter methylation, amplification, and deep deletion might contribute to the abnormal expressions of candidate genes. Moreover, we illustrated downstream-targeted genes of JUN, FOS, FOSB, EGR1, and ZFP36 and demonstrated that these targeted genes were involved in "positive regulation of cell death", "pathways in cancer", "PI3K-Akt signaling pathway", and so on. DISCUSSION & CONCLUSION: We presented differential gene expression profiles among normal, para-cancerous, and BC tissues and further identified candidate genes that might contribute to tumorigenesis and progression of BC, as potential diagnostic and prognostic targets for BC patients.

OTUD7B stabilizes estrogen receptor α and promotes breast cancer cell proliferation.

Breast cancer is the most common malignancy in women worldwide. Estrogen receptor α (ERα) is expressed in ∼70% of breast cancer cases and promotes estrogen-dependent cancer progression. In the present study, we identified OTU domain-containing 7B (OTUD7B), a deubiquitylase belonging to A20 subgroup of ovarian tumor protein superfamily, as a bona fide deubiquitylase of ERα in breast cancer. OTUD7B expression was found to be positively correlated with ERα in breast cancer and associated with poor prognosis. OTUD7B could interact with, deubiquitylate, and stabilize ERα in a deubiquitylation activity-dependent manner. Depletion of OTUD7B decreased ERα protein level, the expression of ERα target genes, and the activity of estrogen response element in breast cancer cells. In addition, OTUD7B depletion significantly decreased ERα-positive breast cancer cell proliferation and migration. Finally, overexpression of ERα could rescue the suppressive effect induced by OTUD7B depletion, suggesting that the ERα status was essential to the function of OTUD7B in breast carcinogenesis. In conclusion, our study revealed an interesting post-translational mechanism between ERα and OTUD7B in ERα-positive breast cancer. Targeting the OTUD7B-ERα complex may prove to be a potential approach to treat patients with ERα-positive breast cancer.

SOX13/TRIM11/YAP axis promotes the proliferation, migration and chemoresistance of anaplastic thyroid cancer.

Anaplastic thyroid cancer (ATC) is one of the most aggressive and virulent solid tumors. The ubiquitin proteasome system presents in all eukaryotic cells and is essential for cellular homeostasis. While its underlying role in ATC remains largely unclear. TRIM11 is an E3 ubiquitin ligase and has been reported to act as an oncogene in several human cancers. The present study aims to reveal the oncogenic function of TRIM11 in ATC. Western blot was used to measure the protein expression of TRIM11 and YAP, while the YAP target genes were measured by real-time PCR. CCK8 assay was used to detect cell viability; wound-healing assay and transwell assay were used to measure the migration ability of ATC. The xeno-graft tumor model was used for in vivo study. Immuno-precipitation assay was used to detect the interaction domain between YAP and TRIM11. And the ubiquitin-based Immuno-precipitation assays were used to detect the specific ubiquitination manner happened on YAP. TRIM11 depletion significantly decreases cell proliferation and migration capabilities of ATC cells, and elevates cell sensitivity to chemotherapy, which effect could be further rescued by YAP overexpression. TRIM11 depletion decreases YAP protein level and YAP/TEAD target genes, such as CTGF, ANKRD1 and CYR61 in ATC. Indicating that TRIM11 is a regulator of Hippo signaling pathway. Immuno-precipitation assay shows that the RING domain of TRIM11 is essential for the interaction with WW domain of YAP. Further mechanistic analysis suggests that TRIM11 promotes the mono-ubiquitination of YAP, thus prolongs its protein half. Furthermore, TRIM11 promoter analysis revealed that SOX13 activates TRIM11 transcription by binding to the promoter of TRIM11. In summary, our study describes the oncogenic function of TRIM11 in ATC, which acts as a post-translational modulating factor of Hippo pathway. Targeting TRIM11 may be a potential therapeutic method for ATC treatment.

TRIM8 inhibits breast cancer proliferation by regulating estrogen signaling.

Breast cancer (BC) is the most common female malignancy worldwide, and 70% of which are estrogen receptor α (ERα) positive. Endocrine treatment, such as tamoxifen, is a primary adjuvant therapy for patients with ER-positive BC. However, some patients will develop acquired resistance following long-time treatment. Further research on estrogen signaling is important to improve the therapy of these patients. In this study, we report that the E3 ubiquitin ligase tripartite motif 8 (TRIM8) acts as a novel regulator of ERα signaling. TRIM8 is downregulated in BC and is associated with poor prognosis. In addition, the protein level of TRIM8 is negatively correlated with ERα. RNA sequencing revealed that estrogen signaling maybe a potential target of TRIM8. Moreover, knockdown of TRIM8 can significantly enhance BC cell proliferation and migration both in vitro and in vivo. And this effect can be reversed by ERα depletion. Further mechanistic studies showed that TRIM8 interacts with AF1 domain of ERα via its RING domain in the cytoplasm and increases poly-ubiquitination of the ERα protein. In conclusion, our study reveals an interesting post-translational mechanism between ERα and TRIM8 in ER-positive BC, which suggests that TRIM8 may be a potential therapeutic target in the treatment of BC.

Identification of a 9-gene prognostic signature for breast cancer.

Breast cancer (BRCA) is the most common cancer among women and is the second leading cause of cancer death in women. In this study, we developed a 9-gene prognostic signature to predict the prognosis of patients with BRCA. GSE20685, GSE42568, GSE20711, and GSE88770 were used as training sets. The Kaplan-Meier plot was constructed to assess survival differences and log-rank test was performed to evaluate the statistical significance. The overall survival (OS) of patients in the low-risk group was significantly higher than that in the high-risk group. ROC analysis indicated that this 9-gene signature shows good diagnostic efficiency both in OS and disease-free survival (DFS). The 9-gene signature was further validated through GSE16446, GSE7390, and TCGA-BRCA datasets. We also established a nomogram that integrates clinicopathological features and 9-gene signature. The analysis of the calibration plot showed that the nomogram has good prognostic performance. More convincingly, real-time reverse transcription-polymerase chain reaction (RT-PCR) results indicated that the protective prognostic factors in BRCA patients were downregulated, whereas the dangerous prognostic factors were upregulated. The innovation of this article is not only constructing a prognostic gene signature, but also combining with clinical information to further establish a nomogram to better predict the survival probability of patients. It is worth mentioning that this signature also does not depend on other clinical factors or variables.

Identification of Important Modules and Biomarkers in Breast Cancer Based on WGCNA.

INTRODUCTION: Breast cancer (BRCA) has the highest incidence among female malignancies, and the prognosis for these patients remains poor. MATERIALS AND METHODS: In this study, core modules and central genes related to BRCA were identified through a weighted gene co-expression network analysis (WGCNA). Gene expression profiles and clinical data of GSE25066 were obtained from the Gene Expression Omnibus (GEO) database. The result was validated with RNA-seq data from The Cancer Genome Atlas (TCGA) and Oncomine database. The top 30 key module genes with the highest intramodule connectivity were selected as the core genes (R2 = 0.40). RESULTS: According to TCGA and Oncomine datasets, seven genes were selected as candidate hub genes. Following further experimental verification, four hub genes (FAM171A1, NDFIP1, SKP1, and REEP5) were retained. CONCLUSION: We identified four hub genes as candidate biomarkers for BRCA. These hub genes may provide a theoretical basis for targeted therapy against BRCA.

An immune-related prognostic signature for predicting breast cancer recurrence.

Breast cancer (BC) is the most common cancer among women worldwide and is the second leading cause of cancer-related deaths in women. Increasing evidence has validated the vital role of the immune system in BC development and recurrence. In this study, we identified an immune-related prognostic signature of BRCA that could help delineate risk scores of poor outcome for each patient. This prognostic signature comprised information on five danger genes-TSLP, BIRC5, S100B, MDK, and S100P-and three protect genes RARRES3, BLNK, and ACO1. Kaplan-Meier survival curve showed that patients classified as low-risk according to optimum cut-off risk score had better prognosis than those identified within the high-risk group. ROC analysis indicated that the identified prognostic signature had excellent diagnostic efficiency for predicting 3- and 5-years relapse-free survival (RFS). Multivariate Cox regression analysis proved that the prognostic signature is independent of other clinical parameters. Stratification analysis demonstrated that the prognostic signature can be used to predict the RFS of BC patients within the same clinical subgroup. We also developed a nomogram to predict the RFS of patients. The calibration plots exhibited outstanding performance. The validation sets (GSE21653, GSE20711, and GSE88770) were used to external validation. More convincingly, the real time RT-PCR results of clinical samples demonstrated that danger genes were significantly upregulated in BC samples, whereas protect genes were downregulated. In conclusion, we developed and validated an immune-related prognostic signature, which exhibited excellent diagnostic efficiency in predicting the recurrence of BC, and will help to make personalized treatment decisions for patients at different risk score.

TRIM11 promotes breast cancer cell proliferation by stabilizing estrogen receptor α.

Breast cancer is the most commonly diagnosed malignancy in female worldwide, over 70% of which are estrogen receptor α (ERα) positive. ERα has a crucial role in the initiation and progression of breast cancer and is an indicator of endocrine therapy, while endocrine resistance is an urgent problem in ER-positive breast cancer patients. In the present study, we identify a novel E3 ubiquitin ligase TRIM11 function to facilitate ERα signaling. TRIM11 is overexpressed in human breast cancer, and associates with poor prognosis. The protein level of TRIM11 is highly correlated with ERα. RNA-seq results suggest that ERα signaling may be an underlying target of TRIM11. Depletion of TRIM11 in breast cancer cells significantly decreases cell proliferation and migration. And the suppression effects can be reversed by overexpressing ERα. In addition, ERα protein level, ERα target genes expression and estrogen response element activity are also dramatically decreased by TRIM11 depletion. Further mechanistic analysis indicates that the RING domain of TRIM11 interacted with the N terminal of ERα in the cytoplasm and promotes its mono-ubiquitination, thus enhances ERα protein stability. Our study describes TRIM11 as a modulating factor of ERα and increases ERα stability via mono-ubiquitination. TRIM11 could be a promising therapeutic target for breast cancer treatment.

Atypical ubiquitin-binding protein SHARPIN promotes breast cancer progression.

Breast cancer ranks first among female malignancies worldwide, and estrogen receptor-positive (ER+) breast cancer is the leading cause of cancer death in women. Abnormal oncogenic signaling has important effects on the development of breast cancer, such as ERα/ ESR1 (estrogen receptor alpha), PTEN (gene of phosphate and tension homology deleted on chromsome ten), NFκB(nuclear factor κB), and tumor protein p53 (p53 / TP53). SHARPIN is a ubiquitin-related protein that has important regulatory functions in inflammation control, immune organ development, and cancer development. SHARPIN is highly expressed in many cancers, especially in breast cancer. It plays an important role in controlling important carcinogenic pathways in breast cancer, such as p53 and ERα. This review emphasizes the functional role of SHARPIN and the recent advances in the molecular mechanisms by which SHARPIN regulates breast cancer development through ubiquitination.