TRIM29 regulates the SETBP1/SET/PP2A axis via transcription factor VEZF1 to promote progression of ovarian cancer

Predictive biomarkers for metachronous gastric cancer development after endoscopic resection of early gastric cancer

OBJECTIVES

We aimed to identify predictive markers for metachronous gastric cancer (MGC) in early gastric cancer (EGC) patients curatively treated with endoscopic submucosal dissection (ESD).

MATERIALS AND METHODS

From EGC patients who underwent ESD, bulk RNA sequencing was performed on non-cancerous gastric mucosa samples at the time of initial EGC diagnosis. This included 23 patients who developed MGC, and 23 control patients without additional gastric neoplasms for over 3 years (1:1 matched by age, sex, and Helicobacter pylori infection state). Candidate differentially-expressed genes were identified, from which biomarkers were selected using real-time quantitative polymerase chain reaction and cell viability assays using gastric cell lines. An independent validation cohort of 55 MGC patients and 125 controls was used for marker validation. We also examined the severity of gastric intestinal metaplasia, a known premalignant condition, at initial diagnosis.

RESULTS

From the discovery cohort, 86 candidate genes were identified of which KDF1 and CDK1 were selected as markers for MGC, which were confirmed in the validation cohort. CERB5 and AKT2 isoform were identified as markers related to intestinal metaplasia and were also highly expressed in MGC patients compared to controls (p < 0.01). Combining these markers with clinical data (age, sex, H. pylori and severity of intestinal metaplasia) yielded an area under the curve (AUC) of 0.91 (95% CI, 0.85-0.97) for MGC prediction.

CONCLUSION

Assessing biomarkers in non-cancerous gastric mucosa may be a useful method for predicting MGC in EGC patients and identifying patients with a higher risk of developing MGC, who can benefit from rigorous surveillance.

The m6A methyltransferase METTL14 promotes cell proliferation via SETBP1-mediated activation of PI3K-AKT signaling pathway in myelodysplastic neoplasms

N6-methyladenosine (m6A) is the most prevalent epitranscriptomic modification in mammalian mRNA. Recent studies have revealed m6A is involved in the pathogenesis of various malignant tumors including hematologic neoplasms. Nevertheless, the specific roles of m6A modification and m6A regulators in myelodysplastic neoplasms (MDS) remain poorly understood. Herein, we demonstrated that m6A level and the expression of m6A methyltransferase METTL14 were elevated in MDS patients with bone marrow blasts ≥5%. Additionally, m6A level and METTL14 expression were upregulated as the disease risk increased and significantly associated with adverse clinical outcomes. Knockdown of METTL14 inhibited cell proliferation and colony formation ability of MDS cells. Moreover, in vivo experiments showed METTL14 knockdown remarkably reduced tumor burden and prolonged the survival of mice. Mechanistically, METTL14 facilitated the m6A modification of SETBP1 mRNA by formation of METTL3-METTL14 complex, leading to increased stabilization of SETBP1 mRNA and subsequent activation of the PI3K-AKT signaling pathway. Overall, this study elucidated the involvement of the METTL14/m6A/SETBP1/PI3K-AKT signaling axis in MDS, highlighting the therapeutic potential of targeting METTL3-METTL14 complex-mediated m6A modification for MDS therapy.

SETBP1 activation upon MDM4-enhanced ubiquitination of NR3C1 triggers dissemination of colorectal cancer cells

Colorectal cancer (CRC) presents a growing concern globally, marked by its escalating incidence and mortality rates, thus imposing a substantial health burden. This investigation delves into the role of nuclear receptor subfamily 3 group C member 1 (NR3C1) in CRC metastasis and explores the associated mechanism. Through a comprehensive bioinformatics analysis, NR3C1 emerged as a gene with diminished expression levels in CRC. This finding was corroborated by observations of a low-expression pattern of NR3C1 in both CRC tissues and cells. Furthermore, experiments involving NR3C1 knockdown revealed an exacerbation of proliferation, migration, and invasion of CRC cells in vitro. Subsequent assessments in mouse xenograft tumor models, established by injecting human HCT116 cells either through the tail vein or at the cecum termini, demonstrated a reduction in tumor metastasis to the lung and liver, respectively, upon NR3C1 knockdown. Functionally, NR3C1 (glucocorticoid receptor) suppressed SET binding protein 1 (SETBP1) transcription by binding to its promoter region. Notably, mouse double minute 4 (MDM4) was identified as an upstream regulator of NR3C1, orchestrating its downregulation via ubiquitination-dependent proteasomal degradation. Further investigations unveiled that SETBP1 knockdown suppressed migration and invasion, and epithelial to mesenchymal transition of CRC cells, consequently impeding in vivo metastasis in murine models. Conversely, upregulation of MDM4 exacerbated the metastatic phenotype of CRC cells, a propensity mitigated upon additional upregulation of NR3C1. In summary, this study elucidates a cascade wherein MDM4-mediated ubiquitination of NR3C1 enables the transcriptional activation of SETBP1, thereby propelling the dissemination of CRC cells.

TRIM29 modulates proteins involved in PTEN/AKT/mTOR and JAK2/STAT3 signaling pathway and suppresses the progression of hepatocellular carcinoma

Tripartite motif-containing 29 (TRIM29), also known as the ataxia telangiectasia group D-complementing (ATDC) gene, has been reported to play an oncogenic or tumor suppressive role in developing different tumors. So far, its expression and biological functions in hepatocellular carcinoma (HCC) remain unclear. We investigated TRIM29 expression pattern in human HCC samples using quantitative RT-PCR and immunohistochemistry. Relationships between TRIM29 expression level, clinical prognostic indicators, overall survival (OS), and disease-free survival (DFS) were evaluated by Kaplan-Meier analysis and Cox proportional hazards model. A series of in vitro experiments and a xenograft tumor model were conducted to detect the functions of TRIM29 in HCC cells. RNA sequencing, western blotting, and immunochemical staining were performed to assess the molecular regulation of TRIM29 in HCC. We found that the mRNA and protein levels of TRIM29 were significantly reduced in HCC samples, compared with adjacent noncancerous tissues, and were negatively correlated with poor differentiation of HCC tissues. Survival analysis confirmed that lower TRIM29 expression significantly correlated with shorter OS and DFS of HCC patients. TRIM29 overexpression remarkably inhibited cell proliferation, migration, and EMT in HCC cells, whereas knockdown of TRIM29 reversed these effects. Moreover, deactivation of the PTEN/AKT/mTOR and JAK2/STAT3 pathways might be involved in the tumor suppressive role of TRIM29 in HCC. Our findings indicate that TRIM29 in HCC exerts its tumor suppressive effects through inhibition of the PTEN/AKT/mTOR and JAK2/STAT3 signaling pathways and may be used as a potential biomarker for survival in patients with HCC.

Conduction and validation of a novel prognostic signature in cervical cancer based on the necroptosis characteristic genes via integrating of multiomics data

The significance of necroptosis in recurrent or metastatic cervical cancer remains unclear. In this study, we utilized various bioinformatics methods to analyze the cancer genome atlas (TCGA) data, gene chip and the single-cell RNA-sequencing (scRNA seq) data. And a necroptosis-related genes signature for prognostic assessment of patients with cervical cancer was constructed successfully. Survival analysis, receiver operating characteristic (ROC) curve, the support vector machine recursive feature elimination (SVM-RFE) algorithm and random forest analysis were performed to validate this signature. Patients in TCGA-CESC cohort were grouped into "high-necroptosis score (H-NCPS)" vs "low-necroptosis score (L-NCPS)" subgroups based on the median of necroptosis score of each patient. Analyses of the tumor microenvironment manifested "H-NCPS" patients associated with lower degree of immune infiltration. Through the utilization of survival analysis, cell communication, and Gene Set Enrichment Analysis (GSEA), PGK1 was determined to be the pivotal gene within the 9-gene signature associated with necroptosis. The high expression of PGK1 in cervical cancer cells was confirmed through the utilization of quantitative real-time polymerase chain reaction (RT-qPCR) and the human protein atlas (HPA). In the interim, PGK1 prompted the transition of M1 macrophages to M2 macrophages and influenced the occurrence and development of necroptosis. In conclusion, the 9-gene signature developed from necroptosis-related genes has shown significant predictive capabilities for the prognosis of cervical cancer, offered valuable guidance for individualized and targeted treatment approaches for patients.

From slides to insights: Harnessing deep learning for prognostic survival prediction in human colorectal cancer histology

Prognostic survival prediction in colorectal cancer (CRC) plays a crucial role in guiding treatment decisions and improving patient outcomes. In this research, we explore the application of deep learning techniques to predict survival outcomes based on histopathological images of human colorectal cancer. We present a retrospective multicenter study utilizing a dataset of 100,000 nonoverlapping image patches from hematoxylin & eosin-stained histological images of CRC and normal tissue. The dataset includes diverse tissue classes such as adipose, background, debris, lymphocytes, mucus, smooth muscle, normal colon mucosa, cancer-associated stroma, and colorectal adenocarcinoma epithelium. To perform survival prediction, we employ various deep learning architectures, including convolutional neural network, DenseNet201, InceptionResNetV2, VGG16, VGG19, and Xception. These architectures are trained on the dataset using a multicenter retrospective analysis approach. Extensive preprocessing steps are undertaken, including image normalization using Macenko's method and data augmentation techniques, to optimize model performance. The experimental findings reveal promising results, demonstrating the effectiveness of deep learning models in prognostic survival prediction. Our models achieve high accuracy, precision, recall, and validation metrics, showcasing their ability to capture relevant histological patterns associated with prognosis. Visualization techniques are employed to interpret the models' decision-making process, highlighting important features and regions contributing to survival predictions. The implications of this research are manifold. The accurate prediction of survival outcomes in CRC can aid in personalized medicine and clinical decision-making, facilitating tailored treatment plans for individual patients. The identification of important histological features and biomarkers provides valuable insights into disease mechanisms and may lead to the discovery of novel prognostic indicators. The transparency and explainability of the models enhance trust and acceptance, fostering their integration into clinical practice. Research demonstrates the potential of deep learning models for prognostic survival prediction in human colorectal cancer histology. The findings contribute to the understanding of disease progression and offer practical applications in personalized medicine. By harnessing the power of deep learning and histopathological analysis, we pave the way for improved patient care, clinical decision support, and advancements in prognostic prediction in CRC.

Deciphering roles of TRIMs as promising targets in hepatocellular carcinoma: current advances and future directions

Tripartite motif (TRIM) family is assigned to RING-finger-containing ligases harboring the largest number of proteins in E3 ubiquitin ligating enzymes. E3 ubiquitin ligases target the specific substrate for proteasomal degradation via the ubiquitin-proteasome system (UPS), which seems to be a more effective and direct strategy for tumor therapy. Recent advances have demonstrated that TRIM genes associate with the occurrence and progression of hepatocellular carcinoma (HCC). TRIMs trigger or inhibit multiple biological activities like proliferation, apoptosis, metastasis, ferroptosis and autophagy in HCC dependent on its highly conserved yet diverse structures. Remarkably, autophagy is another proteolytic pathway for intracellular protein degradation and TRIM proteins may help to delineate the interaction between the two proteolytic systems. In depth research on the precise molecular mechanisms of TRIM family will allow for targeting TRIM in HCC treatment. We also highlight several potential directions warranted further development associated with TRIM family to provide bright insight into its translational values in hepatocellular carcinoma.

Role of the tripartite motif (TRIM) family in female genital neoplasms

The tripartite motif proteins (TRIMs) family represents a class of highly conservative proteins which play a large regulatory role in molecular processes. Recently, increasing evidence has demonstrated a role of TRIMs in female genital neoplasms. Our review thereby aimed to provide an overview of the biological involvement of TRIMs in female genital neoplasms, to provide a better understanding of its role in the development and progression of such diseases, and emphasize its potential as targeted cancer therapy. Overall, our review highlighted that the wide-ranging roles of TRIMs, in not only target protein ubiquitination, tumor migration and/or invasion, epithelial-mesenchymal transition, stemness, cell adhesion, proliferation, cell cycle regulation, and apoptosis, but also in influencing estrogenic, and chemotherapy response.

A Novel pyroptosis-related signature for predicting prognosis and evaluating tumor immune microenvironment in ovarian cancer

Ovarian cancer (OV) is the most fatal gynecological malignant tumor worldwide, with high recurrence rates and great heterogeneity. Pyroptosis is a newly-acknowledged inflammatory form of cell death with an essential role in cancer progression, though studies focusing on prognostic patterns of pyroptosis in OV are still lacking. Our research filtered 106 potential pyroptosis-related genes (PRGs) among the 6406 differentially expressed genes (DEGs) between the 376 TCGA-OV samples and 180 normal controls. Through the LASSO-Cox analysis, the 6-gene prognostic signature, namely CITED2, EXOC6B, MIA2, NRAS, SETBP1, and TRPV46, was finally distinguished. Then, the K-M survival analysis and time-dependent ROC curves demonstrated the promising prognostic value of the 6-gene signature (p-value < 0.0001). Furthermore, based on the signature and corresponding clinical features, we constructed and validated a nomogram model for 1-year, 2-year, and 3-year OV survival, with reliable prognostic values in TCGA-OV (p-value < 0.001) and ICGC-OV cohort (p-value = 0.040). Pathway analysis enriched several critical pathways in cancer, refer to the pyroptosis-related signature, while the m6A analysis indicated greater m6A level in high-risk group. We assessed tumor immune microenvironment through the CIBERSORT algorithm, which demonstrated the upregulation of M1 Macrophages and activated DCs and high expression of key immune checkpoint molecules (CTLA4, PDCD1LG2, and HAVCR2) in high-risk group. Interestingly, the high-risk group exhibited poor sensitivity towards immunotherapy and better sensitivity towards chemotherapies, including Vinblastine, Docetaxel, and Sorafenib. Briefly, the pyroptosis-related signature was a promising tool to predict prognosis and evaluate immune responses, in order to assist decision-making for OV patients in the realm of precision medicine.

The impact of SETBP1 mutations in neurological diseases and cancer

SE translocation (SET) is a cancer-promoting factor whose expression is upregulated in many cancers. High SET expression positively correlates with a poor cancer prognosis. SETBP1 (SET-binding protein 1/SEB/MRD29), identified as SET-binding protein, is the causative gene of Schinzel-Giedion syndrome, which is characterized by severe intellectual disability and a distorted facial appearance. Mutations in these genetic regions are also observed in some blood cancers, such as myelodysplastic syndromes, and are associated with a poor prognosis. However, the physiological role of SETBP1 and the molecular mechanisms by which the mutations lead to disease progression have not yet been fully elucidated. In this review, we will describe the current epidemiological data on SETBP1 mutations and shed light on the current knowledge about the SET-dependent and -independent functions of SETBP1.

TRIM29 knockdown prevented the colon cancer progression through decreasing the ubiquitination levels of KRT5

To investigate the specific role of TRIM29 in colon cancer progression, bioinformatic analysis was performed on TRIM29. Colon cancer tissues were collected and colon cancer cells were cultured for further experiments. Cell viability and proliferation were determined using CCK-8, colony formation, and EDU staining assays. The mRNA and protein levels of TRIM29 and KRT5 were determined using quantitative real-time PCR and western blotting, respectively. The interaction between TRIM29 and KRT5 was detected using a co-immunoprecipitation (CO-IP) assay. Cycloheximide treatment was performed to analyse the stability of KRT5. TRIM29 was upregulated in colon cancer tissues and cells. TRIM29 knockdown decreased the cell viability and proliferation and ubiquitination levels of KRT5 and enhanced the protein stability and expression of KRT5. The CO-IP assay confirmed that TRIM29 and KRT5 binded to each other. KRT5 knockdown neutralises the inhibitory effect of sh-TRIM29 on colon cancer cell growth and TRIM29 knockdown prevented the proliferation of colon cancer cells by decreasing ubiquitination of KRT5, which enhanced the protein stability and expression of KRT5 in cancer cells. Thus, targeting TRIM29-mediated ubiquitination levels of KRT5 might be a new direction for colon cancer therapy.

SETBP1 mutation determines sensitivity to immune checkpoint inhibitors in melanoma and NSCLC

SET binding protein 1 (SETBP1) plays crucial roles in various biological processes; however, its involvement in cancer immune checkpoint inhibitor (ICI) treatments has never been studied. In this study, we collected a total of 631 melanoma and 109 non-small cell lung cancer (NSCLC) samples treated with ICI agents (i.e., anti-CTLA-4, anti-PD-1/PD-L1, or combination therapy). Additionally, we obtained their corresponding somatic mutational profiles. We observed that SETBP1 mutated (SETBP1-MUT) melanoma patients exhibited significantly prolonged ICI survival outcomes compared to wild-type patients (HR: 0.56, 95% CI: 0.38-0.81, P = 0.002). Consistently, an elevated ICI response rate was also noticed in the SETBP1-MUT group (42.9% vs. 29.1%, P = 0.016). The Association of SETBP1 mutations with favorable immunotherapeutic prognosis and response was further supported by an independent NSCLC cohort (both P < 0.05). Additional immunological analyses revealed that favorable immune infiltration, tumor immunogenicity, and immune response circuits were enriched in SETBP1-MUT patients. Overall, our findings suggest that SETBP1 mutations may serve as a new biomarker for stratifying beneficiaries of ICI treatments in melanoma and NSCLC, which provides possible evidence for tailoring clinical immunotherapeutic strategies.

TRIM31: A molecule with a dual role in cancer

Tripartite motif (TRIM) 31 is a new member of the TRIM family and functions as an E3 ubiquitin ligase. Abnormal TRIM31 expression leads to a variety of pathological conditions, such as cancer, innate immunity diseases, sepsis-induced myocardial dysfunction, cerebral ischemic injury, nonalcoholic fatty liver disease and hypertensive nephropathy. In this review, we comprehensively overview the structure, expression and regulation of TRIM31 in cancer. Moreover, we discuss the dual role of TRIM31 in human cancer, and this dual role may be linked to its involvement in the selective regulation of several pivotal cellular signaling pathways: the p53 tumor suppressor, mTORC1, PI3K-AKT, NF-κB and Wnt/β-catenin pathways. In addition, we also discuss the emerging role of TRIM31 in innate immunity, autophagy and its growing sphere of influence across multiple human pathologies. Finally, a better understanding of the dual role of TRIM31 in cancer may provide new therapeutic strategies aimed at inhibiting the cancer-promoting effects of TRIM31 without affecting its tumor suppressor effects.

TRIM family contribute to tumorigenesis, cancer development, and drug resistance

The tripartite-motif (TRIM) family represents one of the largest classes of putative single protein RING-finger E3 ubiquitin ligases. TRIM family is involved in a variety of cellular signaling transductions and biological processes. TRIM family also contributes to cancer initiation, progress, and therapy resistance, exhibiting oncogenic and tumor-suppressive functions in different human cancer types. Moreover, TRIM family members have great potential to serve as biomarkers for cancer diagnosis and prognosis. In this review, we focus on the specific mechanisms of the participation of TRIM family members in tumorigenesis, and cancer development including interacting with dysregulated signaling pathways such as JAK/STAT, PI3K/AKT, TGF-β, NF-κB, Wnt/β-catenin, and p53 hub. In addition, many studies have demonstrated that the TRIM family are related to tumor resistance; modulate the epithelial–mesenchymal transition (EMT) process, and guarantee the acquisition of cancer stem cells (CSCs) phenotype. In the end, we havediscussed the potential of TRIM family members for cancer therapeutic targets.

The Role of SETBP1 in Gastric Cancer: Friend or Foe

Background

Gastric cancer (GC) remains a common disease with a poor prognosis worldwide. The SET binding protein 1 (SETBP1) has been implicated in the pathogenesis of several cancers and plays a dual role as an oncogene and a tumor suppressor gene. However, the role and underlying mechanism of SETBP1 in GC remain unclear.

Materials and Methods

We used next-generation RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) to explore the correlation between SETBP1 expression and tumor progression. We then quantified SETBP1 expression in GC cells with real-time quantitative polymerase chain reactions (RT-qPCR). The chi-square test and logistic regression were used to assess the correlation between SETBP1 expression and clinicopathological features. Kaplan-Meier survival analysis and Cox proportional hazards regression model were used to assess the relationship between SETBP1 expression and survival. Finally, gene set enrichment analyses (GSEA) were used to examine GC-related signaling pathways in low and high SETBP1 expressing samples.

Results

We found SETBP1 expression levels in GC tissues to be significantly lower than in adjacent non-tumor tissues in the TCGA database. In addition, SETBP1 expression differed significantly between groups classified by tumor differentiation. Furthermore, SETBP1 expression in diffuse-type GC was significantly higher than in intestinal-type GC. However, it did not differ significantly across pathological- or T-stage groups. RT-qPCR and comprehensive meta-analysis showed that SETBP1 expression is downregulated in GC cells and tissues. Interestingly, SETBP1 expression in poorly- or un-differentiated GC cells was higher than in well-differentiated GC cells. Moreover, the chi-square test and logistic regression analyses showed that SETBP1 expression correlates significantly with tumor differentiation. Kaplan–Meier curves indicated that patients with relatively high SETBP1 expression had a poor prognosis. Multivariate analyses indicated that SETBP1 expression might be an important predictor of poor overall survival in GC patients. GSEA indicated that 20 signaling pathways were significantly enriched in samples with high and low SETBP1 expression.

Conclusion

SETBP1 may play a dual role in GC progression.

TRIM29 is differentially expressed in colorectal cancers of different primary locations and affects survival by regulating tumor immunity based on retrospective study and bioinformatics analysis

Background

In colorectal cancer (CRC) patients, different primary tumor locations caused distinct prognosis and clinicopathological features. It is necessary to identify specific tumor markers according tumor site. Our previous work has identified differentially expressed genes between CRC and adjacent normal tissues, in which only TRIM29 was differently expressed between right colon cancer (RCC) and left colon cancer (LCC) patients. Rectal cancer (RECC) was not included in this latter study and the effects of TRIM29 on the survival with RCC and LCC patients were not investigated. This study further verified TRIM29 expression through Gene Expression Omnibus (GEO) database and our retrospective study. The role of TRIM29 on survival according tumor sites was also explored. Furthermore, the molecular mechanisms of TRIM29 were explored.

Methods

The GEO dataset was used to confirm the differential expression of TRIM29 in proximal and distal cancers. Moreover, TRIM29 were assess using immunohistochemistry (IHC) in 227 cases to observe the correlation between TRIM29 and tumor site. The relationship between TRIM29 and the clinicopathologic features was investigated according tumor sites. Furthermore, the disease-free survival (DFS) and overall survival (OS) was analyzed using the Kaplan-Meier method to assess the prognostic value of TRIM29. Finally, bioinformatics analysis was used to explore the molecular mechanisms. The Tumor-Immune System Interactions and Drug Bank database (TISIDB) was used to analyze the correlations between TRIM29 expression and tumor immune functions. The correlation of TRIM29 with tumor infiltrating lymphocytes or mismatch-repair-proficient/mismatch-repair-deficient (pMMR/dMMR) status was also investigated.

Results

TRIM29 expression was significantly higher in patients with RCC (P<0.001). RCC patients with high TRIM29 tended to be older, male, in stage III-IV, with N+ staging, and intestinal obstruction (P<0.001, P<0.001, P<0.001, P<0.001, and P=0.010, respectively). High TRIM29 expression was associated with an increased risk of recurrence/metastasis and death, only in RCC patients (P=0.020 and P<0.001). Functional annotations and immune activity analysis showed that TRIM29 is related to tumor infiltrating lymphocytes and immune dysfunction.

Conclusions

TRIM29 plays varying roles in patients with different tumor sites. TRIM29 is correlated with the clinicopathological features and prognosis in RCC patients. Indeed, TRIM29 may serve as a new biomarker for RCC patients.