A robust immune-related lncRNA signature for the prognosis of human colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) is one of the most prevalent malignant cancers worldwide. Immune-related long non-coding RNAs (IRlncRNAs) are proved to be essential in the development and progression of carcinoma. The purpose of the present study was to develop and validate a prognostic IRlncRNA signature for CRC patients. METHODS: Gene expression profiles of CRC samples were downloaded from The Cancer Genome Atlas (TCGA) database. Immune-related genes were obtained from the ImmPort database and were used to identify IRlncRNA by correlation analysis. Through LASSO Cox regression analyses, a prognostic signature was constructed. Functional enrichment analysis was performed by gene set enrichment analysis (GSEA). TIMER2.0 web server and tumor immune dysfunction and exclusion (TIDE) algorithm were employed to analyze the association between our model and tumor-infiltrating immune cells and immunotherapy response. The expression levels of IRlncRNAs in cell lines were detected by quantitative real-time PCR (qPCR). RESULTS: A 9-IRlncRNA signature was developed by a LASSO Cox proportional regression model. Based on the signature, CRC patients were divided into high- and low-risk groups with different prognoses. GSEA results indicated that patients in high-risk group were associated with cancer-related pathways. In addition, patients in low-risk group were found to have more infiltration of anti-tumor immune cells and might show a favorable response to immunotherapy. Finally, the result of qPCR revealed that most IRlncRNAs were differently expressed between normal and tumor cell lines. CONCLUSION: The constructed 9-IRlncRNA signature has potential to predict the prognosis of CRC patients and may be helpful to guide personalized immunotherapy.

Role of oncogenic KRAS in the prognosis, diagnosis and treatment of colorectal cancer.

Colorectal cancer (CRC) is a heterogeneous disease at the cellular and molecular levels. Kirsten rat sarcoma (KRAS) is a commonly mutated oncogene in CRC, with mutations in approximately 40% of all CRC cases; its mutations result in constitutive activation of the KRAS protein, which acts as a molecular switch to persistently stimulate downstream signaling pathways, including cell proliferation and survival, thereby leading to tumorigenesis. Patients whose CRC harbors KRAS mutations have a dismal prognosis. Currently, KRAS mutation testing is a routine clinical practice before treating metastatic cases, and the approaches developed to detect KRAS mutations have exhibited favorable sensitivity and accuracy. Due to the presence of KRAS mutations, this group of CRC patients requires more precise therapies. However, KRAS was historically thought to be an undruggable target until the development of KRASG12C allele-specific inhibitors. These promising inhibitors may provide novel strategies to treat KRAS-mutant CRC. Here, we provide an overview of the role of KRAS in the prognosis, diagnosis and treatment of CRC.

Spotlight on USP4: Structure, Function, and Regulation.

The deubiquitinating enzyme (DUB)-mediated cleavage of ubiquitin plays a critical role in balancing protein synthesis and degradation. Ubiquitin-specific protease 4 (USP4), a member of the largest subfamily of cysteine protease DUBs, removes monoubiquitinated and polyubiquitinated chains from its target proteins. USP4 contains a DUSP (domain in USP)-UBL (ubiquitin-like) domain and a UBL-insert catalytic domain, sharing a common domain organization with its paralogs USP11 and USP15. USP4 plays a critical role in multiple cellular and biological processes and is tightly regulated under normal physiological conditions. When its expression or activity is aberrant, USP4 is implicated in the progression of a wide range of pathologies, especially cancers. In this review, we comprehensively summarize the current knowledge of USP4 structure, biological functions, pathological roles, and cellular regulation, highlighting the importance of exploring effective therapeutic interventions to target USP4.

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

Bladder cancer is a leading cause of morbidity and mortality worldwide. Currently, immunotherapy has become a worthwhile therapy for bladder cancer. Tumor mutation burden (TMB) has been regarded as the most prevalent biomarker to predict immunotherapy. Bladder cancer is reported to have the third highest mutation rate. However, whether these gene mutations are related to TMB and immune response remain unknown. In this study, we downloaded somatic mutation data of bladder cancer from The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) datasets, and found 11 frequently mutated genes were covered by both two cohorts including FGFR3, TTN, XIRP2, CREBBP, PIK3CA, TP53, MUC16, EP300 (E1A binding protein P300), ARID1A, ERBB2, and KDM6A. Among them, EP300 mutation was associated with higher TMB and indicated a favorable clinical prognosis. Furthermore, based on Gene set enrichment analysis (GSEA) and CIBERSORT algorithm, we observed that EP300 mutation upregulated signaling pathways involved in immune system and enhanced antitumor immune response. In conclusion, EP300 is frequently mutated in bladder cancer, and its mutation is associated with increased TMB and promotes antitumor immunity, which may serve as a biomarker to predict immune response.

Profiles of tumor-infiltrating immune cells in renal cell carcinoma and their clinical implications.

Tumor-infiltrating immune cells (TIICs) are crucial for the clinical outcome of renal cell carcinoma (RCC), as they regulate cancer progression. TIICs have therefore the potential to become novel targets of immunotherapies. The present study used CIBERSORT analytical tool, which is a deconvolution algorithm, to comprehensively analyze the composition of immune cells in RCC and normal tissues from The Cancer Genome Atlas (TCGA) cohort, and to determine the prognostic value of TIICs in RCC. A landscape of infiltrating immune cells was determined as containing 13 subpopulations of immune cells, with significant differences between normal and tumor tissues. Subsequently, Kaplan-Meier analysis and log-rank test were used to estimate the prognostic value of TIICs in RCC. The results demonstrated that a higher proportion of regulatory T cells (Tregs) [hazard ratio (HR)=1.596; 95% confidence interval (CI), 1.147-2.222; P=0.006] and follicular helper T cells (HR=1.516; 95% CI, 1.089-2.111; P=0.014) were associated with poor outcome in patients with RCC. Conversely, resting mast cells (HR=0.678; 95% CI, 0.487-0.943; P=0.021) and monocytes (HR=0.701; 95% CI, 0.503-0.977; P=0.036) were associated with a favorable prognosis in patients with RCC. Furthermore, the results from multivariate Cox regression analysis indicated that Tregs and monocytes represented independent risk factors for prognosis in patients with RCC. These findings demonstrated that gene profiling deconvolution by CIBERSORT served to determine the composition of immune cells infiltrated in RCC and may provide some crucial information for the development of immunotherapies.

Exosomes from human-bone-marrow-derived mesenchymal stem cells protect against renal ischemia/reperfusion injury via transferring miR-199a-3p.

Renal ischemia/reperfusion (I/R) injury is the main reason for acute kidney injury (AKI) and is closely related to high morbidity and mortality. In this study, we found that exosomes from human-bone-marrow-derived mesenchymal stem cells (hBMSC-Exos) play a protective role in hypoxia/reoxygenation (H/R) injury. hBMSC-Exos were enriched in miR-199a-3p, and hBMSC-Exo treatment increased the expression level of miR-199a-3p in renal cells. We further explored the function of miR-199a-3p on H/R injury. miR-199a-3p was knocked down in hBMSCs with a miR-199a-3p inhibitor. HK-2 cells cocultured with miR-199a-3p-knockdown hBMSCs were more susceptible to H/R injury and showed more apoptosis than those cocultured with hBMSCs or miR-199a-3p-overexpressing hBMSCs. Meanwhile, we found that HK-2 cells exposed to H/R treatment incubated with hBMSC-Exos decreased semaphorin 3A (Sema3A) and activated the protein kinase B (AKT) and extracellular-signal-regulated kinase (ERK) pathways. However, HK-2 cells cocultured with miR-199a-3p-knockdown hBMSCs restored Sema3A expression and blocked the activation of the AKT and ERK pathways. Moreover, knocking down Sema3A could reactivate the AKT and ERK pathways suppressed by a miR-199a-3p inhibitor. In vivo, we injected hBMSC-Exos into mice suffering from I/R injury; this treatment induced functional recovery and histologic protection and reduced cleaved caspase-3 and Sema3A expression levels, as shown by immunohistochemistry. On the whole, this study demonstrated an antiapoptotic effect of hBMSC-Exos, which protected against I/R injury, via delivering miR-199a-3p to renal cells, downregulating Sema3A expression and thereby activating the AKT and ERK pathways. These findings reveal a novel mechanism of AKI treated with hBMSC-Exos and provide a therapeutic method for kidney diseases.

KRAB zinc-finger protein 382 regulates epithelial-mesenchymal transition and functions as a tumor suppressor, but is silenced by CpG methylation in gastric cancer.

Several studies have recently reported that KRAB zinc finger protein 382 (ZNF382) is downregulated in multiple carcinoma types due to promoter methylation. The exact role of ZNF382 in gastric carcinogenesis, however, remains elusive. In this study, we investigated the alterations and functions of ZNF382 in the pathogenesis of gastric cancer (GC). Semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR), quantitative (real-time) PCR (qPCR) and immunohistochemistry were carried out to detect the expression patterns of ZNF382 in GC cell lines and gastric tissue samples. Furthermore, its methylation status in GC cell lines, tumor tissues and adjacent non-tumor tissues was detected by methylation-specific PCR (MSP). We observed that ZNF382 was silenced due to promoter methylation in MKN45 and SGC7901 cell lines, and that its silencing could be reversed with 5-aza-2'-deoxycytidine, indicating that its downregulation in GC is due to promoter methylation. In addition, the ectopic expression of ZNF382 significantly inhibited gastric tumor cell clonogenicity, proliferation, migration and epithelial-mesenchymal transition (EMT) through the induction of apoptosis. ZNF382 expression downregulated the expression of SNAIL, Vimentin, Twist, NOTCH1, NOTCH2, NOTCH3, NOTCH4, HES-1, JAG1, matrix metalloproteinase (MMP)2 and MMP11, as well as that of the stem cell markers, NANOG, octamer-binding transcription factor 4 (OCT4) and SOX2. ZNF382 also upregulated the expression of E-cadherin. On the whole, the findings of this study suggest that ZNF382 functions as a tumor suppressor in GC cells, but is frequently methylated in both GC cell lines and primary gastric tumors. ZNF382 can reverse the EMT process in GC cells through NOTCH signaling. Our findings further illustrate the molecular pathogenesis of GC and establish potential biomarkers for this type of cancer.

The novel 19q13 KRAB zinc-finger tumour suppressor ZNF382 is frequently methylated in oesophageal squamous cell carcinoma and antagonises Wnt/ß-catenin signalling.

Zinc finger proteins (ZFPs) are the largest transcription factor family in mammals. About one-third of ZFPs are Krüppel-associated box domain (KRAB)-ZFPs and involved in the regulation of cell differentiation/proliferation/apoptosis and neoplastic transformation. We recently identified ZNF382 as a novel KRAB-ZFP epigenetically inactivated in multiple cancers due to frequent promoter CpG methylation. However, its epigenetic alterations, biological functions/mechanism and clinical significance in oesophageal squamous cell carcinoma (ESCC) are still unknown. Here, we demonstrate that ZNF382 expression was suppressed in ESCC due to aberrant promoter methylation, but highly expressed in normal oesophagus tissues. ZNF382 promoter methylation is correlated with ESCC differentiation levels. Restoration of ZNF382 expression in silenced ESCC cells suppressed tumour cell proliferation and metastasis through inducing cell apoptosis. Importantly, ZNF382 suppressed Wnt/ß-catenin signalling and downstream target gene expression, likely through binding directly to FZD1 and DVL2 promoters. In summary, our findings demonstrate that ZNF382 functions as a bona fide tumour suppressor inhibiting ESCC pathogenesis through inhibiting the Wnt/ß-catenin signalling pathway.