Super enhancer associated RAI14 is a new potential biomarker in lung adenocarcinoma

The dual-crosslinked prospective values of RAI14 for the diagnosis and chemosurveillance in triple negative breast cancer

OBJECTIVE

The exploration of non-invasive biomarkers for assessing tumor response is critical to optimize treatment decisions. In this study, we aimed at determining the potential role of RAI14 in the early diagnosis and evaluation of chemotherapy efficacy in triple-negative breast cancer (TNBC).

METHODS

We recruited 116 patients newly diagnosed with breast cancer, 30 patients with benign breast disease and 30 healthy controls. In addition, 57 TNBC patients were collected in serum at different time points (C0, C2 and C4) for chemotherapy monitoring. The expression of serum RAI14 and CA15-3 were quantified by Elisa and electrochemiluminescence assay, respectively. Then we compared the performances of markers with the chemotherapy efficacy assessed by imaging.

RESULTS

RAI14 is significantly overexpressed in TNBC and is linked to adverse clinicopathological features such as tumor burden, CA15-3 levels and the ER, PR, and HER2 status of the patients. ROC curve analysis showed that RAI14 improves the diagnostic performance for CA15-3(AUCRAI14 = 0.934 vs. AUCCA15-3 = 0.836), especially embodied in early-stage breast cancer diagnosis and patients with CA15-3 negativity. Furthermore, RAI14 behaves well in reproducing treatment response which was consistent with clinical Imaging assessment.

CONCLUSIONS

Recent studies showed that RAI14 has a complementary effect to CA15-3 and a test combining the two parameters can improve the detection rate of early triple-negative breast cancer. At the same time, RAI14 plays a more important role in chemotherapy monitoring than CA15-3 as the change in its concentration is in line with the tumor volume variation. Taken together, RAI14 is a reliable novel marker in the early diagnosis and chemotherapy monitoring of triple-negative breast cancer.

RAI14 Promotes Melanoma Progression by Regulating the FBXO32/c-MYC Pathway

Melanoma originates from the malignant transformation of melanocytes. Compared with other skin cancers, melanoma has a higher fatality rate. The 5-year survival rate of patients with early-stage primary melanoma through surgical resection can reach more than 90%. However, the 5-year survival rate of patients with metastatic melanoma is only 25%. Therefore, accurate assessment of melanoma progression is critical. Previous studies have found that Retinoic Acid Induced 14(RAI14) is critical in tumorigenesis. However, the biological function of RAI14 for the development of melanoma is unclear. In this study, RAI14 is highly expressed in melanoma and correlated with prognosis. The expression of RAI14 can affect the proliferation, migration and invasion of melanoma cells. F-Box Protein 32(FBXO32) is an E3 ubiquitin ligase of c-MYC. We found that RAI14 affects the transcriptional expression of FBXO32 and regulates the stability of c-MYC. These results suggest that RAI14 play an important role in the growth of melanoma and is expected to be a therapeutic target for melanoma.

Epigenetic Alterations and Inflammation as Emerging Use for the Advancement of Treatment in Non-Small Cell Lung Cancer

Lung cancer remains one of the most common malignancies in the world. Nowadays, the most common lung cancer is non-small cell lung cancer (NSCLC), namely, adenocarcinoma, squamous cell carcinoma, and large cell lung carcinoma. Epigenetic alterations that refer to DNA methylation, histone modifications, and noncoding RNA expression, are now suggested to drive the genesis and development of NSCLC. Additionally, inflammation-related tumorigenesis also plays a vital role in cancer research and efforts have been attempted to reverse such condition. During the occurrence and development of inflammatory diseases, the immune component of inflammation may cause epigenetic changes, but it is not always certain whether the immune component itself or the stimulated host cells cause epigenetic changes. Moreover, the links between epigenetic alterations and cancer-related inflammation and their influences on the human cancer are not clear so far. Therefore, the connection between epigenetic drivers, inflammation, and NSCLC will be summarized. Investigation on such topic is most likely to shed light on the molecular and immunological mechanisms of epigenetic and inflammatory factors and promote the application of epigenetics in the innovative diagnostic and therapeutic strategies for NSCLC.

High Expression of RAI14 in Triple-Negative Breast Cancer Participates in Immune Recruitment and Implies Poor Prognosis Through Bioinformatics Analyses

Objective: The purpose of current research is to explore the function of retinoic acid-induced protein 14 (RAI14), being a reciprocal protein of carboxypeptidase N1 (CPN1), and as a biomarker for prognosis and immunoregulatory effects in breast cancers.

Methods: Interacting proteins of CPN1 were characterized by co-immunoprecipitation (CO-IP) and mass spectrometry. We evaluated RAI14 expression and related clinical prognosis based on bioinformatics methods. The level of relevance between RAI14 and infiltrating immune cells biomarkers was investigated by using TIMER and certificated by immunohistochemical staining and cytology experiments.

Results: RAI14 is an interacting protein of CPN1. Higher RAI14 expression in TNBC was significantly correlated with poor prognosis in TNBC, especially (RFS: HR = 1.32, p = 0.015; DFS: HR = 1.18, p = 0.035). The estrogen receptor (ER), P53 status, and histological types and triple-negative status were observed and correlated with RAI14 expression. Moreover, the level of RAI14 was positive in relation with the expression of CD163 (M2 macrophages marker, r = 0.393, p = 1.89e-06) and PD-1 (T-cell exhaustion marker, r = 0.626, p = 4.82e-03), indicating RAI14 levels were mainly related to M2 macrophages and T-cell exhaustion infiltration in TNBC. Furthermore, CPN1 overexpression was accompanied by RAI14 and PD-L1 upregulation, and a correlation was found among them.

Conclusions: RAI14 is a potential downstream molecule of CPN1, which may be a potential prognostic biomarker and identification of an immunosuppressive tumor microenvironment in TNBC.

Identification of Four Enhancer-Associated Genes as Risk Signature for Diffuse Glioma Patients

The abnormal expressions of enhancer-associated genes have been reported to be correlated with poor prognosis of tumors, including glioblastoma (GBM). The objective of the current study is to predict prognosis by identifying enhancer-associated genes (EAGs). The profiles of genome-wide expressions of low-grade glioma (LGG) and GBM tissues in The Cancer Genome Atlas (TCGA) dataset were obtained to explore the expression patterns of EAGs in diffuse glioma. The capacity of prognosis prediction was validated by Rembrandt and GSE16011. Moreover, qPCR was utilized to confirm the effect of JQ1 and THZ1 on the EAGs. We detected 35 differentially expressed EAGs, which were predictive of overall survival. These candidate EAGs were then subjected to the multivariate cox regression analysis and were further scoped down to four signature genes, including TRAM2, SMAGP, KDELC2, and C7ORF25. A total of 662 patients were then stratified according to the expression levels of these four signature genes. The high-risk group accounted for poorer prognosis based on the Rembrandt and GSE16011 databases. The results of qPCR also demonstrated that the expression of the four EAGs could be abolished by JQ1 (bromodomain inhibitor) and THZ1 (CDK7 inhibitor) treatment. Our study not only highlights the potential role of EAGs, which can be used to improve clinical prognosis prediction in patients with diffuse glioma, but also sheds light on the specific biomarkers and therapeutic targets for diffuse glioma patients.

A systematic dissection of the epigenomic heterogeneity of lung adenocarcinoma reveals two different subclasses with distinct prognosis and core regulatory networks

BACKGROUND

Lung adenocarcinoma (LUAD) is a highly malignant and heterogeneous tumor that involves various oncogenic genetic alterations. Epigenetic processes play important roles in lung cancer development. However, the variation in enhancer and super-enhancer landscapes of LUAD patients remains largely unknown. To provide an in-depth understanding of the epigenomic heterogeneity of LUAD, we investigate the H3K27ac histone modification profiles of tumors and adjacent normal lung tissues from 42 LUAD patients and explore the role of epigenetic alterations in LUAD progression.

RESULTS

A high intertumoral epigenetic heterogeneity is observed across the LUAD H3K27ac profiles. We quantitatively model the intertumoral variability of H3K27ac levels at proximal gene promoters and distal enhancers and propose a new epigenetic classification of LUAD patients. Our classification defines two LUAD subgroups which are highly related to histological subtypes. Group II patients have significantly worse prognosis than group I, which is further confirmed in the public TCGA-LUAD cohort. Differential RNA-seq analysis between group I and group II groups reveals that those genes upregulated in group II group tend to promote cell proliferation and induce cell de-differentiation. We construct the gene co-expression networks and identify group-specific core regulators. Most of these core regulators are linked with group-specific regulatory elements, such as super-enhancers. We further show that CLU is regulated by 3 group I-specific core regulators and works as a novel tumor suppressor in LUAD.

CONCLUSIONS

Our study systematically characterizes the epigenetic alterations during LUAD progression and provides a new classification model that is helpful for predicting patient prognosis.

RAI14 Is a Prognostic Biomarker and Correlated With Immune Cell Infiltrates in Gastric Cancer

OBJECTIVE

To analyze the expression and clinical significance of retinoic acid-induced protein 14 (RAI14) in gastric cancer and its relationship with immune cell infiltration by mining databases such as Oncomine, TIMER, UALCAN, and Kaplan Meier Plotter.

METHODS

RAI14 expression in various cancer types was analyzed using the Oncomine and TIMER databases. We used the Kaplan-Meier Plotter and UALCAN databases to evaluate the impact of RAI14 on clinicopathological parameters in gastric cancer. The correlation between RAI14 expression and immune cell invasion was studied using TIMER. TIMER was also used to analyze the correlation between RAI14 expression and marker levels of tumor-infiltrating immune cells.

RESULTS

High RAI14 expression in gastric cancer was significantly associated with poor overall survival (OS; hazard ratio [HR] = 1.82, 95% confidence interval [CI] = 1.53-2.15, P < 0.001) and poor progression-free survival (PFS; HR = 2.16, 95% CI = 1.77-2.65, P < 0.001). Furthermore, high RAI14 expression was significantly associated with poor prognosis of patients with stage 2-4 gastric cancer, but not with OS and PFS of stage 1 patients (OS P = 0.17; PFS P = 0.09), and patients with stage N0 PFS had nothing to do (PFS P = 0.238). RAI14 expression was positively correlated with the infiltration levels of monocytes, tumor-associated macrophages, macrophages, neutrophils, and Treg cells in gastric cancer. Besides, RAI14 expression was closely related to various marker genes in immune cells.

CONCLUSION

RAI14 is highly expressed in gastric cancer, and its expression level is correlated with the prognosis of patients with gastric cancer. RAI14 plays also an important role in the recruitment and regulation of infiltrating immune cells and is, thus, expected to become a target for the optimal treatment of gastric cancer.

RAI14 silencing suppresses progression of esophageal cancer via the STAT3 pathway

Esophageal cancer (EC) is an aggressive malignancy that has an unclear molecular pathogenesis. Although retinoic acid induced 14 (RAI14) is involved in various cancer processes, the relationship between EC and RAI14 has not been elucidated. Our study reported the oncogenic function of RAI14 and its underlying mechanisms in EC. The Cancer Genome Atlas (TCGA) database revealed that RAI14 was upregulated in EC, and this upregulation correlated with T stage, histologic grade, and poor clinical prognosis. RAI14 was evaluated in EC cell lines, and the overexpression of RAI14 promoted cell proliferation, migration, and invasion in vitro. Conversely, RAI14 knockdown induced apoptosis and cell cycle arrest. RAI14 activated STAT3, upregulated Mcl-1 and cyclin D1, and inhibited cleaved caspase-3. Inhibition of STAT3 restored the oncogenic effect of RAI14, and RAI14 silencing restrained tumor growth and the protein level of Ki67 in vivo. Our results suggest that RAI14 regulates the STAT3 pathway and acts as an oncogene during EC progression.

Retinoic Acids in the Treatment of Most Lethal Solid Cancers

Although the use of oral administration of pharmacological all-trans retinoic acid (ATRA) concentration in acute promyelocytic leukaemia (APL) patients was approved for over 20 years and used as standard therapy still to date, the same use in solid cancers is still controversial. In the present review the literature about the top five lethal solid cancers (lung, stomach, liver, breast, and colon cancer), as defined by The Global Cancer Observatory of World Health Organization, and retinoic acids (ATRA, 9-cis retinoic acid, and 13-cis retinoic acid, RA) was compared. The action of retinoic acids in inhibiting the cell proliferation was found in several cell pathways and compartments: from membrane and cytoplasmic signaling, to metabolic enzymes, to gene expression. However, in parallel in the most aggressive phenotypes several escape routes have evolved conferring retinoic acids-resistance. The comparison between different solid cancer types pointed out that for some cancer types several information are still lacking. Moreover, even though some pathways and escape routes are the same between the cancer types, sometimes they can differently respond to retinoic acid therapy, so that generalization cannot be made. Further studies on molecular pathways are needed to perform combinatorial trials that allow overcoming retinoic acids resistance.

Downregulation of RAI14 inhibits the proliferation and invasion of breast cancer cells

Retinoic acid-induced 14 (RAI14) is involved in the development of different tumor types, however, its expression and biological function in breast cancer are yet unknown. In the current study, we demonstrated that RAI14 was highly expressed in breast cancer. The high expression of RAI14 is positively correlated with the malignant progression of breast cancer and suggests a worse prognosis. Further, we found that knockdown RAI14 inhibits the proliferation, migration and invasion of breast cancer cells by regulating cell cycle and EMT through Akt/Cyclin D1, MMP2, MMP9 and ZEB1/E-cadhrin/Vimentin pathway. These findings revealed a novel function for RAI14 in breast cancer progression and suggest that RAI14 may become a promising diagnostic and therapeutic target for breast cancer.

Differentiated super-enhancers in lung cancer cells

Super-enhancers (SEs) are regulatory elements with enriched accumulation of key transcription factors. Few studies were done investigating SEs in lung cancers. Here we analyzed epigenetic profiling data to identify SEs in lung cancer cell lines. Enhancers were classified as SEs and typical enhancers (TEs). Most of the TEs were overlapped between normal cell and cancer cells. A great portion of SEs were differentiated comparing these cells. Analysis of GO terms associated with SEs revealed SE remodeling (lost on some sites while gain on others) between normal and lung cancer cells. By comparing the average number of SEs in each GO term in cancer cells with the number in control cells, surprisingly, no GO terms with significantly increased SE number in cancer condition were observed. On the contrary, in aspects such as "cell-cell adhesion", "receptor activity" and "negative regulation of canonical Wnt signaling pathway", the related SEs were significantly reduced in cancer cells. These findings suggest that in lung cancer, cells may not gain decisive gene expression in the related aspect, instead, they may have lost control of the fateful genes. Taken together, our work with the usability of omics data identified SEs in lung cancer cells and further showed cancer-specific features of SE-related terms.

Knockdown of RAI14 suppresses the progression of gastric cancer

Background

Retinoic acid induced 14 (RAI14), also known as NORPEG, is reported as being deregulated in non-small-cell lung cancer, together with having involvement in its cell proliferation as a super enhancer related gene.

Purpose

The objective of this study was to investigate the role of RAI14 in the progression and metastasis of gastric cancer and explore the associated mechanism.

Materials and methods

GEPIA database was used to analyze the expression of RAI14 in gastric cancer. MNK45 and AGS cells were transfected with siRNA-RAI14 to block the expression of RAI14. Cell Counting Kit 8 and colony formation assays were performed to measure cell proliferation. Cell migration and invasion capacities was examined by transwell assay. Apoptosis rate was detected using flow cytometry, and the protein levels of apoptosis-related proteins was determined using Western blot assay. Reverse-transcription PCR assay was used to detect the expressions of RAB31.

Results

Gene expression profiling interactive analysis revealed that RAI14 was substantially upregu-lated in gastric cancer and higher expression of RAI14 was associated with worse prognosis. We also observed that the knockdown of RAI14 by siRNA-RAI14 transfection suppressed growth capacity of MKN45 and AGS cells. Also, RAI14 knockdown inhibited migration and invasion of MKN45 and AGS cells in vitro. Moreover, RAI14 knockdown was observed to accelerate cell apoptosis via down-regulation of Bcl-2 and upregulation of Bax in MKN45 and AGS cells. Furthermore, downregulation of RAI14 inhibited the activation of Akt pathway, and activation of Akt by IGF-1 could restore the reduced proliferation induced by RAI14 knockdown. In addition, we found that RAI14 had a positive correlation with the RAB31 in gastric cancer by GEPIA reverse-transcription PCR and Western blot assays, and the reduced proliferation caused by RAI14 knockdown was restored by RAB31.

Conclusion

RAI14 knockdown inhibited proliferation, migration and invasion and promoted apoptosis by downregulating the Akt pathway in gastric cancer cells, and RAB31 might be a downstream target gene of RAI14, providing a novel sight into the molecular mechanism of RAI14 and a potential target for gastric cancer treatment.

High Expression of Retinoic Acid Induced 14 (RAI14) in Gastric Cancer and Its Prognostic Value

Background

To explore the expression level of retinoic acid induced 14 (RAI14) in gastric cancer (GC) patients and its potentially clinical prognostic value.

Material/Methods

Initially, The Cancer Genome Atlas (TCGA) and Oncomine databases were mined to examine the differential expression levels and clinical prognostic significance of RAI14 mRNA in GC patients. Subsequently, 68 cases of GC and paired adjacent normal tissues were collected retrospectively, and the expression level of RAI14 protein was detected by immunohistochemical staining. In addition, Kaplan-Meier univariate and Cox multivariate survival analyses were used to verify the correlation between RAI14 expression and clinicopathological parameters in GC patients and its clinical prognostic significance.

Results

TCGA and GEO (from Oncomine database) data mining results found that RAI14 mRNA level was remarkably higher in GC than normal gastric tissues (All P<0.05). Besides, immunohistochemical results detected that RAI14 protein level in GC was dramatically higher (P=0.004) compared to that in the matched normal tissues. Moreover, TCGA database and Kaplan-Meier Plotter mining results showed that compared to those with RAI14 low mRNA expression levels, GC patients with RAI14 high mRNA expression levels had remarkably lower time of both overall survival and disease-free survival (All P<0.05). Additionally, based on the immunohistochemical results, Kaplan-Meier univariate and Cox multivariate survival analyses indicated that high expression of RAI14 was the only independent predictor of unfavorable prognosis in patients with gastric cancer (P=0.000).

Conclusions

RAI14 was highly expressed in GC, and the high expression of RAI14 could be an independent predictor of poor prognosis in GC patients.