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Background Copy number variation (CNV) is a type of structural variation, which is a gain or loss event with abnormal changes in copy number. Methods to predict the pathogenicity of CNVs are required to realize the relationship between these variants and clinical phenotypes. ClassifyCNV, X-CNV, StrVCTVRE, etc. have been trained to predict the pathogenicity of CNVs, but few studies have been reported based on the deleterious significance of features. Results From single nucleotide polymorphism (SNP), gene and region dimensions, we collected 79 informative features that quantitatively describe the characteristics of CNV, such as CNV length, the number of protein genes, the number of three prime untranslated region. Then, according to the deleterious significance, we formulated quantitative methods for features, which fall into two categories: the first is variable type, including maximum, minimum and mean; the second is attribute type, which is measured by numerical sum. We used Gradient Boosted Trees (GBT) algorithm to construct dbCNV, which can be used to predict pathogenicity for five-tier classification and binary classification of CNVs. We demonstrated that the distribution of most feature values was consistent with the deleterious significance. The five-tier classification model accuracy for 0.85 and 0.79 in loss and gain CNVs, which proved that it has high discrimination power in predicting the pathogenicity of five-tier classification CNVs. The binary model achieved area under curve (AUC) values of 0.96 and 0.81 in the validation set, respectively, in gain and loss CNVs. Conclusion The performance of the dbCNV suggest that functional deleteriousness-based model of CNV is a promising approach to support the classification prediction and to further understand the pathogenic mechanism.

5-Fluorouracil (5-FU)-based chemotherapy is the first-line treatment for colorectal cancer (CRC) but is hampered by chemoresistance. Despite its impact on patient survival, the mechanism underlying chemoresistance against 5-FU remains poorly understood. Here, we identified serine hydroxymethyltransferase-2 (SHMT2) as a critical regulator of 5-FU chemoresistance in CRC. SHMT2 inhibits autophagy by binding cytosolic p53 instead of metabolism. SHMT2 prevents cytosolic p53 degradation by inhibiting the binding of p53 and HDM2. Under 5-FU treatment, SHMT2 depletion promotes autophagy and inhibits apoptosis. Autophagy inhibitors decrease low SHMT2-induced 5-FU resistance in vitro and in vivo. Finally, the lethality of 5-FU treatment to CRC cells was enhanced by treatment with the autophagy inhibitor chloroquine in patient-derived and CRC cell xenograft models. Taken together, our findings indicate that autophagy induced by low SHMT2 levels mediates 5-FU resistance in CRC. These results reveal the SHMT2–p53 interaction as a novel therapeutic target and provide a potential opportunity to reduce chemoresistance.

Hyperactivation of transforming growth factor-β (TGF-β) signaling pathway is a common feature of hepatocellular carcinoma (HCC) progression. However, the driver factors leading to enhanced TGF-β activity are not well characterized. Here, we explore the mechanisms that loss of Krüppel-like factor 4 (KLF4) exacerbates oncogenic TGF-β signaling in human HCC. The expression of KLF4 and TGF-β signaling components in primary HCC and their clinicopathologic relevance and significance was evaluated by using tissue microarray and immunohistochemistry. Cellular and molecular impacts of altered KLF4 expression and TGF-β signaling were determined using immunofluorescence, western blot, reverse-transcriptase PCR, chromatin immunoprecipitation and promoter reporter assays. Loss of KLF4 expression in primary HCC closely correlated with decreased Smad7 expression, increased p-Smad2/3 expression and independently predicts reduced overall and relapse-free survival after surgery. TGF-β signaling components were expressed in most HCC cells, and activation of TGF-β signaling promoted cell migration and invasion. Enforced KLF4 expression blocked TGF-β signal transduction and inhibited cell migration and invasion via activation of Smad7 transcription, whereas deletion of its C-terminal zinc-finger domain diminished this effect. KLF4 protein physically interacts with the Smad7 promoter. Promoter deletion and point mutation analyses revealed that a region between nucleotides -15 bp and -9 bp of the Smad7 promoter was required for the induction of Smad7 promoter activity by KLF4. Our data indicate that KLF4 suppresses oncogenic TGF-β signaling by activation of Smad7 transcription, and that loss of KLF4 expression in primary HCC may contribute to activation of oncogenic TGF-β signaling and subsequent tumor progression.

Background: Despite advancements in the diagnosis and treatment of colorectal cancer (CRC), many patients die because of tumor metastasis or recurrence. Therefore, identifying new prognostic markers and elucidating the mechanisms of CRC metastasis and recurrence will help to improve the prognosis of the disease. As dysregulation of microRNAs is strongly related to cancer progression, the aim of this study was to identify the role of miR-4775 in the prognosis of CRC patients and the underling mechanisms involved in CRC progression. Methods: qPCR and in situ hybridization were used to evaluate the expression of miR-4775 in 544 pairs of paraffin-embedded normal and CRC tissues. Kaplan-Meier analysis with the log-rank test was used for survival analyses. Immunohistochemical staining was applied to investigate the expression of miR-4775-regulated Smad7/TGF beta pathway-associated markers. In vitro and in vivo invasion and metastasis assays were used to explore the function of miR-4775 in the progression of CRC. Results: miR-4775 was identified as a high-risk factor for CRC metastasis and recurrence, with high levels predicting poor survival among the 544 studied CRC patients. Furthermore, high miR-4775 expression promoted the invasion of CRC cells as well as metastasis and the epithelial to mesenchymal transition (EMT) via Smad7-mediated activation of TGF beta signaling both in vitro and in vivo. Downregulating miR-4775 or overexpressing Smad7 reversed the tumor-promoting roles of miR-4775/ Smad7/TGF beta in vitro and in vivo. Conclusion: miR-4775 promotes CRC metastasis and recurrence in a Smad7/TGF beta signaling-dependent manner, providing a new therapeutic target for inhibiting the metastasis or recurrence of the disease. Funding Agencies|National High Technology Research and Development Program of China [SS2014AA020803]; National Natural Science Foundation of China [81220108021, 81302083, 81272750]; Natural Science Foundation of Shanghai [16ZR1427700]; Project of Shanghai Science and Technology Commission [124119a1700, 14411950502]; Project of Songjiang District [0702 N14001]

The liver transplant (LT) situation represents an attractive model for studying hepatocellular carcinoma (HCC) metastasis. Based on microarray data, we previously found that miR-126 expression was lower in tumor tissues of patients with post-LT HCC recurrence compared with non-recurrence. In this study, we examined the expression of miR-126 in HCC samples from 68 patients who had undergone LT using quantitative real-time PCR and analyzed its correlation with clinicopathological features and prognosis of patients. Furthermore, we performed experimental analyses to explore the involvement of miR-126 in HCC metastasis. We found that miR-126 levels were lower in tumor tissues of patients with post-LT HCC recurrence in comparison to patients with no-recurrence (p = 0.009). Lower expression of miR-126 in HCC was associated significantly with tumor recurrence (p = 0.011) and poor survival (p = 0.009) of patients. Functional studies indicated that ectopic expression of miR-126 significantly inhibits HCC cells migration, invasion, proliferation and colony formation in vitro, and suppresses experimental lung colonization in vivo. Our study revealed that down-regulation of miR-126 plays an important role in HCC metastasis, and suggest a potential application of miR-126 in prognosis prediction and HCC treatment.

Background Meprin displays multiple functions in both health and disease, due in part to its broad proteolytic activity. In this report, we explored the clinical significance and functional relevance of the expression of meprin-ɑ (MEP1A) in colorectal cancer (CRC). Methods The mRNA and protein expression levels of MEP1A in tumor specimens obtained from CRC patients was determined by quantitative real-time PCR and Western blot assay and comparatively paired with adjacent mucosa that presented as normal tissue. ShRNA was used to knock-down MEP1A expression in CRC cell-lines and the effects of dampened expression of MEP1A on the proliferation and invasion were determined by colony formation assays, Cell Counting Kit-8 assays and matrigel invasion assays. Moreover, nude mouse xenograft models were designed to investigate the same effect in vivo. In order to determine whether MEP1A expression correlated with CRC clinicopathologic factors and survival, immunohistochemical staining of a tissue microarray containing 88 paired CRC specimens was performed. Results In CRC, enhanced expression of MEP1A was seen. Additionally, both in vitro and in vivo, CRC cellular proliferation and invasiveness was inhibited by dampened MEP1A expression. Several parameters were associated with enhanced MEP1A expression including tumor size (P = 0.023), staging of CRC by the American Joint Committee on Cancer (AJCC) (P = 0.024), and T (P = 0.032) and N stages (P = 0.001). Moreover, the expression of MEP1A is an independent prognostic factor for overall survival in CRC (HR 3.643; 95 % CI 0.305-5.842; P = 0.007). Conclusion MEP1A was not only found to be functionally important, but it might also serve as an important and unique indicator of patient prognosis and therapeutic targeting in CRC.

Period 3 (PER3), a circadian regulation protein, influences cell cycle, growth, and differentiation. The aim of the present study was to determine whether PER3 expression is associated with colon cancer incidence and progression. PER3 expression was analyzed in the normal and cancerous tissues from patients with colon cancer by establishing a long serial analysis of gene expression (SAGE) database as well as by real-time PCR and immunohistochemistry. As compared with normal tissue, a 2.8-fold decrease in PER3 mRNA levels in colon cancerous tissue was observed. Real-time PCR analysis revealed that PER3 mRNA levels in tumor tissues were lower than in normal tissues (P

In our previous study, we have found that PLCE1 was down-regulated in sporadic colorectal cancer. But the role of PLCE1 in the incidence of colorectal cancer is still not definite. Therefore, in order to validate whether PLCE1 displays a suppressive role, in this study, we examined the expression of PLCE1 in sporadic colorectal cancer with a larger sample size and the effect of PLCE1 overexpression on cancer cell malignant degree. The expression level of PLCE1 in 50 colorectal cancers with their pair-matched normal tissues was measured by RT-PCR, Western blot, and immunohistochemistry. The effect of PLCE1 overexpression on cancer cell malignant degree was measured by MTT assay, plate colony formation assay, soft agar colony formation assay, cell cycle and apoptosis analysis, and xenograft assay. We found that PLCE1 was down-regulated in 42% (21/50) of colorectal cancer tissues compared with pair-matched normal tissues, more frequent in the poor differentiation tumor in patients under 60. Overexpression of PLCE1 significantly inhibited the proliferation of colon cancer cells and degraded its malignant degree. These results suggest that PLCE1 may be involved in the development of sporadic colorectal cancer through its inhibitory effect on cell proliferation. PLCE1 exhibits a suppressive role in incidence of colorectal cancer.

Our previous study observed that the expression of RASSF6, a member of the Ras-association domain family, was down-regulated in gastric cancer cells. The present study further investigated the clinical significance of RASSF6 in gastric cancer. Using real-time PCR, Western blot analysis, tissue microarray (TMA), and immunohistochemical staining, we evaluated RASSF6 mRNA and protein levels in tumor tissues and in the paired adjacent normal mucosa from patients with gastric cancers at different stages. RASSF6 mRNA and protein levels were decreased in gastric cancer tissues compared with the adjacent normal mucosa. Immunohistochemical detection of RASSF6 in a TMA that contained 264 paired specimens showed that a decreased cytoplasmic RASSF6 expression was significantly associated with the extent of cancer invasion, lymph node metastasis, distant metastasis, tumor histological grade, advanced clinical stage, and Ki-67 proliferative index. Moreover, RASSF6 expression in metastatic lymph nodes was lower than in the paired primary tumors. Patients with RASSF6-negative tumors had extremely higher disease recurrence rates and poorer survival than patients with RASSF6-positive tumors even after radical surgery. Stratification analysis revealed RASSF6 as an independent predictor for tumor recurrence in patients with gastric cancers irrespective of tumor stage. RASSF6 might contribute to the progression of gastric carcinogenesis and may function as a novel independent prognostic marker for the prediction of the recurrence of cancer in patients after curative operations.

Musashi1 (Msi-1), a neural RNA-binding protein, plays an important role in regulating cell differentiation in precursor cells. Recently, aberrant expression of Msi-1 has been detected in several malignancies. However, its role in the progression of colon cancer is largely unknown. We used Western blotting to examine Msi-1 protein expression in 8 cases of primary colon cancer lesions and paired normal colonic mucosa. Msi-1 expression and clinicopathological significance were determined by immunohistochemical staining in a tissue microarray (TMA) containing 203 cases of primary colon cancer paired with noncancerous tissue and 66 lymph node metastasis (LNM) tissues. RNAi was used to analyze the biological function of Msi-1 in vitro. LNM tissue exhibited a striking increase in Msi-1 expression when compared with primary colon cancer and adjacent normal mucosa (87.9% vs. 64.5% vs. 16.7%, P

Expression microarrays are widely used for investigating the candidate molecular targets in human cancer. While genome-wide expression signatures screened by gene set enrichment analysis (GSEA) were not performed in Chinese gastric cancer (GC). To gain new molecular targets for GC, GSEA analysis was performed. In the present study, GSEA were used to pick out differentially expressed gene sets of our database. Total RNA of paired tissue samples (n = 48) and a tissue microarray containing 132 paired tissues were used to further validate expression levels of INHBA and its correction with clinicopathological factors. Upregulated INHBA expression in gastric cancer was screened and further confirmed by qPCR and immunostaining analysis. Increased INHBA expression was significantly correlated with the diameter of cancer and depth of tumor invasion. Patients with higher expression levels of INHBA had a shorter disease-free survival rate. It was effective to gain new molecular targets for GC by GSEA analysis. INHBA may be a poor survival indicator of GC.

To investigate the clinicopathologic significance and predictive value of Bmi-1 expression in patients with colon cancer. Bmi-1 expression was assessed by immunohistochemistry, PCR, and western blotting in specimens from 203 patients and by immunohistochemistry in 66 specimens of lymph node metastasis (LNM). Positive staining of Bmi-1 occurred in 7.9% (16/203), 66.5% (135/203), and 86.4% (57/66) of specimens from normal tissue, colon cancer, and LNM, respectively. Staining was significantly correlated with clinical stage, depth of invasion, nodal involvement, distant metastasis, and Ki67 level. Bmi-1 was upregulated at the transcriptional and translational levels. Patients with Bmi-1-positive localized tumors had a much lower 5-year disease-free survival (relative risk 2.919, P

Insulin-like growth factor-II mRNA-binding protein 3 (IMP3) plays a vital role in carcinogenesis; however, its significance and prognostic value in colon cancer remain unclear.In this study, a tissue microarray (TMA) containing 203 samples of primary colon cancer was assessed for IMP3 expression by immunohistochemistry. The TMA included 66 lymph node metastasis (LNM) samples. The mRNA and protein expression levels of IMP3 were evaluated by reverse transcription-PCR and Western blot analysis, respectively.Cytoplasmic immunoreactivity of IMP3 was significantly higher in LNM (93%) than in primary colon cancer (65%) or normal mucosa (3.9%). Increased IMP3 levels were significantly correlated with higher clinical stage, T classification, LNM, presence of distant metastasis, and Ki-67 positivity. IMP3 was up-regulated in colon cancer compared with paired normal colonic mucosa. IMP3 expression was associated with an 11-fold increased risk of distant metastases (hazard ratio (HR) 10.7; 95% confidence interval (CI) 3.3-34.5; P0.0001). Patients with IMP3-positive localized tumors had lower 5-year disease-free survival (DFS) (HR 2.87; 95% CI 1.65-4.98; P0.0001) and overall survival (OS) (HR 4.2; 95% CI 2.51-10.17; P0.0001) than those with IMP3-negative tumors. Multivariate survival analysis showed that IMP3 was an independent prognostic marker for DFS (HR 1.92; 95% CI 1.06-3.47; P = 0.03) and OS (HR 2.37; 95% CI 1.2-4.7; P = 0.014).IMP3 may play an important role in colon cancer progression and could serve as a prognostic biomarker to identify patients at risk of developing metastasis or recurrence after colonectomy.

Background Karyopherin alpha 2 (KPNA2), a member of the karyopherin family, plays a vital role in carcinogenesis. Yet its role in colon cancer is poorly characterized. We sought to clarify the clinical significance of its dysregulated expression in human colon tumor specimens. Methods We evaluated KPNA2 mRNA and protein expression by real-time polymerase chain reaction and Western blotting in 40 primary colon cancer tissues and paired adjacent normal colon mucosa specimens. KPNA2 protein expression in colon tissue microarray of tumor and normal tissue specimens and lymph node metastasis specimens obtained from 195 colon cancer patients were analyzed immunohistochemically. The effect of KPNA2 knockdown on carcinogenesis potential of human colon cancer cells was determined using Cell Counting Kit-8 (CCK8), colony formation, cell migration, and tumorigenesis in nude mice. Results KPNA2 was expressed at higher levels in colon tumors and lymph node metastasis specimens than in normal tissues. Patients with KPNA2-positive tumors were significantly correlated with the American Joint Committee on Cancer (AJCC) stage (p = 0.01), T-classification (p = 0.018), regional lymph node metastasis (p = 0.025), distant metastasis (p = 0.014), and differentiated degree (p = 0.001). KPNA2 was shown to be an independent prognostic indicator of disease-free survival (HR 1.681; 95 % CI: 1.170–2.416; p = 0.005) and overall survival (HR 2.770; 95 % CI: 1.314–5.837; p = 0.007) for patients with colon cancer. Knockdown of KPNA2 expression inhibited colon cancer cell proliferation, colony formation, and migration. Conclusion KPNA2 might play an important role in colorectal carcinogenesis and functions as a novel prognostic indicator and a potential therapeutic target for colorectal cancer.

Cullin 4B (CUL4B), a scaffold protein of the Cullin4B-RING E3 ligase complex, functions in proteolysis. The present study aims to investigate its expression pattern and evaluate whether CUL4B expression was associated with histopathological and prognosis in the patients with colon cancer. Real-time PCR and western blot were used to identify CUL4B expression in tumor tissue and the paired adjacent normal mucosa from patients with colon cancer. Immunohistochemistry on a tissue microarray containing 203 cases of colon cancer was performed to analyze the association between CUL4B expression and clinicopathological features. Results indicated that CUL4B mRNA and protein levels in tumor tissues were both higher than that in normal mucosae (P

Homeobox (HOX) gene family is known to be classic examples of the intimate relationship between embryogenesis and tumorigenesis. However, less is known about the involvement of HOX gene family with gastric cancerogenesis. Here, we screened the expression of HOX gene family in gastric cancers and explored the relationships between them by cDNA microarray. We found several differentially expressed HOX genes in gastric cancers, especially HOXA10 (11/12) and HOXA13 (11/12) with significantly higher expression in the cancerous tissues. Furthermore, we validated HOXA13 as a novel prognostic marker in gastric cancer based on immunohistochemistry and statistical analysis. HOXA13 expression was significantly up-regulated in cancerous tissues compared with the corresponding non-cancerous mucosa (P < 0.001). Up-expression of HOXA13 was significantly correlated with T stage (P = 0.002), M stage (P = 0.024), advanced UICC stage (P < 0.001), histological differentiation (P = 0.005), and relapse (P = 0.001). Patients with positive HOXA13 expression had a obviously lower overall survival (OS) and disease-free survival (DFS) rate than patients with negative HOXA13 expression (HR 3.331, 95 % CI 1.722-6.442, P < 0.001; HR 3.289, 95 % CI 1.703-6.351, P < 0.001, respectively). Univariate and multivariate Cox analysis confirmed that HOXA13 could serve as a significant independent prognostic factor for DFS and OS. Therefore, our results indicated that several HOX genes might be closely involved in the process of the gastric tumorigenesis. Furthermore, up-expression of HOXA13 might be associated with highly aggressive phenotype of gastric cancer. HOXA13 was a significant independent prognostic factor and could serve as a putative biomarker for diagnosis and prognosis of gastric cancer.