Tumor-associated Gene Expression Research Articles

Trim family and tumor

Studies show that some Trim family proteins are associated with tumorigenesis and cancer progression. Trim members are differently expressed in various cancers including lung cancer, hepatocellular carcinoma, colon cancer, stomach cancer and breast cancer. Trim proteins are found to be involved in tumor progess by modulating the expression of tumor associated genes via several signaling pathways such as p53 and NF-κB pathway. Members of Trim family can be used as oncogenes or anti-oncogenes in the biological processes such as tumor cell proliferation, cell differentiation, cell apoptosis and metastasis. Key words: Ubiquitination; Neoplasms; Genes, p53; Tripartite-motif protein

Prognosis of lymph node-negative breast cancer: Association with clinicopathological factors and tumor associated gene expression

The aim of the present study was to investigate the association between the prognosis of lymph node-negative breast cancer patients and clinicopathological factors, as well as the association between tumor-associated gene expression and prognosis. Clinical data and survival information was collected for 341 patients with lymph node-negative breast cancer, admitted to the Cancer Hospital of the Chinese Academy of Medical Sciences (Beijing, China) from 1995 to 1999. Kaplan-Meier survival analysis and Log-rank tests were used to evaluate the association of clinical parameters and prognosis. In addition, the gene expression of HER2, TOP2A and CCND1 in patients with good [disease-free survival (DFS), ≥5 years] and poor (DFS, <5 years) prognoses was analyzed. The clinicopathological factors of the 341 lymph node-negative breast cancer patients were determined. The 5-year DFS and overall survival rate (OS) in patients >35 years old was higher as compared with those of patients under the age of 35. Tumor size significantly affected the 5-year DFS. Patients with smaller tumors (≤2 cm) had a significantly higher DFS rate as compared with patients with larger tumors (>2 cm). Estrogen receptor (ER)-positive patients had a significantly higher 5-year DFS and OS rate as compared with ER-negative patients. By contrast, there were no significant differences in the 5-year DFS and OS rates between progesterone receptor-positive and -negative patients. The 5-year DFS and OS rates were significantly higher in patients treated with adjuvant hormone therapy, as compared with patients without hormone therapy. The expression of HER2 protein was higher in patients with a poor prognosis as compared with those with a good prognosis; however, there were no differences in the protein expression of CCND1 and TOP2A between patients with a good and poor prognosis. The results of quantitative polymerase chain reaction showed that the gene expression of HER2 and CCND1 was higher in patients with a poor prognosis as compared with that in patients with a good prognosis. TOP2A gene expression was not significantly different between patients with a poor and good prognosis. The age at diagnosis, tumor size, ER status and hormone therapy were associated with prognosis in patients with lymph node-negative breast cancer. The molecular biomarker, HER2, but not CCND1 or TOP2A, may be a critical factor for predicting prognosis.

A comprehensive look at transcription factor gene expression changes in colorectal adenomas

BackgroundBiological processes are controlled by transcription networks. Expression changes of transcription factor (TF) genes in precancerous lesions are therefore crucial events in tumorigenesis. Our aim was to obtain a comprehensive picture of these changes in colorectal adenomas.MethodsUsing a 3-pronged selection procedure, we analyzed transcriptomic data on 34 human tissue samples (17 adenomas and paired samples of normal mucosa, all collected with ethics committee approval and written, informed patient consent) to identify TFs with highly significant tumor-associated gene expression changes whose potential roles in colorectal tumorigenesis have been under-researched. Microarray data were subjected to stringent statistical analysis of TF expression in tumor vs. normal tissues, MetaCore-mediated identification of TF networks displaying enrichment for genes that were differentially expressed in tumors, and a novel quantitative analysis of the publications examining the TF genes’ roles in colorectal tumorigenesis.ResultsThe 261 TF genes identified with this procedure included DACH1, which plays essential roles in the proper proliferation and differentiation of retinal and leg precursor cell populations in Drosophila melanogaster. Its possible roles in colorectal tumorigenesis are completely unknown, but it was found to be markedly overexpressed (mRNA and protein) in all colorectal adenomas and in most colorectal carcinomas. However, DACH1 expression was absent in some carcinomas, most of which were DNA mismatch-repair deficient. When networks were built using the set of TF genes identified by all three selection procedures, as well as the entire set of transcriptomic changes in adenomas, five hub genes (TGFB1, BIRC5, MYB, NR3C1, and TERT) where identified as putatively crucial components of the adenomatous transformation process.ConclusionThe transcription-regulating network of colorectal adenomas (compared with that of normal colorectal mucosa) is characterized by significantly altered expression of over 250 TF genes, many of which have never been investigated in relation to colorectal tumorigenesis.

The Homeobox Gene MEIS1 Is Methylated in BRAFp.V600E Mutated Colon Tumors

Development of colorectal cancer (CRC) can occur both via gene mutations in tumor suppressor genes and oncogenes, as well as via epigenetic changes, including DNA methylation. Site-specific methylation in CRC regulates expression of tumor-associated genes. Right-sided colon tumors more frequently have BRAF p.V600E mutations and have higher methylation grades when compared to left-sided malignancies. The aim of this study was to identify DNA methylation changes associated with BRAF p.V600E mutation status. We performed methylation profiling of colon tumor DNA, isolated from frozen sections enriched for epithelial cells by macro-dissection, and from paired healthy tissue. Single gene analyses comparing BRAF p.V600E with BRAF wild type revealed MEIS1 as the most significant differentially methylated gene (log2 fold change: 0.89, false discovery rate-adjusted P-value 2.8*10-9). This finding was validated by methylation-specific PCR that was concordant with the microarray data. Additionally, validation in an independent cohort (n=228) showed a significant association between BRAF p.V600E and MEIS1 methylation (OR: 13.0, 95% CI: 5.2 - 33.0, P<0.0001). MEIS1 methylation was associated with decreased MEIS1 gene expression in both patient samples and CRC cell lines. The same was true for gene expression of a truncated form of MEIS1, MEIS1 D27, which misses exon 8 and has a proposed tumor suppression function. To trace the origin of MEIS1 promoter methylation, 14 colorectal tumors were flow-sorted. Four out of eight BRAF p.V600E tumor epithelial fractions (50%) showed MEIS1 promoter methylation, as well as three out of eight BRAF p.V600E stromal fractions (38%). Only one out of six BRAF wild type showed MEIS1 promoter methylation in both the epithelial tumor and stromal fractions (17%). In conclusion, BRAF p.V600E colon tumors showed significant MEIS1 promoter methylation, which was associated with decreased MEIS1 gene expression.

Research Advance in Antitumor Activities of Artemisinin and Its Derivatives

Artemisinin and its derivatives are highly effective in fighting against malaria. Notably, these drugs have shown potent anti-timor activities by arresting cellular growth, enhancing apoptosis, inhibiting angiogenesis, and regulating the expression of tumor-associated genes, although the underlying mechanisms remain unclear.

Apoptin induces apoptosis in nude mice allograft model of human bladder cancer by altering multiple bladder tumor-associated gene expression profiles

Bladder cancer (BC) is one of the most common human malignancies that account for major death in the world. Apoptin that is derived from chicken anemia virus (CAV) has displayed tumor-specific cytotoxic activity in a variety of human carcinomas. However, the magical function of apoptin in bladder carcinoma cell lines has not been identified yet. In our study, we delivered apoptin into bladder-originating T24, EJ, and HCV29 cell lines by adenovirus system. The selective cytotoxic effect of apoptin was determined by cell viability assay, active caspase-3 measurement, and annexin V/PI double staining. Importantly, we have examined the differential expression patterns of tumor-associated genes including Ki67, C-erbB-2, Rb, and nm23 by flow cytometry and western blot in vitro. In an animal study, apoptin was infused into animal models by AAV system, and immunohistochemistry and quantitative real-time PCR (qRT-PCR) were employed to validate results in vivo. The results indicated that apoptin could selectively induce apoptosis in bladder tumorigenic cells coupled with tumor-specific nucleus accumulation in vitro. Interestingly, apoptin could downregulate expression levels of Ki67 and C-erbB-2 and upregulate the expression of Rb both in vitro and in vivo. Moreover, the animal models treated with AAV-apoptin have shown smaller tumor volumes and displayed better prognosis than controls. In conclusion, apoptin could selectively induce apoptosis in bladder tumor cells through altering expression profiles of tumor-associated genes.

Pathogen-driven gastrointestinal cancers: Time for a change in treatment paradigm?

The regulation of cancerous tumor development is converged upon by multiple pathways and factors. Besides environmental factors, gastrointestinal (GI) tract cancer can be caused by chronic inflammation, which is generally induced by bacteria, viruses, and parasites. The role of these inducers in cancer development, cell differentiation and transformation, cell cycle deregulation, and in the expression of tumor-associated genes cannot be ignored. Although Helicobacter pylori activates many oncogenic pathways, particularly those in gastric and colorectal cancers, the role of viruses in tumor development is also significant. Viruses possess significant oncogenic potential to interfere with normal cell cycle control and genome stability, stimulating the growth of deregulated cells. An increasing amount of recent data also implies the association of GI cancers with bacterial colonization and viruses. This review focuses on host-cell interactions that facilitate primary mechanisms of tumorigenesis and provides new insights into novel GI cancer treatments.

Phenotypic and Differentiation Stability of Human Embryonic Stem Cell-Derived Osteoblasts

Purpose: To ensure the efficiency and safety of transplanted human embryonic stem cell (hESC)-derived osteoblast-like cells (hESC-OS) for bone regeneration, this study was designed to determine the effects of continuous cell expansion on the osteoblastic differentiation stability, pluripotency, and tumorigenic potential of long-term expanded hESC-OS. Methods: hESCs manually harvested as cell aggregates or enzymatically dissociated as single cells were directly incubated in osteogenic medium and serially passaged to passage 25. Expression of osteoblast-related genes, pluripotent regulator genes, and genes related to tumorigenesis were examined at the primary passage and every 5 passages thereafter. hESC-OS were subcutaneously transplanted into nude mice for 4–24 weeks to test for teratoma formation. hESC-OS were recultivated in hESC culture conditions to evaluate the extent to which reverse differentiation back to the undifferentiated stage may occur. Results: hESC-OS derived from hESC aggregates and dissociated cells exhibited comparable osteoblast differentiation patterns. Expression levels of osteoblast-related genes reached plateau levels at passages 5–10 before declining in higher passages. Expression of tumor-associated genes was not significantly increased. Only hESC-OS at primary and first passages formed teratomas after 4 weeks in vivo. The hESC-OS were not able to revert to hESCs. Conclusions: Expanded hESC-OS demonstrated lineage-specific differentiation stability, did not maintain the pluripotency of hES cells, and were genetically stable. Thus, hESC-OS may be considered for large animal preclinical studies.

Abstract 3041: Focal amplification of chromosome 9p13 is associated with progression risk and activation of multiple oncogenes in oral precancers

Abstract Oral squamous cell carcinoma, the most common form of head and neck cancer, has a dismal five year survival rate of ∼50%. This is largely due to the late stage of diagnosis and high rates of recurrence. A better understanding of the mechanisms driving early oral tumorigenesis is an essential first step towards increasing survival rates, which have not improved in decades. Specifically, by characterizing genetic alterations in early oral premalignant lesions (OPLs), we will better understand mechanisms of disease progression and discover targets for timely therapeutic intervention that could ultimately improve oral cancer outcomes. Methods: Whole genome DNA copy number profiling was undertaken on a rare panel of OPLs with extensive longitudinal data (including known progression status for invasive disease). Recurring alterations were characterized and gene lists were refined using independent tumor-associated gene expression datasets. The functional significance of remaining gene candidates was then assessed using lentiviral shRNA and expression vectors in cell model systems. Results: Analysis of genomic data from OPLs identified four focal recurrent alterations. Three of these alterations were associated with previously identified oncogenes: cMYC, EGFR, and KRAS. The fourth was a novel 2.04 Mbp amplification at chromosome 9p13. Based on our results and publicly available gene expression data, four candidate genes were found in this region: VCP, DCTN3, STOML2, and TLN1. Independent manipulation of each of these genes in cell models revealed changes in oncogenicity (based on changes in rate of proliferation and the degree of anchorage independence), suggesting a critical role in malignant processes associated with cancer progression. Conclusion: We have shown that a recurring, focal 9p13 amplicon in OPLs is associated with progression to invasive oral cancer. Further, our data indicate that this region spans multiple genes with oncogenic potential. Taken together, our results suggest that a single amplification event may dysregulate multiple genes that drive progression to invasive oral cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3041. doi:10.1158/1538-7445.AM2011-3041

Alpha-fetoprotein and human telomerase reverse transcriptase mRNA levels in peripheral blood of patients with hepatocellular carcinoma

Tumor-associated gene expression in peripheral blood reflects the presence of circulating hepatocellular carcinoma (HCC) cells and might be associated with aggressive features of HCC. We assessed the prognostic significance of alpha-fetoprotein (AFP) and human telomerase reverse transcriptase protein (hTERT) mRNA expression in the peripheral blood of HCC patients. About 343 HCC patients, treated at the National Cancer Center, Korea, were included in this study. We measured AFP and hTERT mRNA levels in peripheral blood using quantitative real-time reverse transcription polymerase chain reaction. The association between the expression of each gene and survival was analyzed. AFP and hTERT mRNA were detected in 204 (59.5%) and 48 (14.0%) patients with HCC, respectively. The mean AFP copy number was 203 copies/microL (range 0-19992 copies/microL) and that of hTERT was 26 copies/microL (0-1711 copies/microL). AFP mRNA expression was correlated with the number of tumors (P = 0.05), but there were no significant association between hTERT expression and clinical features. There was also no relationship between overall survival and AFP (P = 0.08) or hTERT (P = 0.67) mRNA expression. This is the first report to evaluate the association between peripheral blood hTERT mRNA expression, and survival of HCC patients. The results indicate that AFP and hTERT mRNA expression in peripheral blood may not be useful HCC prognostic markers.

Carcinoma ex pleomorphic adenoma of the salivary gland: an immunohistochemical study

The proliferative activity of the tumor cells and the expression of tumor-associated genes and sex steroid hormone receptors were investigated immunohistochemically in ten cases of carcinoma ex pleomorphic adenoma (Ca-ex-PA) of the salivary glands. These were analyzed in benign and malignant components separately, and then were compared with ten cases of the other malignant tumors [adenocarcinomas, not otherwise specified (ACN) and salivary duct carcinomas (SDC)] and ten cases of pleomorphic adenomas (PA). The results obtained in this study were as follows: (1) malignant component of Ca-ex-PA showed a higher incidence of PCNA and Ki67 than benign component of Ca-ex-PA. A significant difference between benign component of Ca-ex-PA and PA was not observed. (2) A significant difference in the incidence of p53, c-erbB-2, EGFR overexpression was observed only between malignant component of Ca-ex-PA and benign component of Ca-ex-PA. (3) The incidence of PCNA, Ki67, p53, c-erbB-2 overexpression in malignant component of Ca-ex-PA showed the highest data among the four groups. These results suggest that Ca-ex-PA acquired the particular biological behavior in contrast to the other salivary neoplasms in the long-standing process while PA undergoes malignant transformation.

Effect of oxidized lipids and antioxidants on the expression of tumor-associated genes in colorectal adenoma cells

Effect of oxidized lipids and antioxidants on the expression of tumor-associated genes in colorectal adenoma cells

Glycodelin reduces carcinoma-associated gene expression in endometrial adenocarcinoma cells

Glycodelin is a major secretory glycoprotein of differentiated endometrial epithelium, rarely expressed in proliferative endometrium or endometrial cancer. We aimed to elucidate its role in growth and gene expression of endometrial adenocarcinoma cells, and hypothesized that glycodelin affects cell growth and tumor-associated gene expression. Endometrial adenocarcinoma HEC-1B cells were transfected with glycodelin cDNA in both antisense and sense orientations. Cellular morphology, cell proliferation, and gene expression were compared between native and transfected cells. Compared with native and antisense-transfected carcinoma cells, sense-transfected, glycodelin-producing carcinoma cells showed reduced proliferation, morphologic changes, and altered expression of cancer-related genes. Notably, anti-apoptotic Bcl-XL and MUC1 genes were down-regulated. Reduction by glycodelin transfection of carcinoma cell proliferation and expression of MUC1 and Bcl-XL is significant because these genes are often overexpressed in human cancers--MUC1 is linked to invasive growth and metastases, and both confer resistance to chemotherapy. These results suggest a novel mechanism whereby malignant growth of endometrial adenocarcinoma cells is regulated.

Epigenetic modification regulates both expression of tumor-associated genes and cell cycle progressing in human colon cancer cell lines: Colo-320 and SW1116.

The aim of this study is to assess the effects of DNA methylation and histone acetylation, alone or in combination, on the expression of several tumor-associated genes and cell cycle progression in two established human colon cancer cell lines: Colo-320 and SW1116. Treatments with 5-aza-2-deoxycytidine (5-aza-dC) and trichostatin A, alone or in combination, were applied respectively. The methylation status of the CDKN2A promoter was determined by methylation-specific PCR, and the acetylated status of the histones associated with the p21WAF1 and CDKN2A genes was examined by chromatin immunoprecipitation. The expression of the CDKN2A, p21WAF1, p53, p73, APC, c-myc, c-Ki-ras and survivin genes was detected by real-time RT-PCR and RT-PCR. The cell cycle profile was established by flow cytometry. We found that along with the demethylation of the CDKN2A gene promoter in both cell lines induced by 5-aza-dC alone or in combination with TSA, the expression of both CDKN2A and APC genes increased. The treatment of TSA or sodium butyrate up-regulated the transcription of p21WAF1 significantly by inducing the acetylation of histones H4 and H3, but failed to alter the acetylation level of CDKN2A-associated histones. No changes in transcription of p53, p73, c-myc, c-Ki-ras and survivin genes were observed. In addition, TSA or sodium butyrate was shown to arrest cells at the G1 phase. However, 5-aza-dC was not able to affect the cell cycle progression. In conclusion, regulation by epigenetic modification of the transcription of tumor-associated genes and the cell cycle progression in both human colon cancer cell lines Colo-320 and SW1116 is gene-specific.

Regulation of epigenetics on cell cycle progression and expression of tumor-associated genes in human colon cancer cells

Regulation of epigenetics on cell cycle progression and expression of tumor-associated genes in human colon cancer cells

Thalidomide up-regulates prostate-specific antigen secretion from LNCaP cells.

Thalidomide has been shown to have species- and metabolic-dependent antiangiogenic activity in vitro and in vivo, suggesting its potential in treating human angiogenesis-dependent pathologies such as solid tumors. Based on promising preclinical studies, thalidomide has entered phase II clinical trials for prostate, brain, breast cancer, and Kaposi's sarcoma. However, the antiangiogenic mechanism of action is largely unresolved, as are its effects on tumor-associated gene expression, cytokine secretion, etc. We have investigated the effects of thalidomide on: 1) the secretion of prostate-specific antigen (PSA) in a human androgen-dependent prostate cell line; 2) growth and viability of human prostate cells; and 3) differential gene expression profiles of thalidomide-treated vs untreated human prostate cells. A human androgen-dependent prostate carcinoma cell line (LNCaP) and a human androgen-independent prostate carcinoma cell line (PC-3) were incubated with thalidomide 0.6, 6, or 60 microg/mL for 5-6 days. Secreted PSA from LNCaP cells was measured using a commercial enzyme-linked immunosorbant assay. Cell viability studies were conducted in both LNCaP and PC-3 cells using the same thalidomide concentrations. Furthermore, the differential gene expression of thalidomide-treated LNCaP cells was compared to that of untreated control cells using a commercially available human cancer cDNA expression array system. Thalidomide-treated LNCaP cells demonstrated increased PSA/cell levels at all concentrations tested compared to untreated control cells. Thalidomide demonstrated a cytostatic effect in LNCaP cells but had no appreciable effect on PC-3 cell viability compared to untreated control cells. Comparison of cDNA expression arrays hybridized with thalidomide-treated LNCaP cDNA probes suggests that thalidomide may up- or downregulate expression of angiogenesis-related genes, i.e., vitronectin, but these differential effects require further verification. Thalidomide over a range of doses has demonstrated nontoxic, cytostatic activity in LNCaP cells and significant upregulation of LNCaP cell PSA secretion in vitro. Furthermore, preliminary data from cDNA nucleic acid arrays of thalidomide-treated LNCaP cells suggest that thalidomide upregulates a potential angiogenic modulatory protein, the vitronectin precursor, which may eventually link thalidomide's antiangiogenic activity with modulation of angiogenic vascular integrin pathways.

Tumor promoters induce a transient expression of tumor-associated genes in both basal and differentiated cells of the mouse epidermis.

The effect of tumor promoters on the in vivo expression of tumor-associated, overexpressed genes was studied. Two of the tumor-associated genes, mal 1 and mal 2 were overexpressed already in the benign papilloma stage of mouse skin carcinogenesis. Overexpression of the other two genes, mal 4 and transin, was specific for the malignant state. Treatment of the normal adult epidermis with the complete tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) and the incomplete, second-stage promoter 12-O-retinylphorbol-13-acetate (RPA) enhanced transiently the expression of the mal sequences and transin. Fractionation of the adult epidermis on Percoll gradients into basal cells and differentiated, suprabasal cells showed that expression of the mal sequences was enhanced by TPA in both basal and differentiated cells. In contrast, transin expression, which was undetectable in cells of the normal epidermis, was enhanced in only the basal cells of the TPA-treated epidermis. The non-tumor-promoting hyperplastic agent, ethylphenyl propiolate (EPP), applied to the skin at a hyperplastic dose level did not enhance the expression of the mal 4 or transin sequences in the epidermis and had only a slight enhancing effect on the levels of mal 1 and mal 2 transcripts in the epidermis. Our results suggest that the observed stimulated expression of mal 1 and mal 2 is related to proliferative processes, whereas stimulated expression of mal 4 and transin reflects tumor-promoter-specific responses.