Tissue-specific gene expression of head and neck squamous cell carcinoma in vivo by complementary DNA microarray analysis

A Personalized Genomics Approach of the Prostate Cancer

Decades of research identified genomic similarities among prostate cancer patients and proposed general solutions for diagnostic and treatments. However, each human is a dynamic unique with never repeatable transcriptomic topology and no gene therapy is good for everybody. Therefore, we propose the Genomic Fabric Paradigm (GFP) as a personalized alternative to the biomarkers approach. Here, GFP is applied to three (one primary—“A”, and two secondary—“B” & “C”) cancer nodules and the surrounding normal tissue (“N”) from a surgically removed prostate tumor. GFP proved for the first time that, in addition to the expression levels, cancer alters also the cellular control of the gene expression fluctuations and remodels their networking. Substantial differences among the profiled regions were found in the pathways of P53-signaling, apoptosis, prostate cancer, block of differentiation, evading apoptosis, immortality, insensitivity to anti-growth signals, proliferation, resistance to chemotherapy, and sustained angiogenesis. ENTPD2, AP5M1 BAIAP2L1, and TOR1A were identified as the master regulators of the “A”, “B”, “C”, and “N” regions, and potential consequences of ENTPD2 manipulation were analyzed. The study shows that GFP can fully characterize the transcriptomic complexity of a heterogeneous prostate tumor and identify the most influential genes in each cancer nodule.

The MAL Protein, an Integral Component of Specialized Membranes, in Normal Cells and Cancer

The MAL gene encodes a 17-kDa protein containing four putative transmembrane segments whose expression is restricted to human T cells, polarized epithelial cells and myelin-forming cells. The MAL protein has two unusual biochemical features. First, it has lipid-like properties that qualify it as a member of the group of proteolipid proteins. Second, it partitions selectively into detergent-insoluble membranes, which are known to be enriched in condensed cell membranes, consistent with MAL being distributed in highly ordered membranes in the cell. Since its original description more than thirty years ago, a large body of evidence has accumulated supporting a role of MAL in specialized membranes in all the cell types in which it is expressed. Here, we review the structure, expression and biochemical characteristics of MAL, and discuss the association of MAL with raft membranes and the function of MAL in polarized epithelial cells, T lymphocytes, and myelin-forming cells. The evidence that MAL is a putative receptor of the epsilon toxin of Clostridium perfringens, the expression of MAL in lymphomas, the hypermethylation of the MAL gene and subsequent loss of MAL expression in carcinomas are also presented. We propose a model of MAL as the organizer of specialized condensed membranes to make them functional, discuss the role of MAL as a tumor suppressor in carcinomas, consider its potential use as a cancer biomarker, and summarize the directions for future research.

Collagen Type XI Alpha 1 (COL11A1): A Novel Biomarker and a Key Player in Cancer

Collagen type XI alpha 1 (COL11A1), one of the three alpha chains of type XI collagen, is crucial for bone development and collagen fiber assembly. Interestingly, COL11A1 expression is increased in several cancers and high levels of COL11A1 are often associated with poor survival, chemoresistance, and recurrence. This review will discuss the recent discoveries in the biological functions of COL11A1 in cancer. COL11A1 is predominantly expressed and secreted by a subset of cancer-associated fibroblasts, modulating tumor-stroma interaction and mechanical properties of extracellular matrix. COL11A1 also promotes cancer cell migration, metastasis, and therapy resistance by activating pro-survival pathways and modulating tumor metabolic phenotype. Several inhibitors that are currently being tested in clinical trials for cancer or used in clinic for other diseases, can be potentially used to target COL11A1 signaling. Collectively, this review underscores the role of COL11A1 as a promising biomarker and a key player in cancer.

Differential gene expression analysis of HNSCC tumors deciphered tobacco dependent and independent molecular signatures

Head and neck cancer is the sixth most common cancer worldwide, with tobacco as the leading cause. However, it is increasing in non-tobacco users also, hence limiting our understanding of its underlying molecular mechanisms. RNA-seq analysis of cancers has proven as effective tool in understanding disease etiology. In the present study, RNA-Seq of 86 matched Tumor/Normal pairs, of tobacco smoking (TOB) and non-smokers (N-TOB) HNSCC samples analyzed, followed by validation on 375 similar datasets. Total 2194 and 2073 differentially expressed genes were identified in TOB and N-TOB tumors, respectively. GO analysis found muscle contraction as the most enriched biological process in both TOB and N-TOB tumors. Pathway analysis identified muscle contraction and salivary secretion pathways enriched in both categories, whereas calcium signaling and neuroactive ligand-receptor pathway was more enriched in TOB and N-TOB tumors respectively. Network analysis identified muscle development related genes as hub node i. e. ACTN2, MYL2 and TTN in both TOB and N-TOB tumors, whereas EGFR and MYH6, depicts specific role in TOB and N-TOB tumors. Additionally, we found enriched gene networks possibly be regulated by tumor suppressor miRNAs such as hsa-miR-29/a/b/c, hsa-miR-26b-5p etc., suggestive to be key riboswitches in regulatory cascade of HNSCC. Interestingly, three genes PKLR, CST1 and C17orf77 found to show opposite regulation in each category, hence suggested to be key genes in separating TOB from N-TOB tumors. Our investigation identified key genes involved in important pathways implicated in tobacco dependent and independent carcinogenesis hence may help in designing precise HNSCC diagnostics and therapeutics strategies.

A Transcriptional Sequencing Analysis of Islet Stellate Cell and Pancreatic Stellate Cell

BACKGROUND

Our previous studies have shown that islet stellate cell (ISC), similar to pancreatic stellate cell (PSC) in phenotype and biological characters, may be responsible for the islet fibrosis in type 2 diabetes. To further identify the differences between PSC and ISC and for better understanding of the physiological function of ISC, we employed genome-wide transcriptional analysis on the PSCs and ISCs of Wistar rats.

METHOD

PSCs and ISCs from each rat were primarily cultured at the same condition. Genome-wide transcriptional sequence of stellate cells was generated. The identified differentially expressed genes were validated using RT-PCR.

RESULTS

32 significant differentially expressed genes between PSCs and ISCs were identified. Moreover, collagen type 11a1 (COL11A1), was found to be expressed 2.91-fold higher in ISCs compared with PSCs, indicating that COL11A1 might be a potential key gene modulating the differences between PSC and ISC.

CONCLUSIONS

Our study identified and validated the differences between PSC and ISC in genome-wide transcriptional scale, confirming the assumption that ISC and PSC are similar other than identical. Moreover, our data might be instrumental for further investigation of ISC and islet fibrosis, and some differential expressed genes may provide an insight into new therapeutic targets for type 2 diabetes.

COL11A1/(pro)collagen 11A1 expression is a remarkable biomarker of human invasive carcinoma-associated stromal cells and carcinoma progression

The COL11A1 human gene codes for the α1 chain of procollagen 11A1 and mature collagen 11A1, an extracellular minor fibrillar collagen. Under regular conditions, this gene and its derived products are mainly expressed by chondrocytes and mesenchymal stem cells as well as osteoblasts. Normal epithelial cells and quiescent fibroblasts from diverse locations do not express them. Mesenchyme-derived tumors and related conditions, such as scleroderma and keloids, are positive for COL11A1/(pro)collagen 11A1 expression, as well as high-grade human gliomas/glioblastomas. This expression is almost absent in benign pathological processes such as breast hyperplasia, sclerosing adenosis, idiopathic pulmonary fibrosis, cirrhosis, pancreatitis, diverticulitis, and inflammatory bowel disease. By contrast, COL11A1/(pro)collagen 11A1 is highly expressed by activated stromal cells of the desmoplastic reaction of different human invasive carcinomas, and this expression is correlated with carcinoma aggressiveness and progression, and lymph node metastasis. COL11A1 upregulation has been shown to be associated to TGF-β1, Wnt, and Hh signaling pathways, which are especially active in cancer-associated stromal cells. At the front of invasive carcinomas, neoplastic epithelial cells, putatively undergoing epithelial-to-mesenchymal transition, and carcinoma-derived cells with highly metastatic capabilities, can express COL11A1. Thus, in established metastases, the expression of COL11A1/(pro)collagen 11A1 could rely on both the metastatic epithelial cells and/or the accompanying activated stromal cells. COL11A1/(pro)collagen 11A1 expression is a remarkable biomarker of human carcinoma-associated stromal cells and carcinoma progression.

Tumor matrix protein collagen XIα1 in cancer

The extracellular matrix is increasingly recognized as an essential player in cancer development and progression. Collagens are one of the most important components of the extracellular matrix, and have themselves been implicated in many aspects of neoplastic transformation. Collagen XI is a minor collagen whose main physiologic function is to regulate the diameter of major collagen fibrils. The α1 chain of collagen XI (colXIα1) has known pathogenic roles in several musculoskeletal disorders. Recent research has highlighted the importance of colXIα1 in many types of cancer, including its roles in metastasis, angiogenesis, and drug resistance, as well as its potential utility in screening tests and as a therapeutic target. High levels of colXIα1 overexpression have been reported in multiple expression profile studies examining differences between cancerous and normal tissue, and between beginning and advanced stage cancer. Its expression has been linked to poor progression-free and overall survival. The consistency of these data across cancer types is particularly striking, including colorectal, ovarian, breast, head and neck, lung, and brain cancers. This review discusses the role of collagen XIα1 in cancer and its potential as a target for cancer therapy.

Validation of COL11A1/procollagen 11A1 expression in TGF-β1-activated immortalised human mesenchymal cells and in stromal cells of human colon adenocarcinoma

Background

The human COL11A1 gene has been shown to be up-regulated in stromal cells of colorectal tumours, but, so far, the immunodetection of procollagen 11A1, the primary protein product of COL11A1, has not been studied in detail in human colon adenocarcinomas. Some cancer-associated stromal cells seem to be derived from bone marrow mesenchymal cells; the expression of the COL11A1 gene and the parallel immunodetection of procollagen 11A1 have not been evaluated in these latter cells, either.

Methods

We used quantitative RT-PCR and/or immunocytochemistry to study the expression of DES/desmin, VIM/vimentin, ACTA2/αSMA (alpha smooth muscle actin) and COL11A1/procollagen 11A1 in HCT 116 human colorectal adenocarcinoma cells, in immortalised human bone marrow mesenchymal cells and in human colon adenocarcinoma-derived cultured stromal cells. The immunodetection of procollagen 11A1 was performed with the new recently described DMTX1/1E8.33 mouse monoclonal antibody. Human colon adenocarcinomas and non-malignant colon tissues were evaluated by immunohistochemistry as well. Statistical associations were sought between anti-procollagen 11A1 immunoscoring and patient clinicopathological features.

Results

Procollagen 11A1 was immunodetected in human bone marrow mesenchymal cells and in human colon adenocarcinoma-associated spindle-shaped stromal cells but not in colon epithelial or stromal cells of the normal colon. This immunodetection paralleled, in both kinds of cells, that of the other mesenchymal-related biomarkers studied: vimentin and alpha smooth muscle actin, but not desmin. Thus, procollagen 11A1⁺ adenocarcinoma-associated stromal cells are similar to “activated myofibroblasts”. In the series of human colon adenocarcinomas here studied, a high procollagen 11A1 expression was associated with nodal involvement (p = 0.05), the development of distant metastases (p = 0.017), and advanced Dukes stages (p = 0.047).

Conclusion

The immunodetection of procollagen 11A1 in cancer-associated stromal cells could be a useful biomarker for human colon adenocarcinoma characterisation.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2407-14-867) contains supplementary material, which is available to authorized users.

Collagen type XI α1 facilitates head and neck squamous cell cancer growth and invasion

BACKGROUND

Although it is well established that the extracellular matrix affects tumour progression, not much is known about the various components and their effect on head and neck squamous cell carcinoma (HNSCC) progression. Levels of collagen type XI α1 (colXIα1), a minor fibrillar collagen, have been shown to be increased in tumour compared with normal tissue in several cancers, including colorectal, breast, and non-small cell lung cancer. Currently, the functional significance of colXIα1 is not understood.

METHODS

We examined the expression levels of colXIα1 mRNA and elucidated the functional role of colXIα1 in HNSCC. Cell proliferation, invasion, and migration were examined with and without colXIα1 knockdown with siRNA in HNSCC cells.

RESULTS

Our data demonstrate that colXIα1 expression is increased in tumour samples compared with levels in normal adjacent tissue in 16/23 HNSCC patients. In addition, colα11 is increased in HNSCC cell lines compared with normal immortalised epithelial cells and is increased in tumour-derived fibroblasts compared with normal fibroblasts. Using an siRNA approach, we demonstrate that colXIα1 contributes to proliferation, migration, and invasion of HNSCC.

CONCLUSION

Our cumulative findings suggest that colXIα1 contributes to HNSCC tumorigenesis and may serve as a potential therapeutic target.

Gene expression profiling for the purposes of biomarker discovery in oral potentially malignant lesions: a systematic review

Early and accurate diagnosis of oral potentially malignant lesions (OPML) is of critical importance in preventing malignant transformation. Although histopathological interpretation of the degree of epithelial dysplasia is considered the gold standard for diagnosis, this method is subjective and lacks sensitivity. Therefore, many attempts have been made to identify objective molecular biomarkers to improve diagnosis. Microarray technology has the advantage of screening the expression of the whole genome making it one of the best tools for searching for novel biomarkers. However, microarray studies of OPMLs are limited, and no review has been published to highlight and compare their findings. In this paper, we systematically review all studies that have incorporated microarray analyses in the investigation of gene profile alterations in OPMLs and suggest a set of commonly dysregulated genes across multiple gene expression profile studies. This list of common genes may help focus selection of markers for further analysis regarding their importance in the diagnosis and prognosis of OPMLs.

Overexpression of COL11A1 by cancer-associated fibroblasts: clinical relevance of a stromal marker in pancreatic cancer

BACKGROUND

The collagen11A1 (COL11A1) gene is overexpressed in pancreatic cancer. The expression of COL11A1 protein could be involved in desmoplastic events in pancreatic cancer, but an antibody that specifically stains the COL11A1 protein is not currently available.

METHODS AND FINDINGS

A total of 54 pancreatic ductal adenocarcinomas (PDAC), 23 chronic pancreatitis (CP) samples, and cultured peritumoral stromal cells of PDAC (passages 3-6) were studied. Normal human pancreas tissue samples were obtained through a cadaveric organ donation program. 1) Validation of COL11A1 gene overexpression by q-RT-PCR.

FINDINGS

the expression of COL11A1 gene is significantly increased in PDAC samples vs. normal and CP samples. 2) Analysis of COL11A1 by immunohistochemistry using highly specific anti-proCOL11A1 antibodies.

FINDINGS

anti-proCOL11A1 stains stromal cells/cancer-associated fibroblasts (CAFs) of PDAC but it does not stain chronic benign condition (chronic pancreatitis) stromal cells, epithelial cells, or normal fibroblasts. 3) Evaluation of the discrimination ability of the antibody.

FINDINGS

anti-proCOL11A1 immunostaining accurately discriminates between PDAC and CP (AUC 0.936, 95% CI 0.851, 0.981). 4) Phenotypic characterization of proCOL11A1+ stromal cells co-staining with mesenchymal, epithelial and stellate cell markers on pancreatic tissue samples and cultured peritumoral pancreatic cancer stromal cells.

FINDINGS

ProCOL11A1+ cells present co-staining with mesenchymal, stellate and epithelial markers (EMT phenotype) in different proportions.

CONCLUSIONS/SIGNIFICANCE

Detection of proCOL11A1 through immunostaining with this newly-developed antibody allows for a highly accurate distinction between PDAC and CP. Unlike other available antibodies commonly used to detect CAFs, anti-proCOL11A1 is negative in stromal cells of the normal pancreas and almost absent in benign inflammation. These results strongly suggest that proCOL11A1 is a specific marker for CAFs, and thus, anti-proCOL11A1 is a powerful new tool for cancer research and clinical diagnostics.

Expression, purification and molecular analysis of the human ZNF706 protein

Background

The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3).

Findings

ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis.

Conclusions

We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis.

Analysis of RNA from brush cytology detects changes in B2M, CYP1B1 and KRT17 levels with OSCC in tobacco users

RNA expression analysis of oral keratinocytes can be used to detect early oral cancer, but a limitation is the inability to obtain high quality RNA from oral tissue without using biopsies. While oral cytology cell samples can be obtained from patients in a minimally invasive manner, they have not been validated for quantitative analysis of RNA expression. Earlier we showed RNA from brush cytology of hamster Oral Squamous Cell Carcinoma (OSCC) demonstrated differential expression of B2M and CYP1B1 using real time RT-PCR in a dibenz[a,I]pyrene, tobacco carcinogen, induced model of this disease. Here we show reproducibility of this approach to measuring gene expression in humans. Cytology brush samples from 12 tobacco and betel related OSCC and 17 nonmalignant oral lesions revealed B2M mRNA was enriched in tumor samples while CYP1B1 mRNA was reduced, similar to what was seen in the model system. Additionally, we showed that KRT17 mRNA, a gene linked to OSCC in another brush cytology study, was also enriched in OSCC versus nonmalignant lesions, again supporting the promise of using RNA from brush oral cytology to reproducibly monitor oral gene expression.

Transcriptional activities of histone H3, cyclin D1 and claudin 7 encoding genes in laryngeal cancer

Uncontrolled proliferation and a decrease in cell-cell adhesion are one of the most important characteristics of malignancy. Determination of replication-dependent histone H3 can be applied as a proliferative marker. Cyclin D1 (CCND1) regulates the cell cycle by participating in the control of the G1/S phase transition. Claudins (CLDN) are components of tight junctions and may play an essential role in the loss of tissue cohesion. The aim of the study was to assess the mRNA expression of histone H3, cyclin D1, and claudin 7 genes in laryngeal squamous cell carcinoma (LSCC) and adjacent nonneoplastic tissues. The study group consisted of 32 patients with LSCC. Adjacent nonneoplastic tissues of incision lines were used as controls. Quantification of H3, CCND1 and CLDN7 mRNAs was performed by the use of real-time QRT-PCR assay. Molecular analysis showed a significantly higher expression of CCND1 (P = 0.0001; Wilcoxon test) and H3 (P = 0.0141) genes in tumor tissues than in surrounding nonneoplastic tissues. On the contrary, transcriptional activity of claudin 7 gene was higher in histologically normal tissues; however, this difference was not statistically significant (P = 0.1499). The data obtained indicate that laryngeal cancer is characterized by high proliferative potential mediated by increase in cyclin D1 and H3 mRNAs expression.

Clinical relevance of nine transcriptional molecular markers for the diagnosis of head and neck squamous cell carcinoma in tissue and saliva rinse

BACKGROUND

Analysis of 23 published transcriptome studies allowed us to identify nine genes displaying frequent alterations in HNSCC (FN1, MMP1, PLAU, SPARC, IL1RN, KRT4, KRT13, MAL, and TGM3). We aimed to independently confirm these dysregulations and to identify potential relationships with clinical data for diagnostic, staging and prognostic purposes either at the tissue level or in saliva rinse.

METHODS

For a period of two years, we systematically collected tumor tissue, normal matched mucosa and saliva of patients diagnosed with primary untreated HNSCC. Expression levels of the nine genes of interest were measured by RT-qPCR in tumor and healthy matched mucosa from 46 patients. MMP1 expression level was measured by RT-qPCR in the salivary rinse of 51 HNSCC patients and 18 control cases.

RESULTS

Dysregulation of the nine genes was confirmed by the Wilcoxon test. IL1RN, MAL and MMP1 were the most efficient diagnostic markers of HNSCC, with ROC AUC > 0.95 and both sensitivity and specificity above 91%. No clinically relevant correlation was found between gene expression level in tumor and T stage, N stage, tumor grade, global survival or disease-free survival. Our preliminary results suggests that with 100% specificity, MMP1 detection in saliva rinse is potentially useful for non invasive diagnosis of HNSCC of the oral cavity or oropharynx, but technical improvement is needed since sensitivity was only 20%.

CONCLUSION

IL1RN, MAL and MMP1 are prospective tumor diagnostic markers for HNSCC. MMP1 overexpression is the most promising marker, and its detection could help identify tumor cells in tissue or saliva.

T-lymphocyte maturation-associated protein gene as a candidate metastasis suppressor for head and neck squamous cell carcinomas

Previous gene expression profiles revealed the T-lymphocyte maturation-associated protein (MAL) gene as being frequently downregulated in head and neck cancer. To define the relationship between the MAL gene and the metastatic process, we evaluated the expression status of the gene in matched primary and metastatic tumors of head and neck cancer by semiquantitative reverse transcription-polymerase chain reaction. Furthermore, we aimed to identify potential genetic and epigenetic mechanisms associated with downregulation of MAL, including loss of heterozygosity (LOH), mutation, and hypermethylation. Thirty-five cell lines of University of Turko squamous cell carcinoma (UT-SCC) series derived from head and neck cancer, including nine pairs from matched primary and metastatic tumors, and 30 pairs of matched primary and metastatic tumor samples were analyzed. Twenty out of 35 (57%) cell lines showed downregulation of MAL expression, whereas no expression was found in 10 cell lines (29%). Considering matched primary and metastatic tumor-derived cell-line pairs, four pairs showed decreased expression only in metastasis-derived cells compared with their primary counterparts. Expression analysis of 21 tissue samples demonstrated decreased or no expression of MAL mRNA in 43% of metastatic tumors compared with matched primary tumors. Relating to mechanisms of downregulation, LOH was observed in 30% of primary tumors and 38% of their metastatic counterparts by a MAL-specific microsatellite marker. Furthermore, we found restoration of MAL mRNA after treatment with demethylating agent (5-aza-2'-deoxycytidine) in 9 (45%) out of 20 cell lines. No mutation was found in UT-SCC cell lines. In conclusion, our findings indicate selective downregulation of MAL expression in metastatic cells, suggesting the MAL gene as a new metastasis-suppressor candidate for head and neck cancer. LOH and hypermethylation appeared to be important mechanisms for inactivation of MAL function.

Drug-eluting polymer implants in cancer therapy

BACKGROUND

Drug-eluting polymer implants present a compelling parenteral route of administration for cancer chemotherapy. With potential for minimally invasive, image-guided placement and highly localized drug release, these delivery systems are playing an increasingly important role in cancer management. This is particularly true as the use of labile proteins and other bioactive molecules is likely to increase in the upcoming years.

OBJECTIVE

In this review, we present the current trends in the application of Pre-formed and in situ-forming systems as drug-eluting implants for cancer chemotherapy.

METHODS

We outline the clinically available options as well as up-and-coming technologies and their advantages and challenges. We also describe ongoing related innovations with image-guided drug delivery, mathematical modeling of implanted delivery systems and implanted drug delivery in combination with other therapies.

RESULTS/CONCLUSION

Whether used alone or combined with other minimally invasive procedures, drug-eluting polymeric implants will play a significant role in the future of cancer management.

Searching for molecular markers in head and neck squamous cell carcinomas (HNSCC) by statistical and bioinformatic analysis of larynx-derived SAGE libraries

BACKGROUND

Head and neck squamous cell carcinoma (HNSCC) is one of the most common malignancies in humans. The average 5-year survival rate is one of the lowest among aggressive cancers, showing no significant improvement in recent years. When detected early, HNSCC has a good prognosis, but most patients present metastatic disease at the time of diagnosis, which significantly reduces survival rate. Despite extensive research, no molecular markers are currently available for diagnostic or prognostic purposes.

METHODS

Aiming to identify differentially-expressed genes involved in laryngeal squamous cell carcinoma (LSCC) development and progression, we generated individual Serial Analysis of Gene Expression (SAGE) libraries from a metastatic and non-metastatic larynx carcinoma, as well as from a normal larynx mucosa sample. Approximately 54,000 unique tags were sequenced in three libraries.

RESULTS

Statistical data analysis identified a subset of 1,216 differentially expressed tags between tumor and normal libraries, and 894 differentially expressed tags between metastatic and non-metastatic carcinomas. Three genes displaying differential regulation, one down-regulated (KRT31) and two up-regulated (BST2, MFAP2), as well as one with a non-significant differential expression pattern (GNA15) in our SAGE data were selected for real-time polymerase chain reaction (PCR) in a set of HNSCC samples. Consistent with our statistical analysis, quantitative PCR confirmed the upregulation of BST2 and MFAP2 and the downregulation of KRT31 when samples of HNSCC were compared to tumor-free surgical margins. As expected, GNA15 presented a non-significant differential expression pattern when tumor samples were compared to normal tissues.

CONCLUSION

To the best of our knowledge, this is the first study reporting SAGE data in head and neck squamous cell tumors. Statistical analysis was effective in identifying differentially expressed genes reportedly involved in cancer development. The differential expression of a subset of genes was confirmed in additional larynx carcinoma samples and in carcinomas from a distinct head and neck subsite. This result suggests the existence of potential common biomarkers for prognosis and targeted-therapy development in this heterogeneous type of tumor.

Differentially expressed serum haptoglobin alpha chain isoforms with potential application for diagnosis of head and neck cancer

BACKGROUND

The discovery of molecular biomarkers is crucial to the diagnosis of head and neck squamous cell cancer (HNSCC).

METHODS

Proteins from pre-surgery serum samples of patients with HNSCC and healthy individuals were analyzed by 2-dimensional gel electrophoresis (2-DE) using a 17 cm-long immobilized pH gradient gel strip (large gel). The differentially expressed protein spots were detected by statistical analysis. Because 2 haptoglobin (Hp) alpha chains were found to be differentially expressed, the genotypic distribution of Hp alpha chains in patients and healthy individuals was assayed by polymerase chain reaction. The protein expression levels of Hp alpha chains in individuals carrying different Hp alleles were analyzed by 2-DE with a small gel.

RESULTS

Two isoforms of haptoglobin alpha2 chain (Hp alpha2) in patients' sera were found from 2-DE analysis to be up-regulated, while the isoforms of haptoglobin alpha1 chain (Hp alpha1) were significantly down-regulated. Apolipoprotein AII and 2 isoforms of apolipoprotein CII were also differentially expressed in the sera of patients with HNSCC. The Hp alpha2 chain was significantly up-regulated in the patients carrying at least one haptoglobin 2 allele, according to the spot intensities from scanned images of small-gel 2-DE.

CONCLUSIONS

The expression pattern of seven differentially expressed polypeptides and the up-regulation of Hp alpha2 in individuals with the Hp 2 allele are potential biomarkers.

Institutional and Comprehensive Review of Laryngeal Leukoplakia

Objectives:

The nature and interpretation of vocal fold leukoplakia has been limited by small study sizes. The present study reviewed institutional data and the published literature to better characterize vocal fold leukoplakia.

Methods:

At our institution, the histopathology, age, and malignant conversion rates of 136 patients (208 biopsies) with vocal fold leukoplakia from 1990 to 2005 were reviewed.

Results:

No dysplasia (ND), mild and/or moderate dysplasia (MM), and severe dysplasia and/or squamous cell carcinoma in situ (SS) was identified in, respectively, 110 of 208 (53%), 38 of 208 (18%), and 31 of 208 (15%) biopsies. After 30 months (range, 1 to 134 months), malignant transformation was observed in 8 patients on subsequent biopsies. Additionally, a literature search was performed from 1960 to 2005 for the medical subject headings (MeSH) premalignant laryngeal lesions, laryngeal dysplasia, laryngeal leukoplakia, vocal cord dysplasia, and hyperkeratosis of the larynx. Fifteen reports were included for review. When these were combined with our institutional data, 1,173 of 2,188 biopsies (53.6%) revealed ND. Mild and/or moderate dysplasia and SS were present in 717 of 2,140 (33.5%) and 375 of 2,471 (15.2%) biopsies, respectively. Squamous cell carcinoma developed in 52 of 1,388 (3.7%), 83 of 824 (10.1%), and 56 of 310 (18.1%) patients whose initial biopsies demonstrated ND, MM, or SS.

Conclusions:

More than half of the reported leukoplakia lesions with biopsies showed ND. However, even lesions characterized as ND were associated with an increased risk of development of squamous cell carcinoma. Importantly, the risk of developing malignancy appears to correlate with the severity of dysplasia present on initial biopsy. Because clinical examination does not accurately predict the risk of malignancy, future studies, including genomic evaluation of this lesion, may be necessary to further characterize its biologic behavior.

Metastasis of squamous cell carcinoma of the oral tongue

Squamous cell carcinoma of the oral tongue (SCCOT) is one of the most prevalent tumors of the head and neck region. Despite advances in treatment, the survival of patients with SCCOT has not significantly improved over the past several decades. Most frequently, treatment failure takes the form of local and regional recurrences, but as disease control in these areas improves, SCCOT treatment failures are occurring more often as distant metastasis. The presence of cervical lymph node metastasis is the most reliable adverse prognostic factor in patients with SCCOT, and extracapsular spread (ECS) of cervical lymph nodes metastasis is a particularly reliable predictor of regional and distant recurrence and death from disease. Decisions regarding the elective and therapeutic management of cervical lymph node metastases are made mainly on clinical grounds as we cannot always predict cervical lymph node metastasis from the size and extent of invasion of the primary tumors. Therefore, the treatment of these metastases in the management of SCCOT remains controversial. The promise of basing treatment decisions on biomarkers has yet to be fully realized because of our poor understanding of the mechanisms of regional and distant metastases of SCCOT. Here we summarize the current status of investigations of SCCOT metastases and the potential of these studies to have a positive impact on the clinical management of SCCOT in the future.

Tumor-specific genetic expression profile of metastatic oral squamous cell carcinoma

BACKGROUND

Metastasis is the most important predictor of survival in patients with oral squamous cell carcinoma (OSCC). We tested the hypothesis that there is a genetic expression profile associated with OSCC metastasis.

METHODS

We obtained samples from 6 OSCC node-positive primary tumors and their matched metastatic lymph nodes, and 5 OSCC node-negative primary tumors. Using laser capture microdissection, we isolated OSCC cells from metastatic lymph nodes and compared them with those from matched primary tumors and unmatched node-negative primary tumors using Affymetrix Human Genome Focus arrays.

RESULTS

Comparison of tumor cells from the lymph nodes with those from the unmatched, node-negative primary tumors revealed differential expression of 160 genes. Hierarchical clustering and principal component analysis using this 160-gene set showed that the node-negative samples were distinguishable from both, node-positive primary tumors and tumors in the lymph nodes. Many of the expression changes found in the metastatic cells from the lymph nodes were also found in the node-positive primary tumors. Immunohistochemical analysis for transglutaminase-3 and keratin 16 confirmed the differential genetic expression for these genes.

CONCLUSION

These preliminary results suggest that there may be a metastatic gene expression profile present in node-positive primary OSCC.

Differences in the expression of genes between normal tissue and squamous cell carcinomas of head and neck using cancer-related gene cDNA microarray

CONCLUSION

This study clearly showed the molecular characteristics of head and neck squamous cell carcinoma (HNSCC) on the basis of gene expression patterns.

OBJECTIVE

cDNA microarray has recently been shown to have the ability to represent the expression patterns of large numbers of genes from a small amount of tissue, potentially enabling definition of groups of patients with similar biological behavior of cancer. Although gene expression profiling using this technique has proven helpful for predicting the prognosis in various cancers, little is known regarding HNSCC. The aim of this study was to investigate the differences in the expression of various genes between normal tissue and cancers of patients with HNSCC by cDNA microarray.

PATIENTS AND METHODS

We extracted mRNA from 17 HNSCC patients and used cDNA microarray analysis to investigate the gene expression patterns. The present study was not designed to perform an inclusive search for genes but rather to focus on cancer-related genes.

RESULTS

Seven independent genes were found to be up-regulated in cancer tissues: matrix metalloproteinase-1, -3, and -10, interleukin-8, cadherin 3, hexabrachion, and interferon gamma-inducible protein 10. Hyaluronic acid-binding protein 2, keratin 4, and keratin 13 were categorized as down-regulated. The hierarchical clustering and dendrogram for 17 cancer samples and 425 genes could be grouped into three clusters.

Molecular markers of head and neck squamous cell carcinoma: promising signs in need of prospective evaluation

BACKGROUND

The aim of this article is to review recent developments in the biological understanding of head and neck squamous cell carcinomas.

METHODS AND RESULTS

We describe the markers according to their function and their prognostic or predictive roles. Some associations can be found between molecular markers and invasiveness, aggressiveness, degree of differentiation, and tumor stage, but only a few clinical studies have shown an impact on prognosis. In addition, despite an increasing number of articles relating to this topic, the small number of patients included in the studies reported reduces the clinical implications of these results. Few studies applied a more comprehensive molecular analysis approach, such as DNA microarrays or differential expression profiling by polymerase chain reaction, to identify a combination of markers that could be more informative than a single molecular marker.

CONCLUSION

Some progress has been made with respect to molecular markers and head and neck cancers. Translational and prospective, hypothesis-driven research must proceed with sufficient rigor to facilitate the clinical applicability of such results.

Association between high collagenase-3 expression levels and poor prognosis in patients with head and neck cancer

BACKGROUND

Squamous cell carcinoma of the head and neck (HNSCC) is a common cancer type. The ability for curative treatment with surgery and radiotherapy (RT) is usually highly dependent on tumor stage at the time of diagnosis.

METHODS

The purpose of this study was to determine whether the expression of a cancer-specific proteinase, collagenase-3 (matrix metalloproteinase-13 [MMP-13]), is associated with survival parameters in patients with HNSCC. We studied MMP-13 expression in tumors of 81 patients with stage I-IV HNSCC treated with surgery alone or in combination with radiotherapy.

RESULTS

We found a subgroup of patients with high MMP-13 expression level in their tumors (>/=90% MMP-13-positive tumor cells) associated with unfavorable prognosis (median overall survival [OS], 11.8 vs 19.6 months, p = .032). In addition, the median disease-specific survival (DSS) time was markedly reduced in this subgroup (13.8 months vs 40.7 months, p = .062). When the subgroup of patients treated with a curative intent was studied, the same association was found in OS (13.8 vs 24.6 months, p = .023) and DSS (p = .004). In addition, there was a trend for association between >/=90% MMP-13 positivity and a recurrent tumor (p = .078) in curatively treated patients.

CONCLUSIONS

The short survival time associated with high MMP-13 expression levels could not be predicted by tumor size or local lymph node invasion. These results show that a high MMP-13 expression level is associated with aggressiveness of HNSCC and may have prognostic value in patient evaluation.

Pilot Study of Mucosal Genetic Differences in Early Smokers and Nonsmokers

BACKGROUND

Global gene expression analysis is proving to be an important means of assessing human tumors and may identify key components of carcinogenesis or clinical prognosis. This technique has been successfully applied to head and neck squamous cell carcinoma (HNSCC) and thyroid carcinomas; however, little has been done to evaluate premalignant states.

METHODS

Human buccal mucosal cells were sampled from smokers and nonsmokers using a noninvasive brush technique. The method was validated by assessing the quantity and quality of RNA obtained. The purified RNA was then assayed using cDNA microarrays containing 27,323 cDNA clones to examine the buccal mucosa in these patients for differences in gene expression patterns. Using unsupervised and supervised hierarchical clustering methods, we developed a gene profile signature for an initial training set of smokers and nonsmokers and then used this to predict smoking status in a subsequent test set of subjects. Selected genes were then cross-referenced with previously published gene sets found in HNSCC identified by our group.

RESULTS

Nineteen subjects were used in this pilot analysis, 9 smokers and 10 nonsmokers. Smoking among the study group ranged from 1 to 60 pack years. RNA purified from buccal mucosal brushing demonstrated a high degree of similarity in gene expression profiles among independent samples. Through the application of supervised clustering techniques, we were able to identify 113 genes whose expression differed significantly between samples from smokers and nonsmokers (t test, P < .001). This expression signature was able to accurately predict who within the second set of subjects were smokers, with the exception of one person who had a minimal tobacco history and clustered with the nonsmokers. Cross-referencing data with that found in HNSCC, we were able to identify a tumor suppressor gene involved in the c-myc pathway (Mxi1) that was similarly under-expressed in smokers and cancer patients with progressive disease.

CONCLUSIONS

Although the sample size was small in this preliminary dataset, our analysis revealed several groups of genes that were either over- or under-expressed in the smokers and which could be used to predict smoking exposure. Many of these represent genes of possible interest as early molecular markers for head and neck carcinogenesis.

The extracellular matrix in oral squamous cell carcinoma: friend or foe?

Oral squamous cell carcinoma is a disfiguring, highly invasive and metastatic cancer. Despite advances in detection and therapy, many patients will continue to face a poor prognosis. It is well established that the predominate factor determining overall survival in patients with oral squamous cell carcinoma is lymph node involvement. Tumor growth and progression to invasive cancer requires tumor cell interactions with the extracellular matrix. An understanding of how the extracellular matrix influences tumor development and invasion is fundamental in the development of new prognostic indicators and treatment strategies for oral squamous cell carcinoma. In this review, we summarize how changes in the extracellular matrix contribute to oral cancer development.

OMICS-driven biomarker discovery in nutrition and health

While traditional nutrition research has dealt with providing nutrients to nourish populations, it nowadays focuses on improving health of individuals through diet. Modern nutritional research is aiming at health promotion and disease prevention and on performance improvement. As a consequence of these ambitious objectives, the disciplines "nutrigenetics" and "nutrigenomics" have evolved. Nutrigenetics asks the question how individual genetic disposition, manifesting as single nucleotide polymorphisms, copy-number polymorphisms and epigenetic phenomena, affects susceptibility to diet. Nutrigenomics addresses the inverse relationship, that is how diet influences gene transcription, protein expression and metabolism. A major methodological challenge and first pre-requisite of nutrigenomics is integrating genomics (gene analysis), transcriptomics (gene expression analysis), proteomics (protein expression analysis) and metabonomics (metabolite profiling) to define a "healthy" phenotype. The long-term deliverable of nutrigenomics is personalised nutrition for maintenance of individual health and prevention of disease. Transcriptomics serves to put proteomic and metabolomic markers into a larger biological perspective and is suitable for a first "round of discovery" in regulatory networks. Metabonomics is a diagnostic tool for metabolic classification of individuals. The great asset of this platform is the quantitative, non-invasive analysis of easily accessible human body fluids like urine, blood and saliva. This feature also holds true to some extent for proteomics, with the constraint that proteomics is more complex in terms of absolute number, chemical properties and dynamic range of compounds present. Apart from addressing the most complex "-ome", proteomics represents the only platform that delivers not only markers for disposition and efficacy but also targets of intervention. The Omics disciplines applied in the context of nutrition and health have the potential to deliver biomarkers for health and comfort, reveal early indicators for disease disposition, assist in differentiating dietary responders from non-responders, and, last but not least, discover bioactive, beneficial food components. This paper reviews the state-of-the-art of the three Omics platforms, discusses their implication in nutrigenomics and elaborates on applications in nutrition and health such as digestive health, allergy, diabetes and obesity, nutritional intervention and nutrient bioavailability. Proteomic developments, applications and potential in the field of nutrition have been specifically addressed in another review issued by our group.

Genomic screening of head and neck cancer and its implications for therapy planning

Despite great technical improvements in radiotherapy and surgery, survival for patients with squamous cell carcinoma of the head and neck (SCCHN) has still not improved significantly over the last decades. Management of SCCHN has mainly been based on the TNM staging and site over this time period, even though we know that there are individual differences independent of the TNM status. Individual patients with small tumors might have a poor outcome, and patients with large tumors may end up with a favorable prognosis, despite their respective TNM classification. Recent molecular studies indicate that underlying genetic abnormalities may reflect such individual differences independently of TNM status. Individualization of treatment based on such biological properties of the tumors might result in less over as well as under treatment. However, the optimal panel of biomarkers to be used for the individualization of treatment is yet to be defined. A variety of laboratory techniques have been used in studies that investigate the individual biological features, spanning from methods that screen the genome for chromosomal and genetic abnormalities, e.g., cytogenetics, CGH, SKY and cDNA micro array, to detailed studies of specific aberrations. The purpose of this review of the literature is to summarize what has been studied so far by methods for genetic screening and to relate these results to the prediction of the clinical outcome. We conclude that it is time to focus future prospective studies on how treatment can be individualized based on biomarkers in combination with the macroscopic features of SCCHN.

Molecular predictors of clinical outcome in patients with head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) involves the upper aerodigestive tract and can destroy the structure and function of organs involved in voice, speech, taste, smell and hearing, as well as vital structures necessary for survival. HNSCC has long been a treatment challenge because of the high rate of recurrences and of advanced disease at the time of diagnosis. Molecular identification of tissue biomarkers in diagnostic biopsy specimens may not only identify patients at risk for developing HNSCC but may also select patients that may benefit from more aggressive treatment modalities. Several biomarkers studied to date such as the proteins p53, cyclin D1, p16, Cox-2 enzyme, epidermal growth factor and vascular endothelial growth factor receptors, matrix metalloproteinases and the Fhit marker for genomic instability could be manipulated for the therapeutic benefit of these patients. This review presents the most updated information on molecular biomarkers with the greatest prognostic potential in HNSCC and discusses some factors that contribute to the controversy concerning their prognostic importance.

Genetic expression profiles and biologic pathway alterations in head and neck squamous cell carcinoma

Head and neck squamous cell carcinoma (HNSCC) is associated with considerable mortality and morbidity and is a major public health concern worldwide. To date, > 20 studies incorporating DNA microarray analyses have examined genomewide genetic expression changes associated with the development of HNSCC. The authors identified published reports of genetic expression profiles of HNSCC by Medline database search. They performed a review of the reports to identify genes that have been found repeatedly to exhibit substantially altered expression in HNSCC. Genes with altered expression were subsequently examined in the context of defined biologic systems with the use of GenMapp 2.0 pathway analysis software. Genes most commonly found to exhibit altered expression were those encoding for cytoskeletal and extracellular matrix proteins, inflammatory mediators, proteins involved in epidermal differentiation, and cell adhesion molecules. Results of GenMapp 2.0 analysis suggested global down-regulation of genes that encode for ribosomal proteins and enzymes in the cholesterol biosynthesis pathway; and up-regulation of genes that encode for matrix metalloproteinases and genes that bear on the inflammatory response. The review indicated that there are several genes and pathways that exhibit substantially altered expression in cancerous versus noncancerous states across studies. Further investigation into the genomic, proteomic, and functional consequences of these gene expression alterations may provide insight into the pathophysiology of HNSCC.

Gene Expression Profile in Oral Squamous Cell Carcinoma: A Pilot Study

PURPOSE

To study the gene expression profile of oral squamous cell carcinomas.

MATERIALS AND METHODS

Gene expression profile was investigated in oral squamous cell carcinomas in 5 patients using the Atlas Glass Human 3.8 I Microarray (which detects cDNA obtained from cellular total RNA) (Clontech Laboratories, Palo Alto, CA). Data were normalized by the LOWESS method. Statistical significances of deviations from a 1:1 ratio were evaluated by t tests, with P<.05.

RESULTS

Of the 3,757 genes analyzed, 322 (8.6%) were significantly overexpressed in tumoral tissue with respect to normal tissue, while 104 (2.8%) were significantly underexpressed. The affected genes fell into a wide range of functional categories.

CONCLUSION

We consider that cDNA microarrays are of clear value for investigating the biology of these tumors, and that this technology may help in the molecular classification of oral squamous cell carcinomas and in the identification of targets for gene therapy.

Bioinformatics in Otolaryngology

This article reviews the recent literature on microarray analysis, bioinformatics techniques, and genomics in relation to the study of carcinogenesis of head and neck cancers.

Profiling early head and neck cancer

Head and neck squamous-cell carcinoma (HNSCC) is the sixth most common cancer worldwide and, disappointingly, survival rates are not improving. Moreover, HNSCC has a severe impact on the quality of life of patients and survivors, and the significant morbidity subsequent to treatment often mandates long-term multidisciplinary care, which places significant financial pressures on the treating institution. Therefore, prevention and early diagnosis of high-risk pre-malignant lesions are high priorities for reducing deaths due to head and neck cancer. Recent advances have begun to elucidate the different aetiologies of HNSCCs in relation to previous pre-malignancies and to identify which pre-malignant lesions are likely to progress to malignancy.

Gene profiling in squamous cell carcinoma of the head and neck

Survival for patients with squamous cell carcinoma of the head and neck (SCCHN) is still poor, despite great technical improvements in radiotherapy and surgery. A possible explanation for this is the lack of individualization in treatment based on biological properties of the tumors, resulting in over- as well as under treatment. Management of SCCHN has mainly been based on TNM classification over the last decades. However, a large amount of studies have shown that biomarkers may add prognostic information, independently of the TNM system, indicating that biological aggressiveness is not entirely reflected by the T- and N-status of the tumor. A conclusion to draw from this is that the present standardized treatment based on macroscopic features of the tumor in many cases will result in suboptimal treatment since important underlaying genetic properties of the tumors are not taken into consideration. A variety of laboratory techniques have been used in studies that investigate the individual biological features, spanning from methods that screen the genome for chromosomal and genetic abnormalities, e.g. cytogenetics, CGH, SKY, cDNA micro array to detailed studies of specific aberrations, e.g. southern, northern and western blotting, PCR based analysis and immunohistochemistry. Dysregulation of genes involved in e.g. cell cycle control, proliferation, drug resistance, and metastasis have been linked to outcome of treatment and survival. The purpose of this review of the literature was to summarize what has been studied so far by cDNA micro array techniques with regards to genetic screening in general and biomarkers that relate to response to therapy and prediction of clinical outcome in particular. We conclude that the majority of investigations that focus on gene profiling have a descriptive character, e.g. comparisons of tumor and normal cells, metastatic and non-metastatic properties, and differences between sub-sites and grades of differentiation. There are just a handful studies that so far have investigated how gene profiling can be used to predict clinical course.

Association between gene expression profile and tumor invasion in oral squamous cell carcinoma

There are limited studies attempting to correlate the expression changes in oral squamous cell carcinoma with clinically relevant variables. We determined the gene expression profile of 16 tumor and 4 normal tissues from 16 patients by means of Affymetrix Hu133A GeneChips. The hybridized RNA was isolated from cells obtained with laser capture microdissection, then was amplified and labeled using T7 polymerase-based in vitro transcription. The expression of 53 genes was found to differ significantly (33 upregulated, 20 downregulated) in normal versus tumor tissues under two independent statistical methods. The expression changes in four selected genes (LGALS1, MMP1, LAGY, and KRT4) were confirmed with reverse transcriptase polymerase chain reaction. Two-dimensional hierarchical clustering of the 53 genes resulted in the samples clustering according to the extent of tumor infiltration: normal epithelial tissue, tumors less than or equal to 4 cm in dimension, and tumors more than 4 cm in dimension (P = 0.0014). The same pattern of clustering was also observed for the 20 downregulated genes. We did not observe any associations with lymph node metastasis (P = 0.097).