Profiling of chromosomal changes in potentially malignant and malignant oral mucosal lesions from South and South-East Asia using array-comparative genomic hybridization.

BACKGROUND/AIM: Using array-CGH, the present study aimed to explore genome-wide profiles of chromosomal aberrations in samples of oral cancer (OC), oral submucous fibrosis (OSF) and their corresponding normal oral mucosa from Indian (n=18) and OC from Sri Lankan (n=12) patients with history of BQ use, and correlate the findings to other clinicopathological parameters. A second aim was to verify the results from the array-CGH by selecting a candidate gene, S100A14, and examine its expression and genetic polymorphisms by immunohistochemistry (IHC) and restriction fragment length polymorphism (RFLP) using samples from both populations and from multi-national archival DNA and paraffin-embedded samples of OC. RESULTS: In OC and OSF samples, 80 chromosomal regions (harboring 349 genes) were found as deleted or amplified. Out of the 349 genes, 34 (including several S100 gene family members) were found to be deleted and 30 (containing NOTCH4, TP53 and ERBB2) were found as amplified in OSF and OC cases. 285 genes (including TP53, ERBB2 and BRCA1) were found either as deleted in one population or amplified in the other. Few chromosomal alterations were found to be exclusive to either OC or OSF samples alone. IHC demonstrated down-regulation and transfer of S100A14 protein expression from membrane to cytoplasmic. RFLP showed differential distribution between Asian samples compared to African and Western samples at 461 G>A SNP. CONCLUSION: The present study provides findings on chromosomal aberrations likely to be involved in pathogenesis of OC and OSF. Findings of chromosomal changes harboring genes previously found in OC examined from Western, African and Asian populations demonstrate the importance of these changes in development of OC, and the existence of common gene-specific amplifications/deletions, regardless of source of samples or attributed risk factors. We report a down-regulation of S100A14 expression to be a significant marker in association with loss of 1q21 in 70% of OC samples.

S100A14 inhibits proliferation of oral carcinoma derived cells through G1-arrest.

Altered expression of S100A14 has been reported in various human cancers including oral squamous cell carcinomas (OSCCs). Its biological functions in carcinogenesis, however, are largely unknown. This study aimed to investigate the functional role of S100A14 in tumor cell proliferation and its possible functional association with p53. S100A14 protein was found to be gradually down-regulated during the transition from normal to dysplastic and carcinoma cells in an in vitro human OSCC progression model. When over-expressed by employing retroviral expression vector, S100A14 inhibited proliferation of CaLH3 and OSCC1, OSCC cell-lines harboring wild type (wt) p53, by inducing G1-arrest. This G1-arrest correlated with up-regulation of p21 both in the CaLH3 and OSCC1 cell-lines. shRNA mediated silencing of p53 led to partial suppression of p21 in S100A14 over-expressing CaLH3 cells, indicating that p21 up-regulation was, at least, partly dependent on p53. We further demonstrated that nuclear accumulation of p53 occurred with over-expression of S100A14 in CaLH3 cells. Our data suggest a novel role of S100A14 in OSCC cell proliferation by inducing G1-arrest and also indicate a functional link between S100A14 and the tumor suppressor protein p53.

S100A14 regulates the invasive potential of oral squamous cell carcinoma derived cell-lines in vitro by modulating expression of matrix metalloproteinases, MMP1 and MMP9.

Despite the differential expression of S100A14 (a newly identified S100 member) in various human cancers including oral squamous cell carcinomas (OSCCs), its biological role in tumour invasion has not been characterised. The aim of this study was thus to investigate the possible role of S100A14 in OSCC cell invasion. Using immunohistochemistry in normal (n=13), dysplastic (n=10) and OSCC (n=16) archival tissues, S100A14 protein was found to be down-regulated/lost with concomitant membrane to cytoplasmic translocation in OSCCs, especially in the invading tumour islands. These expression data were corroborated by profiling S100A14 mRNA expression using quantitative RT-PCR (qRT-PCR) in an in vitro human OSCC progression model consisting of cell-lines derived from normal (n=3), dysplastic (n=3) and OSCC (n=8) tissues. Employing in vitro Matrigel invasion assay, we demonstrated that retroviral vector mediated over-expression of S100A14 resulted in significant decrease in the invasive potential of OSCC derived CaLH3 and H357 cell-lines whereas siRNA mediated knockdown resulted in significant increase in the invasive potential of CaLH3 cell-line. Pathway focused PCR array and validation using qRT-PCR revealed that S100A14 over-expression was associated with down-regulation of MMP1 and MMP9 mRNAs in both CaLH3 and H357 cell-lines. Further, S100A14 over-expression was found to be associated with suppression of MMP9 gelatinolytic activity in CaLH3 cell-line. Additionally, an inverse correlation between mRNA expression levels of MMP1 and MMP9 with S100A14 was found in 19 cases of OSCCs. Collectively, these data provide the first evidence for a role of S100A14 protein in regulation of OSCC cell invasion by modulating expression of MMP1 and MMP9.

Presence of human papilloma virus, herpes simplex virus and Epstein-Barr virus DNA in oral biopsies from Sudanese patients with regard to toombak use.

Using PCR/DNA sequencing, we investigated the prevalence of human papillomavirus (HPV), herpes simplex virus (HSV) and Epstein-Barr virus (EBV) DNA in brush biopsies obtained from 150 users of Sudanese snuff (toombak) and 25 non-users of toombak in formalin-fixed paraffin-embedded tissue samples obtained from 31 patients with oral dysplasias (25 toombak users and 6 non-users), and from 217 patients with oral cancers (145 toombak users and 72 non-users). In the brush tissue samples from toombak users, HPV was detected in 60 (40%), HSV in 44 (29%) and EBV in 97 (65%) of the samples. The corresponding figures for the 25 samples from non-users were 17 (68%) positive for HPV, 6 (24%) positive for HSV and 21 (84%) for EBV. The formalin-fixed samples with oral dysplasias were all negative for HPV. In the 145 oral cancer samples from toombak users, HPV was detected in 39 (27%), HSV in 15 (10%) and EBV in 53 (37%) of the samples. The corresponding figures for the samples from non-users were 15 (21%) positive for HPV, 5 (7%) for HSV and 16 (22%) for EBV. These findings illustrate that prevalence of HSV, HPV and EBV infections are common and may influence oral health and cancer development. It is not obvious that cancer risk is increased in infected toombak users. These observations warrant further studies involving toombak-associated oral lesions, to uncover the possible mechanisms of these viral infections in the development of oral cancer, and the influence of toombak on these viruses.

Gene expression analysis by cDNA microarray in oral cancers from two Western populations.

BACKGROUND: In this work, gene expression profile was examined in 19 cases of oral cancer (OC) obtained from patients from Sweden (n=8) and UK (n=11) and the findings were tested for correlation to patient's clinicopathological data. MATERIALS AND METHODS: Following total RNA extraction, cDNA synthesis, labeling with fluorescent dyes and hybridization to the 21 k human oligonucleotide microarrays, slides were scanned and images were subjected to Genepix and J-Express analysis. Results for selected genes were validated by quantitative reverse transcriptase polymerase chain reaction (Q-RT-PCR). RESULTS: 42 genes were identified as being differentially expressed. These included 39 genes of known functions (such as fatty acid synthase (FASN), 5' nucleotidase, ecto (NT5E), high mobility group AT-hook (HMGA1), and v-fos FBJ murine osteosarcoma viral oncogene homolog (FOS)) and 3 novel genes; 26 (67%) of the 39 genes with known functions were previously reported in oral/head and neck tumors examined from other populations. Hierarchical clustering of the samples using the 42 genes demonstrated that samples mainly clustered in the same population. CONCLUSION: These results illustrate that microarrays can be used to identify distinct patterns of gene expression in different populations, but with no direct association to clinicopathological parameters. The fact that 67% of the 39 genes with known functions found in this work were previously reported in oral/head and neck tumors from other populations provides clear evidence that development of these tumors follows the same biological pathways irrespective of the source of the samples used.

Chromosomal aberrations in head and neck squamous cell carcinomas in Norwegian and Sudanese populations by array comparative genomic hybridization.

We used microarray-based comparative genomic hybridization to explore genome-wide profiles of chromosomal aberrations in 26 samples of head and neck cancers compared to their pair-wise normal controls. The samples were obtained from Sudanese (n=11) and Norwegian (n=15) patients. The findings were correlated with clinicopathological variables. We identified the amplification of 41 common chromosomal regions (harboring 149 candidate genes) and the deletion of 22 (28 candidate genes). Predominant chromosomal alterations that were observed included high-level amplification at 1q21 (harboring the S100A gene family) and 11q22 (including several MMP family members). Regions of copy number increase was also identified at 6p21 (p21), 7p12 (EGFR), 17p13 (p53) and 19p13.2 (p19INK4d), while regions showing deletion included among others 3p25.2 (RAF1) and 9p21 (p15, p16). We found genes from four common biological pathways (MAPK signaling, cytokine-cytokine receptor interaction, ECM-receptor interaction and Jak-STAT signaling) to be predominantly over-represented in areas of gain and loss. The current study provides valuable information on chromosomal aberrations likely to be involved in the pathogenesis of head and neck cancers. An increased copy number of the S100A and MMP gene family members, known to be involved in invasion and metastasis, may play an important role in the development of the tumors. Hierarchical clustering of the chromosomal alterations with clinicopathological parameters showed little correlation, suggesting an occurrence of gains/losses regardless of ethnic differences and clinicopathological status between the patients from the two countries. Our findings indicate the existence of common gene-specific amplifications/deletions in these tumors, regardless of the source of the samples or attributed carcinogenic risk factors.

Expression profile of the S100 gene family members in oral squamous cell carcinomas.

BACKGROUND: Several of the S100 gene members have been reported to be differentially expressed in many human pathological conditions, in particular, the malignancies. Identification and quantification of the differentially expressed S100 gene members in oral squamous cell carcinoma (OSCC) might facilitate their use as potential diagnostic and/or prognostic markers or targets for therapy. METHODS: we examined the expression profile of 16 members of the S100 gene family at the mRNA level by semiquantitative reverse transcription-polymerase chain reaction (sRT-PCR) in 27 cases of OSCCs/their pair-wised normal controls obtained from Sudanese patients, and confirmed the sRT-PCR results by performing quantitative real time-polymerase chain reaction (qRT-PCR) for 6 of the 16 genes examined. RESULTS: With sRT-PCR, 4 (25%; S100A4, S100A6, S100A8, S100A14) out of the 16 S100 gene members examined were found to be significantly down-regulated (P < 0.05) in the tumors compared to the normal controls. None of the S100 gene members examined were found to be significantly up-regulated in the tumors. qRT-PCR results confirmed the significant down-regulation of the S100A4, S100A6, and S100A14 genes in the tumors examined. CONCLUSION: S100 gene family members might play an important role in the pathogenesis of the OSCCs examined. Findings of the present work warrant in-depth studies of the S100 gene family members, in particular, the S100A4, S100A6, S100A8, and S100A14 to further understand their possible role(s) in OSCC tumorigenesis.

Gene expression profile of oral squamous cell carcinomas from Sri Lankan betel quid users.

Oral squamous cell carcinoma (OSCC) is one of the major health problems in Sri Lanka and the disease is associated with the habit of Betel Quid (BQ) chewing. Using 35k oligo microarrays, we analyzed the gene expression profile of 15 Sri Lankan patients diagnosed with OSCCs and pair-wised normal controls and correlated the findings with the clinicopathological data. Following the recording of the scanned array images and data analysis, results for selected candidate genes were verified using QRT-PCR. Upon analysis, a total of 263 genes [71 (27%) of unknown functions previously not reported in OSCCs and 192 (73%) of known functions] were found as differentially expressed between tumors and controls. For the genes with known functions, 66 (34%; such as COL4A1, MMP1, MMP3, PLAU, SPARC and KRT19) were previously reported in OSCC and for the remaining 126 (66%; such as CD47, APOL3, RRAGC, BPIL1 and AZGP1) this is the first report in OSCCs. Hierarchical clustering of the differentially expressed 263 genes grouped the samples into several clusters with the larger one being dominated by tumors of stage 3 and 4. Two cases (a verrucous SCC and an advanced SCC), did not cluster with any of the other samples. We found two main biological pathways (cell communication and integrin-mediated cell adhesion) and 5 gene ontology categories (transcription regulator activity, structural molecule activity, intracellular signaling, cytoskeleton and signal transduction) of relevance to the OSCCs examined. Results from the QRT-PCR verified the results from the microarray experiment. This study provides valuable information on gene expression profile of OSCCs of habitual users of BQ from Sri Lanka. Of particular interest were the list of genes of known and unknown functions and the two biological pathways that we suggest as candidate genes in oral cancers associated with BQ chewing in Southeast Asia, in particular Sri Lanka. The suggested candidate genes might be used as molecular biomarkers in the early detection of the alarming problem of OSCCs in Southeast Asia in association with BQ use. These findings provide valuable information that might help in the selection of possible biomarkers that can be used in early detection of the alarming problem of oral cancer in Southeast Asia.

Gene expression profiles of head and neck carcinomas from Sudanese and Norwegian patients reveal common biological pathways regardless of race and lifestyle.

PURPOSE: To explore possible range of gene expression profiles in head and neck squamous cell carcinomas (HNSCC) and pairwised normal controls from Sudanese (n = 72) and Norwegian (n = 45) patients using a 15K cDNA microarray and to correlate the findings with clinicopathologic variables. EXPERIMENTAL DESIGN: Samples from Sudan were grouped according to anatomic location/patients' habit of toombak (snuff) use, and 37 pools of 2 to 11 tumors matched to 37 pools of their normal controls from the same patients, respectively, were prepared. For Norway, eight pools of 3 to 11 tumors matched to eight pools of their normal controls from the same patients, respectively, were prepared according to anatomic location. Pools (n = 45) were hybridized to microarrays. For controls, 33 of the pools were hybridized against Human Reference RNA. Scanned array images were recorded, and data analysis was done in groups. For verification, results for selected genes were analyzed using quantitative real-time PCR/immunohistochemistry. RESULTS: We identified 136 genes from Sudan and 154 from Norway as differentially expressed between tumors and controls. Changes of the genes found were confirmed in >70% of the pools by hybridization against Reference RNA. Seventy-three genes and three main pathways (signal transduction, cell communication, and ligand-receptor interaction) were of relevance to the HNSCCs from both countries. Hierarchical clustering of the 73 genes identified subclasses of mixed tumors from the two populations, two independent subgroups for Norwegian tumors by their anatomic sites, and five subgroups for Sudanese tumors by their toombak habits. Quantitative real-time PCR/immunohistochemistry validated the microarray-based data. CONCLUSIONS: Differences in gene expression between tumor and nontumor tissues were identified in HNSCCs. Analysis of the two population groups revealed a common set of 73 genes within three main biological pathways. This indicates that the development of HNSCCs is mediated by similar biological pathways regardless of differences related to race, ethnicity, lifestyle, and/or exposure to environmental carcinogens. Of particular interest, however, was the valuable association of gene expression signature found with toombak use and anatomic site of the tumors.

Expression of p53, cyclin D1 and Ki-67 in pre-malignant and malignant oral lesions: association with clinicopathological parameters.

In this study, a possible association was examined between the immunoexpressions of p53, cyclin D1, Ki-67 and tobacco exposure and the risk of oral cancer (OC) in premalignant and malignant formalin-fixed, paraffin-embedded oral mucosal tissue specimens from patients from Yemen (n=24, all were pre-malignant) and India (n=16, 11 were OCs). Overexpressions of p53, cyclin D1 and Ki-67 were found in 100%, 45.5% and 80% of the OCs, compared to 65.5%, 82.8% and 85.1% of the pre-malignant lesions, respectively. In the pre-malignant lesions, a statistically significant correlation was found between histopathological grading and expressions of cyclin D1 (p = 0.001) and Ki-67 (p = 0.03), and between anatomical site and expression of Ki-67 (p = 0.01). Coexpressions of the three proteins in the cases examined was found to correlate significantly to each other (cyclin D1: p53, r = 0.48, p = 0.002; p53: Ki-67, r = 0.41, p = 0.008) except for cyclin D1: Ki-67. These findings suggest that the expressions of p53, cyclin D1 and Ki-67 might contribute to OC susceptibility in oral mucosal lesions examined from Yemen and India. The importance of the three proteins examined as biomarkers in OC and pre-malignant lesions deserves particular attention because it might offer further understanding of the development of these lesions, particularly in populations heavily exposed to tobacco habits. Abnormalities of both cyclin D1 and Ki-67 might play an important role in the development of oral pre-malignant lesions and warrant further studies. Larger studies are, therefore, necessary in the two countries to examine the role of these biomarkers in OCs and premalignant oral mucosal lesions.

Mutations of the cell cycle arrest gene p21WAF1, but not the metastasis-inducing gene S100A4, are frequent in oral squamous cell carcinomas from Sudanese toombak dippers and non-snuff-dippers from the Sudan, Scandinavia, USA and UK.

PCR and direct DNA sequencing methods were used to analyse the prevalence of mutations in exon 2 of the p21waf1 gene in 14 oral squamous cell carcinomas (OSCCs) and 8 non-malignant oral mucosal lesions from Sudanese toombak dippers. For comparison, OSCCs (14 from the Sudan, 16 from Norway, 11 from Sweden, 21 from the USA and 14 from the UK) and non-malignant oral mucosal lesions (3 from the Sudan) from non-snuff-dippers were included. The prevalence of mutations in exons 2 & 3 of the S100A4 gene were analysed in the 14 OSCCs from toombak-dippers and in 25 cases of OSCCs from the control non-snuff-dippers. Of the 14 OSCCs investigated from toombak-dippers, mutations in the p21waf1 exon 2 were found in 43% (6 out of 14), compared to 14% (2 out of 14), 22% (6 out of 27) and 14% (5 out of 35) found in those from non-snuff-dippers from the Sudan, Scandinavia and the USA/UK, respectively. OSCCs from toombak-dippers showed 13 different mutations distributed as 10 (77%) transitions and 3 (23%) transversions. OSCCs from non-snuff-dippers from the Sudan, Scandinavia, the USA and the UK showed 33 different mutations distributed as 14 (42%) transitions and 19 (58%) transversions. In the OSCCs examined, cases with mutations in the p21waf1 also had p53 gene mutations. Only exon 2 of the S100A4 gene was found mutated in 3 cases of OSCCs (one from a toombak-dipper and two from the non-snuff-dippers). The toombak-dipper OSCC had 4 mutations (one transition, 3 transversions), compared to the OSCCs from non-snuff-dippers which showed 3 mutations each (one transition, 2 transversions). All these 3 cases were negative for mutations in the p21waf1 and p53 genes. No mutations of p21waf1 or S100A4 were found in the non-malignant oral mucosal lesions from the snuff-dippers/non-dippers. These findings suggest that; (i) p21waf1, together with p53, is a target gene of oral carcinogenesis in OSCCs from toombak-dippers, with the tobacco specific nitrosamines present in toombak possibly acting as principal carcinogens in these OSCCs; (ii) findings of p21waf1 exon 2 mutations in the OSCCs unrelated to snuff use further demonstrate that this gene may play an important role during the pathogenesis of OSCCs caused by smoked tobacco use; (iii) mutations in the S100A4 gene are rare in OSCCs, but appears to be complementary to p21waf1 and p53 mutations. Since molecular analysis of OSCCs can provide clues to endogenous or environmental factors contributing to the high risk of OSCCs, further analysis of the role of the p21waf1 gene mutations as a biomarker of malignant transformation, which is linked to the p53 gene, is necessary, especially in habitual users of toombak from the Sudan.