Analysis of Salivary Mycobiome in a Cohort of Oral Squamous Cell Carcinoma Patients From Sudan Identifies Higher Salivary Carriage of Malassezia as an Independent and Favorable Predictor of Overall Survival.

Background: Microbial dysbiosis and microbiome-induced inflammation have emerged as important factors in oral squamous cell carcinoma (OSCC) tumorigenesis during the last two decades. However, the "rare biosphere" of the oral microbiome, including fungi, has been sparsely investigated. This study aimed to characterize the salivary mycobiome in a prospective Sudanese cohort of OSCC patients and to explore patterns of diversities associated with overall survival (OS). Materials and Methods: Unstimulated saliva samples (n = 72) were collected from patients diagnosed with OSCC (n = 59) and from non-OSCC control volunteers (n = 13). DNA was extracted using a combined enzymatic-mechanical extraction protocol. The salivary mycobiome was assessed using a next-generation sequencing (NGS)-based methodology by amplifying the ITS2 region. The impact of the abundance of different fungal genera on the survival of OSCC patients was analyzed using Kaplan-Meier and Cox regression survival analyses (SPPS). Results: Sixteen genera were identified exclusively in the saliva of OSCC patients. Candida, Malassezia, Saccharomyces, Aspergillus, and Cyberlindnera were the most relatively abundant fungal genera in both groups and showed higher abundance in OSCC patients. Kaplan-Meier survival analysis showed higher salivary carriage of the Candida genus significantly associated with poor OS of OSCC patients (Breslow test: p = 0.043). In contrast, the higher salivary carriage of Malassezia showed a significant association with favorable OS in OSCC patients (Breslow test: p = 0.039). The Cox proportional hazards multiple regression model was applied to adjust the salivary carriage of both Candida and Malassezia according to age (p = 0.029) and identified the genus Malassezia as an independent predictor of OS (hazard ratio = 0.383, 95% CI = 0.16-0.93, p = 0.03). Conclusion: The fungal compositional patterns in saliva from OSCC patients were different from those of individuals without OSCC. The fungal genus Malassezia was identified as a putative prognostic biomarker and therapeutic target for OSCC.

Expression of circadian clock genes and proteins in urothelial cancer is related to cancer-associated genes.

BACKGROUND: The purpose of this study was to evaluate invasive and metastatic potential of urothelial cancer by investigating differential expression of various clock genes/proteins participating in the 24 h circadian rhythms and to compare these gene expressions with transcription of other cancer-associated genes. METHODS: Twenty seven paired samples of tumour and benign tissue collected from patients who underwent cystectomy were analysed and compared to 15 samples of normal bladder tissue taken from patients who underwent cystoscopy for benign prostate hyperplasia (unrelated donors). Immunohistochemical analyses were made for clock and clock-related proteins. In addition, the gene-expression levels of 22 genes (clock genes, casein kinases, oncogenes, tumour suppressor genes and cytokeratins) were analysed by real-time quantitative PCR (qPCR). RESULTS: Considerable up- or down-regulation and altered cellular distribution of different clock proteins, a reduction of casein kinase1A1 (CSNK1A1) and increase of casein kinase alpha 1 E (CSNK1E) were found. The pattern was significantly correlated with simultaneous up-regulation of stimulatory tumour markers, and a down-regulation of several suppressor genes. The pattern was mainly seen in aneuploid high-grade cancers. Considerable alterations were also found in the neighbouring bladder mucosa. CONCLUSIONS: The close correlation between altered expression of various clock genes and common tumour markers in urothelial cancer indicates that disturbed function in the cellular clock work may be an important additional mechanism contributing to cancer progression and malignant behaviour.

Urokinase-type plasminogen activator receptor (uPAR) expression is associated with T-stage and survival in urothelial carcinoma of the bladder.

OBJECTIVES: To evaluate the expression-and localization pattern of the urokinase-type plasminogen activator receptor (uPAR), focusing on its clinical implications in patients with urothelial neoplasia of the bladder treated with radical cystectomy. uPAR is a central molecule in tissue remodeling during cancer invasion and metastasis and is an established prognostic marker in cancer. The expression and localization of uPAR and its prognostic significance is only limitedly investigated in urothelial bladder neoplasia. MATERIALS AND METHODS: The expression-and localization pattern of uPAR was investigated in formalin-fixed paraffin-embedded tumor tissue from 149 patients treated with radical cystectomy between 1988 and 2005. uPAR expression was determined by immunohistochemistry and scored as either negative or positive. Separate values were obtained for cancer cells, macrophages, and myofibroblasts at the invasive front and tumor core, respectively. Statistical analyses were performed to evaluate the association of uPAR localization and score with clinicopathologic covariates and survival. RESULTS: uPAR positivity was seen in 122/137 (89%) and 118/149 (74%) of the neoplasias at the invasive front and tumor core, respectively. uPAR was primarily expressed by myofibroblasts and macrophages in the surrounding stroma as well as some cancer cells. A significant association between uPAR positivity and T-stage as well as grade was found for all 3 cell types in tumor core (P ≤ 0.04 for all comparisons). In univariate analysis, the uPAR positive group had a shorter survival than the uPAR negative group (hazard ratio = 2.39; 95% CI: 1.15-5.01; P = 0.020). CONCLUSIONS: The expression of uPAR is a possible prognostic marker that could be useful in identification of patients with aggressive, highly invasive tumors that could benefit from additional chemotherapy or more intensive follow-up after cystectomy.

Time-dependent biological differences in molecular markers of high-grade urothelial cancer over 7 decades (ras proteins, pTEN, uPAR, PAI-1 and MMP-9).

The aim of this study was to evaluate changes and correlations between various molecular markers related to growth regulation and invasiveness in urothelial carcinomas in samples collected from 1932 to 2004. Paraffin-embedded autopsy/biopsy tissues from 144 patients were stained with antibodies against H-K-N ras proteins, pTEN protein, urokinase plasminogen activator receptor (uPAR), plasminogen activator inhibitor-1 (PAI-1) and matrix metalloproteinase-9 (MMP-9) and analyzed by in situ hybridization. Statistical analysis was performed by SPSS using cross tabulation and logistic regression. While the presence of K-ras, N-ras, PAI-1, and loss of pTEN increased over the last few decades, uPAR expression decreased during the same period. The increase in K-ras expression associated positively with the increase in expression of the other two ras proteins, H-ras and N-ras, and the loss of pTEN. A strong positive correlation was also observed between PAI-1 and uPAR, PAI-1 and previously detected markers, EGFR (epidermal growth factor receptor) and p53. Presence of uPAR was found to be positively associated with p16 expression. Multivariate analysis with clinical parameters revealed a positive correlation between PAI-1 expression and tumour grade, CkHMW (high molecular weight cytokeratin) and tumour grade, CkHMW and metastasis, EGFR and metastasis. mRNA could be detected in samples from the last 50 years while older samples were negative, indicating its complete degradation during longer storage. In conclusion, increased accumulation of K-ras, N-ras, and PAI-1 together with loss of pTEN in bladder carcinomas of grades II and III seems to be more dominant in recent times, suggesting an altered malignant potential in these neoplasms.

Immunohistochemical markers in urinary bladder carcinomas from paraffin-embedded archival tissue after storage for 5-70 years.

OBJECTIVE: To evaluate archival tissue specimens from bladder tumours and seek molecular changes in samples collected over seven decades previously, as although the frequencies of some cancer types have remained stable during the last 50 years, the incidence of others, including bladder tumours, has increased significantly, and molecular analyses of bladder cancer over periods with an increasing incidence are of interest as the findings might reflect varying external influences. MATERIALS AND METHODS: Immunohistochemical staining with the biological markers p53 protein, p16 protein, epidermal growth factor receptor (EGFR), cytokeratin 7 and high molecular weight 34betaE12 cytokeratin (HMW-cytokeratin, characteristic of basal cells) was used on archival, paraffin wax-embedded autopsy/biopsy tissue material collected from 144 patients with invasive bladder cancer (World Health Organisation grade II and III). The cases were selected from the periods 1932-48, 1950-59, 1960-70 and 1990-2004. Control immunohistochemistry was done on available normal tissue (i.e. connective and fatty tissue, heart, lungs and normal urinary bladder epithelium) obtained from the autopsies. RESULTS: The normal tissues were all largely negative for EGFR, had <1% positively stained nuclei for p53 and strong positive reactions for p16, and in epithelial tissues the two cytokeratins were detected. The positive scores for HMW-cytokeratin in the tumour tissue decreased significantly from approximately 90% to 30% over the 70 years. For p53 there was a higher fraction of positive scores (borderline significant) with time. The p16-positive tumours showed no significant variation, with the highest frequency of positive scores in recent years. Overexpression of EGFR in the tumours was significantly correlated with the occurrence of HMW-cytokeratin and decreased from approximately 85% to 65% (not significant), with the lowest frequency in the samples from 1990 to 2004. Autolysis after death or long storage periods did not compromise good quality in the histochemical analyses of the autopsy tissue. CONCLUSION: The higher frequency of HMW-cytokeratin, lower p53 accumulation and more EGFR expression in grade II and III urinary bladder carcinomas from the 1930s could indicate different phenotypes in bladder cancer during this 70-year period. The successful detection of these protein markers in old archival material allows larger retrospective studies that might increase the understanding of molecular carcinogenesis in bladder cancer.