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Supplementary Methods, Figure Legends 1-4 from Global Methylation Pattern of Genes in Androgen-Sensitive and Androgen-Independent Prostate Cancer Cells

Supplementary Figures 1-4 from Global Methylation Pattern of Genes in Androgen-Sensitive and Androgen-Independent Prostate Cancer Cells

Promoter DNA methylation of CpG islands is an important epigenetic mechanism in cancer development. We have characterized the promoter methylation profile of 82 genes in three prostate cancer cell lines (LNCaP, PC3, and DU145) and two normal prostate cell lines (RWPE1 and RWPE2). The methylation pattern was analyzed using a Panomics gene array system that consists of immobilized probes of known gene promoters on a nitrocellulose membrane. Methylation binding protein–purified methylated DNA was hybridized on the membrane and detected by the chemiluminescence method. We analyzed methylation profile in normal (RWPE1) versus cancerous cells and androgen receptor (AR)–sensitive (LNCaP) versus AR-negative cells (DU145 and PC3). Our study shows that >50% of the genes were hypermethylated in prostate cancer cells compared with 13% in normal cell lines. Among these were the tumor suppressor (RB, TMS1, DAPK, RBL1, PAX6, and FHIT), cell cycle (p27KIP1 and CDKN2A), transporters (MDR1, MLC1, and IGRP), and transcription factor (STAT1, CIITA, MYOD, and NPAT) genes. Relative methylation pattern shows that most of these genes were methylated from 5-fold to >10-fold compared with the normal prostate cells. In addition, promoter methylation was detected for the first time in target genes such as RIOK3, STAT5, CASP8, SRBC, GAGE1, and NPAT. A significant difference in methylation pattern was observed between AR-sensitive versus AR-negative cancer cells for the following genes: CASP8, GPC3, CD14, MGMT, IGRP, MDR1, CDKN2A, GATA3, and IFN. In summary, our study identified candidate genes that are methylated in prostate cancer. Mol Cancer Ther; 9(1); 33–45

Urban community parks have significant benefits for city residents, both physical and spiritual. This is especially true in developing countries, such as China. The purpose of our study is to describe the current situation of the community parks in five main districts of Jinan City while recognizing features of the community parks that influence usage patterns. Our study also means to determine the desired improvements of visitors that promote access to and use of community parks on the basis of the Chinese context. We conducted a survey among 542 community park visitors and obtained valid responses. The findings of respondents show that community parks are mostly used by people over 55 years (34.7%) and children under 10 years (23.6%). The main motives for using community parks are for exercise (24.2%) and to socialize with others (21.6%). The majority of respondents (65.7%) rated the community park as satisfactory and considered only a few improvements needed. Regarding the desired improvements, numerous respondents mentioned adding more physical training facilities (13.3%) and activity areas (7.6%), as well as emergency call buttons in areas frequented by children and older people (7.6%). Furthermore, most of the respondents (79.9%) indicated that they would like to use the community parks more frequently if there is additional progress to make the parks more attractive, cleaner, and friendlier. These results can help park designers, government agencies, and community groups to provide the planning and design strategies for community parks to promote their upgrading in China.

MicroRNAs have been proposed as novel biomarkers for the diagnosis and treatment of many types of cancer. The levels of five candidate microRNAs (miRNAs) (miR-99a-5p, miR-31-5p, miR-138-5p, miR-21-5p, and miR-375-3p) in sera from oral cancer patients and paired tumor and normal tissues were detected by real-time qPCR. The diagnostic power of these miRNAs was analyzed by receiver operating characteristic (ROC) curves. Patient-derived xenograft (PDX) models of oral cancer were established and utilized to verify the potential therapeutic effect of miR-31-5p. Candidate miRNAs were screened from our previous studies and verified in 11 paired oral cancer and adjacent normal tissues. Only serum miR-31-5p levels were significantly different between oral cancer patients and healthy controls and between pre- and postoperative patients. Based on the logistic regression model, this panel of five miRNAs distinguished oral cancer patients from healthy control, with an area under the ROC curve (AUC) of 0.776 (sensitivity = 76.8% and specificity = 73.6%). Furthermore, a miR-31-5p mimic enhanced the proliferation of normal epithelial cells, and antagomiR-31-5p inhibited the proliferation of oral cancer cells in vitro. In vivo, antagomiR-31-5p significantly inhibited tumor growth in oral cancer PDX models. Our findings suggest that circulating miR-31-5p might act as an independent biomarker for oral cancer diagnosis and could serve as a therapeutic target for oral cancer. Keywords: oral cancer, biomarker, circulating miRNA, miR-31-5p, target therapy

Oral tongue squamous cell carcinoma (TSCC) is a complex disease with extensive genetic and epigenetic defects, including microRNA deregulation. The aims of the present study were to test the feasibility of performing the microRNA profiling analysis on archived TSCC specimens and to assess the potential diagnostic utility of the identified microRNA biomarkers for the detection of TSCC. TaqMan array-based microRNA profiling analysis was performed on 10 archived TSCC samples and their matching normal tissues. A panel of 12 differentially expressed microRNAs was identified. Eight of these differentially expressed microRNAs were validated in an independent sample set. A random forest (RF) classification model was built with miR-486-3p, miR-139-5p, and miR-21, and it was able to detect TSCC with a sensitivity of 100% and a specificity of 86.7% (overall error rate = 6.7%). As such, this study demonstrated the utility of the archived clinical specimens for microRNA biomarker discovery. The feasibility of using microRNA biomarkers (miR-486-3p, miR-139-5p, and miR-21) for the detection of TSCC was confirmed.

Wounds within the oral mucosa are known to heal more rapidly than skin wounds. Recent studies suggest that differences in the microRNAome profiles may underlie the exceptional healing that occurs in oral mucosa. Here, we test whether skin wound-healing can be accelerating by increasing the levels of oral mucosa-specific microRNAs. A panel of 57 differentially expressed high expresser microRNAs were identified based on our previously published miR-seq dataset of paired skin and oral mucosal wound-healing [Sci. Rep. (2019) 9:7160]. These microRNAs were further grouped into 5 clusters based on their expression patterns, and their differential expression was confirmed by TaqMan-based quantification of LCM-captured epithelial cells from the wound edges. Of these 5 clusters, Cluster IV (consisting of 8 microRNAs, including miR-31) is most intriguing due to its tissue-specific expression pattern and temporal changes during wound-healing. The in vitro functional assays show that ectopic transfection of miR-31 consistently enhanced keratinocyte proliferation and migration. In vivo, miR-31 mimic treatment led to a statistically significant acceleration of wound closure. Our results demonstrate that wound-healing can be enhanced in skin through the overexpression of microRNAs that are highly expressed in the privileged healing response of the oral mucosa.

Oral mucosal wounds heal faster than skin wounds, yet the role of microRNAs in this differential healing has never been examined. To delineate the role of microRNAs in this site-specific injury response, we first compared the microRNAome of uninjured skin and oral mucosa in mice. A total of 53 tissue-specific microRNAs for skin and oral mucosa epithelium were identified. The most striking difference was the high abundance of miR-10a/b in skin (accounting for 21.10% of the skin microRNAome) as compared to their low expression in oral mucosa (2.87%). We further examined the dynamic changes of microRNAome throughout the time course of skin and oral mucosal wound healing. More differentially expressed microRNAs were identified in skin wounds than oral wounds (200 and 33, respectively). More specifically, miR-10a/b was significantly down-regulated in skin but not oral wounds. In contrast, up-regulation of miR-21 was observed in both skin and oral wounds. The therapeutic potential of miR-10b and miR-21 in accelerating wound closure was demonstrated in in vitro assays and in a murine skin wound model. Thus, we provided the first site-specific microRNA profile of skin and oral mucosal wound healing, and demonstrate the feasibility of a microRNA-based therapy for promoting wound closure.

The mechanisms underlying reprogramming of growth factor signaling and metabolic pathways during bone metastasis of breast cancer are not clear. The Runt-related transcription factor (Runx2) regulates cell signaling during mammary epithelial morphogenesis and promotes invasion; therefore, we investigated its role in cell growth and metabolic signaling in bone-seeking breast cancer cells. We performed systemic inoculation of control or Runx2 knockdown invasive MDA-MB-231 cells in NOD/SCID mice, and compared parental and bone-derived variants for phenotypic and molecular alterations. The Runx2 knockdown showed early (0-2 weeks) inhibition of metastatic spread but late (4-6 weeks) outgrowth, suggesting Runx2-dependent bi-phasic response and reprogramming of metastatic cells. The late-stage tumor outgrowth of bone-derived Runx2 knockdown cells was associated with increased insulin-like growth factor- 1Rβ (IGF-1Rβ) levels. Interestingly, glucose uptake and glycolysis were reduced in the bone-derived Runx2 knockdown cells that could be further reduced by extracellular-regulated protein kinase (Erk1/2) inhibition. Furthermore, the Runx2 knockdown cells displayed activation of AMP-activated protein kinase (AMPKα), the sensor of cellular metabolism. Importantly, the Runx2 knockdown in bone-derived cells resulted in increased sensitivity to both Erk1/2 inhibition and AMPKα activation by PD184161 and metformin, respectively, despite increased IGF-1Rβ and AMPKα levels. Our results reveal that Runx2 promotes metastatic spread of mammary tumor cells. The growth of late-stage tumor cells can be targeted by Runx2 knockdown in combination with Mek-Erk1/2 inhibition and metformin treatment.

The oral mucosa exhibits exceptional healing capability when compared to skin. Recent studies suggest that intrinsic differences in coding genes and regulatory small non-coding RNA (sncRNA) genes (e.g., microRNAs) may underlie the exceptional healing that occurs in the oral mucosa. Here, we investigate the role of a novel class of sncRNA&mdash, Piwi-interacting RNA (piRNA)&mdash, in the tissue-specific differential response to injury. An abundance of piRNAs was detected in both skin and oral mucosal epithelium during wound healing. The expression of PIWI genes (the obligate binding partners of piRNAs) was also detected in skin and oral wound healing. This data suggested that PIWI-piRNA machinery may serve an unknown function in the highly orchestrated wound healing process. Furthermore, unique tissue-specific piRNA profiles were obtained in the skin and oral mucosal epithelium, and substantially more changes in piRNA expression were observed during skin wound healing than oral mucosal wound healing. Thus, we present the first clue suggesting a role of piRNA in wound healing, and provide the first site-specific piRNA profile of skin and oral mucosal wound healing. These results serve as a foundation for the future investigation of the functional contribution(s) of piRNA in wound repair and tissue regeneration.

MicroRNAs are ~22 nucleotide-long noncoding RNAs influencing many cellular processes (including wound healing) by their regulatory functions on gene expression. The ability to analyze microRNA in different cells at the wound site is essential for understanding the critical role(s) of microRNA during various phases of wound healing. Laser capture micro-dissection (LCM) is an effective method to distinguish between relevant and non-relevant cells or tissues and enables the researcher to obtain homogeneous, ultra-pure samples from heterogeneous starting material. We present here our protocol for procuring epithelial cells from a mouse wound healing model using a Leica LMD7000 Laser Microdissection system, as well as the RNA isolation and downstream microRNA analysis. Using this method, researchers can selectively and routinely analyze regions of interest down to single cells to obtain results that are relevant, reproducible, and specific.

Previous evidence has indicated an increased cancer risk in individuals with diabetes mellitus (DM). The aim of this study was to investigate the relationship between DM (high glucose) and tongue squamous cell carcinoma (TSCC) and how high glucose mediated the metastatic potential of TSCC. The relationship between DM and TSCC was assessed in a retrospective study. The role and its mechanism of high glucose on the proliferation, metastatic potential of TSCC were investigated in vitro and in vivo. The prevalence rate of DM in patients with TSCC was 12.84%, which was significantly higher than that (9.7%) in the general population in China. Although no significant difference was observed in the overall survival (OS) rate, TSCC patients with DM have a 1.38-fold increase in relative risk affecting 5-year OS compared to patients without DM. High glucose enhanced the TSCC cell proliferation, migration, invasion and upregulated PKM2 (pyruvate kinase M2) expression. Whereas, these effect was abolished after knockdown of PKM2 in TSCC cells. High glucose promoted tumour growth and lung metastasis of TSCC in a DM animal model. Our results confirm DM as a risk factor for the development of TSCC. High glucose enhances the metastatic potential of TSCC through stimulation of the PKM2 pathway.

Crosstalk among mitogen-activated protein kinase (MAPK) and phosphatidyl inositol 3′ kinase (PI3K) signaling pathways integrates extracellular cues to regulate mammary epithelial cell growth, proliferation, differentiation, and survival. The runt-related transcription factor, Runx2, is expressed in normal mammary epithelium and promotes differentiation, however, its function in regulation of the MAPK and PI3K signaling crosstalk is not known. We determined the function of Runx2 expression in growth factor-mediated phosphorylation of Erk1/2 and Akt, key downstream kinases in MAPK and PI3K pathway crosstalk in MCF-10A mammary epithelial cells. The Runx2-mediated alterations in cell signaling and associated changes in phenotype were determined by real-time quantitative PCR, Western blotting, immunofluorescence, and flow cytometry approaches. The results revealed that ectopic Runx2 expression differentially downregulates the growth factor (EGF vs. IGF or insulin)-induced pErk1/2 and pAkt levels. Additionally, the ectopic Runx2 expression increases FOXO1 levels, cell cycle G1 stage and promotes survival of MCF-10A cells. Furthermore, we demonstrate that Runx2 expression increases EGF-induced phosphorylation of epidermal growth factor receptor (pEGFR) and relieves Mek/Erk-mediated negative regulation of pEGFR and pAkt levels. Altogether, our results identify functions of Runx2 in MAPK and PI3K signaling crosstalk in MCF-10A cells that could be critical in understanding the mammary epithelial cell growth and survival. J. Cell. Biochem. 115: 2208–2217, 2014. © 2014 Wiley Periodicals, Inc.

BACKGROUND Vitamin D plays a role in cancer tumorogenesis and acts through the vitamin D receptor (VDR). Although African Americans have the lowest serum vitamin D levels, supplementation has not yielded a significant improvement in cancer. Gene polymorphisms in VDR may play a role. There is a dearth of information on VDR gene polymorphisms and colorectal cancer (CRC) among under-represented ethnic groups. In this study, the authors examined whether VDR gene single nucleotide polymorphisms (SNPs) were associated with CRC in predominately African American and Hispanic study participants. METHODS Blood samples were collected from 378 participants, including a group of 78 patients with CRC (cases), a group of 230 noncancer participants without polyps (controls without polyps), and a group of 70 noncancer participants with polyps (controls with polyps). The 4 polymorphic SNPs in VDR (FokI, BsmI, TaqI, and ApaI) were assessed using the polymerase chain reaction-restriction fragment length polymorphism method. RESULTS There was a significant association of the VDR-FokI FF genotype with CRC cases (odds ratio, 2.9; P = .036) compared with the controls without polyps. The most common VDR-FokI genotype in the overall study population was the FF genotype (46%). However, upon breakdown by ethnicity, the FF genotype was the most common in African American participants (61%), and the Ff genotype was the most common in Hispanic/Latino participants (49%). When the association was assessed in a multivariate model, there was no significant association with any VDR polymorphism and CRC cases (P > .05). The other 3 polymorphic variants of VDR (BsmI, TaqI, and ApaI) were not associated with CRC. CONCLUSIONS The results from this study suggest that genetic variation of the VDR-FokI SNPs may influence CRC risk, particularly in African American cohorts. Cancer 2014;120:1387–1393. © 2014 American Cancer Society.

Background Oral tongue squamous cell carcinoma (OTSCC) is one of the most aggressive forms of head and neck/oral cancer (HNOC), and is a complex disease with extensive genetic and epigenetic defects, including microRNA deregulation. Identifying the deregulation of microRNA-mRNA regulatory modules (MRMs) is crucial for understanding the role of microRNA in OTSCC. Methods A comprehensive bioinformatics analysis was performed to identify MRMs in HNOC by examining the correlation among differentially expressed microRNA and mRNA profiling datasets and integrating with 12 different sequence-based microRNA target prediction algorithms. Confirmation experiments were performed to further assess the correlation among MRMs using OTSCC patient samples and HNOC cell lines. Functional analyses were performed to validate one of the identified MRMs: miR-21-15-Hydroxyprostaglandin Dehydrogenase (HPGD) regulatory module. Results Our bioinformatics analysis revealed 53 MRMs that are deregulated in HNOC. Four high confidence MRMs were further defined by confirmation experiments using OTSCC patient samples and HNOC cell lines, including miR-21-HPGD regulatory module. HPGD is a known anti-tumorigenic effecter, and it regulates the tumorigenic actions of Prostaglandin E2 (PGE2) by converts PGE2 to its biologically inactive metabolite. Ectopic transfection of miR-21 reduced the expression of HPGD in OTSCC cell lines, and the direct targeting of the miR-21 to the HPGD mRNA was confirmed using a luciferase reporter gene assay. The PGE2-mediated upregulation of miR-21 was also confirmed which suggested the existence of a positive feed-forward loop that involves miR-21, HPGD and PGE2 in OTSCC cells that contribute to tumorigenesis. Conclusions We identified a number of high-confidence MRMs in OTSCC, including miR-21-HPGD regulatory module, which may play an important role in the miR-21-HPGD-PGE2 feed-forward loop that contributes to tumorigenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2716-0) contains supplementary material, which is available to authorized users.

Summary Objective We previously performed a meta-analysis of microRNA profiling studies on head and neck/oral cancer (HNOC), and identified 11 consistently dysregulated microRNAs in HNOC. Here, we evaluate the diagnostic values of these microRNAs in oral tongue squamous cell carcinoma (OTSCC) using oral cytology samples. Materials and methods The levels of 11 microRNAs were assessed in 39 oral cytology samples (19 OTSCC and 20 normal subjects), and 10 paired OTSCC and adjacent normal tissues. The predictive power of these microRNAs was analyzed by receiver operating characteristic curve (ROC) and random forest (RF) model. A classification and regression trees (CART) model was generated using miR-21 and miR-375, and further validated using both independent oral cytology validation sample set (14 OTSCC and 11 normal subjects) and tissue validation sample set (12 paired OTSCC and adjacent normal tissues). Results Differential expression of miR-21, miR-100, miR-125b and miR-375 was validated in oral cytology training sample set. Based on the RF model, the combination of miR-21 and miR-375 was selected which provide best prediction of OTSCC. A CART model was constructed using miR-21 and miR-375, and was tested in both oral cytology and tissue validation sample sets. A sensitivity of 100% and specificity of 64% was achieved in distinguishing OTSCC from normal in the oral cytology validation set, and a sensitivity of 83% and specificity of 83% was achieved in the tissue validation set. Conclusion The utility of microRNA from oral cytology samples as biomarkers for OTSCC detection is successfully demonstrated in this study.

Lists of 97 differentially expressed mRNA transcripts and 9 microRNAs in OTSCC based on our previous genomic profiling studies [15, 16]. (DOC 140 kb)

Summary Objectives MicroRNA deregulation is a critical event in head and neck squamous cell carcinoma (HNSCC). Several microRNA profiling studies aimed at deciphering the microRNA signatures of HNSCC have been reported, but there tends to be poor agreement among studies. The objective of this study was to survey the published microRNA profiling studies on HNSCC, and to assess the commonly deregulated microRNAs in an independent sample set. Materials and methods Meta-analysis of 13 published microRNA profiling studies was performed to define microRNA signatures in HNSCC. Selected microRNAs (including members of miR-99 family) were evaluated in an independent set of HNSCC cases. The potential contributions of miR-99 family to the tumorigenesis of HNSCC were assessed by in vitro assays. Results We identified 67 commonly deregulated microRNAs. The up-regulation of miR-21, miR-155, miR-130b, miR-223 and miR-31, and the down-regulation of miR-100, miR-99a and miR-375 were further validated in an independent set of HNSCC cases with quantitative RT-PCR. Among these validated microRNAs, miR-100 and miR-99a belong to the miR-99 family. Our in vitro study demonstrated that restoration of miR-100 to the HNSCC cell lines suppressed cell proliferation and migration, and enhanced apoptosis. Furthermore, ectopic transfection of miR-99 family members down-regulated the expression of insulin-like growth factor 1 receptor (IGF1R) and mechanistic target of rapamycin (mTOR) genes. Conclusion In summary, we described a panel of frequently deregulated microRNAs in HNSCC, including members of miR-99 family. The deregulation of miR-99 family contributes to the tumorigenesis of HNSCC, in part by targeting IGF1R and mTOR signaling pathways.

DNA repair system plays an indispensable role in maintaining genomic integrity, and its ability to mediate and repair carcinogen-induced DNA lesion is a key determinant of susceptibility to carcinogenesis. Increasing evidence has demonstrated that reduced DNA repair capacity might play a central role in cancer development. Enhanced proliferation is a hall mark of cancer cells. In this study, we aim to test the association between reduction in DNA repair and enhancement in cell proliferation in HNSCC. The expression of base excision repair pathway genes (XRCC1 and OGG1) and a proliferation marker, Ki-67, was studied in a cohort of 50 HNSCC patients and controls, using real-time PCR in order to determine the potential prognostic significance of these factors. Using real-time PCR, statistically significant downregulation of XRCC1 (p < 0.01) and OGG1 (p < 0.04) was observed in HNC tumor samples compared to control samples. Ki-67 was also overexpressed (p < 0.03) in HNC tumor samples versus control samples. Additionally, to explore gene–gene relationship, we observed a positive Spearmen correlation between XRCC1 versus OGG1 (r = 0.554***, p < 0.0001) and a negative correlation between XRCC1 versus Ki-67 (r = −0.377**, p < 0.007) in HNC cases. OGG1 also showed negative correlation with Ki-67, but this correlation was statistically not significant. In this study, we have found that the deregulation of BER genes (XRCC1 and OGG1) in relation to excessive proliferation (as measured by proliferation marker Ki-67) may be considered as important factors in the development of head and neck cancer in Pakistani population.

Enhancer of Zeste homolog 2 (EZH2) is a critical component of the polycomb-repressive complex 2 (PRC2) that regulates many essential biological processes, including embryogenesis and many developmental events. The oncogenic role of EZH2 has recently been implicated in several cancer types. In this study, we first confirmed that the over-expression of EZH2 is a frequent event in oral tongue squamous cell carcinoma (OTSCC). We further demonstrated that EZH2 over-expression is correlated with advanced stages of the disease and is associated with lymph node metastasis. Statistical analysis revealed that EZH2 over-expression was correlated with reduced overall survival. Furthermore, over-expression of EZH2 was correlated with reduced expression of tumor suppressor gene E-cadherin. These observations were confirmed in vitro, in which knockdown of EZH2-induced E-cadherin expression and reduced cell migration and invasion. In contrast, ectopic transfection of EZH2 led to reduced E-cadherin expression and enhanced cell migration and invasion. Furthermore, EZH2 may act on cell migration in part by suppressing the E-cadherin expression. Taken together, these data suggest that EZH2 plays major roles in the progression of OTSCC, and may serve as a biomarker or therapeutic target for patients at risk of metastasis.

Down-regulation of miR-138 (microRNA-138) has been frequently observed in various cancers, including HNSCC (head and neck squamous cell carcinoma). Our previous studies suggest that down-regulation of miR-138 is associated with mesenchymal-like cell morphology and enhanced cell migration and invasion. In the present study, we demonstrated that these miR-138-induced changes were accompanied by marked reduction in E-cad (E-cadherin) expression and enhanced Vim (vimentin) expression, characteristics of EMT (epithelial–mesenchymal transition). On the basis of a combined experimental and bioinformatics analysis, we identified a number of miR-138 target genes that are associated with EMT, including VIM, ZEB2 (zinc finger E-box-binding homeobox 2) and EZH2 (enhancer of zeste homologue 2). Direct targeting of miR-138 to specific sequences located in the mRNAs of the VIM, ZEB2 and EZH2 genes was confirmed using luciferase reporter gene assays. Our functional analyses (knock-in and knock-down) demonstrated that miR-138 regulates the EMT via three distinct pathways: (i) direct targeting of VIM mRNA and controlling the expression of VIM at a post-transcriptional level, (ii) targeting the transcriptional repressors (ZEB2) which in turn regulating the transcription activity of the E-cad gene, and (iii) targeting the epigenetic regulator EZH2 which in turn modulates its gene silencing effects on the downstream genes including E-cad. These results, together with our previously observed miR-138 effects on cell migration and invasion through targeting RhoC (Rho-related GTP-binding protein C) and ROCK2 (Rho-associated, coiled-coil-containing protein kinase 2) concurrently, suggest that miR-138 is a multi-functional molecular regulator and plays major roles in EMT and in HNSCC progression.

Author(s): Mishra, Dhruva K; Wu, Yanyuan; Sarkissyan, Marianna; Sarkissyan, Suren; Chen, Zujian; Shang, Xiying; Ong, May; Heber, David; Koeffler, H Phillip; Vadgama, Jaydutt V | Abstract: BackgroundVitamin D plays a role in cancer development and acts through the vitamin D receptor (VDR). Although African-Americans have the lowest levels of serum vitamin D, there is a dearth of information on VDR gene polymorphisms and breast cancer among African-Americans and Hispanics. This study examines whether VDR gene polymorphisms are associated with breast cancer in these cohorts.MethodsBlood was collected from 232 breast cancer patients (Cases) and 349 non-cancer subjects (Controls). Genotyping for four polymorphic variants of VDR (FokI, BsmI, TaqI and ApaI) was performed using the PCR-RFLP method.ResultsAn increased association of the VDR-Fok1 f allele with breast cancer was observed in African-Americans (OR = 1.9, p = 0.07). Furthermore, the FbTA, FbtA and fbtA haplotypes were associated with breast cancer among African-Americans (pl0.05). Latinas were more likely to have the VDR-ApaI alleles (Aa or aa) (p = 0.008). The VDR-ApaI aa genotype was significantly associated with poorly-differentiated breast tumors (p = 0.04) in combined Cases. Kaplan-Meier survival analysis showed decreased 5-year disease-free-survival (DFS) in breast cancer patients who had the VDR-Fok1 FF genotype (pl0.05). The Cox regression with multivariate analysis revealed the independent predictor value of the VDR-FokI polymorphism for DFS. The other three variants of VDR (BsmI, TaqI and ApaI) were not associated with disease outcome.ConclusionsVDR haplotypes are associated with breast cancer in African-Americans, but not in Hispanic/Latinas. The VDR-FokI FF genotype is linked with poor prognosis in African-American women with breast cancer.

Objective: The aim of this study was to investigate the role of glycolysis (HK2/PKM2) in the development of tongue squamous cell carcinoma (TSCC) and elucidate how hyperglycaemia stimulate HK2 and PKM2 and enhance migration/invasion potential in TSCC. Methods: A total of 501 patients which diagnosed as TSCC between 1998 and 2004 were enrolled in the retrospective study. The expression of HK2/PKM2 was examined by IHC and the relationship between TSCC and diabetes mellitus (DM) was investigated. We then investigated the role of HK2/PKM2 in the migration and invasion of TSCC and relevant pathways (the SOD2-H2O2 pathway and miR-138 pathway). Finally, we investigated whether hyperglycaemia enhance migratory/invasive potential of TSCC through stimulating glycolysis. Results: The prevalent rate of TSCC patients with diabetes was 13.97%, which was significantly higher than the incidence rate of DM (11.6%) in China. Cox analysis revealed that the HR for patients with DM vs without DM was 1.32. IHC results confirmed that the up-regulation of PKM2/HK2 expression was correlated with tumor stage, clinical stages, diabetes, lymph node metastasis and associated with reduced overall survival. PKM2/HK2/AKT1 overexpression increased cell migration and invasion, SOD2 activities and intracellular H2O2. The siRNA-based PKM2/HK2 knockdown inhibited cell migration and invasion, reduced activities of SOD2 and intracellular H2O2, and also inhibited tumor growth and lung metastasis in vivo. Luciferase assays revealed that PKM2/AKT1 was directly targeted by miR-138 and miR-138 can reduce the expression of the PKM2/AKT1 gene. High glucose enhanced the migration/invasion ability, miR-138/PKM2/HK2 expression and increased SOD2 activities and intracellular H2O2. Conclusions: Our results confirm that DM may be a risk factor in the development of TSCC. PKM2/HK2 plays an important role in the progression of TSCC, and may serve as a biomarker or therapeutic target for patients with TSCC. High glucose stimulates glycolysis (PKM2/HK2) and enhances migration/invasion potential in TSCC. Citation Format: Anxun Wang, Wei Wang, Luodan Zhao, Qianting He, Jingjing Sun, Zhonghua Liu, Zujian Chen, Xiaofeng Zhou. Hyperglycemia stimulates glycolysis and enhances migratory/invasive potential in tongue squamous cell carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 704.

MicroRNAs are post-transcriptional regulators that control mRNA stability and the translation efficiency of their target genes. Mature microRNAs are approximately 22-nucleotide in length. They mediate post-transcriptional gene regulation by binding to the imperfect complementary sequences (a.k.a. microRNA regulatory elements, MRE) in the target mRNAs. It is estimated that more than one-third of the protein-coding genes in the human genome are regulated by microRNAs. The experimental methods to examine the interaction between the microRNA and its targeting site(s) in the mRNA are important for understanding microRNA functions. The luciferase reporter gene assay has recently been adapted to test the effect of microRNAs. In this chapter, we use a previously identified miR-138 targeting site in the 3'-untranslated region (3'-UTR) of the RhoC mRNA as an example to describe a quick method for testing the interaction of microRNA and mRNA.

Angiotensin II AT(2) receptor interacting protein 1 (ATIP1) has been recently identified as a tumor suppressor. In the present study, a 2.2 kb fragment of the 5' flanking region of the human ATIP1 gene was cloned, and its promoter activity was confirmed. Two putative p53 binding sites were identified in the minimal promoter. Cisplatin treatment and ectopic expression of p53 led to enhanced ATIP1 expression. Knockdown of p53 reduced the ATIP1 expression. The direct interaction of p53 and the ATIP1 promoter was confirmed by reporter gene and chromatin-immunoprecipitation assays. When the p53 sites were mutated, the effect of p53 on ATIP1 promoter was eliminated. The results suggest that the ATIP1 gene is regulated by p53 at the transcriptional level, and that it may play an important role in cancer initiation and progression.

MicroRNA-138 is one of the most frequently down-regulated microRNAs in cancer. We recently identified 51 candidate targets of microRNA-138 (Jiang, L., Dai, Y., Liu, X., Wang, C., Wang, A., Chen, Z., Heidbreder, C. E., Kolokythas, A., and Zhou, X. (2011) Hum. Genet. 129, 189–197). Among these candidates, Fos-like antigen 1 (FOSL1) is a member of Fos gene family and is a known proto-oncogene. In this study, we first confirmed the microRNA-138-mediated down-regulation of FOSL1 in squamous cell carcinoma cell lines. We then demonstrated the effect of this microRNA-138-FOSL1 regulatory module on downstream genes (homolog of Snail 2 (Snai2) expression and the Snai2-mediated repression of E-cadherin expression), as well as its contributions to tumorigenesis. The microRNA-138-directed recruitment of FOSL1 mRNA to the RNAi-induced silencing complex was confirmed by a ribonucleoprotein-immunoprecipitation assay. Three canonical and three high affinity non-canonical microRNA-138 (miR-138) targeting sites were identified on the FOSL1 mRNA: one in the 5′-UTR, three overlapping sites in the coding sequences, and two overlapping sites in the 3′-UTR. The direct targeting of miR-138 to these sites was confirmed using luciferase reporter gene assays. In summary, we describe an important microRNA regulatory module, which may play an important role in cancer initiation and progression. Our results also provide evidence that microRNAs target both canonical and non-canonical targeting sites located in all areas of the mRNA molecule (e.g. 5′-UTR, coding sequences, and 3′-UTR).

miR-7 (microRNA-7) has been characterized as a tumour suppressor in several human cancers. It targets a number of proto-oncogenes that contribute to cell proliferation and survival. However, the mechanism(s) by which miR-7 suppresses tumorigenesis in TSCC (tongue squamous cell carcinoma) is unknown. The present bioinformatics analysis revealed that IGF1R (insulin-like growth factor 1 receptor) mRNA is a potential target for miR-7. Ectopic transfection of miR-7 led to a significant reduction in IGF1R at both the mRNA and protein levels in TSCC cells. Knockdown of miR-7 in TSCC cells enhanced IGF1R expression. Direct targeting of miR-7 to three candidate binding sequences located in the 3′-untranslated region of IGF1R mRNA was confirmed using luciferase-reporter-gene assays. The miR-7mediated down-regulation of IGF1R expression attenuated the IGF1 (insulin-like growth factor 1)-induced activation of Akt (protein kinase B) in TSCC cell lines, which in turn resulted in a reduction in cell proliferation and cell-cycle arrest, and an enhanced apoptotic rate. Taken together, the present results demonstrated that miR-7 regulates the IGF1R/Akt signalling pathway by post-transcriptional regulation of IGF1R. Our results indicate that miR-7 plays an important role in TSCC and may serve as a novel therapeutic target for TSCC patients.

MicroRNA deregulation is a critical event in tumor initiation and progression. The down-regulation of microRNA-138 has been frequently observed in various cancers, including tongue squamous cell carcinoma (TSCC). Our previous studies suggest that deregulation of miR-138 is associated with the enhanced proliferation and invasion in TSCC cells. Here, we seek to identify the targets of miR-138 in TSCC, and explore their functional relevance in tumorigenesis. Our genome-wide expression profiling experiments identified a panel of 194 unique transcripts that were significantly down-regulated in TSCC cells transfected with miR-138. A comprehensive screening using six different sequence-based microRNA target prediction algorithms revealed that 51 out of these 194 down-regulated transcripts are potential direct targets for miR-138. These targets include: chloride channel, nucleo-tide-sensitive, 1A (CLNS1A), G protein alpha inhibiting activity polypeptide 2 (GNAI2), solute carrier family 20, member 1 (SLC20A1), eukaryotic translation initiation factor 4E binding protein 1 (EIF4EBP1), and Rho-related GTP-binding protein C (RhoC). GNAI2 is a known proto-oncogene that is involved in the initiation and progression of several different types of tumors. Direct targeting of miR-138 to two candidate binding sequences located in the 3′-untranslated region of GNAI2 mRNA was confirmed using luciferase reporter gene assays. Knockdown of miR-138 in TSCC cells enhanced the expression of GNAI2 at both mRNA and protein levels. In contrast, ectopic trans-fection of miR-138 reduced the expression of GNAI2, which, in consequence, led to reduced proliferation, cell cycle arrest and apoptosis. In summary, we identified a number of high-confident miR-138 target genes, including proto-oncogene GNAI2, which may play an important role in TSCC initiation and progression.

Promoter DNA methylation of CpG islands is an important epigenetic mechanism in cancer development. We have characterized the promoter methylation profile of 82 genes in three prostate cancer cell lines (LNCaP, PC3, and DU145) and two normal prostate cell lines (RWPE1 and RWPE2). The methylation pattern was analyzed using a Panomics gene array system that consists of immobilized probes of known gene promoters on a nitrocellulose membrane. Methylation binding protein–purified methylated DNA was hybridized on the membrane and detected by the chemiluminescence method. We analyzed methylation profile in normal (RWPE1) versus cancerous cells and androgen receptor (AR)–sensitive (LNCaP) versus AR-negative cells (DU145 and PC3). Our study shows that >50% of the genes were hypermethylated in prostate cancer cells compared with 13% in normal cell lines. Among these were the tumor suppressor (RB, TMS1, DAPK, RBL1, PAX6, and FHIT), cell cycle (p27KIP1 and CDKN2A), transporters (MDR1, MLC1, and IGRP), and transcription factor (STAT1, CIITA, MYOD, and NPAT) genes. Relative methylation pattern shows that most of these genes were methylated from 5-fold to >10-fold compared with the normal prostate cells. In addition, promoter methylation was detected for the first time in target genes such as RIOK3, STAT5, CASP8, SRBC, GAGE1, and NPAT. A significant difference in methylation pattern was observed between AR-sensitive versus AR-negative cancer cells for the following genes: CASP8, GPC3, CD14, MGMT, IGRP, MDR1, CDKN2A, GATA3, and IFN. In summary, our study identified candidate genes that are methylated in prostate cancer. Mol Cancer Ther; 9(1); 33–45

A major outcome from Taxol treatment is induction of tumor cell apoptosis. However, metabolic responses to Taxol-induced apoptosis are poorly understood. In this study, we hypothesize that alterations in specific amino acid transporters may affect the Taxol-induced apoptosis in breast cancer cells. In this case, the activity of the given transporter may serve as a biomarker that could provide a biological assessment of response to drug treatment. We have examined the mechanisms responsible for Taxol-induced neutral amino acid uptake by breast cancer cells, such as MCF-7, BT474, MDAMB231 and T47D. The biochemical and molecular studies include: (1) growth-inhibition (MTT); (2) transport kinetics: (3) substrate-specific inhibition; (4) effect of thiol-modifying agents NEM and NPM; (5) gene expression of amino acid transporters; and (6) apoptotic assays. Our data show that Taxol treatment of MCF-7 cells induced a transient increase in Na(+)-dependent transport of the neutral amino acid transporter B0 at both gene and protein level. This increase was attenuated by blocking the transporter in the presence of high concentrations of the substrate amino acid. Other neutral amino acid transporters such as ATA2 (System A) and ASC were not altered. Amino acid starvation resulted in the expected up-regulation of System A (ATA2) gene, but not for B0 and ASC. B0 was significantly down regulated. Taxol treatment had no significant effect on the uptake of arginine and glutamate as measured by System y(+) and X(-) (GC) respectively. Tunel assays and FACS cell cycle analysis demonstrated that both Taxol- and doxorubicin-induced upregulation of B0 transporter gene with accompanying increase in cell apoptosis, could be reversed partially by blocking the B0 transporter with high concentration of alanine, and/or by inhibiting the caspase pathway. Both Taxol and doxorubicin treatment caused a significant decrease in S-phase of the cell cycle. However, Taxol-induced an increase primarily in the G2 fraction while doxorubicin caused increase in G1/G0 together with a small increase in G2. In summary, our study showed that Taxol induced apoptosis in several breast cancer cells results in activation of amino acid transporter System B0 at both gene and protein level. Similar response was observed with another chemotherapeutic agent Doxorubicin, suggesting that this increase is in response to apoptosis, and not only due to changes in cell cycle related events.

The metastasis of breast cancer cells to bones is a leading cause of cancer-related deaths. The bone microenvironment presents a vital source of several growth factors that could promote survival and proliferation of metastatic cancer cells. The bone-derived insulin-like growth factor-1 (IGF-1) binds to insulin-like growth factor receptor (IGF-1R) to initiate intracellular signaling. The downstream signaling events in response to IGF-1R stimulation include activation of Phosphatidyl Inositol 3’ Kinase (PI3K) and Mitogen Activated Protein Kinase (MAPK) pathways. However, the inhibition of these signaling pathways has shown modest benefit in recent clinical trials necessitating the need to identify regulatory mechanisms to successfully block breast cancer-associated bone metastasis. The Runt-related transcription factor, Runx2, is required for normal bone development but is also aberrantly expressed at higher levels in invasive mammary epithelial cells and promotes invasive properties. Previously, we have identified a mechanism wherein Runx2 promotes survival of parental population of invasive breast cancer MDA-MB-231cells by promoting phosphorylation of serine/threonine kinase Akt (pAkt) via mammalian target of rapamycin complex-2 proteins. To determine the implications of Runx2-mediated pAkt regulation in bone metastasis of breast cancers, we harvested Runx2 knockdown or control MDA-MB-231 cells from bones 7 weeks post intracardiac injections in NOD/SCID mice. The gene and protein expression levels of IGF-1R/Akt pathway effectors in the bone seeking subpopulation were determined by real-time PCR and western blotting approaches. The bone-derived Runx2 knockdown cells showed increased IGF-1Rβ levels compared to controls. The Runx2 knockdown MDA-MB-231 cells showed an increase in pIGF1R-β and pAkt levels in response to IGF-1 stimulation that could be inhibited with IGF-1Rβ inhibitor OSI-906 (Linsitinib). However, despite inhibition of IGF-1R and Akt activity with OSI-906 treatment, no alterations were observed in growth or survival of bone-seeking cells. Interestingly, in contrast to IGF-1Rβ and pAkt, the Erk 1/2 levels were reduced in bone-derived Runx2 knockdown MDA-MB-231 cells compared to parental MDA-MB-231 cells. The treatment of cells with Erk 1/2 inhibitor PD184161 reduced cell proliferation and clonogenic potential. Furthermore, the Runx2 protein levels were also reduced in bone seeking subpopulation compared to parental MDA-MB-231cells. Taken together, our studies indicate Runx2-mediated suppression of IGF-1Rβ and Akt but upregulation of Erk signaling in bone seeking breast cancer cells compared to parental MDA-MB-231 cells. Our results suggest that the growth of bone metastatic cancer cells could be effectively blocked by inhibition of Runx2 and Erk pathway. Citation Format: Manish Tandon, Zujian Chen, Jitesh Pratap. Crosstalk between Runx2 regulatory network and insulin-like growth factor receptor/Akt signaling pathway in bone metastasis of breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 3349. doi:10.1158/1538-7445.AM2014-3349

The miR-99 family is one of the evolutionarily most ancient microRNA families, and it plays a critical role in developmental timing and the maintenance of tissue identity. Recent studies, including reports from our group, suggested that the miR-99 family regulates various physiological processes in adult tissues, such as dermal wound healing, and a number of disease processes, including cancer. By combining 5 independent genome-wide expression profiling experiments, we identified a panel of 266 unique transcripts that were down-regulated in epithelial cells transfected with miR-99 family members. A comprehensive bioinformatics analysis using 12 different sequence-based microRNA target prediction algorithms revealed that 81 out of these 266 down-regulated transcripts are potential direct targets for the miR-99 family. Confirmation experiments and functional analyses were performed to further assess 6 selected miR-99 target genes, including mammalian Target of rapamycin (mTOR), Homeobox A1 (HOXA1), CTD small phosphatase-like (CTDSPL), N-myristoyltransferase 1 (NMT1), Transmembrane protein 30A (TMEM30A), and SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 5 (SMARCA5). HOXA1 is a known proto-oncogene, and it also plays an important role in embryonic development. The direct targeting of the miR-99 family to two candidate binding sequences located in the HOXA1 mRNA was confirmed using a luciferase reporter gene assay and a ribonucleoprotein-immunoprecipitation (RIP-IP) assay. Ectopic transfection of miR-99 family reduced the expression of HOXA1, which, in consequence, down-regulated the expression of its downstream gene (i.e., Bcl-2) and led to reduced proliferation and cell migration, as well as enhanced apoptosis. In summary, we identified a number of high-confidence miR-99 family target genes, including proto-oncogene HOXA1, which may play an important role in regulating epithelial cell proliferation and migration during physiological disease processes, such as dermal wound healing and tumorigenesis.

Breast cancer is not only most commonly diagnosed in women worldwide but its metastasis shows serious life threatening consequences. The cell survival and mitogenesis via phosphatidyl inositol 3’ kinase (PI3K) and mitogen activated protein kinase (MAPK) signaling pathways are critical for breast cancer cell survival, proliferation, metabolism and metastasis. A de-regulation of osteogenic Runt-related transcription factor-2 (Runx2) is recently implicated in mammary carcinogenesis. We found that Runx2 differentially regulates the serine/threonine kinase Akt phosphorylation (pAkt), a downstream effecter of PI3K signaling, in non-tumorigenic and invasive mammary epithelial cell lines. The decline in pAkt upon Runx2 suppression in invasive MDA-MB-231 cells was completely abrogated by PI3K inhibitor LY294002. In contrast, the MAPK inhibitor, U0126, showed partial restoration of pAkt upon Runx2 depletion suggesting that Runx2-mediated crosstalk stimulates feedback mechanism within the PI3K and MAPK signaling pathways. The expression analysis of kinases and phosphatases functional in pAkt regulation revealed that the decline in pAkt upon Runx2 knockdown in MDA-MB-231 cells is due to the reduction in PI3K p85 subunit and mammalian target of rapamycin complex-2 (mTORC2). Additionally, we find altered expression of FOXO1, a downstream molecule of PI3K/Akt signaling, due to Runx2-mediated regulation of pAkt levels in MCF-10A and MDA-MB-231 cell lines. To examine the phenotypic effects of Runx2 and PI3K/Akt pathway crosstalk, we evaluated the Runx2-depleted MDA-MB-231 cells for survival under stress conditions. These studies revealed an altered morphology coupled with increased rounding and sub-G1 population in response to glucose- and serum-deprivation upon Runx2 knockdown. The increase in sub-G1 population was restored by glucose and serum re-constitution in the culture media. An increase in Annexin V staining, decline in pAkt levels and cleavage of caspase-3 confirmed the induction of apoptotic cell death. To understand the Runx2-mediated regulation of PI3K/Akt signaling pathway in breast cancer metastasis, the control or Runx2-depleted MDA-MB-231 cells were inoculated intra-cardiacally into immunodeficient mice. The tumors at lung and bone metastatic sites were harvested, FACS-sorted and examined for pAkt levels. Interestingly, to this end, the in-vivo metastatic tumor-derived Runx2 knockdown MDA-MB-231 cells showed an increase in pAkt levels in contrast to in-vitro cultured Runx2 knockdown MDA-MB-231 cells. The data suggests that the mechanism of pAkt activation might involve a dynamic requirement of transcriptional control and feedback regulation within PI3K/Akt and MAPK signaling pathways during different phases of tumor growth in primary and metastatic microenvironment. Citation Format: Manish Tandon, Zujian Chen, Jitesh Pratap. The requirement of Runx2-dependent Akt phosphorylation in breast cancer cell survival and metastasis. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 551. doi:10.1158/1538-7445.AM2013-551

The Runt-related transcription factor Runx2 is essential for skeletal development but is also aberrantly expressed in several cancers (e.g., breast, prostate and osteosarcoma) where it promotes cell migration, invasive and growth properties of cancer cells. The phosphatidylinositol 3′ kinase (PI3K)/Akt signaling pathway is linked to Runx2-dependent skeletogenesis, however, the mechanisms of Runx2 role in PI3K-Akt signaling in breast cancers, and its implication in cancer progression remains under investigated. To mechanistically determine the function of Runx2 in epidermal growth factor (EGF)-induced PI3K/Akt signaling and concomitantly ensuing downstream signaling events, we modulated Runx2 expression levels in immortalized normal MCF-10A and invasive MDA-MB-231 cells via lentiviral vector-mediated gene delivery. The Runx2 over-expression in EGF-stimulated MCF-10A cells increased the cellular response towards PI3K inhibitor LY294002 as indicated by a decline in Akt (Serine 473) phosphorylation (pAkt) levels. This effect could be restored by Runx2 suppression indicating the specificity of Runx2 function in Akt regulation. In MDA-MB-231 cells, Runx2 over-expression and, surprisingly, suppression profoundly inhibited pAkt suggesting that a threshold level of Runx2 is required for phosphorylation of Akt. The Runx2-mediated decline in pAkt was completely reversed by the Runx2-DNA binding mutant over-expression indicating that Runx2 DNA binding domain is essential for Akt inhibition. To further dissect the mechanism of Runx2-mediated regulation of pAkt levels in MDA-MB-231 cells, we examined the protein levels of phosphatases and kinases associated with PI3K/Akt signaling pathway. These analyses revealed that PH domain and leucine rich repeat protein phosphatase 1 (PHLPP1) levels were directly responsive to Runx2. Chromatin immunoprecipitation studies showed Runx2 recruitment on the proximal promoter of PHLPP1 suggesting that Runx2 mediates its effect on Akt activity, in part by regulating PHLPP1 expression. Furthermore, Runx2 overexpression increased nuclear translocation of a forkhead box transcription factor FoxO1, a downstream molecule of PI3K/Akt signaling indicating an indirect Runx2 affect on FoxO1 transcriptional activity in MDA-MB-231 cells as examined by western blot analysis and immunofluorescence studies. Together, our results identified clinically relevant and novel mechanisms of Runx2 regulatory network in PI3K/Akt signaling pathway that could have important consequences in targeting breast cancer-associated cell survival and invasive properties. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3081. doi:1538-7445.AM2012-3081