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1.  Potentially functional variants of p14 ARF are associated with HPV-positive oropharyngeal cancer patients and survival after definitive chemoradiotherapy 
Carcinogenesis  2013;35(1):62-68.
Since p14 ARF and human papillomavirus (HPV) 16 E6/E7 oncoproteins are important regulators participating in the p53/Rb pathways, genetic variations of p14 ARF may modify tumor HPV16 status and survival of HPV16-positive squamous cell carcinoma of the oropharynx (SCCOP) patients. We determined tumor HPV16 status and expression of p14/p53 and genotyped p14 ARF-rs3731217 and -rs3088440 polymorphisms in 552 incident SCCOP patients. We found that patients having variant genotypes for each p14 ARF polymorphism were approximately two or three times as likely to have HPV16-positive tumors compared with patients with corresponding common homozygous genotype, and such an association was particularly pronounced in patients with variant genotypes of both polymorphisms. After definitive chemoradiotherapy, patients having p14 ARF rs3731217 TG/GG variant genotypes had significantly better overall, disease-specific and disease-free survival than those having TT genotype, respectively. Multivariable analysis found that patients with p14 ARF-rs3731217 TT genotype had an ~7-, 11- and 3-fold increased risk for death overall, death due to SCCOP and recurrence than those with TG/GG variant genotypes, respectively. Furthermore, such significantly prognostic effect was also found when survival analysis was limited to HPV16-positive patients. Additionally, potentially functional relevance of the two variants was characterized to explore the genotype–phenotype correlation. Our findings indicate p14 ARF variants may predict tumor HPV16-positive SCCOP patients and survival.
PMCID: PMC3871940  PMID: 24104554
2.  MicroRNA-503 Acts as a Tumor Suppressor in Osteosarcoma by Targeting L1CAM 
PLoS ONE  2014;9(12):e114585.
Deregulated microRNAs and their roles in tumorigenesis have attracted much attention in recent years. Although miR-503 was shown to be important in tumorigenesis, its role in osteosarcoma remains unknown. In this study, we focused on the expression and mechanisms of miR-503 in osteosarcoma development. We found that miR-503 was down-regulated in osteosarcoma cell lines and primary tumor samples, and the restoration of miR-503 reduced cell proliferation, migration and invasion. Low level of miR-503 in patients with osteosarcoma was associated with considerably shortened disease-free survival. Furthermore, bioinformatic prediction and experimental validation revealed that the anti-tumor effect of miR-503 was probably exerted through targeting and repressing of L1CAM expression. L1CAM was up-regulated in osteosarcoma cell lines and primary tumor samples and the expression level of L1CAM were negatively correlated with miR-503 levels in osteosarcoma tissues. Collectively, our data identify the important roles of miR-503 in osteosarcoma pathogenesis, indicating its potential application in cancer therapy.
PMCID: PMC4275157  PMID: 25536034
3.  Association of TBX2 and P21 expression with clinicopathological features and survival of laryngeal squamous cell carcinoma 
Background: The expression of P21 and TBX2 in laryngeal squamous cell carcinoma (LSCC) and their corresponding adjacent normal laryngeal tissues, as well as their association with clinical pathological features and survival remain unclear. Method: we used the RT-PCR and immunohistochemistry to detect their mRNA and protein levels in 75 LSCC patients. We also use log-rank test and Cox models to compare survival among different groups. Results: The mRNA expression level of TBX2 was up-regulated, while P21 was down-regulated in LSCC compared with their matched adjacent laryngeal tissues (All P < 0.001). The expression of P21 was correlated with tumor stage, lymph node metastasis and smoking; and TBX2 expression was associated with lymph node metastasis, differentiation degree and smoking (All P < 0.05). Patients with high TBX2 and low P21 expression had significantly worse survival than those with low TBX2 and high P21 expression, respectively (All P < 0.05). A significant correlation between expression of TBX2 and P21 (Pearson, P < 0.05) was observed. Furthermore, multivariable analysis showed that patients with low TBX2 and high P21 expression alone had a significantly reduced risk for overall death compared with those with low TBX2 and high P21 expression. The risk for overall death was even lower for patients with both low and high expression of both genes than any other co-expression status of both genes (HR, 0.1; 95% CI, 0.0-0.9). Conclusion: These results suggest that abnormal expression of P21 and TBX2 in tumors may jointly, or individually, predict poor prognosis of LSCC.
PMCID: PMC4307495  PMID: 25664048
P21; TBX2; LSCC; survival
4.  Mechanisms of methotrexate resistance in osteosarcoma cell lines and strategies for overcoming this resistance 
Oncology Letters  2014;9(2):940-944.
The aim of the present study was to investigate the underlying mechanisms of methotrexate (MTX) resistance in the human osteosarcoma cell line, Saos-2/MTX4.4, and to evaluate various methods of overcoming the resistance to this chemotherapeutic agent. MMT assays were performed to determine the resistance of the primary (Saos-2) and resistant (Saos-2/MTX4.4) cell lines to MTX, cisplatin [cis-diamminedichloroplatinum II (DDP)], ifosfamide (IFO), Adriamycin (ADM), epirubicin (EPI) and theprubicin (THP). The Saos-2/MTX4.4 cells exhibited a low resistance to IFO, ADM, EPI and THP; however, no resistance to DDP was identified. Overall, the Saos-2/MTX4.4 cells exhibited a greater resistance to all the chemotherapeutic agents investigated compared with the Saos-2 cells. Rhodamine 123 (R123) fluorescence was measured in the Saos-2/MTX4.4 and Saos-2 cells 30 and 60 min after the addition of R123, and R123 plus verapamil (VER). VER administration increased the intracellular accumulation of R123. In addition, reverse transcription-quantitative polymerase chain reaction was performed to determine the mRNA expression levels of multidrug resistance gene 1 (MDR1) in the two cell lines. Although the Saos-2/MTX4.4 cells were more resistant to the chemotherapeutic agents than the Saos-2 cells, no significant difference was identified between the relative mRNA expression levels of MDR1 in the Saos-2/MTX4.4 and Saos-2 cells (0.4350±0.0354 vs. 0.3886±0.0456; P>0.05).
PMCID: PMC4301490  PMID: 25621072
osteosarcoma cell lines; drug resistance; methotrexate; overcoming resistance
5.  Human Papillomavirus and WHO Type I Nasopharyngeal Carcinoma 
The Laryngoscope  2010;120(10):1990-1997.
Nasopharyngeal carcinoma (NPC) is a rare cancer in the United States. An association between NPC and Epstein-Barr virus (EBV) is well-established for World Health Organization (WHO) types II and III (WHO-II/III) NPC but less well-established for WHO type I (WHO-I) NPC. Given the rise in oropharyngeal tumors positive for high-risk human papillomavirus (HPV) and the unique biology of WHO-I NPC, we examined the relationship between HPV and WHO-I NPC.
Study Design
Retrospective case-comparison study.
A search of a large multidisciplinary cancer center tumor registry identified 183 patients seen from January 1999 to December 2008 with incident NPC and no prior cancer. Available paraffin-embedded tumor specimens (N=30) were analyzed for oncogenic HPV status by in-situ hybridization (ISH) and polymerase chain reaction (PCR) for HPV-16 and HPV-18; EBV status by ISH; and p16 expression by immunohistochemistry. Demographic parameters, including race and smoking, were obtained from the medical records.
Among the 18 WHO-I NPC patients, 66% (N=12) were smokers and 17% (N=3) Asian; among the 165 WHO-II/III NPC patients, 44% (N=73) were smokers and 24% (N=39) Asian. Eight WHO-I NPC patients had available paraffin blocks; 5 of 6 were HPV-16-positive by PCR and 4 of 8 were HPV-positive by ISH; only 2 of 8 (25%) were EBV-positive. Twenty-two WHO-II/III NPC patients had available paraffin blocks; only 1 was HPV-positive by ISH, and 13 of 22 (60%) were EBV-positive.
These results suggest that WHO-I NPC is associated with oncogenic HPV, though larger studies are needed to verify these findings.
PMCID: PMC4212520  PMID: 20824783
Human papillomavirus; Nasopharyngeal Carcinoma; WHO Type; In-situ hybridization; Polymerase chain reaction
6.  eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes 
Cancer Informatics  2014;13(Suppl 2):105-112.
Identifying clinically relevant subtypes of a cancer using gene expression data is a challenging and important problem in medicine, and is a necessary premise to provide specific and efficient treatments for patients of different subtypes. Matrix factorization provides a solution by finding checker-board patterns in the matrices of gene expression data. In the context of gene expression profiles of cancer patients, these checkerboard patterns correspond to genes that are up- or down-regulated in patients with particular cancer subtypes. Recently, a new matrix factorization framework for biclustering called Maximum Block Improvement (MBI) is proposed; however, it still suffers several problems when applied to cancer gene expression data analysis. In this study, we developed many effective strategies to improve MBI and designed a new program called enhanced MBI (eMBI), which is more effective and efficient to identify cancer subtypes. Our tests on several gene expression profiling datasets of cancer patients consistently indicate that eMBI achieves significant improvements in comparison with MBI, in terms of cancer subtype prediction accuracy, robustness, and running time. In addition, the performance of eMBI is much better than another widely used matrix factorization method called nonnegative matrix factorization (NMF) and the method of hierarchical clustering, which is often the first choice of clinical analysts in practice.
PMCID: PMC4213194  PMID: 25374455
matrix factorization; biclustering; microarray analysis; cancer classification; iterative method; consensus clustering
7.  Telomere length in peripheral blood lymphocytes contributes to the development of HPV-associated oropharyngeal carcinoma 
Cancer research  2013;73(19):5996-6003.
Sexual transmission of human papillomavirus, particularly HPV16, has been associated with an increasing incidence of oropharyngeal squamous cell carcinoma (OPC). Telomere shortening results in chromosomal instability, subsequently leading to cancer development. Given that HPV16 can affect telomerase activity and telomere length (TL), we conjectured that TL in peripheral blood lymphocytes (PBLs) may affect the risk of HPV16-associated OPC and tumor HPV16 status in patients. TL in PBLs and HPV16 serological status were measured in peripheral blood samples in 188 patients with OPC, 137 patients with oral cavity cancer (OCC) and 335 controls of non-Hispanic whites. Tumor HPV status was determined in 349 OPC cases. Odds ratios and 95% confidence intervals were calculated in univariate and multivariable logistic regression models. Overall, compared with long TL, short TL was associated significantly with a moderately increased risk of OPC but no increased risk of OCC. When we stratified the data by HPV16 serological status, using long TL and HPV16 seronegativity as the reference group, we found that the risk associated with HPV16 seropositivity was higher among OPC patients with short TL. Notably, such risk was particularly pronounced in never smokers, never drinkers and those >50 years of age. Furthermore, short TL was also associated significantly with tumor HPV-positive OPC. Together, our findings suggest that TL in PBLs may be associated with higher risk of HPV16-associated OPC and tumor HPV16 status, particularly in certain patient subgroups. Larger studies are needed to validate these findings.
PMCID: PMC3790860  PMID: 23928994
telomere length; HPV; molecular epidemiology; oropharyngeal cancer
8.  Differences in Imaging Characteristics of HPV-Positive and HPV-Negative Oropharyngeal Cancers: A Blinded Matched-Pair Analysis 
Human papillomavirus–positive oropharyngeal cancers typically have younger age of onset, limited tobacco exposure, and more favorable prognosis than HPV-negative oropharyngeal cancers. We assessed whether HPV-positive and HPV-negative oropharyngeal cancers have consistent differences in pretreatment imaging characteristics.
A retrospective review of 136 pretreatment CT examinations of paired HPV-positive and HPV-negative oropharyngeal cancers matched for T stage, tumor subsite, and smoking status was performed with the reviewing radiologist blinded to HPV status and clinical stage. Demographic/clinical characteristics and imaging characteristics of primary lesions and metastatic nodal disease were compared by use of Fisher exact testing. The McNemar χ2 test was used for the matched-pair analysis.
By imaging, HPV-negative tumors were more likely to demonstrate invasion of adjacent muscle (26% versus 6%, P = .013). HPV-positive primary tumors were more likely to be enhancing and exophytic with well-defined borders, whereas HPV-negative primary tumors were more likely to be isoattenuated and demonstrate ill-defined borders, though these results were not statistically significant. HPV-positive tumors were more likely to demonstrate cystic nodal metastases than HPV-negative tumors (36% versus 9%, P = .002).
In this matched and blinded analysis of the imaging differences between HPV-positive and HPV-negative oropharyngeal cancers, HPV-positive carcinomas often had primary lesions with well-defined borders and cystic nodal metastases, whereas HPV-negative primaries more often had poorly defined borders and invasion of adjacent muscle.
PMCID: PMC3951375  PMID: 23660291
9.  Surgical management of cervical esophageal carcinoma with larynx preservation and reconstruction 
Objectives: There is no generally accepted treatment strategy for cervical esophageal carcinoma. The purpose of this study was to evaluate the operative outcomes of reconstruction after resection of cervical esophageal and hypopharynx-esophagus junction carcinoma with larynx preservation. Methods: We retrospectively reviewed the data of 79 patients with carcinoma of the hypopharynx-esophagus junction and cervical esophagus. Transhiatal total esophagectomy without thoracotomy was carried out in 67 patients who underwent gastric pull-up (GP) or colon interposition (CI) techniques. Transcervical limited pharyngo-cervical esophagectomy was performed in the patients with the pectoralis major flap alone or combined with the split graft (PMF/CWSG) for reconstruction. Seventy-two patients received postoperative adjuvant therapy. Results: The 3-year and 5-year overall survival rates were 66.4% and 45.5%, respectively. The average time to resumption of oral feeding was 25.2 days. All patients had preserved laryngeal function. The overall incidence of complications was 29.1% (23/79), which included cervical fistula, abdominal wound dehiscence, liquefaction necrosis of abdominal fat, and pleural effusion. Conclusions: Surgical resection of cervical esophageal carcinoma and laryngeal preservation is possible. Complete esophagectomy should be performed when the resection extends below the thoracic inlet. The reconstruction methods we performed were safe and effective for the immediate restoration of alimentary continuity after resection of cervical esophageal and pharyngo-cervical esophageal carcinoma; and the patients with PMF/CWSG reconstruction had a better survival than those with GP or CI reconstruction. Combined with radiotherapy, the resectability rate and survival rate of cervical esophageal carcinoma can be improved.
PMCID: PMC4211788  PMID: 25356138
Carcinoma; cervical esophagus; gastric pull-up; colon interposition; larynx preservation; oral cancer
10.  Comparison of neuroendocrine differentiation and KRAS/NRAS/BRAF/PIK3CA/TP53 mutation status in primary and metastatic colorectal cancer 
Neuroendocrine differentiation of tumor tissue has been recognized as an important prerequisite for new targeted therapies. To evaluate the suitability of colorectal cancer (CRC) tissue for these treatment approaches and to find a possible link to pretherapeutic conditions of other targeted strategies, we compared neuroendocrine differentiation and KRAS/NRAS/BRAF/PIK3CA/TP53 mutational status in primary and metastatic CRC. Immunohistochemical expression analysis of neuroendocrine markers chromogranin A and synaptophysin was performed on archival CRC tissue, comprising 116 primary tumors, 258 lymph node metastases and 72 distant metastases from 115 patients. All CRC samples but 30 distant metastases were subjected to mutation analysis of KRAS, NRAS, BRAF, PIK3CA, and TP53. Neuroendocrine marker expression was found significantly less frequently in lymph node metastases compared to primary tumors and distant metastases (20%, 31%, 28%, respectively, P = 0.044). KRAS mutation rates increased significantly from primary tumors to lymph node metastases and distant metastases within the neuroendocrine negative CRC group (44%, 53%, 64%, respectively, P = 0.042). Neuroendocrine differentiation was significantly less concordant than KRAS/NRAS/BRAF/PIK3CA/TP53 mutational status in primary tumor/lymph node metastases pairs (65% versus 88%-99%; P < 0.0001) and primary tumor/distant metastases pairs (64% versus 83%-100%; P = 0.027 and P < 0.0001, respectively). According to these data, therapeutic targeting of neuroendocrine tumor cells can be considered only for a subset of CRC patients and biopsies from the metastatic site should be used to guide therapy. A possible importance of lacking neuroendocrine differentiation for progression of KRAS mutant CRC should be further investigated.
PMCID: PMC4203208  PMID: 25337237
Neuroendocrine differentiation; KRAS mutations; colorectal cancer
11.  Occupational Exposure to Welding Fume among Welders: Alterations of Manganese, Iron, Zinc, Copper, and Lead in Body Fluids and the Oxidative Stress Status 
Welders in this study were selected from a vehicle manufacturer; control subjects were from a nearby food factory. Airborne manganese levels in the breathing zones of welders and controls were 1.45 ± SD1.08 mg/m3 and 0.11 ± 0.07 μg/m3, respectively. Serum levels of manganese and iron in welders were 4.3-fold and 1.9-fold, respectively, higher than those of controls. Blood lead concentrations in welders increased 2.5-fold, whereas serum zinc levels decreased 1.2-fold, in comparison with controls. Linear regression revealed the lack of associations between blood levels of five metals and welder’s age. Furthermore, welders had erythrocytic superoxide dismutase activity and serum malondialdehyde levels 24% less and 78% higher, respectively, than those of controls. These findings suggest that occupational exposure to welding fumes among welders disturbs the homeostasis of trace elements in systemic circulation and induces oxidative stress.
PMCID: PMC4126160  PMID: 15091287
12.  Modeling Gene-Environment Interactions in Oral Cavity and Esophageal Cancers Demonstrates a Role for the p53 R72P Polymorphism in Modulating Susceptibility 
Molecular carcinogenesis  2013;53(8):648-658.
A large number of epidemiological studies have linked a common single nucleotide polymorphism (SNP) in the human p53 gene to risk for developing a variety of cancers. This SNP encodes either an arginine or proline at position 72 (R72P) of the p53 protein, which can alter the apoptotic activity of p53 via transcriptional and non-transcriptional mechanisms. This SNP has also been reported to modulate the development of human papilloma virus (HPV)-driven cancers through differential targeting of the p53 variant proteins by the E6 viral oncoprotein. Mouse models for the p53 R72P polymorphism have recently been developed but a role for this SNP in modifying cancer risk in response to viral and chemical carcinogens has yet to be established experimentally. Here we demonstrate that the p53 R72P polymorphism modulates the hyperprolferative, apoptotic and inflammatory phenotypes caused by expression of the HPV16 E6 and E7 oncoproteins. Moreover, the R72P SNP also modifies the carcinogenic response to the chemical carcinogen 4NQO, in the presence and absence of the HPV16 transgene. Our findings confirm several human epidemiological studies associating the codon 72 proline variant with increased risk for certain cancers but also suggest that there are tissue-specific differences in how the R72P polymorphism influences the response to environmental carcinogens.
PMCID: PMC3926899  PMID: 23475592
13.  Variants in nucleotide excision repair core genes and susceptibility to recurrence of squamous cell carcinoma of the oropharynx 
Genetically determined capacity for NER may modulate both cancer risk and prognosis. Thus, we evaluated associations of seven selected variants in the NER core genes with recurrence risk in 658 SCCOP patients treated principally by radiation. The seven polymorphisms in the core NER genes (XPC-rs2228000, XPC-rs2228001, XPD-rs1799793, XPD-rs13181, XPG-rs17655, ERCC1-rs3212986, and XPA-rs1800975) were genotyped using PCR-RFLP method and log-rank test and multivariable Cox models were used to evaluate the associations in both dominant and recessive genetic models. In a dominant model, we found that polymorphisms of XPC-rs2228000, XPD-rs1799793, and XPG-rs17655 were significantly associated with disease-free survival (log-rank, P = 0.014; P = 0.00008; and P = 0.0007, respectively), and these polymorphisms were significantly associated with recurrence risk of SCCOP (HR = 1.6, 95% CI, 1.1–2.3 for XPC-rs2228000; HR = 0.4, 95%, 0.3–0.6 for XPD-rs1799793; and HR = 0.5, 95% CI, 0.4–0.8 for XPG-rs17655) after multivariable adjustment. Moreover, the borderline significant or significant associations were also found for these three polymorphisms in HPV16/18-positive SCCOP patients (HR= 1.6, 95% CI, 1.0–4.1 for XPC-rs2228000; HR = 0.2, 95%, 0.1–0.5 for XPD-rs1799793; and HR = 0.1, 95% CI, 0.0–0.9 for XPG-rs17655). However, similarly significant associations were not found for these polymorphisms in a recessive model. These findings suggest that polymorphisms of XPC-rs2228000, XPD-rs1799793, and XPG-rs17655 in the NER core genes may contribute to recurrence risk of SCCOP, particularly HPV-positive SCCOP, in a dominant but not in a recessive model. However, validation of these results is warranted.
PMCID: PMC3663873  PMID: 23335232
genetic variants; nucleotide excision repair; human papillomavirus; oropharyngeal cancer; recurrence; DNA repair
14.  Incidence and Pattern of Second Primary Malignancies in Patients with Index Oropharyngeal Cancers versus Index Non-oropharyngeal Head and Neck Cancers 
Cancer  2013;119(14):2593-2601.
A recent review of the SEER registry suggested that patients with index squamous cell carcinoma (SCC) of the oropharynx (SCCOP) are less likely to develop second primary malignancies (SPM) than patients with index SCC of non-oropharyngeal sites (oral cavity, larynx, hypopharynx). The purpose of this study was to determine the impact of index primary tumor site on SPM risk and explore factors potentially affecting this risk within a large prospectively accrued cohort of patients with index SCC of the head and neck (SCCHN).
A cohort of 2230 patients with incident SCCHN was reviewed for development of SPM. Kaplan-Meier analysis, log-rank testing, and Cox proportional hazards models were used to detect the impact of various factors, including index tumor site, on SPM risk.
The SPM rate was lower for patients with index SCCOP than for patients with index non-oropharyngeal cancer (P<.001). Among SCCOP patients, former-smokers had a 50% greater risk of SPM and current-smokers had a 100% greater risk of SPM than never-smokers (Ptrend=.008). Among SCCOP patients, those with classic SCCHN phenotype had SPM risk similar to that of patients with index non-oropharyngeal cancers; those with typical HPV phenotype had very low SPM risk. SPM most commonly occurred at non-tobacco-related sites in patients with index SCCOP and at tobacco-related sites in patients with index non-oropharyngeal cancers.
In patients with SCCHN, index cancer site and smoking status affect the risk and distribution of SPM.
PMCID: PMC3909962  PMID: 23605777
Head and neck neoplasms; second primary malignancy; smoking; oropharyngeal cancer; oral cancer; laryngeal cancer; human papillomavirus
15.  Genetic variants in p53-related genes confer susceptibility to second primary malignancy in patients with index squamous cell carcinoma of head and neck 
Carcinogenesis  2013;34(7):1551-1557.
Because of their important roles in mediating the stabilization and expression of p53, we hypothesized that high-risk genotypes of polymorphisms in p53-related genes, including p53, p73, p14ARF, MDM2 and MDM4, may be associated with an increased risk of second primary malignancy (SPM) after index squamous cell carcinoma of the head and neck (SCCHN). We analyzed data from a cohort of 1283 patients with index SCCHN who were recruited between 1995 and 2007 at MD Anderson Cancer Center and followed for SPM development. Patients were genotyped for nine polymorphisms of p53-related genes. A log-rank test and Cox models were used to compare SPM-free survival and risk. Our results demonstrated that each p53-related polymorphism had a moderate effect on increased SPM risk, but when we combined risk genotypes of these nine polymorphisms together, we found that SPM-free survival was significantly shorter among risk groups with a greater number of combined risk genotypes. SPM risk increased with increasing number of risk genotypes (P < 0.0001 for trend). Compared with the low-risk group (0–3 combined risk genotypes), both the medium-risk (4–5 combined risk genotypes) and high-risk (6–9 combined risk genotypes) groups had significantly increased SPM risk [hazard ratio (HR): 1.6; 95% confidence interval (CI): 1.0–2.6 and HR: 3.0; 95% CI: 1.8–5.0, respectively]. Moreover, such significant associations were even higher in several subgroups. Our findings suggest that combined risk genotypes of p53-related genes may jointly modify SPM risk, especially in patients who are smokers and those with index non-oropharyngeal cancers. However, larger studies are needed to validate our findings.
PMCID: PMC3697893  PMID: 23508638
16.  Elucidation of Operon Structures across Closely Related Bacterial Genomes 
PLoS ONE  2014;9(6):e100999.
About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.
PMCID: PMC4069176  PMID: 24959722
17.  Low risk of second primary malignancies among never smokers with human papillomavirus-associated index oropharyngeal cancers 
Head & neck  2012;35(6):794-799.
Among index oropharyngeal cancer patients, second primary malignancies (SPMs) may be less common in human papillomavirus (HPV)-associated tumors than HPV-negative tumors. Further modification of these SPM risks by smoking has not been reported.
SPM outcomes of 356 incident oropharyngeal cancer patients were analyzed using Cox proportional hazards and Kaplan-Meier models. SPM risk and SPM-free survival were compared in HPV-seronegative patients, HPV-seropositive never smokers, and HPV-seropositive ever smokers.
HPV-seropositive patients had a lower 5-year SPM rate than HPV-seronegative patients (5.6% vs. 14.6%, p=0.051). Compared to HPV-seronegative patients, HPV-seropositive never smokers had a 73% reduced SPM risk, and HPV-seropositive ever smokers had a 27% reduced SPM risk (trend p=0.028). While HPV-seronegative patients had SPMs in traditional locations, 70% of SPMs among HPV-seropositive patients were outside typical tobacco-related sites.
HPV serologic status and smoking may stratify patients with index oropharyngeal cancers in terms of risk and location of SPMs.
PMCID: PMC3459137  PMID: 22711172
Head and neck neoplasms; second primary; smoking; oropharyngeal cancer; human papillomavirus
18.  Free posterior tibial flap reconstruction for hypopharyngeal squamous cell carcinoma 
The aim of this article was to determine outcomes in patients with squamous cell carcinoma of the hypopharynx (SCCHP) in whom the free posterior tibial flap was used for primary reconstruction of hypopharynx defects after cancer resection.
Subjects and methods
Between August 2009 and February 2012, 10 patients with SCCHP underwent posterior tibial flap reconstruction for hypopharynx defects. The corresponding clinical data were retrospectively collected and analyzed.
Despite the multistep and time-consuming procedure, the posterior tibial flap survival rate was 100%. Operation-induced complications did not occur in four patients. Six patients developed postoperative hypoproteinemia, four patients developed postoperative pulmonary infections, and four patients developed pharyngeal fistula. The pharyngeal and laryngeal functions of all patients were preserved.
Our experience demonstrates that the posterior tibial flap is a safe and reliable choice for the reconstruction of hypopharynx defects.
PMCID: PMC4038592  PMID: 24884631
Hypopharyngeal cancer; Posterior tibial flap; Reconstruction
19.  Significance of MDM2 and P14ARF polymorphisms in susceptibility to differentiated thyroid carcinoma 
Surgery  2012;153(5):711-717.
Murine double minute 2 (MDM2) oncoprotein and p14ARF tumor suppressor play pivotal roles in regulating p53 and function in the MAPK pathway, which is frequently mutated in differentiated thyroid carcinoma (DTC). We hypothesized that functional polymorphisms in the promoters of MDM2 and p14ARF contribute to the inter-individual difference in predisposition to DTC.
MDM2-rs2279744, MDM2-rs937283, p14ARF-rs3731217, and p14ARF-rs3088440 were genotyped in 303 patients with DTC and 511 cancer-free controls. Multivariate logistic regression analysis was performed to calculate odds ratios (ORs) and 95% confidence intervals (CIs).
MDM2-rs2279744 and p14ARF-rs3731217 were associated with a significantly increased risk of DTC (MDM2-rs2279744: TT vs. TG/GG, OR = 1.5, 95% CI, 1.1–2.0; p14ARF-rs3731217: TG/GG vs. TT, OR = 1.7, 95% CI, 1.2–2.3). No association was found for MDM2-rs937283 or p14ARF-rs3088440. Individuals carrying 3–4 risk genotypes of MDM2 and p14ARF had 2.2 times (95% CI, 1.4–3.5) the DTC risk of individuals carrying 0–1 risk genotypes (Ptrend = 0.021). The combined effect of MDM2 and p14ARF on DTC risk was confined to young subjects (≤45 years), non-smokers, non-drinkers, and subjects with a first-degree family history of cancer. These associations were quite similar in strength when cases were restricted to those with papillary thyroid cancer.
Our results suggest that polymorphisms of MDM2 and p14ARF contribute to the inter-individual difference in susceptibility to DTC, either alone or more likely jointly. The observed associations warrant further confirmation in independent studies.
PMCID: PMC3610784  PMID: 23218882
papillary thyroid carcinoma; p53 pathway; case-control study
20.  Pre-microRNA variants predict HPV16-positive tumors and survival in patients with squamous cell carcinoma of the oropharynx 
Cancer letters  2012;330(2):233-240.
To identify non-tumor biomarkers for prediction of tumor HPV status and prognosis of patients with squamous cell carcinoma of the oropharynx (SCCOP), we evaluated the association of single nucleotide polymorphisms (SNPs) in pre-miRNAs with HPV16 status and survival for SCCOP patients. We analyzed HPV16 status in tumor specimens and genotyped four SNPs in pre-miRNAs (hsa-mir-146a rs2910164 G>C, hsa-mir-149 rs2292832 G>T, hsa-mir-196a2 rs11614913 C>T, and hsa-mir-499 rs3746444 A>G) in 309 SCCOP patients. Unconditional logistic regression models were used for calculation of odds ratio (OR) and 95% confidence intervals (CIs), and Kaplan-Meier analysis and Cox proportional hazards regression were used to evaluate associations. We found that statistically significant associations with HPV16-positive SCCOP and survival were found for hsa-mir-146a rs2910164 and hsa-mir-196a2 rs11614913, while such similar associations were not observed for hsa-mir-149 rs2292832 and hsa-mir499 rs3746444. Compared with those with corresponding hsa-mir-146a CG/CC and has-mir-196a2 CC genotypes, the hsa-mir-146a GG and hsa-mir-196a2 CT/TT wild-type genotypes were significantly associated with HPV16-positive tumor status (adjusted OR, 2.4; 95% CI, 1.4–4.1 and adjusted OR, 2.1, 95% CI, 1.2–3.6), respectively. Patients having hsa-mir-146a rs2910164 GG and hsa-mir196a2 rs11614913 CT/TT genotypes had significantly better overall, disease-specific, and disease-free survival compared with those having the corresponding CG/CC and CC genotypes, respectively. Furthermore, these genotypes were significantly associated with reduced risk of overall death, death owing to disease, and recurrence after adjustment for important prognostic confounders including HPV status, smoking, and stage. Our findings indicate pre-miRNA polymorphisms may predict tumor HPV16-positive SCCOP cases and may be prognostic biomarkers for SCCOP.
PMCID: PMC3563870  PMID: 23219900
MicroRNA polymorphisms; genetic susceptibility; oropharyngeal cancer; molecular epidemiology; survival
21.  The Impacts of Read Length and Transcriptome Complexity for De Novo Assembly: A Simulation Study 
PLoS ONE  2014;9(4):e94825.
Transcriptome assembly using RNA-seq data - particularly in non-model organisms has been dramatically improved, but only recently have the pre-assembly procedures, such as sequencing depth and error correction, been studied. Increasing read length is viewed as a crucial condition to further improve transcriptome assembly, but it is unknown whether the read length really matters. In addition, though many assembly tools are available now, it is unclear whether the existing assemblers perform well enough for all data with different transcriptome complexities. In this paper, we studied these two open problems using two high-performing assemblers, Velvet/Oases and Trinity, on several simulated datasets of human, mouse and S.cerevisiae. The results suggest that (1) the read length of paired reads does not matter once it exceeds a certain threshold, and interestingly, the threshold is distinct in different organisms; (2) the quality of de novo assembly decreases sharply with the increase of transcriptome complexity, all existing de novo assemblers tend to corrupt whenever the genes contain a large number of alternative splicing events.
PMCID: PMC3988101  PMID: 24736633
22.  Upregulation of DMT1 expression in choroidal epithelia of the blood–CSF barrier following manganese exposure in vitro 
Brain research  2006;1097(1):1-10.
Divalent metal transporter 1 (DMT1), whose mRNA possesses a stem-loop structure in 3′-untranslated region, has been identified in most organs and responsible for transport of various divalent metal ions. Previous work from this laboratory has shown that manganese (Mn) exposure alters the function of iron regulatory protein (IRP) and increases iron (Fe) concentrations in the cerebrospinal fluid (CSF). This study was designed to test the hypothesis that Mn treatment, by acting on protein–mRNA binding between IRP and DMT1 mRNA, altered the expression of DMT1 in an immortalized choroidal epithelial Z310 cell line which was derived from rat choroid plexus epithelia, leading to a compartmental shift of Fe from the blood to the CSF. Immunocytochemistry confirmed the presence of DMT1 in Z310 cell. Following in vitro exposure to Mn at 100 μM for 24 and 48 h, the expression of DMT1 mRNA in Z310 cells was significantly increased by 45.4% (P < 0.05) and 78.1% (P < 0.01), respectively, as compared to controls. Accordingly, Western blot analysis revealed a significant increase of DMT1 protein concentrations at 48 h after Mn exposure (100 μM). Electrophoretic mobility shift assay (EMSA) showed that Mn exposure increased binding of IRP to DMT1 mRNA in cultured choroidal Z310 cells. Moreover, real-time RT-PCR revealed no changes in DMT1 heterogeneous nuclear RNA (hnRNA) levels following Mn exposure. These data suggest that Mn appears to stabilize the binding of IRP to DMT1 mRNA, thereby increasing the expression of DMT1. The facilitated transport of Fe by DMT1 at the blood–CSF barrier may partly contribute to Mn-induced neurodegenerative Parkinsonism.
PMCID: PMC3980874  PMID: 16729984
Manganese; Choroid plexus; Z310 cell; Blood; CSF barrier; Divalent metal transporter 1; Iron responsive element
23.  A furin inhibitor downregulates osteosarcoma cell migration by downregulating the expression levels of MT1-MMP via the Wnt signaling pathway 
Oncology Letters  2014;7(4):1033-1038.
This study aimed to explore the exact mechanism of the effect of a furin inhibitor on the migration and invasion of MG-63 and Saos-2 osteosarcoma cells. MG-63 and Saos-2 osteosarcoma cells were treated with regular culture medium in the presence or absence of 480 nM α1-antitrypsin Portland (α1-PDX). Wound-healing and Transwell assays were used for the detection of the effects of α1-PDX on MG-63 and Saos-2 osteosarcoma cell migration and invasion. Western blot analysis and reverse transcription-polymerase chain reaction were performed to detect the expression levels of membrane type I matrix metalloproteinase (MT1-MMP), Wnt and β-catenin. A chromatin immunoprecipitation assay was used for detection of the levels of MT1-MMP gene transcription activity. The results showed that α1-PDX treatment significantly reduced the migration and invasion ability of the cells. Notably, the expression levels of MT1-MMP decreased evidently upon α1-PDX treatment, paralleled with reductions in the expression levels of Wnt and β-catenin. Further analysis of the transcriptional activity of MT1-MMP revealed that the α1-PDX-induced downregulation of the levels of MT1-MMP was mediated by the Wnt signaling pathway. These data suggest that α1-PDX plays a vital role in inhibiting MG-63 and Saos-2 osteosarcoma cell migration and invasion by downregulating the expression levels of MT1-MMP via the Wnt signaling pathway.
PMCID: PMC3961323  PMID: 24944664
α1-PDX; osteosarcoma MG-63 and Saos-2; migration; MT1-MMP; Wnt; β-catenin
24.  Phase II Trial of Induction Chemotherapy Followed by Surgery for Squamous Cell Carcinoma of the Oral Tongue in Young Adults 
Head & neck  2011;34(9):1255-1262.
We conducted a phase II clinical trial of induction chemotherapy followed by surgery ± radiotherapy for squamous cell carcinoma of the oral tongue (SCCOT) in young adults.
From September 2001 to October 2004, 23 patients aged 18–49 years with clinical T2-3N0-2M0 SCCOT and no prior radiotherapy, chemotherapy, or neck dissection underwent induction chemotherapy (paclitaxel, ifosfamide, and carboplatin) followed by glossectomy and neck dissection ± radiotherapy and chemotherapy.
On final surgical pathology, 9 (39%) patients had a complete/major (2 complete) histologic response at the primary tumor site; 8 (35%) had no response or progression. Similarly, 9 (39%) patients had a complete response in the neck or remained node negative; 6 (26%) had an increase in nodal category. No treatment-associated deaths occurred, and toxicity was modest. At a median follow-up from the end of treatment of 52 months (minimum, 23 months), 10 (43%) patients developed recurrence, and all 10 died of cancer. Crude recurrence/cancer death rates were associated with ≤ a partial response at the tongue (P = .029), poor histologic differentiation (P = .012), and multiple adverse features on final surgical pathology (P = .040).
Response rates and overall survival with this induction chemotherapy regimen were limited, but complete/major response at the tongue was associated with excellent prognosis. Additionally, improved patient selection and predictive tumor biomarkers will be needed for induction chemotherapy to be routinely incorporated into the treatment of oral tongue cancer in young adults.
PMCID: PMC3893095  PMID: 22009800
Oral tongue cancer; Young adults; Induction chemotherapy
25.  An evolution in demographics, treatment, and outcomes of oropharyngeal cancer at a major cancer center: A staging system in need of repair 
Cancer  2012;119(1):81-89.
This retrospective review examines demographic/clinical characteristics and overall survival of patients with squamous cell carcinoma of the oropharynx (SCCOP) at a tertiary cancer center and reports the characteristics influencing any observed survival trends over time.
The study included 3891 newly diagnosed, previously untreated patients presenting to our institution between 1955 and 2004.
Over time, patients presented at younger ages and were more likely to have base of tongue or tonsil tumors and to be never or former smokers. Patients diagnosed in 1995–2004 were almost half as likely to die as those diagnosed before 1995 (HR,0.6; 95% CI,0.6–0.8). In both multivariable and recursive partitioning survival analyses, the TNM staging system predicted survival of patients treated before 1995 but not of patients treated in 1995–2004.
Survival among patients with SCCOP improved substantially over the past 50 years. The main contributing factors were changes in clinical characteristics, in particular surrogates for HPV positivity. The current TNM staging system for SCCOP is inadequate. Incorporation of HPV status and perhaps smoking status is encouraged.
PMCID: PMC3469778  PMID: 22736261
head and neck cancer; head and neck neoplasms; human papillomavirus; oropharyngeal cancer; neoplasm staging

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