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1.  Simultaneous analysis of large-scale RNAi screens for pathogen entry 
BMC Genomics  2014;15(1):1162.
Large-scale RNAi screening has become an important technology for identifying genes involved in biological processes of interest. However, the quality of large-scale RNAi screening is often deteriorated by off-targets effects. In order to find statistically significant effector genes for pathogen entry, we systematically analyzed entry pathways in human host cells for eight pathogens using image-based kinome-wide siRNA screens with siRNAs from three vendors. We propose a Parallel Mixed Model (PMM) approach that simultaneously analyzes several non-identical screens performed with the same RNAi libraries.
We show that PMM gains statistical power for hit detection due to parallel screening. PMM allows incorporating siRNA weights that can be assigned according to available information on RNAi quality. Moreover, PMM is able to estimate a sharedness score that can be used to focus follow-up efforts on generic or specific gene regulators. By fitting a PMM model to our data, we found several novel hit genes for most of the pathogens studied.
Our results show parallel RNAi screening can improve the results of individual screens. This is currently particularly interesting when large-scale parallel datasets are becoming more and more publicly available. Our comprehensive siRNA dataset provides a public, freely available resource for further statistical and biological analyses in the high-content, high-throughput siRNA screening field.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-1162) contains supplementary material, which is available to authorized users.
PMCID: PMC4326433  PMID: 25534632
High-throughput high-content RNAi screening; Pathogen entry; Linear mixed model; Hit detection
2.  Prophylactic vaccination against human papillomaviruses to prevent cervical cancer and its precursors 
This is the protocol for a review and there is no abstract. The objectives are as follows:
To evaluate the immunogenicity, clinical efficacy, and safety of prophylactic HPV vaccines in females. The assessment of clinical efficacy will address protection against HPV infection (for homologous and heterologous HPV types), against re-infection, against cervical cancer and its precursors (high-grade CIN (grade 2 or grade 3), adenocarcinoma in situ) in women previously not exposed to HPV infection (negative at enrolment for both HPV DNA and antibodies against the vaccine HPV types). We will assess clinical effectiveness by evaluating outcomes in all women, irrespective of the HPV DNA or serology status at enrolment. Evaluation by fine age and time since sexual debut categories is also planned.
PMCID: PMC4176676  PMID: 25267916
3.  Prognostic Significance of Overexpressed p16INK4a in Patients with Cervical Cancer: A Meta-Analysis 
PLoS ONE  2014;9(9):e106384.
p16INK4a is a tumor suppressor protein which is induced in cells upon the interaction of high-risk HPV E7 with the retinoblastoma protein by a positive feedback loop, but cannot exert its suppressing effect. Previous reports suggested that p16INK4a immunostaining allows precise identification of even small CIN or cervical cancer lesions in biopsies. The prognostic value of overexpressed p16INK4a in cervical cancer has been evaluated for several years while the results remain controversial. We performed a systematic review and meta-analysis of studies assessing the clinical and prognostic significance of overexpression of p16INK4a in cervical cancer.
Identification and review of publications assessing clinical or prognostic significance of p16INK4a overexpression in cervical cancer until March 1, 2014. A meta-analysis was performed to clarify the association between p16INK4a overexpression and clinical outcomes.
A total of 15 publications met the criteria and comprised 1633 cases. Analysis of these data showed that p16INK4a overexpression was not significantly associated with tumor TNM staging (I+II vs. III+IV) (OR = 0.75, 95% confidence interval [CI]: 0.35–1.63, P = 0.47), the tumor grade (G1+ G2 vs. G3) (OR = 0.78, 95% CI: 0.39–1.57, P = 0.49), the tumor size (<4 vs. ≥4 cm) (OR = 1.10, 95% CI: 0.45–2.69, P = 0.83), or vascular invasion (OR = 1.20, 95% CI: 0.69–2.08, P = 0.52). However, in the identified studies, overexpression of p16INK4a was highly correlated with no lymph node metastasis (OR = 0.51, 95% CI: 0.28–0.95, P = 0.04), increased overall survival (relative risk [RR]: 0.42, 95% CI: 0.24–0.72, P = 0.002) and increased disease free survival (RR: 0.60, 95% CI: 0.44–0.82, P = 0.001).
This meta-analysis shows overexpression of p16INK4a in cervical cancer is connected with increased overall and disease free survival and thus marks a better prognosis.
PMCID: PMC4154680  PMID: 25188353
4.  Depletion of the cdk Inhibitor p16INK4a Differentially Affects Proliferation of Established Cervical Carcinoma Cells 
Journal of Virology  2014;88(10):5256-5262.
Infections with high-risk human papillomaviruses (hrHPV) contribute to cervical carcinoma. The cdk inhibitor and tumor suppressor p16INK4A is consistently upregulated in cervical carcinoma cells for reasons that are poorly understood. We report here that downregulation of p16INK4A gene expression in three different cervical carcinoma cell lines reduced expression of the E7 oncogene, suggesting a positive feedback loop involving E7 and p16INK4A. p16INK4A depletion induced cellular senescence in HeLa but not CaSki and MS-751 cervical carcinoma cells.
IMPORTANCE This study demonstrates that the cdk inhibitor p16INK4A, frequently used as surrogate marker for transforming infections by human papillomaviruses of the high-risk group, is required for high-level expression of the E7 oncoproteins of HPV-16, HPV-18, and HPV-45 in cervical carcinoma cells. It is also demonstrated that depletion of p16INK4A induces senescence in HeLa but not CaSki or MS-751 cervical carcinoma cells.
PMCID: PMC4019144  PMID: 24599991
5.  Human Papillomavirus prevalence and probable first effects of vaccination in 20 to 25 year-old women in Germany: a population-based cross-sectional study via home-based self-sampling 
Estimates of Human Papillomavirus (HPV) prevalence in a population prior to and after HPV vaccine introduction are essential to evaluate the short-term impact of vaccination.
Between 2010 and 2012 we conducted a population-based cross-sectional study in Germany to determine HPV prevalence, genotype distribution and risk factors for HPV-infection in women aged 20-25 years. Women were recruited by a two-step cluster sampling approach. A home-based self-collection of cervicovaginal lavages was used. Specimens were analysed using a general primer GP5+/GP6+-based polymerase chain reaction and genotyped for 18 high-risk and 6 low-risk HPV- strains by Luminex-based multiplexed genotyping.
Among 787 included women, 512 were not vaccinated against HPV. In the non-vaccinated population, HPV prevalence of any type was 38.1%, with HPV 16 (19.5%) being the most prevalent genotype. Prevalence of any high-risk type was 34.4%, and in 17.4% of all women, more than one genotype was identified. A higher number of lifetime sexual partners and low educational status were independently associated with HPV-infection. In 223 vaccinated women, prevalence of HPV 16/18 was significantly lower compared to non-vaccinated women (13.9% vs. 22.5%, p = 0.007). When stratifying by age groups, this difference was only significant in women aged 20-21 years, who at time of vaccination were on average younger and had less previous sexual contacts than women aged 22-25 years.
We demonstrate a high prevalence of high-risk HPV genotypes in non-vaccinated women living in Germany that can be potentially prevented by vaccination. Probable first vaccination effects on the HPV prevalence were observed in women who were vaccinated at younger age. This finding reinforces the recommendation to vaccinate girls in early adolescence.
PMCID: PMC3933406  PMID: 24552260
HPV; Cervical cancer; Genotype distribution; Self-sampling; Epidemiology
6.  Post-Translational Control of IL-1β via the Human Papillomavirus Type 16 E6 Oncoprotein: A Novel Mechanism of Innate Immune Escape Mediated by the E3-Ubiquitin Ligase E6-AP and p53 
PLoS Pathogens  2013;9(8):e1003536.
Infections with high-risk human papillomaviruses (HPVs) are causally involved in the development of anogenital cancer. HPVs apparently evade the innate immune response of their host cells by dysregulating immunomodulatory factors such as cytokines and chemokines, thereby creating a microenvironment that favors malignancy. One central key player in the immune surveillance interactome is interleukin-1 beta (IL-1β) which not only mediates inflammation, but also links innate and adaptive immunity. Because of its pleiotropic physiological effects, IL-1β production is tightly controlled on transcriptional, post-translational and secretory levels. Here, we describe a novel mechanism how the high-risk HPV16 E6 oncoprotein abrogates IL-1β processing and secretion in a NALP3 inflammasome-independent manner. We analyzed IL-1β regulation in immortalized keratinocytes that harbor the HPV16 E6 and/or E7 oncogenes as well as HPV-positive cervical tumor cells. While in primary and in E7-immortalized human keratinocytes the secretion of IL-1β was highly inducible upon inflammasome activation, E6-positive cells did not respond. Western blot analyses revealed a strong reduction of basal intracellular levels of pro-IL-1β that was independent of dysregulation of the NALP3 inflammasome, autophagy or lysosomal activity. Instead, we demonstrate that pro-IL-1β is degraded in a proteasome-dependent manner in E6-positive cells which is mediated via the ubiquitin ligase E6-AP and p53. Conversely, in E6- and E6/E7-immortalized cells pro-IL-1β levels were restored by siRNA knock-down of E6-AP and simultaneous recovery of functional p53. In the context of HPV-induced carcinogenesis, these data suggest a novel post-translational mechanism of pro-IL-1β regulation which ultimately inhibits the secretion of IL-1β in virus-infected keratinocytes. The clinical relevance of our results was further confirmed in HPV-positive tissue samples, where a gradual decrease of IL-1β towards cervical cancer could be discerned. Hence, attenuation of IL-1β by the HPV16 E6 oncoprotein in immortalized cells is apparently a crucial step in viral immune evasion and initiation of malignancy.
Author Summary
Persistently high-risk HPV-infected individuals have an increased risk to develop anogenital cancer. HPV encodes the viral proteins E6 and E7 that interact with and induce the degradation of the cell cycle regulators p53 and pRb, respectively, priming immortalized keratinocytes towards malignant transformation. In early antiviral immune response, IL-1β is an important factor for the initiation of inflammation and activation of immune cells such as macrophages and T cells. Our study describes a post-translationally controlled pathway where E6 mediates proteasomal degradation of IL-1β in HPV16-immortalized human keratinocytes. This process depends on the cellular ubiquitin ligase E6-AP and p53 highlighting a novel molecular mechanism of a virus-host interaction that is critical for evading innate immune defense. IL-1β dysregulation is also found in tissue sections which represent different stages of virus-induced carcinogenesis, underlining the clinical relevance of our findings.
PMCID: PMC3731255  PMID: 23935506
7.  Protocadherin PCDH10, Involved in Tumor Progression, is a Frequent and Early Target of Promoter Hypermethylation in Cervical Cancer 
Genes, chromosomes & cancer  2009;48(11):983-992.
Cervical cancer (CC) is the second most common cancer in women. Currently no tractable molecular based therapeutic targets exist for patients with invasive CC and no predictive markers of risk assessment for progression of precancerous lesions are identified. New molecular insights into CC pathogenesis are urgently needed. Towards this goal, we first determined the copy number alterations of chromosome 4 and then examined the role of PCDH10 mapped to 4q28 as a candidate tumor suppressor gene. We identified monosomy 4 in 47% of 81 invasive CC studied by SNP array and found that 91% of 130 invasive CC harboring methylation in the promoter region of the PCDH10 gene. We then showed that aberrant promoter hypermethylation of PCDH10 is associated with down-regulation of gene expression and cell lines exposed to demethylating agent resulted in profound reactivated gene expression. We also showed that the promoter methylation in the PCDH10 gene occurs at an earliest identifiable stage of low-grade squamous intraepithelial lesion (LSIL). Our studies demonstrate that inactivation of PCDH10 may be a critical event in CC progression and form a potentially useful therapeutic target for CC.
PMCID: PMC3430375  PMID: 19681120
8.  The 2′-O-methylation status of a single guanosine controls transfer RNA–mediated Toll-like receptor 7 activation or inhibition 
Bacterial transfer RNA can suppress the immunostimulatory activity of other bacterial tRNAs as a result of the presence of a guanosine modification.
Foreign RNA serves as pathogen-associated molecular pattern (PAMP) and is a potent immune stimulator for innate immune receptors. However, the role of single bacterial RNA species in immune activation has not been characterized in detail. We analyzed the immunostimulatory potential of transfer RNA (tRNA) from different bacteria. Interestingly, bacterial tRNA induced type I interferon (IFN) and inflammatory cytokines in mouse dendritic cells (DCs) and human peripheral blood mononuclear cells (PBMCs). Cytokine production was TLR7 dependent because TLR7-deficient mouse DCs did not respond and TLR7 inhibitory oligonucleotides inhibited tRNA-mediated activation. However, not all bacterial tRNA induced IFN-α because tRNA from Escherichia coli Nissle 1917 and Thermus thermophilus were non-immunostimulatory. Of note, tRNA from an E. coli knockout strain for tRNA (Gm18)-2′-O-methyltransferase (trmH) regained immunostimulatory potential. Additionally, in vitro methylation of this immunostimulatory Gm18-negative tRNA with recombinant trmH from T. thermophilus abolished its IFN-α inducing potential. More importantly, Gm18-modified tRNA acted as TLR7 antagonist and blocked IFN-α induction of influenza A virus–infected PBMCs.
PMCID: PMC3280869  PMID: 22312111
9.  Cervicovaginal Self-Sampling Is a Reliable Method for Determination of Prevalence of Human Papillomavirus Genotypes in Women Aged 20 to 30 Years▿ 
Journal of Clinical Microbiology  2011;49(10):3519-3522.
Self-sampling by cervicovaginal lavage could be an attractive method to detect high-risk human papillomavirus (hr-HPV) infections to identify women with a risk of cervical precancer. The objective of our study was to use self-sampling for the first time in a cross-sectional approach to determine HPV prevalence and genotype distribution. We evaluated participants' acceptance and laboratory results from self-obtained samples versus endocervical brush samples obtained by gynecologists. To determine the sensitivity of both sampling methods in presumed high- and low-prevalence settings, two groups of women 20 to 30 years of age with (n = 55) and without (n = 101) a recent suspicious cytological smear were compared. Overall, 76% (95% confidence interval [95% CI], 65 to 88) of women with and 40% (95% CI, 30 to 49) of women without a recent suspicious cytological smear tested HPV positive. The prevalences of high-risk HPV strains were 71% (95% CI, 59 to 83) and 32% (95% CI, 22 to 41), respectively, for these two groups. The agreement for hr-HPV between the two sampling methods for women with and without suspicious cytology was 84% (κ = 0.65; 95% CI, 0.44 to 0.86) and 91% (κ = 0.78; 95% CI, 0.64 to 0.92), respectively. Participants rated the user-friendliness of the self-sampling method on a visual analog scale from 0 (easy) to 100 (difficult) with a median of 12. In conclusion, self-sampling by cervicovaginal lavage is a reliable method to determine hr-HPV prevalence and is well accepted by young adult females.
PMCID: PMC3187348  PMID: 21813722
10.  Detection of Human Papillomavirus Type 18 E7 Oncoprotein in Cervical Smears: a Feasibility Study 
Journal of Clinical Microbiology  2012;50(2):246-257.
Persistent infections by high-risk human papillomaviruses (HPVs) are the main etiological factor for cervical cancer, and expression of HPV E7 oncoproteins was suggested to be a potential marker for tumor progression. The objective of this study was to generate new reagents for the detection of the HPV18 E7 oncoprotein in cervical smears. Rabbit monoclonal antibodies against recombinant E7 protein of HPV type 18 (HPV18) were generated and characterized using Western blotting, epitope mapping, indirect immunofluorescence, and immunohistochemistry. One clone specifically recognizing HPV18 E7 was used for the development of a sandwich enzyme-linked immunosorbent assay (ELISA). The assay was validated using recombinant E7 proteins of various HPV types and lysates from E7-positive cervical carcinoma cells. A total of 14 HPV18 DNA-positive cervical swab specimens and 24 HPV DNA-negative-control specimens were used for the determination of E7 protein levels by the newly established sandwich ELISA. On the basis of the average absorbance values obtained from all 24 negative controls, a cutoff above which a clinical sample can be judged E7 positive was established. Significant E7 signals 6- to 30-fold over background were found in 7 out of 14 abnormal HPV18 DNA-positive cervical smear specimens. This feasibility study demonstrates for the first time that HPV18 E7 oncoprotein can be detected in cervical smears.
PMCID: PMC3264166  PMID: 22135254
11.  Tacaribe Virus but Not Junin Virus Infection Induces Cytokine Release from Primary Human Monocytes and Macrophages 
The mechanisms underlying the development of disease during arenavirus infection are poorly understood. However, common to all hemorrhagic fever diseases is the involvement of macrophages as primary target cells, suggesting that the immune response in these cells may be of paramount importance during infection. Thus, in order to identify features of the immune response that contribute to arenavirus pathogenesis, we have examined the growth kinetics and cytokine profiles of two closely related New World arenaviruses, the apathogenic Tacaribe virus (TCRV) and the hemorrhagic fever-causing Junin virus (JUNV), in primary human monocytes and macrophages. Both viruses grew robustly in VeroE6 cells; however, TCRV titres were decreased by approximately 10 fold compared to JUNV in both monocytes and macrophages. Infection of both monocytes and macrophages with TCRV also resulted in the release of high levels of IL-6, IL-10 and TNF-α, while levels of IFN-α, IFN-β and IL-12 were not affected. However, we could show that the presence of these cytokines had no direct effect on growth of either TCRV of JUNV in macrophages. Further analysis also showed that while the production of IL-6 and IL-10 are dependent on viral replication, production of TNF-α also occurs after exposure to UV-inactivated TCRV particles and is thus independent of productive virus infection. Surprisingly, JUNV infection did not have an effect on any of the cytokines examined indicating that, in contrast to other viral hemorrhagic fever viruses, macrophage-derived cytokine production is unlikely to play an active role in contributing to the cytokine dysregulation observed in JUNV infected patients. Rather, these results suggest that an early, controlled immune response by infected macrophages may be critical for the successful control of infection of apathogenic viruses and prevention of subsequent disease, including systemic cytokine dysregulation.
Author Summary
It remains unclear how arenavirus infection causes disease; however, for other hemorrhagic fever viruses, infection has been linked to over-production of numerous cytokines by macrophages that can then affect vascular integrity. In order to determine if a similar mechanism might contribute to arenavirus pathogenesis, we have examined the infection and subsequent cytokine production in human monocytes and macrophages by two closely related arenaviruses: the apathogenic Tacaribe virus (TCRV) and the hemorrhagic fever-causing Junin virus (JUNV). We found that both viruses infected primary monocyte and macrophage cultures; however, only, in the case of TCRV was infection accompanied by the production of cytokines. These cytokines would have the potential to stimulate an antiviral response to infection, including the production of antibodies, which are known to be protective during infection. Surprisingly, in contrast to what is observed in other viral hemorrhagic fevers, we found that JUNV infection did not have any effect on the expression of these cytokines. This suggests that an early, strong immune response by infected macrophages may be critical for the control of infection by apathogenic arenaviruses and the prevention of subsequent disease.
PMCID: PMC3091837  PMID: 21572983
12.  Evidence for Epithelial-Mesenchymal Transition in Cancer Stem Cells of Head and Neck Squamous Cell Carcinoma 
PLoS ONE  2011;6(1):e16466.
Initiation, growth, recurrence, and metastasis of head and neck squamous cell carcinomas (HNSCC) have been related to the behavior of cancer stem cells (CSC) that can be identified by their aldehyde-dehydrogenase-isoform-1 (ALDH1) activity. We quantified and enriched ALDH1+ cells within HNSCC cell lines and subsequently characterized their phenotypical and functional properties like invasion capacity and epithelial-mesenchymal transition (EMT). Spheroid culture enriched CSC from five HNSCC cell lines by up to 5-fold. In spheroid-derived cells (SDC) and the parental monolayer-derived cell line ALDH1, CD44, CD24, E-Cadherin, α-SMA, and Vimentin expression was compared by flow-cytometry and immunofluorescence together with proliferation and cell cycle analysis. Invasion activity was evaluated by Matrigel assay and expression of stemness-related transcription factors (TF) Nanog, Oct3/4, Sox2 and EMT-related genes Snail1 and 2, and Twist by real-time PCR. All cell lines formed spheroids that could self-renew and be serially re-passaged. ALDH1 expression was significantly higher in SDC. ALDH1+ cells showed increased colony-formation. The proportion of cells with a putative CSC marker constellation of CD44+/CD24− was highly variable (0.5% to 96%) in monolayer and spheroid cultures and overlapped in 0%–33% with the CD44+/CD24−/ALDH1+ cell subset. SDC had significantly higher invading activity. mRNA of the stemness-related genes Sox2, Nanog, and Oct3/4 was significantly increased in SDC of all cell lines. Twist was significantly increased in two while Snail2 showed a significant increase in one and a significant decrease in SDC of two cell lines. SDC had a higher G0 phase proportion, showed high-level expression of α-SMA and Vimentin, but significantly decreased E-Cadherin expression. HNSCC-lines harbor potential CSC, characterized by ALDH1 and stemness marker TF expression as well as properties like invasiveness, quiescence, and EMT. CSC can be enriched by anchorage-independent culture techniques, which may be important for the investigation of their contribution to therapy resistance, tumor recurrence and metastasis.
PMCID: PMC3029362  PMID: 21304586
13.  A Quest for Initiating Cells of Head and Neck Cancer and Their Treatment 
Cancers  2010;2(3):1528-1554.
The biology of head and neck squamous cell carcinomas (HNSCC) and other cancers have been related to cancer stem-like cells (CSC). Specific markers, which vary considerably depending on tumor type or tissue of origin, characterize CSC. CSC are cancer initiating, sustaining and mostly quiescent. Compared to bulk tumors, CSC are less sensitive to chemo- and radiotherapy and may have low immunogenicity. Therapeutic targeting of CSC may improve clinical outcome. HNSCC has two main etiologies: human papillomavirus, a virus infecting epithelial stem cells, and tobacco and alcohol abuse. Here, current knowledge of HNSCC-CSC biology is reviewed and parallels to CSC of other origin are drawn where necessary for a comprehensive picture.
PMCID: PMC3837320  PMID: 24281171
metastasis; stemness; ALDH1; Sox2; Nanog; Oct3/4; human papillomavirus; immunotherapy; chemoresistance; radioresistance; epithelial mesenchymal transition
14.  Of Bars and Rings: Hof1-Dependent Cytokinesis in Multiseptated Hyphae of Ashbya gossypii▿ §  
Molecular and Cellular Biology  2008;29(3):771-783.
We analyzed the development of multiple septa in elongated multinucleated cells (hyphae) of the filamentous ascomycete Ashbya gossypii in which septation is apparently uncoupled from nuclear cycles. A key player for this compartmentalization is the PCH protein Hof1. Hyphae that are lacking this protein form neither actin rings nor septa but still elongate at wild-type speed. Using in vivo fluorescence microscopy, we present for the first time the coordination of cytokinesis and septation in multiseptated and multinucleated cells. Hof1, the type II myosin Myo1, the landmark protein Bud3, and the IQGAP Cyk1 form collars of cortical bars already adjacent to hyphal tips, thereby marking the sites of septation. While hyphae continue to elongate, these proteins gradually form cortical rings. This bar-to-ring transition depends on Hof1 and Cyk1 but not Myo1 and is required for actin ring assembly. The Fes/CIP4 homology (FCH) domain of Hof1 ensures efficient localization of Hof1, whereas ring integrity is conferred by the Src homology 3 (SH3) domain. Up to several hours after site selection, actin ring contraction leads to membrane invagination and subsequent cytokinesis. Simultaneously, a septum forms between the adjacent hyphal compartments, which do not separate. During evolution, A. gossypii lost the homologs of two enzymes essential for cell separation in Saccharomyces cerevisiae.
PMCID: PMC2630676  PMID: 19029253
15.  Semantic Integration of Cervical Cancer Data Repositories to Facilitate Multicenter Association Studies: The ASSIST Approach 
Cancer Informatics  2009;8:31-44.
The current work addresses the unification of Electronic Health Records related to cervical cancer into a single medical knowledge source, in the context of the EU-funded ASSIST research project. The project aims to facilitate the research for cervical precancer and cancer through a system that virtually unifies multiple patient record repositories, physically located in different medical centers/hospitals, thus, increasing flexibility by allowing the formation of study groups “on demand” and by recycling patient records in new studies. To this end, ASSIST uses semantic technologies to translate all medical entities (such as patient examination results, history, habits, genetic profile) and represent them in a common form, encoded in the ASSIST Cervical Cancer Ontology. The current paper presents the knowledge elicitation approach followed, towards the definition and representation of the disease’s medical concepts and rules that constitute the basis for the ASSIST Cervical Cancer Ontology. The proposed approach constitutes a paradigm for semantic integration of heterogeneous clinical data that may be applicable to other biomedical application domains.
PMCID: PMC2664695  PMID: 19458792
association studies; cervical cancer; coding systems; data unification; semantic integration
16.  Integrative genomics analysis of chromosome 5p gain in cervical cancer reveals target over-expressed genes, including Drosha 
Molecular Cancer  2008;7:58.
Copy number gains and amplifications are characteristic feature of cervical cancer (CC) genomes for which the underlying mechanisms are unclear. These changes may possess oncogenic properties by deregulating tumor-related genes. Gain of short arm of chromosome 5 (5p) is the most frequent karyotypic change in CC.
To examine the role of 5p gain, we performed a combination of single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and gene expression analyses on invasive cancer and in various stages of CC progression.
The SNP and FISH analyses revealed copy number increase (CNI) of 5p in 63% of invasive CC, which arises at later stages of precancerous lesions in CC development. We integrated chromosome 5 genomic copy number and gene expression data to identify key target over expressed genes as a consequence of 5p gain. One of the candidates identified was Drosha (RNASEN), a gene that is required in the first step of microRNA (miRNA) processing in the nucleus. Other 5p genes identified as targets of CNI play a role in DNA repair and cell cycle regulation (BASP1, TARS, PAIP1, BRD9, RAD1, SKP2, and POLS), signal transduction (OSMR), and mitochondrial oxidative phosphorylation (NNT, SDHA, and NDUFS6), suggesting that disruption of pathways involving these genes may contribute to CC progression.
Taken together, we demonstrate the power of integrating genomics data with expression data in deciphering tumor-related targets of CNI. Identification of 5p gene targets in CC denotes an important step towards biomarker development and forms a framework for testing as molecular therapeutic targets.
PMCID: PMC2440550  PMID: 18559093
17.  Promoter hypermethylation-mediated inactivation of multiple Slit-Robo pathway genes in cervical cancer progression 
Molecular Cancer  2006;5:16.
Cervical Cancer (CC) exhibits highly complex genomic alterations. These include hemizygous deletions at 4p15.3, 10q24, 5q35, 3p12.3, and 11q24, the chromosomal sites of Slit-Robo pathway genes. However, no candidate tumor suppressor genes at these regions have been identified so far. Slit family of secreted proteins modulates chemokine-induced cell migration of distinct somatic cell types. Slit genes mediate their effect by binding to its receptor Roundabout (Robo). These genes have shown to be inactivated by promoter hypermethylation in a number of human cancers.
To test whether Slit-Robo pathway genes are targets of inactivation at these sites of deletion, we examined promoter hypermethylation of SLIT1, SLIT2, SLIT3, ROBO1, and ROBO3 genes in invasive CC and its precursor lesions. We identified a high frequency of promoter hypermethylation in all the Slit-Robo genes resulting in down regulated gene expression in invasive CC, but the inhibitors of DNA methylation and histone deacetylases (HDACs) in CC cell lines failed to effectively reactivate the down-regulated expression. These results suggest a complex mechanism of inactivation in the Slit-Robo pathway in CC. By analysis of cervical precancerous lesions, we further show that promoter hypermethylation of Slit-Robo pathway occurs early in tumor progression.
Taken together, these findings suggest that epigenetic alterations of Slit-Robo pathway genes (i) play a role in CC development, (ii) further delineation of molecular basis of promoter methylation-mediated gene regulation provides a potential basis for epigenetic-based therapy in advanced stage CC, and (iii) form epigenetic signatures to identify precancerous lesions at risk to progression.
PMCID: PMC1482714  PMID: 16700909
18.  From Function to Shape: A Novel Role of a Formin in Morphogenesis of the Fungus Ashbya gossypiiV⃞ 
Molecular Biology of the Cell  2006;17(1):130-145.
Morphogenesis of filamentous ascomycetes includes continuously elongating hyphae, frequently emerging lateral branches, and, under certain circumstances, symmetrically dividing hyphal tips. We identified the formin AgBni1p of the model fungus Ashbya gossypii as an essential factor in these processes. AgBni1p is an essential protein apparently lacking functional overlaps with the two additional A. gossypii formins that are nonessential. Agbni1 null mutants fail to develop hyphae and instead expand to potato-shaped giant cells, which lack actin cables and thus tip-directed transport of secretory vesicles. Consistent with the essential role in hyphal development, AgBni1p locates to tips, but not to septa. The presence of a diaphanous autoregulatory domain (DAD) indicates that the activation of AgBni1p depends on Rho-type GTPases. Deletion of this domain, which should render AgBni1p constitutively active, completely changes the branching pattern of young hyphae. New axes of polarity are no longer established subapically (lateral branching) but by symmetric divisions of hyphal tips (tip splitting). In wild-type hyphae, tip splitting is induced much later and only at much higher elongation speed. When GTP-locked Rho-type GTPases were tested, only the young hyphae with mutated AgCdc42p split at their tips, similar to the DAD deletion mutant. Two-hybrid experiments confirmed that AgBni1p interacts with GTP-bound AgCdc42p. These data suggest a pathway for transforming one axis into two new axes of polar growth, in which an increased activation of AgBni1p by a pulse of activated AgCdc42p stimulates additional actin cable formation and tip-directed vesicle transport, thus enlarging and ultimately splitting the polarity site.
PMCID: PMC1345653  PMID: 16236798
19.  Influence of N-Glycans on Processing and Biological Activity of the Nipah Virus Fusion Protein 
Journal of Virology  2004;78(13):7274-7278.
Nipah virus (NiV), a new member of the Paramyxoviridae, codes for a fusion (F) protein with five potential N-glycosylation sites. Because glycans are known to be important structural components affecting the conformation and function of viral glycoproteins, we analyzed the effect of the deletion of N-linked oligosaccharides on cell surface transport, proteolytic cleavage, and the biological activity of the NiV F protein. Each of the five potential glycosylation sites was removed either individually or in combination, revealing that four sites are actually utilized (g2 and g3 in the F2 subunit and g4 and g5 in the F1 subunit). While the removal of g2 and/or g3 had no or little effect on cleavage, surface transport, and fusion activity, the elimination of g4 or g5 reduced the surface expression by more than 80%. Similar to a mutant lacking all N-glycans, g4 deletion mutants in which the potential glycosylation site was destroyed by introducing a glycine residue were neither cleaved nor transported to the cell surface and consequently were not able to mediate cell-to-cell fusion. This finding indicates that in the absence of g4, the amino acid sequence around position 414 is important for folding and transport.
PMCID: PMC421684  PMID: 15194804

Results 1-19 (19)