Relevant bibliographies by topics / Spdef

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Academic literature on the topic 'Spdef'

Author: Grafiati
Published: 4 June 2021
Last updated: 29 January 2023

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Journal articles on the topic "Spdef"

1

Vatanmakanian, Mousa, Sweaty Koul, Thangavel Chellappagounder, and Hari K. Koul. "Abstract A081: Epigenetic regulation of SPDEF gene in RCC7/T cells, a line of malignant African-American prostate epithelial cells." Cancer Epidemiology, Biomarkers & Prevention 32, no. 1_Supplement (2023): A081. http://dx.doi.org/10.1158/1538-7755.disp22-a081.

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Abstract Background: Prostate cancer (PCa) in African American (AA) men has an earlier onset, more aggressiveness with higher metastasis and mortality rate than in Caucasian men. SAM-pointed domain-containing Ets-like factor (SPDEF) has been identified as a possible suppressor of metastasis in castration-resistant prostate cancer (CRPC) in earlier investigations. Ongoing studies in our lab are focused on deciphering the role of SPDEF in PCa progression and metastasis with special emphasis on PCa in AA men. We discovered that SPDEF expression is lost in RCC7/T cells, and re-expression of SPDEF limits metastatic properties of these cells, however, the regulatory mechanisms underlying the loss of SPDEF have not been elucidated. In the current study, we investigated the role of epigenetic modulators (DNA methylation and histone modifications) in driving the loss of SPDEF. Methods: We analyzed publicly available data sets from TCGA (GDC TCGA Prostate Cancer, and TCGA Prostate Cancer (PRAD) for DNA methylation using Xena UCSC genome browser (https://xena.ucsc.edu/). We also analyzed histone ChIP-seq data from PCa cell lines using cistrome project (http://cistrome.org/db/#/). RCC7/T cells were grown in DMEM and maintained at 37°C in a humidified incubator. We used bisulfite sequencing (BSP) to examine DNA methylation in SPDEF gene in SPDEF proficient (LNCaP) and deficient (RCC7/T) cells. We also employed the ChIP-qPCR to reveal the active and repressive key histone marks (H3K4me3, H3K27ac, and H3K27me3) across the SPDEF gene. Results: In the clinical cohorts, SPDEF expression showed an inverse correlation with the degree of DNA methylation and expression of the epigenetic writer enzymes such as DNMT1 and EZH2. Our results revealed that the CpG islands in SPDEF gene are hyper-methylated in RCC7/T cells compared to LNCaP cells. Our analysis of the data from the cistrome project revealed an elevated enhancer repressive mark H3K27me3 (marked by EZH2) and a decreased promoter active mark, H3K4me3, in PC3 cells as compared with less metastatic LNCaP cells. Our results from ChIP-qPCR confirmed these findings. Moreover, we observed the methylation profiles in RCC7/T cells were similar to those of PC3 cells. Additionally, combination treatment with 5-aza-2-deoxycytidine (DNMT inhibitor) and GSK-126 (EZH2 inhibitor) increased the PDEF expressions levels and also restricted colony formation, migration and invasion in RCC7/T cells. Conclusion: Overall, these findings reveal an inverse correlation between expression of epigenetic writers (DNMT1 and EZH2) and SPDEF expression in PCa. Our results also suggest that SPDEF expression in PCa is regulated in part by epigenetic modifications, and that combined inhibition of DNMT1 and EZH2 may offer a therapeutic benefit in subsets of PCa patients including in AA men. Acknowledgements: These studies were funded in part by NIH/NCI-7R01CA242839 (HK) and unrestricted funds from the LSU-LCMC Cancer Center, School of Medicine -LSUHSC, New Orleans (HK). Grateful to LCU-LCMC Genomics core for DNA sequencing Citation Format: Mousa Vatanmakanian, Sweaty Koul, Thangavel Chellappagounder, Hari K. Koul. Epigenetic regulation of SPDEF gene in RCC7/T cells, a line of malignant African-American prostate epithelial cells [abstract]. In: Proceedings of the 15th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2022 Sep 16-19; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2022;31(1 Suppl):Abstract nr A081.
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Song, Juan, David Cano-Rodriquez, Melanie Winkle, et al. "Targeted epigenetic editing of SPDEF reduces mucus production in lung epithelial cells." American Journal of Physiology-Lung Cellular and Molecular Physiology 312, no. 3 (2017): L334—L347. http://dx.doi.org/10.1152/ajplung.00059.2016.

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Airway mucus hypersecretion contributes to the morbidity and mortality in patients with chronic inflammatory lung diseases. Reducing mucus production is crucial for improving patients’ quality of life. The transcription factor SAM-pointed domain–containing Ets-like factor ( SPDEF) plays a critical role in the regulation of mucus production and, therefore, represents a potential therapeutic target. This study aims to reduce lung epithelial mucus production by targeted silencing SPDEF using the novel strategy, epigenetic editing. Zinc fingers and CRISPR/dCas platforms were engineered to target repressors (KRAB, DNA methyltransferases, histone methyltransferases) to the SPDEF promoter. All constructs were able to effectively suppress both SPDEF mRNA and protein expression, which was accompanied by inhibition of downstream mucus-related genes [anterior gradient 2 ( AGR2), mucin 5AC ( MUC5AC)]. For the histone methyltransferase G9A, and not its mutant or other effectors, the obtained silencing was mitotically stable. These results indicate efficient SPDEF silencing and downregulation of mucus-related gene expression by epigenetic editing, in human lung epithelial cells. This opens avenues for epigenetic editing as a novel therapeutic strategy to induce long-lasting mucus inhibition.
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Tonelli, Claudia, Georgi N. Yordanov, Yuan Hao, et al. "Abstract 6081: The transcription factor SPDEF promotes the survival of mucinous pancreatic ductal adenocarcinoma of the classical subtype." Cancer Research 82, no. 12_Supplement (2022): 6081. http://dx.doi.org/10.1158/1538-7445.am2022-6081.

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Abstract Pancreatic ductal adenocarcinoma (PDA) is characterized by intra-tumoral heterogeneity. Using single-cell RNA sequencing, we reveal multiple tumor subpopulations distinguished by their differentiation state and associated with different stages of tumor progression. We identify SPDEF as a factor required for tumorigenesis in pancreatic cancer cells of epithelial and mucinous nature. SPDEF levels correlate with glandular differentiation and high secretory activity, which are characteristic features of human PDA of the classical subtype. SPDEF can drive mucus production in pancreatic cancer cells and is essential for the growth of mucus-secreting tumors by regulating endoplasmic reticulum (ER) activity. These findings offer insights into the factors controlling differentiation in PDA and may inform new therapeutic strategies with improved efficacy. Citation Format: Claudia Tonelli, Georgi N. Yordanov, Yuan Hao, Astrid Deschênes, Erin Brosnan, Abishek Doshi, Youngkyu Park, Jonathan Preall, David A. Tuveson. The transcription factor SPDEF promotes the survival of mucinous pancreatic ductal adenocarcinoma of the classical subtype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6081.
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4

Li, Xueqing, Yuanzheng Chen, Cong Fu, et al. "Characterization of epigenetic and transcriptional landscape in infantile hemangiomas with ATAC-seq and RNA-seq." Epigenomics 12, no. 11 (2020): 893–905. http://dx.doi.org/10.2217/epi-2020-0060.

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Aim: This study was conducted to reveal epigenetic landscape in infantile hemangiomas (IHs) and identify transcription factors (TFs) and their downstream genes active in IHs. Materials & methods: We performed Assay for Transposase Accessible Chromatin (ATAC-seq) with RNA-seq in three pairs of IHs and their adjacent normal tissues. Functions of candidate TFs were investigated in human umbilical vein endothelial cells (HUVECs). Results: Chromatin of IH tissues is less compact. Some candidate genes and TFs were identified. In HUVECs, SPDEF inhibited cell viability and tube formation, and promoted apoptosis; SOX4 exerted the opposite effect. SPDEF may act through EPHA5, ZBTB46 and SASH1; SOX4 may act through MMP12 and HIVEP3. Conclusion: Epigenetics plays a role in IHs. SPDEF and SOX4 may act in IHs.
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Kim, Sanga, Hee-Won Kim, Seok-Hwan Chang, Kang-Hyun Leem, and Hae-Jeong Park. "Bee Venom Prevents Mucin 5AC Production through Inhibition of AKT and SPDEF Activation in Airway Epithelia Cells." Toxins 13, no. 11 (2021): 773. http://dx.doi.org/10.3390/toxins13110773.

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IL-13 induces mucus metaplasia, which causes airway obstruction in asthma. Bee venom (BV) and its components have shown anti-inflammatory effects in allergic diseases such as atopic dermatitis and asthma. In this study, we investigated the effect of BV on IL-13-induced mucus metaplasia through activation of the signal transducer and activator of transcription (STAT6), and regulation of SAM-pointed domain containing Ets-like factor (SPDEF) and forkhead box A2 (FOXA2) in the airway epithelia cell line A549. In A549 cells, BV (1.0 µg/mL) inhibited IL-13 (10 ng/mL)-induced AKT phosphorylation, increase in SPDEF protein expression, and decrease in FOXA2 protein expression—but not STAT6 phosphorylation. BV also prevented the IL-13-induced increase in mucin 5AC (MUC5AC) mRNA and protein expression. Moreover, we observed that inhibition of phosphoinositide 3 kinase (PI3K)/AKT using LY294002 (50 µM) could reverse the alterations in FOXA2 and MUC5AC expression -by IL-13 and BV. However, LY294002 did not affect IL-13- and BV-induced changes in SPDEF expression. These findings indicate that BV inhibits MUC5AC production through the regulation of SPDEF and FOXA2. The inhibition of MUC5AC production through FOXA2 is mediated via the suppression of PI3K/AKT activation by BV. BV may be helpful in the prevention of mucus metaplasia in asthma.
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Horinaka, Mariko, Jun Shoji, Akiko Tomioka, Yukiko Tonozuka, Noriko Inada, and Satoru Yamagami. "Alterations in Mucin-Associated Gene Expression on the Ocular Surface in Active and Stable Stages of Atopic and Vernal Keratoconjunctivitis." Journal of Ophthalmology 2021 (May 31, 2021): 1–8. http://dx.doi.org/10.1155/2021/9914786.

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Purpose. To evaluate the presence of ocular surface mucin in patients with atopic and vernal keratoconjunctivitis (AKC/VKC), we investigated the mRNA expression levels of SAM-pointed domain-containing ETS-like factor (SPDEF) and mucin-related genes on the ocular surface. Methods. Nineteen patients with AKC or VKC were divided into two groups based on the severity of the disease as determined by their clinical scores for AKC/VKC: the stable group and the active group. Impression cytology was performed in all patients using filter paper, and the expression levels of SPDEF, MUC1, MUC4, MUC5AC, MUC16, and eotaxin-2 mRNA were determined by real-time reverse-transcription polymerase chain reaction. Results. The results showed that the expression levels of SPDEF and MUC5AC mRNA in the active group were significantly decreased compared with those in the stable group. Furthermore, clinical scores were significantly negatively correlated with the expression levels of SPDEF mRNA and significantly positively correlated with the expression levels of eotaxin-2, which is a biomarker for eosinophilic inflammation on the ocular surface. Cluster analysis classified the patients with AKC/VKC into three clusters, and the stable group was divided into two clusters according to the condition of ocular surface mucin. Conclusions. Ocular surface mucin in patients with AKC/VKC is altered in accordance with the clinical severity of the disease.
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Shoji, Jun, Noriko Inada, Akiko Tomioka, and Satoru Yamagami. "Assessment of mucin-related gene alterations following treatment with rebamipide ophthalmic suspension in Sjögren’s syndrome-associated dry eyes." PLOS ONE 15, no. 11 (2020): e0242617. http://dx.doi.org/10.1371/journal.pone.0242617.

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Ocular surface mucins are thought to play vital roles in maintaining the homeostasis of the pre-ocular surface tear film. We performed ocular surface tests with impression cytology to assess the expression levels of mucin-related genes on the ocular surface in healthy eyes. In addition, we investigated alterations in mucin-related gene expression secondary to treatment with rebamipide ophthalmic suspension in patients with Sjögren’s syndrome-associated dry eyes (SS-DE). Thirty-three healthy individuals (control group) and 13 patients from our hospital with SS-DE were enrolled. Impression cytology was performed using Schirmer’s test paper for RNA sampling. The mRNA levels of SAM-pointed domain-containing ETS-like factor (SPDEF), mucin 5AC (MUC5AC), and mucin 16 (MUC16) were determined using a real-time reverse transcription-polymerase chain reaction. The ocular surface test was performed once for the control group, and at baseline as well as 2, 4, 8, and 12 weeks after treatment in the Sjögren’s syndrome-associated dry eyes group. mRNA levels of SPDEF, MUC5AC, and MUC16 were not significantly different between the control and SS-DE groups before rebamipide ophthalmic suspension treatment. SPDEF mRNA levels in control subjects were significantly correlated with levels of MUC5AC. Among SS-DE patients, SPDEF mRNA levels were significantly increased at 2, 4, and 8 weeks after treatment compared with baseline levels. MUC16 mRNA levels were significantly decreased from baseline levels at 4 and 8 weeks post-treatment. Ocular surface test using impression cytology is a clinically useful tool for assessing mucous conditions on the ocular surface and can be used to determine the effects of instillation treatment with eye drops that affect mucin production at the ocular surface.
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Uchida, Shiro, and Takashi Sugino. "In Silico Identification of Genes Associated with Breast Cancer Progression and Prognosis and Novel Therapeutic Targets." Biomedicines 10, no. 11 (2022): 2995. http://dx.doi.org/10.3390/biomedicines10112995.

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Molecular mechanisms underlying breast cancer (BC) progression are complex and remain unclear. In this study, we used bioinformatic tools to identify genes associated with tumor progression mechanisms and novel therapeutic targets in BC. We identified genes with stepwise upregulated expression overlapping between the T and N stages during BC progression using LinkedOmics. We compared the expression level of each gene in BC tissues with that in normal breast tissues and evaluated differences in expression in their intrinsic subtypes and their prognostic value using UALCAN and GEPIA2. We also investigated the dependency of BC cell lines on these genes and whether they are potential therapeutic targets using DepMap. SPDEF, TRIM3, ABCB9, HSPB1, RHBG, SPINT1, EPN3, LRFN2, and PRPH were found to be involved in BC progression. High expression of ABCB9 and SPINT1 was associated with a poor prognosis. SPDEF, TRIM3, ABCB9, RHBG, SPINT1, and PRPH were found to be essential for survival in some BC cell lines (gene effect score < −0.5). PRPH was newly discovered to be involved in the progression of BC and the growth and survival of BC cell lines. Hence, SPDEF, TRIM3, ABCB9, RHBG, SPINT1, and PRPH may serve as novel potential therapeutic targets in BC.
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Nagashima, Akimichi, Masaharu Shinkai, Masahiro Shinoda, et al. "Clarithromycin Suppresses Chloride Channel Accessory 1 and Inhibits Interleukin-13-Induced Goblet Cell Hyperplasia in Human Bronchial Epithelial Cells." Antimicrobial Agents and Chemotherapy 60, no. 11 (2016): 6585–90. http://dx.doi.org/10.1128/aac.01327-16.

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ABSTRACTActivation of the interleukin-13 (IL-13) receptor leads to signal transducer and activator of transcription 6 (STAT6) activation and subsequent induction of SAM pointed domain containing ETS transcription factor (SPDEF) and chloride channel accessory 1 (CLCA1), increasing secretion of the gel-forming mucin MUC5AC. Activation of the epidermal growth factor receptor (EGFR) also leads to MUC5AC production via extracellular signal-regulated kinase (ERK1/2). We examined the effect of clarithromycin IL-13 signaling leading to production. Normal human bronchial epithelial (NHBE) cells were grown for 14 days at an air-liquid interface (ALI) with IL-13 and/or clarithromycin. Histochemical analysis was performed using hematoxylin and eosin (HE) staining and MUC5AC immunostaining. MUC5AC, SPDEF, and CLCA1 mRNA expression were evaluated by real-time PCR. Western analysis was used to assess phosphorylation of STAT6 and ERK1/2. Clarithromycin decreased IL-13-induced goblet cell hyperplasia and MUC5AC mRNA expression in a dose-dependent manner. Clarithromycin decreased IL-13-stimulated SPDEF and CLCA1 mRNA expression in a dose-dependent manner, and at 32 μg/ml CLCA1 was profoundly decreased (P< 0.001). Although clarithromycin had no effect on STAT6 phosphorylation induced by IL-13, it decreased constitutive phosphorylation of ERK1/2 (P< 0.05).
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Sivaprasad, Umasundari, David Askew, Mark Ericksen, et al. "A non-redundant role for Serpinb3a in the induction of mucus production in asthma (141.17)." Journal of Immunology 184, no. 1_Supplement (2010): 141.17. http://dx.doi.org/10.4049/jimmunol.184.supp.141.17.

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Abstract Asthma is a major public health burden worldwide. Excessive mucus production and mucus plugging are key pathologic features of asthma, yet the mechanisms responsible for mucus production remain largely unknown and therapies to effectively target mucus hypersecretion are lacking. Using a murine asthma model, we showed that SerpinB3a, the mouse ortholog of the serine protease inhibitors, SERPINB4 and B3, contribute to house dust mite induced airway hyperresponsiveness (AHR), mucus production and goblet cell hyperplasia and expression of SPDEF, a transcription factor that mediates goblet cell differentiation. Microarray analysis revealed attenuated expression of multiple IL-13 regulated genes that contribute to mucus production in the Serpinb3a null mice and IL-13 treated mice showed attenuated AHR and mucus production. Our data have revealed a novel non-redundant role for SERPINB4 and B3 in mediating mucus production through regulation of SPDEF expression.
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Dissertations / Theses on the topic "Spdef"

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Gao, Chen. "Role of SPDEF in Prostate Cancer." University of Cincinnati / OhioLINK, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1343051932.

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Tuusa, J. (Jussi). "Transkriptiotekijöiden sitoutumiskohtien laskennallisesta määrittämisestä:ETS-faktorit ERG ja SPDEF." Master's thesis, University of Oulu, 2013. http://urn.fi/URN:NBN:fi:oulu-201305131259.

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Tässä opinnäytetyössä tarkasteltiin ja sovellettiin laskennallisia menetelmiä transkriptiotekijöiden (TF) sitoutumiskohtien (TFBS) määrittämiseen. TF:t ovat geenien säätelyyn osallistuvia proteiineja, jotka tunnistavat spesifisen nukleotidijärjestyksen sisältävän DNA-jakson eli TFBS:n sitoutuen siihen. Saman TF:n eri TFBS:t eivät ole identtisiä, vaan ainoastaan samankaltaisia. Laskennallisten menetelmät perustuvat malleihin, joissa DNA:n rakenneosasten eli nukleotidien esiintyminen kussakin TFBS:n paikassa noudattaa jotakin todennäköisyysjakaumaa. Opinnäytetyö jakaantuu kirjallisuus- ja soveltavaan osaan. Ensimmäisessä luodaan yleiskatsaus tutkimusaiheen biologiseen taustaan, esitetään aiheen kannalta keskeisiä matemaattisia määritelmiä ja kaavoja sekä perehdytään erilaisiin TFBS-määrittelyihin, kuten konsensussekvenssi, paikkapainomatriisi (PWM) ja Markov-matriisimallit. TFBS-määrittelyn löytämiseksi kehitetyistä algoritmeista esitellään MEME-menetelmä. Toiseksi kuvataan pistemääräfunktio, jonka avulla etsitään uusia sitoutumiskohtia tunnetun TFBS-määrittelyn avulla ja jota hyödynnetään sovelletun osan MATCH-algoritmissa. Esimerkkinä laskennallisten menetelmien matemaattisesta pätevyydestä esitetään MEME-menetelmän käyttämän EM-(odotusarvo-maksimointi)-algoritmin suppenemistarkastelu todistuksineen. Tämän tarkastelun päälähde on ’Wu, C. (1983) On the Convergence Properties of the EM Algorithm. The Annals of Statistics, 11: 95–103.’ Tutkielman soveltavassa osassa tutkittiin MATCH-algoritmin käyttökelpoisuutta paikannettaessa ETS-transkriptiotekijöiden ERG ja SPDEF sitoutumiskohtia joukosta kromosomaalisia DNA-sekvenssejä, joiden tiedettiin sitovan kyseisiä transkriptiotekijöitä ihmisen eturauhassyöpäsoluissa CHIP-seq-analyysin perusteella (Wei et al.(2010), EMBO J., 29: 2147–2160.) MATCH-algoritmi perustuu oletukseen TFBS:n nukleotidien multinomisesta ja toisistaan riippumattomasta jakaantumisesta. Tri Gonghong Wei ystävällisesti auttoi algoritmissa käytettyjen, alunperin MEME-algoritmilla in vitro (koeputki) -sidontakokeiden tuloksista määritettyjen PWM-matriisien hankkimisessa. Datan analyysissä käytetyt skriptit ja funktiot laadittiin itse Matlab-ympäristössä. Olennaisena osana tähän kuului MATCH-algoritmin lisäksi permutaatioanalyysi, jonka avulla arvioitiin löydettyjen TFBS-kandidaattien tilastollista merkitsevyyttä. Tutkimuksessa analysoitiin 195 ERG-tekijän ja 193 SPDEF-tekijän sitomaa sekvenssiä analysoimalla DNA:n kumpikin juoste erikseeen. Tilastollisesti merkitseviä ERG-TFBS:iä löydettiin vain kaksi ja SPDEF-TFBS:iä viisi kappaletta kaikki eri sekvensseistä. Kun ERG-sekvenssien analyysissä käytettiin in vitro -sidontakokeista saadun PWM:n sijasta in vivo (solussa tapahtuva) -määritettyä edellisestä hieman poikkeavaa PWM:ää, tilastollisesti merkitseviä TFBS-kandidaatteja löydettiin 50 sekvenssistä yhteensä 58 kappaletta. ETS-transkriptiotekijöiden sitomat DNA-sekvenssit sisältävät ainoastaan viiden nukleotidin mittaisen (C/A)GGA(A/T) -ydinjakson, joka on yhteinen suurimmalle osalle näiden proteiinien sitoutumiskohtia. Koska käytetyssä mallissa oletettiin nukleotidien esiintymisen todennäköisyysjakauma riippumattomaksi ympäröivistä nukleotideista, on ymmärrettävää, että MATCH-algoritmi tuottaa tilastollisesti merkitseviä löydöksiä vain, jos kohdesekvenssi on hyvin lähellä PWM-matriisin määräämää konsensussekvenssiä. Tällöin menetetään TFBS- kandidaatit, joissa ydinjakson ulkopuolisten nukleotidien yhteisesiintyminen puhtaasti sattumalta on epätodennäköistä, vaikka erillisinä tapahtumina, riippumattomuusoletuksen vallitessa, esiintyminen ei poikkea tilastollisesti merkitsevästi taustasta. Täten tämä tutkimus vahvistaa käsitystä, että uusia TFBS-kandidaatteja etsittäessä olisi syytä käyttää malleja, jotka sallivat riippuvuuden TFBS:n eri nukleotidipaikkojen välillä<br>The computational methods used in the analysis of transcription factor binding sites were reviewed and utilized in this Pro gradu thesis. Transcription factors (TF) are proteins that regulate the activity of genes. They bind specific DNA sequences, hereafter transcription factor binding sites (TFBS), which share the similar but usually not identical sequences of DNA building block nucleotides. Computational methods are based on models, where the presence of certain nucleotide at the specific position of the TFBS obeys some probability distribution. The thesis consists of a literature review and an applied study. First, a general review of biological background and key mathematical definitions and formulas are given. Secondly, different TFBS definitions like a consensus sequence, a position weight matrix (PWM) and markovian matrix models are presented. MEME is described as an example of an algorithm for extracting matrix form TFBS definition from DNA sequences which are known to bind a specific transcription factor. The solidity of the mathematical basis of MEME is illustrated by showing the proof for the convergence of the EM-algorithm used in MEME. Finally the principles of using a scoring function in the search of novel TFBS are presented. In the applied part of this thesis, the MATCH algorithm is used in the search for human ERG and SPDEF transcription factor binding sites in chromosomal DNA. The analysed sequences come from CHIP-seq analysis (Wei et al.(2010), EMBO J., 29: 2147–2160.) which represent real binding events in human cells. The MATCH algorithm is based on the assumption of independent and multinomial distribution of nucleotides in each TFBS position. Dr Gonghong Wei kindly helped to access the ERG and SPDEF specific PWMs used in this study. These PWMs have been produced by the MEME analysis of in vitro binding data. All the scripts and functions used in the data analysis were written in Matlab environment. In addition to the MATCH algorithm, the permutation analysis was compiled and used to estimate the statistical significance of found TFBS candidates. Altogether 195 ERG specific and 193 SPDEF specific sequences were analysed (both strands). Only two ERG TFBSs and five SPDEF TFBSs were found with statistical significance. When the in vitro PWM was replaced with an in vivo PWM which originated from CHIP-seq analysis, the analysis of ERG specific sequences provided 58 TFBS from 50 different sequences. The poor efficiency of the MATCH algorithm is obviously a consequence from the pre-assumptions of the algorithm. In contrast to the independent distribution of nucleotides postulated in the MATCH algorithm, the binding specificities of ETS-factors are likely dependent on the co-presence of multiple nucleotides. Therefore, models which take account the dependence between the nucleotide positions in the TFBS, should be preferred in the future analysis
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Chen, Gang. "Critical roles of Foxa2 and Spdef in regulating innate immunity and goblet cell differentiation in the lung." University of Cincinnati / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1276537438.

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Zickgraf, Franziska Maria [Verfasser], and Andreas [Akademischer Betreuer] Trumpp. "SPDEF is a mediator of tumorigenicity in SSEA1- tumor-initiating cells in high grade serous ovarian cancer / Franziska Maria Zickgraf ; Betreuer: Andreas Trumpp." Heidelberg : Universitätsbibliothek Heidelberg, 2021. http://d-nb.info/1230067167/34.

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Haller, Andrew Clayton. "The roles of the E26 transcription family member, SAM pointed domain-containing ETS transcription factor (SPDEF), in early stage prostate cancer and the development of castration recurrent disease." Thesis, State University of New York at Buffalo, 2013. http://pqdtopen.proquest.com/#viewpdf?dispub=3565756.

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<p> One of the greatest problems in prostate cancer management today is accurate identification of patients who require treatment for aggressive disease versus those with indolent disease who are suitable for observational strategies. Histological appearance of the tumor, called Gleason score in the prostate cancer field, is the most predictive measure currently used. However, recent studies in multiple tumor types have shown that histological appearance does not always reflect the underlying molecular phenotype of the lesion. Therefore, in prostate cancer specifically, assessment of a molecular marker of androgen receptor driven epithelial differentiation may have clinical predicative capabilities. SAM pointed domain-containing Ets transcription factor (SPDEF) is a potential AR target gene that has shown to be necessary and sufficient for epithelial cell differentiation in many tissues. Although generally associated with good prognosis, SPDEF's role in cancer in unclear. This study demonstrates, through retrospective immunohistochemical analysis, the utility of SPDEF as a predictive biomarker for patients that have an extended benefit from androgen deprivation therapy (ADT). Furthermore, dual roles of SPDEF to inhibit the initiation and supporting the progression of castrate recurrent disease through novel androgen receptor expression regulation in castrate conditions are shown. In ADT na&iuml;ve patients, SPDEF did not associate with metastatic disease or an induction of epithelial to mesenchymal transition. However, aggressive tumors tended to be larger, have greater SPDEF variability, and lack vimentin expression; a phenotype that could be explained by a partial EMT. In conclusion, SPDEF may be clinically useful to assess the epithelial phenotype of tumors, and could have utility identifying patients that will respond well to androgen deprivation therapy.</p>
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Kratky, Joseph J. "SERIES EXPANSION FOR SEMI-SPDES WITH REMARKS ON HYPERBOLIC SPDES ON THE LATTICE." Kent State University / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=kent1310614464.

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Tzitzili, Efthalia. "Numerical approximation of Stratonovich SDEs and SPDEs." Thesis, Heriot-Watt University, 2015. http://hdl.handle.net/10399/2883.

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We consider the numerical approximation of stochastic differential and partial differential equations S(P)DEs, by means of time-differencing schemes which are based on exponential integrator techniques. We focus on the study of two numerical schemes, both appropriate for the simulation of Stratonovich- interpreted S(P)DEs. The first, is a basic strong order 1=2 scheme, called Stratonovich Exponential Integrators (SEI). Motivated by SEI and aiming at benefiting both from the higher order of the standard Milstein scheme and the efficiency of the exponential schemes when dealing with stiff problems, we develop a new Milstein type scheme called Milstein Stratonovich Exponential Integrators (MSEI). We prove strong convergence of the SEI scheme for high-dimensional semilinear Stratonovich SDEs with multiplicative noise and we use SEI as well as the MSEI scheme to approximate solutions of the stochastic Landau-Lifschitz- Gilbert (LLG) equation in three dimensions. We examine the L2(Ω ) approximation error of the SEI and MSEI schemes numerically and we prove analytically that MSEI achieves a higher order of convergence than SEI. We generalise SEI so that it is suited not only for Stratonovich SDEs, but also for It^o and for SDEs interpreted by the 'in-between' calculi. Moreover, we provide a general expression for the predictor contained in SEI and we study the theoretical convergence for the generalised version of the scheme. We show that the order of the scheme used in order to obtain the predictor as well as the stochastic integral interpretation do not affect the overall order of the scheme. We extend the convergence results for SEI to a space-time context by considering a second order semilinear Stratonovich SPDE with multiplicative noise. We discretise in space with the nite element method and we use SEI for discretising in time. We consider the case where we have trace class noise and we examine analytically the strong order of convergence for SEI. We implement SEI as a time discretisation scheme and present the results when simulating SPDEs with stochastic travelling wave solutions. Then, we use an alternative method, called 'freezing' method, for approximating wave solutions and estimating the speed of the waves for the stochastic Nagumo and FitzHugh-Nagumo models. The wave position and hence the speed is found by minimising the L2 distance between a reference function and the travelling wave. While the results obtained from the two different approaches agree, we observe that the behaviour of the wave solution is captured in a smaller computational domain, when we use the freezing method, making it more efficient for long time simulations.
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Fontes, Ramiro. "Applications of Allouba's differentiation theory and semi-SPDEs." [Kent, Ohio] : Kent State University, 2010. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=kent1271438954.

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Fontes, Ramiro C. "Applications of Allouba's Differentiation Theory and Semi-SPDEs." Kent State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=kent1271438954.

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Martin, Jörg. "Refinements of the Solution Theory for Singular SPDEs." Doctoral thesis, Humboldt-Universität zu Berlin, 2018. http://dx.doi.org/10.18452/19329.

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Diese Dissertation widmet sich der Untersuchung singulärer stochastischer partieller Differentialgleichungen (engl. SPDEs). Wir entwickeln Erweiterungen der bisherigen Lösungstheorien, zeigen fundamentale Beziehungen zwischen verschiedenen Ansätzen und präsentieren Anwendungen in der Finanzmathematik und der mathematischen Physik. Die Theorie parakontrollierter Systeme wird für diskrete Räume formuliert und eine schwache Universalität für das parabolische Anderson Modell bewiesen. Eine fundamentale Relation zwischen Hairer's modellierten Distributionen und Paraprodukten wird bewiesen: Wir zeigen das sich der Raum modellierter Distributionen durch Paraprodukte beschreiben lässt. Dieses Resultat verallgemeinert die Fourierbeschreibung von Hölderräumen mittels Littlewood-Paley Theorie. Schließlich wird die Existenz von Lösungen der stochastischen Schrödingergleichung auf dem ganzen Raum bewiesen und eine Anwendung Hairer's Theorie zur Preisermittlung von Optionen aufgezeigt.<br>This thesis is concerned with the study of singular stochastic partial differential equations (SPDEs). We develop extensions to existing solution theories, present fundamental interconnections between different approaches and give applications in financial mathematics and mathematical physics. The theory of paracontrolled distribution is formulated for discrete systems, which allows us to prove a weak universality result for the parabolic Anderson model. This thesis further shows a fundamental relation between Hairer's modelled distributions and paraproducts: The space of modelled distributions can be characterized completely by using paraproducts. This can be seen a generalization of the Fourier description of Hölder spaces. Finally, we prove the existence of solutions to the stochastic Schrödinger equation on the full space and provide an application of Hairer's theory to option pricing.
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Books on the topic "Spdef"

1

Khoshnevisan, Davar, and René Schilling. From Lévy-Type Processes to Parabolic SPDEs. Edited by Frederic Utzet and Lluis Quer-Sardanyons. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-34120-0.

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Flandoli, Franco. Regularity theory and stochastic flows for parabolic SPDEs. Gordon and Breach, 1995.

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Flandoli, Franco. Regularity theory and stochastic flows for parabolic SPDEs. Gordon & Breach, 1995.

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Albeverio, Sergio, Franco Flandoli, and Yakov G. Sinai. SPDE in Hydrodynamic: Recent Progress and Prospects. Edited by Giuseppe Da Prato and Michael Rückner. Springer Berlin Heidelberg, 2008. http://dx.doi.org/10.1007/978-3-540-78493-7.

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Cohen, Samuel N., István Gyöngy, Gonҫalo dos Reis, David Siska, and Łukasz Szpruch, eds. Frontiers in Stochastic Analysis–BSDEs, SPDEs and their Applications. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-22285-7.

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C, I. M. E. Summer School (2005 Cetraro Italy ). SPDE in hydrodynamic: Recent progress and prospects lectures given at the C.I.M.E. Summer School held in Cetraro, Italy August 29 - September 3, 2005. Springer, 2008.

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Giuseppe, Da Prato, Flandoli Franco, Röckner Michael, and Centro internazionale matematico estivo, eds. SPDE in hydrodynamic: Recent progress and prospects lectures given at the C.I.M.E. Summer School held in Cetraro, Italy August 29 - September 3, 2005. Springer, 2008.

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Sergio Albeverio,Franco Flandoli,Yakov G. Sinai. Spde in Hydrodynamics. Springer, 2008.

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Eency Weency Spder-XL Edition. Piggy Toes Press, 2005.

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United States. National Aeronautics and Space Administration., ed. SPDE/SPRE final summary report. National Aeronautics and Space Administration, 1993.

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Book chapters on the topic "Spdef"

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Goodair, Daniel. "Existence and Uniqueness of Maximal Solutions to a 3D Navier-Stokes Equation with Stochastic Lie Transport." In Mathematics of Planet Earth. Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-031-18988-3_7.

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AbstractWe present here a criterion to conclude that an abstract SPDE possesses a unique maximal strong solution, which we apply to a three dimensional Stochastic Navier-Stokes Equation. Motivated by the work of Kato and Lai we ask that there is a comparable result here in the stochastic case whilst facilitating a variety of noise structures such as additive, multiplicative and transport. In particular our criterion is designed to fit viscous fluid dynamics models with Stochastic Advection by Lie Transport (SALT) as introduced in Holm (Proc R Soc A: Math Phys Eng Sci 471(2176):20140963, 2015). Our application to the Incompressible Navier-Stokes equation matches the existence and uniqueness result of the deterministic theory. This short work summarises the results and announces two papers (Crisan et al., Existence and uniqueness of maximal strong solutions to nonlinear SPDEs with applications to viscous fluid models, in preparation; Crisan and Goodair, Analytical properties of a 3D stochastic Navier-Stokes equation, 2022, in preparation) which give the full details for the abstract well-posedness arguments and application to the Navier-Stokes Equation respectively.
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Khoshnevisan, Davar. "SPDEs." In Advanced Courses in Mathematics - CRM Barcelona. Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-34120-0_16.

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Zambotti, Lorenzo. "SPDEs and Renormalisation." In Stochastic Partial Differential Equations and Related Fields. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-74929-7_16.

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Čoupek, Petr, Bohdan Maslowski, and Jana Šnupárková. "SPDEs with Volterra Noise." In Stochastic Partial Differential Equations and Related Fields. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-74929-7_7.

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Röckner, Michael. "Kolmogorov operators and SPDEs." In Spectral Structures and Topological Methods in Mathematics. European Mathematical Society Publishing House, 2019. http://dx.doi.org/10.4171/197-1/2.

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Kusuoka, Shigeo. "Term structure and SPDE." In Advances in Mathematical Economics. Springer Japan, 2000. http://dx.doi.org/10.1007/978-4-431-67909-7_4.

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Gubinelli, Massimiliano, and Nicolas Perkowski. "An Introduction to Singular SPDEs." In Stochastic Partial Differential Equations and Related Fields. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-74929-7_4.

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Liu, Wei, and Michael Röckner. "SPDEs with Locally Monotone Coefficients." In Stochastic Partial Differential Equations: An Introduction. Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-22354-4_5.

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Cioica, Petru A., Stephan Dahlke, Nicolas Döhring, et al. "Adaptive Wavelet Methods for SPDEs." In Extraction of Quantifiable Information from Complex Systems. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-08159-5_5.

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Lototsky, Sergey V., and Boris L. Rozovsky. "Parameter Estimation for Diagonal SPDEs." In Universitext. Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-58647-2_6.

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Conference papers on the topic "Spdef"

1

Haitchi, Hans Michael, Donna E. Davies, Stephen T. Holgate, P. H. Howarth, and Jeffrey A. Whitsett. "The SPDEF Network Regulates Mucus Cell Differentiation In Asthma." In American Thoracic Society 2011 International Conference, May 13-18, 2011 • Denver Colorado. American Thoracic Society, 2011. http://dx.doi.org/10.1164/ajrccm-conference.2011.183.1_meetingabstracts.a2771.

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Haitchi, Hans Michael, Elizabeth R. Davies, Gang Chen, et al. "The Airway Mucus Regulating Transcription Factor SPDEF Is Increased In BALF In Asthma." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a1398.

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Lo, Yuan-Hung, Taeko Noah, Min-Shan Chen, Winnie Zou та Noah Shroyer. "Abstract 2012: SPDEF enforces tumor quiescence by shifting the transcriptional targets of activated β-catenin". У Proceedings: AACR 107th Annual Meeting 2016; April 16-20, 2016; New Orleans, LA. American Association for Cancer Research, 2016. http://dx.doi.org/10.1158/1538-7445.am2016-2012.

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Koh, K. D., L. R. Bonser, W. L. Eckalbar, et al. "Identification and Characterization of an IL-13-Inducible SPDEF Enhancer in Human Airway Secretory Cells." In American Thoracic Society 2019 International Conference, May 17-22, 2019 - Dallas, TX. American Thoracic Society, 2019. http://dx.doi.org/10.1164/ajrccm-conference.2019.199.1_meetingabstracts.a3810.

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Song, Juan, Karolin Meyer, Loes E. M. Kistemaker, et al. "Targeted silencing of master transcription factor SPDEF to reduce mucus production in airway diseases by epigenetic editing." In Annual Congress 2015. European Respiratory Society, 2015. http://dx.doi.org/10.1183/13993003.congress-2015.oa486.

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Xu, Zhibo B., Ann E. Tilley, Jacqueline Salit, and Ronald G. Crystal. "SPDEF, A Transcription Factor Regulator Of Goblet Cell Differentiation, Is Up-regulated By Smoking In Human Small Airway Epithelium." In American Thoracic Society 2010 International Conference, May 14-19, 2010 • New Orleans. American Thoracic Society, 2010. http://dx.doi.org/10.1164/ajrccm-conference.2010.181.1_meetingabstracts.a6760.

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Haitchi, Hans Michael, Nicole Bedke, Julian Legg, et al. "The Induction Of The SPDEF Network By Rhinovirus Infection Of Primary Bronchial Epithelial Cells From Cystic Fibrosis Patients And Healthy Control Subjects." In American Thoracic Society 2012 International Conference, May 18-23, 2012 • San Francisco, California. American Thoracic Society, 2012. http://dx.doi.org/10.1164/ajrccm-conference.2012.185.1_meetingabstracts.a2806.

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Montgomery, M. T., C. M. Moore, J. L. Everman, et al. "Single Cell RNA-seq Characterization of SPDEF Knock-Out in the Mucociliary Epithelium Reveals Mechanisms of Mucus Cell Differentiation in Both the Healthy and Inflamed Airways." In American Thoracic Society 2020 International Conference, May 15-20, 2020 - Philadelphia, PA. American Thoracic Society, 2020. http://dx.doi.org/10.1164/ajrccm-conference.2020.201.1_meetingabstracts.a6147.

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GUBINELLI, MASSIMILIANO. "A PANORAMA OF SINGULAR SPDES." In International Congress of Mathematicians 2018. WORLD SCIENTIFIC, 2019. http://dx.doi.org/10.1142/9789813272880_0140.

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Kolokoltsov, Vassili N., and Marianna Troeva. "Regularity and sensitivity for McKean-Vlasov SPDEs." In PROCEEDINGS OF THE 3RD INTERNATIONAL CONFERENCE ON CONSTRUCTION AND BUILDING ENGINEERING (ICONBUILD) 2017: Smart Construction Towards Global Challenges. Author(s), 2017. http://dx.doi.org/10.1063/1.5012668.

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Reports on the topic "Spdef"

1

Cao, Yanzhao. Numerical Solutions for Optimal Control under SPDE Constraints. Defense Technical Information Center, 2008. http://dx.doi.org/10.21236/ada479338.

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Chi, Hongmei, and Yanzhao Cao. Numerical Solution of Optimal Control Problem under SPDE Constraints. Defense Technical Information Center, 2011. http://dx.doi.org/10.21236/ada564030.

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Cao, Yanzhao. Numerical Solutions for Optimal Control Problems Under SPDE Constraints. Defense Technical Information Center, 2006. http://dx.doi.org/10.21236/ada458787.

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Cao, Yanzhao. Numerical Solutions for Optimal Control Problems Under SPDE Constraints. Defense Technical Information Center, 2008. http://dx.doi.org/10.21236/ada480192.

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Gunzburger, Max. Advanced Numerical Methods for Computing Statistical Quantities of Interest from Solutions of SPDES. Defense Technical Information Center, 2012. http://dx.doi.org/10.21236/ada563949.

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Cohen, Albert, Ronald DeVore, and Christoph Schwab. Convergence Rates of Best N-term Galerkin Approximations for a Class of Elliptic sPDEs. Defense Technical Information Center, 2010. http://dx.doi.org/10.21236/ada522055.

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