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Pfister N.T.,Columbia University | Fomin V.,Columbia University | Regunath K.,Columbia University | Zhou J.Y.,Columbia University | And 16 more authors.
Genes and Development | Year: 2015

Mutant p53 impacts the expression of numerous genes at the level of transcription to mediate oncogenesis. We identified vascular endothelial growth factor receptor 2 (VEGFR2), the primary functional VEGF receptor that mediates endothelial cell vascularization, as a mutant p53 transcriptional target in multiple breast cancer cell lines. Up-regulation of VEGFR2 mediates the role of mutant p53 in increasing cellular growth in two-dimensional (2D) and three-dimensional (3D) culture conditions. Mutant p53 binds near the VEGFR2 promoter transcriptional start site and plays a role in maintaining an open conformation at that location. Relatedly, mutant p53 interacts with the SWI/SNF complex, which is required for remodeling the VEGFR2 promoter. By both querying individual genes regulated by mutant p53 and performing RNA sequencing, the results indicate that >40% of all mutant p53-regulated gene expression is mediated by SWI/SNF. We surmise that mutant p53 impacts transcription of VEGFR2 as well as myriad other genes by promoter remodeling through interaction with and likely regulation of theSWI/SNFchromatin remodeling complex. Therefore, not only might mutant p53-expressing tumors be susceptible to antiVEGFtherapies, impacting SWI/SNF tumor suppressor function in mutant p53 tumors may also have therapeutic potential. © 2015, Pfister et al.

MORRISVILLE, N.C., March 01, 2017 (GLOBE NEWSWIRE) -- Novan, Inc. (“the Company” or “Novan”) (NASDAQ:NOVN) today announced that preclinical data demonstrating the anti-viral effects of the Company’s nitric oxide-releasing drug candidates will be presented at the 31st International Papillomavirus Conference in Cape Town, South Africa. Thomas Broker, Ph.D., and Louise Chow, Ph.D., both of the University of Alabama at Birmingham, or UAB, are scheduled to present “Antiviral Efficacy of Nitric Oxide-Releasing Drug Candidates in Suppressing Productive Infection by HPV-18 in the Organotypic Epithelial Raft Culture Model System” on Thursday, Mar. 2. Drs. Broker and Chow are professors in the Department of Biochemistry and Molecular Genetics at UAB’s School of Medicine. The Broker-Chow research program has been focused on human papillomavirus, or HPV, for more than 33 years. “We are very excited by the continuing success of the investigational nitric oxide-releasing agents against HPV infections,” said Dr. Broker. “The data we are presenting showed significant inhibition of the high-risk HPV-18 genotype and reduction of the E6 viral protein in the raft culture model. We are quite pleased that the testing results from our laboratory have had a very constructive impact in elucidating some of the probable mechanisms of action and the affected cellular and viral pathways.” Published studies have demonstrated that the E6 protein impedes the body’s ability to recognize HPV-infected cells and disrupts the cells’ ability to repair DNA damage and prevent abnormal cellular replication. As a result, E6 is believed to be a primary driver of HPV-related cancers and other abnormal growths. “The findings generated in Broker-Chow’s human tissue model support the novel mechanism of action of Novan’s topical SB206 anti-viral development program,” said Nathan Stasko, Ph.D., President and Chief Executive Officer of Novan. “HPV affects millions of Americans, and we believe nitric oxide-releasing drug candidates have incredible potential not only for the topical treatment of genital, common and plantar warts caused by HPV, but also against cancers associated with high-risk HPV subtypes.” Top-line results from Novan’s Phase 2 clinical trial with SB206 for the treatment of genital warts caused by HPV were announced in November 2016. HPV refers to a large family of double-stranded DNA viruses that induce abnormal growths on the skin or mucosal surfaces. HPV affects nearly 80 million Americans, and an estimated 14 million new cases of the virus are reported each year, according to the Centers for Disease Control and Prevention, or CDC. There are over 100 subtypes of the virus, characterized as low-risk or high-risk based on their cancer-causing potential. The virus is typically transmitted via direct skin-to-skin contact through disruptions in the normal skin barrier. All warts are caused by HPV, including genital and perianal warts, common warts and plantar warts. Genital warts are among the world's most common sexually transmitted diseases. Genital warts are usually flesh-colored growths that can be raised, flat or cauliflower-shaped and are typically found on the surface of the external genitalia or in and around the anus. In males, they can appear on the surface of the penis and scrotum, and in females inside the vagina or on the cervix. Genital warts carry a substantial psychosocial burden due to the shame and embarrassment related to having a sexually transmitted disease as well as the inconvenience and discomfort of current treatment modalities. Current treatment options for genital warts consist of ablative procedures that cut, burn or freeze the warts but do not address the underlying viral infection, and there are no currently approved oral or topical prescription products indicated for the treatment of genital warts with a direct anti-viral mechanism of action. Novan, Inc. is a late-stage pharmaceutical company focused on redefining the standard of care in dermatology through the development and commercialization of innovative therapies using the Company’s nitric oxide-releasing platform. Nitric oxide plays a vital role in the natural immune system response against microbial pathogens and is a critical regulator of inflammation. Our ability to harness nitric oxide and its multiple mechanisms of action has enabled us to create a platform with the potential to generate differentiated, first-in-class product candidates. We are rapidly advancing programs in five dermatological conditions with significant unmet medical need. We believe that our ability to conveniently deploy nitric oxide on demand in topical formulations allows us the potential to significantly improve patient outcomes in a variety of skin diseases and positions us to be a commercially successful leader in the dermatology market. For more information, visit the Company’s website at This press release contains forward-looking statements including, but not limited to, statements related to pharmaceutical development of nitric oxide-releasing product candidates, expected performance of our product candidates, publication and presentation of our trial results in the medical community and future prospects of our business and our product candidates. Forward-looking statements are subject to a number of risks and uncertainties that could cause actual results to differ materially from our expectations, including, but not limited to, uncertainties and risks in the clinical development process, including, among others, length, expense, ability to enroll patients, reliance on third parties, and that results of earlier research and preclinical or clinical trials may not be predictive of results, conclusions or interpretations of later research or trials; the lengthy and unpredictable nature of the U.S. Food and Drug Administration’s drug approval process; whether we will be able to obtain additional funding when needed; and other risks and uncertainties described in our prospectus dated Sept. 20, 2016, filed with the Securities and Exchange Commission, or SEC, in our quarterly report filed with the SEC on Form 10-Q for the three months ended Sept. 30, 2016, and in any subsequent filings with the SEC. These forward-looking statements speak only as of the date of this press release, and Novan disclaims any intent or obligation to update these forward-looking statements to reflect events or circumstances after the date of such statements, except as may be required by law.

Kurosaki T.,University of Rochester | Li W.,Biochemistry and Molecular Genetics | Hoque M.,Biochemistry and Molecular Genetics | Popp M.W.-L.,University of Rochester | And 3 more authors.
Genes and Development | Year: 2014

Nonsense-mediated mRNA decay (NMD) controls the quality of eukaryotic gene expression and also degrades physiologic mRNAs. How NMD targets are identified is incompletely understood. A central NMD factor is the ATP-dependent RNA helicase upframeshift 1 (UPF1). Neither the distance in space between the termination codon and the poly(A) tail nor the binding of steady-state, largely hypophosphorylated UPF1 is a discriminating marker of cellular NMD targets, unlike for premature termination codon (PTC)-containing reporter mRNAs when compared with their PTC-free counterparts. Here, we map phosphorylated UPF1 (p-UPF1)-binding sites using transcriptomewide footprinting or DNA oligonucleotide-directed mRNA cleavage to report that p-UPF1 provides the first reliable cellular NMD target marker. p-UPF1 is enriched on NMD target 3' untranslated regions (UTRs) along with suppressor with morphogenic effect on genitalia 5 (SMG5) and SMG7 but not SMG1 or SMG6. Immunoprecipitations of UPF1 variants deficient in various aspects of the NMD process in parallel with Förster resonance energy transfer (FRET) experiments reveal that ATPase/helicase-deficient UPF1 manifests high levels of RNA binding and disregulated hyperphosphorylation, whereas wild-type UPF1 releases from nonspecific RNA interactions in an ATP hydrolysis-dependent mechanism until an NMD target is identified. 3' UTR-associated UPF1 undergoes regulated phosphorylation on NMD targets, providing a binding platform for mRNA degradative activities. p-UPF1 binding to NMD target 3' UTRs is stabilized by SMG5 and SMG7. Our results help to explain why steady-state UPF1 binding is not a marker for cellular NMD substrates and how this binding is transformed to induce mRNA decay. © 2014 Kurosaki et al.

Stern P.L.,Paterson Institute for Cancer Research | van der Burg S.H.,Leiden University | Hampson I.N.,University of Manchester | Broker T.R.,Biochemistry and Molecular Genetics | And 4 more authors.
Vaccine | Year: 2012

This chapter reviews the current treatment of chronic and neoplastic human papillomavirus (HPV)-associated conditions and the development of novel therapeutic approaches. Surgical excision of HPVassociated lower genital tract neoplasia is very successful but largely depends on secondary prevention programmes for identification of disease. Only high-risk HPV-driven chronic, pre-neoplastic lesions and some very early cancers cannot be successfully treated by surgical procedures alone. Chemoradiation therapy of cervical cancer contributes to the 66-79% cervical cancer survival at 5 years. Outlook for those patients with persistent or recurrent cervical cancer following treatment is very poor. Topical agents such as imiquimod (immune response modifier), cidofovir (inhibition of viral replication; induction apoptosis) or photodynamic therapy (direct damage of tumour and augmentation of anti-tumour immunity) have all shown some useful efficacy (~50-60%) in treatment of high grade vulvar intraepithelial neoplasia (VIN). Provider administered treatments of genital warts include cryotherapy, trichloracetic acid, or surgical removal which has the highest primary clearance rate. Patient applied therapies include podophyllotoxin and imiquimod. Recurrence after "successful" treatment is 30-40%. Further improvements could derive from a rational combination of current therapy with new drugs targeting molecular pathways mediated by HPV in cancer. Small molecule inhibitors targeting the DNA binding activities of HPV E1/E2 or the antiapoptotic consequences of E6/E7 oncogenes are in preclinical development. Proteasome and histone deacetylase inhibitors, which can enhance apoptosis in HPV positive tumour cells, are being tested in early clinical trials. Chronic high-risk HPV infection/neoplasia is characterised by systemic and/or local immune suppressive regulatory or escape factors. Recently two E6/E7 vaccines have shown some clinical efficacy in high grade VIN patients and this correlated with strong and broad systemic HPV-specific T cell response and modulation of key local immune factors. Treatments that can shift the balance of immune effectors locally in combination with vaccination are now being tested. © 2012 Elsevier Ltd. All rights reserved.

Lea M.A.,Biochemistry and Molecular Genetics | Guzman Y.,Biochemistry and Molecular Genetics | Desbordes C.,City University of New York
Anticancer research | Year: 2016

Enhanced glycolysis in cancer cells presents a target for chemotherapy. Previous studies have indicated that proliferation of cancer cells can be inhibited by treatment with phenformin and with an inhibitor of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB) namely 3-(3-pyridinyl)-1-(4-pyridinyl)-2-propen-1-one (3PO). In the present work, the action of two inhibitors that are effective at lower concentrations than 3PO, namely 1-(3-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PQP) and 1-(4-pyridinyl)-3-(2-quinolinyl)-2-propen-1-one (PFK15) were investigated. The inhibitors of lactate dehydrogenase (LDHA) studied in order of half-maximal inhibitory concentrations were methyl 1-hydroxy-6-phenyl-4-(trifluoromethyl)-1H-indole-2-carboxylate (NHI-2) < isosafrole < oxamate. In colonic and bladder cancer cells, additive growth inhibitory effects were seen with the LDHA inhibitors, of which NHI-2 was effective at the lowest concentrations. Growth inhibition was generally greater with PFK15 than with PQP. The increased acidification of the culture medium and glucose uptake caused by phenformin was blocked by combined treatment with PFKFB3 or LDHA inhibitors. The results suggest that combined treatment with phenformin and inhibitors of glycolysis can cause additive inhibition of cell proliferation and may mitigate lactic acidosis caused by phenformin when used as a single agent. Copyright© 2016 International Institute of Anticancer Research (Dr. John G. Delinassios), All rights reserved.

Jin Y.,Harvard University | Geisberg J.V.,Harvard University | Moqtaderi Z.,Harvard University | Ji Z.,Harvard University | And 3 more authors.
Current Protocols in Molecular Biology | Year: 2015

Most eukaryotic genes are transcribed into mRNAs with alternative poly(A) sites. Emerging evidence suggests that mRNA isoforms with alternative poly(A) sites can perform critical regulatory functions in numerous biological processes. In recent years, a number of strategies utilizing high-throughput sequencing technologies have been developed to aid in the identification of genome-wide poly(A) sites. This unit describes a modified protocol for a recently published 3'READS (3' region extraction and deep sequencing) method that accurately identifies genome-wide poly(A) sites and that can be used to quantify the relative abundance of the resulting 3' mRNA isoforms. This approach minimizes nonspecific sequence reads due to internal priming and typically yields a high percentage of sequence reads that are ideally suited for accurate poly(A) identification. © 2015 by John Wiley & Sons, Inc.

Zheng D.,Biochemistry and Molecular Genetics | Liu X.,Biochemistry and Molecular Genetics | Tian B.,Biochemistry and Molecular Genetics
RNA | Year: 2016

Sequencing of the 3′ end of poly(A)+ RNA identifies cleavage and polyadenylation sites (pAs) and measures transcript expression. We previously developed a method, 3′ region extraction and deep sequencing (3′READS), to address mispriming issues that often plague 3′ end sequencing. Here we report a new version, named 3′READS+, which has vastly improved accuracy and sensitivity. Using a special locked nucleic acid oligo to capture poly(A)+ RNA and to remove the bulk of the poly(A) tail, 3′READS+ generates RNA fragments with an optimal number of terminal A's that balance data quality and detection of genuine pAs. With improved RNA ligation steps for efficiency, the method shows much higher sensitivity (over two orders of magnitude) compared to the previous version. Using 3′READS+, we have uncovered a sizable fraction of previously overlooked pAs located next to or within a stretch of adenylate residues in human genes and more accurately assessed the frequency of alternative cleavage and polyadenylation (APA) in HeLa cells (∼50%). 3′READS+ will be a useful tool to accurately study APA and to analyze gene expression by 3′ end counting, especially when the amount of input total RNA is limited. © 2016 Zheng et al.

Silver B.,Biochemistry and Molecular Genetics | Zhu H.,Biochemistry and Molecular Genetics
Virologica Sinica | Year: 2014

Varicella zoster virus (VZV) is the causative agent of varicella (chicken pox) and herpes zoster (shingles). After primary infection, the virus remains latent in sensory ganglia, and reactivates upon weakening of the cellular immune system due to various conditions, erupting from sensory neurons and infecting the corresponding skin tissue. The current varicella vaccine (v-Oka) is highly attenuated in the skin, yet retains its neurovirulence and may reactivate and damage sensory neurons. The reactivation is sometimes associated with postherpetic neuralgia (PHN), a severe pain along the affected sensory nerves that can linger for years, even after the herpetic rash resolves. In addition to the older population that develops a secondary infection resulting in herpes zoster, childhood breakthrough herpes zoster affects a small population of vaccinated children. There is a great need for a neuro-attenuated vaccine that would prevent not only the varicella manifestation, but, more importantly, any establishment of latency, and therefore herpes zoster. The development of a genetically-defined live-attenuated VZV vaccine that prevents neuronal and latent infection, in addition to primary varicella, is imperative for eventual eradication of VZV, and, if fully understood, has vast implications for many related herpesviruses and other viruses with similar pathogenic mechanisms. © 2014, Wuhan Institute of Virology, CAS and Springer-Verlag Berlin Heidelberg.

Rogers M.B.,Biochemistry and Molecular Genetics | Shah T.A.,Biochemistry and Molecular Genetics | Shaikh N.N.,Biochemistry and Molecular Genetics
Journal of Cellular Biochemistry | Year: 2015

The concentration, location, and timing of bone morphogenetic protein 2 (BMP2, HGNC:1069, GeneID: 650) gene expression must be precisely regulated. Abnormal BMP2 levels cause congenital anomalies and diseases involving the mesenchymal cells that differentiate into muscle, fat, cartilage, and bone. The molecules and conditions that influence BMP2 synthesis are diverse. Understandably, complex mechanisms control Bmp2 gene expression. This review includes a compilation of agents and conditions that can induce Bmp2. The currently known trans-regulatory factors and cis-regulatory elements that modulate Bmp2 expression are summarized and discussed. Bone morphogenetic protein 2 (BMP2, HGNC:1069, GeneID: 650) is a classical morphogen; a molecule that acts at a distance and whose concentration influences cell behavior. In mesenchymal cells, the concentration of BMP2 influences myogenesis, adipogenesis, chondrogenesis, and osteogenesis. Because the amount, timing, and location of BMP2 synthesis influence the allocation of cells to muscle, fat, cartilage, and bone, the mechanisms that regulate the Bmp2 gene are crucial. Key early mesodermal events that require precise Bmp2 regulation include heart specification and morphogenesis. Originally named for its osteoinductive properties, healing fractures requires BMP2. The human Bmp2 gene also has been linked to osteoporosis and osteoarthritis. In addition, all forms of pathological calcification in the vasculature and in cardiac valves involve the pro-osteogenic BMP2. The diverse tissues, mechanisms, and diseases influenced by BMP2 are too numerous to list here (see OMIM: 112261). However, in all BMP2-influenced pathologies, changes in the behavior and differentiation of pluripotent mesenchymal cells are a recurring theme. Consequently, much effort has been devoted to identifying the molecules and conditions that influence BMP2 synthesis and the complex mechanisms that control Bmp2 gene expression. This review begins with an overview of the Bmp2 gene's chromosomal neighborhood and then summarizes and evaluates known regulatory mechanisms and inducers. J. Cell. Biochem. 116: 2127-2138, 2015. © 2015 Wiley Periodicals, Inc.

Lea M.A.,Biochemistry and Molecular Genetics
Journal of Cellular Biochemistry | Year: 2015

Flavonols comprise a group of flavonoid molecules that are widely distributes in fruits and vegetables. There is epidemiological data to suggest that consumption of flavonols can be accompanied by decreased cancer incidence. The anti-oxidant activity of flavonols may have an important role in preventing carcinogenesis. Therapeutic potential of flavonols is indicated by their growth inhibitory action accompanied by a decrease in several hallmarks of cancer such as resistance to apoptosis. Multiple mechanisms of action have been reported for the action of flavonols on cancer cells. Particular emphasis has been directed to inhibitory effects on several protein kinases and on the potential for prooxidant effects. The diversity of actions presents a problem in trying to elucidate primary and secondary effects but it may be a strength of the therapeutic potential of flavonols that it renders development of resistance more difficult for cancer cells. Cancer chemotherapy is usually characterized by the use of drug combinations. Some additive or synergistic combinations have been identified for flavonols and this is an area of ongoing investigation. As with other polyphenolic molecules there have been questions of cellular uptake and bioavailability. Several investigations have been and are being conducted to modify the structures of flavonols with the goal of increasing bioavailability. At present many investigators are sufficiently encouraged by past observations that they are responding to the challenge to optimize the dietary and therapeutic use of flavonols in cancer prevention and treatment. J. Cell. Biochem. 116: 1190-1194, 2015. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

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