Stony Brook University Medical School

Stony Brook, NY, United States

Stony Brook University Medical School

Stony Brook, NY, United States
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Leen E.N.,Imperial College London | Rex Kwok K.Y.,Imperial College London | Birtley J.R.,Imperial College London | Birtley J.R.,University of Massachusetts Medical School | And 19 more authors.
Journal of Virology | Year: 2013

We report the solution structures of the VPg proteins from feline calicivirus (FCV) and murine norovirus (MNV), which have been determined by nuclear magnetic resonance spectroscopy. In both cases, the core of the protein adopts a compact helical structure flanked by flexible N and C termini. Remarkably, while the core of FCV VPg contains a well-defined three-helix bundle, the MNV VPg core has just the first two of these secondary structure elements. In both cases, the VPg cores are stabilized by networks of hydrophobic and salt bridge interactions. The Tyr residue in VPg that is nucleotidylated by the viral NS7 polymerase (Y24 in FCV, Y26 in MNV) occurs in a conserved position within the first helix of the core. Intriguingly, given its structure, VPg would appear to be unable to bind to the viral polymerase so as to place this Tyr in the active site without a major conformation change to VPg or the polymerase. However, mutations that destabilized the VPg core either had no effect on or reduced both the ability of the protein to be nucleotidylated and virus infectivity and did not reveal a clear structure-activity relationship. The precise role of the calicivirus VPg core in virus replication remains to be determined, but knowledge of its structure will facilitate future investigations. © 2013, American Society for Microbiology.

Bestman J.E.,Scripps Research Institute | Lee-Osbourne J.,Stony Brook University Medical School | Cline H.T.,Scripps Research Institute | Cline H.T.,University of Nebraska Medical Center
Journal of Comparative Neurology | Year: 2012

We analyzed the function of neural progenitors in the developing central nervous system of Xenopus laevis tadpoles by using in vivo time-lapse confocal microscopy to collect images through the tectum at intervals of 2-24 hours over 3 days. Neural progenitor cells were labeled with fluorescent protein reporters based on expression of endogenous Sox2 transcription factor. With this construct, we identified Sox2-expressing cells as radial glia and as a component of the progenitor pool of cells in the developing tectum that gives rise to neurons and other radial glia. Lineage analysis of individual radial glia and their progeny demonstrated that less than 10% of radial glia undergo symmetric divisions resulting in two radial glia, whereas the majority of radial glia divide asymmetrically to generate neurons and radial glia. Time-lapse imaging revealed the direct differentiation of radial glia into neurons. Although radial glia may guide axons as they navigate to the superficial tectum, we find no evidence that radial glia function as a scaffold for neuronal migration at early stages of tectal development. Over 3 days, the number of labeled cells increased 20%, as the fraction of radial glia dropped and the proportion of neuronal progeny increased to approximately 60% of the labeled cells. Tadpoles provided with short-term visual enhancement generated significantly more neurons, with a corresponding decrease in cell proliferation. Together these results demonstrate that radial glial cells are neural progenitors in the developing optic tectum and reveal that visual experience increases the proportion of neurons generated in an intact animal. J. Comp. Neurol. 520:401-433, 2012. © 2011 Wiley Periodicals, Inc.

Wang L.,University of California at San Francisco | Perera B.G.K.,University of Washington | Hari S.B.,University of Washington | Bhhatarai B.,University of Miami | And 6 more authors.
Nature Chemical Biology | Year: 2012

Under endoplasmic reticulum stress, unfolded protein accumulation leads to activation of the endoplasmic reticulum transmembrane kinase/endoRNase (RNase) IRE1α. IRE1α oligomerizes, autophosphorylates and initiates splicing of XBP1 mRNA, thus triggering the unfolded protein response (UPR). Here we show that IRE1α's kinase-controlled RNase can be regulated in two distinct modes with kinase inhibitors: one class of ligands occupies IRE1α's kinase ATP-binding site to activate RNase-mediated XBP1 mRNA splicing even without upstream endoplasmic reticulum stress, whereas a second class can inhibit the RNase through the same ATP-binding site, even under endoplasmic reticulum stress. Thus, alternative kinase conformations stabilized by distinct classes of ATP-competitive inhibitors can cause allosteric switching of IRE1α's RNase - either on or off. As dysregulation of the UPR has been implicated in a variety of cell degenerative and neoplastic disorders, small-molecule control over IRE1α should advance efforts to understand the UPR's role in pathophysiology and to develop drugs for endoplasmic reticulum stress-related diseases. © 2012 Nature America, Inc. All rights reserved.

Feldman H.C.,University of Washington | Tong M.,Stony Brook University Medical School | Wang L.,University of California at San Francisco | Meza-Acevedo R.,University of California at San Francisco | And 9 more authors.
ACS Chemical Biology | Year: 2016

The accumulation of unfolded proteins under endoplasmic reticulum (ER) stress leads to the activation of the multidomain protein sensor IRE1α as part of the unfolded protein response (UPR). Clustering of IRE1α lumenal domains in the presence of unfolded proteins promotes kinase trans-autophosphorylation in the cytosol and subsequent RNase domain activation. Interestingly, there is an allosteric relationship between the kinase and RNase domains of IRE1α, which allows ATP-competitive inhibitors to modulate the activity of the RNase domain. Here, we use kinase inhibitors to study how ATP-binding site conformation affects the activity of the RNase domain of IRE1α. We find that diverse ATP-competitive inhibitors of IRE1α promote dimerization and activation of RNase activity despite blocking kinase autophosphorylation. In contrast, a subset of ATP-competitive ligands, which we call KIRAs, allosterically inactivate the RNase domain through the kinase domain by stabilizing monomeric IRE1α. Further insight into how ATP-competitive inhibitors are able to divergently modulate the RNase domain through the kinase domain was gained by obtaining the first structure of apo human IRE1α in the RNase active back-to-back dimer conformation. Comparison of this structure with other existing structures of IRE1α and integration of our extensive structure activity relationship (SAR) data has led us to formulate a model to rationalize how ATP-binding site ligands are able to control the IRE1α oligomeric state and subsequent RNase domain activity. © 2016 American Chemical Society.

Lee S.-W.,University of Texas Health Science Center at Houston | Lee S.-W.,University of Houston | Li C.-F.,Chi Mei Foundational Medical Center | Li C.-F.,National Health Research Institute | And 16 more authors.
Molecular Cell | Year: 2015

LKB1 is activated by forming a heterotrimeric complex with STRAD and MO25. Recent studies suggest that LKB1 has pro-oncogenic functions, besides acting as a tumor suppressor. How the LKB1 activity is maintained and how LKB1 regulates cancer development are largely unclear. Here we show that K63-linked LKB1 polyubiquitination by Skp2-SCF ubiquitin ligase is critical for LKB1 activation by maintaining LKB1-STRAD-MO25 complex integrity. We further demonstrate that oncogenic Ras acts upstream of Skp2 to promote LKB1 polyubiquitination by activating Skp2-SCF ubiquitin ligase. Moreover, Skp2-mediated LKB1 polyubiquitination is required for energy-stress-induced cell survival. We also detected overexpression of Skp2 and LKB1 in late-stage hepatocellular carcinoma (HCC), and their overexpression predicts poor survival outcomes. Finally, we show that Skp2-mediated LKB1 polyubiquitination is important for HCC tumor growth invivo. Our study provides new insights into the upstream regulation of LKB1 activation and suggests a potential target, the Ras/Skp2/LKB1 axis, for cancer therapy. © 2015 Elsevier Inc.

Salmoirago-Blotcher E.,University of Massachusetts Medical School | Fitchett G.,Rush University Medical Center | Hovey K.M.,State University of New York at Buffalo | Schnall E.,Yeshiva University | And 7 more authors.
Annals of Epidemiology | Year: 2013

Purpose: Spirituality has been associated with better cardiac autonomic balance, but its association with cardiovascular risk is not well studied. We examined whether more frequent private spiritual activity was associated with reduced cardiovascular risk in postmenopausal women enrolled in the Women's Health Initiative Observational Study. Methods: Frequency of private spiritual activity (prayer, Bible reading, and meditation) was self-reported at year 5 of follow-up. Cardiovascular outcomes were centrally adjudicated, and cardiovascular risk was estimated from proportional hazards models. Results: Final models included 43,708 women (mean age, 68.9 ± 7.3 years; median follow-up, 7.0 years) free of cardiac disease through year 5 of follow-up. In age-adjusted models, private spiritual activity was associated with increased cardiovascular risk (hazard ratio [HR], 1.16; 95% confidence interval [CI], 1.02-1.31 for weekly vs. never; HR, 1.25; 95% CI, 1.11-1.40 for daily vs. never). In multivariate models adjusted for demographics, lifestyle, risk factors, and psychosocial factors, such association remained significant only in the group with daily activity (HR, 1.16; 95% CI, 1.03-1.30). Subgroup analyses indicate this association may be driven by the presence of severe chronic diseases. Conclusions: Among aging women, higher frequency of private spiritual activity was associated with increased cardiovascular risk, likely reflecting a mobilization of spiritual resources to cope with aging and illness. © 2013 Elsevier Inc.

Fung H.,Dana-Farber Cancer Institute | Demple B.,Stony Brook University Medical School
Journal of Biological Chemistry | Year: 2011

Ionizing radiation (IR) and bleomycin (BLM) are used to treat various types of cancers. Both agents generate cytotoxic double strand breaks (DSB) and abasic (apurinic/apyrimidinic (AP)) sites in DNA. The human AP endonuclease Ape1 acts on abasic or 3′-blocking DNA lesions such as those generated by IR or BLM. We examined the effect of siRNA-mediated Ape1 suppression on DNA repair and cellular resistance to IR or BLM in human B-lymphoblastoid TK6 cells and HCT116 colon tumor cells. Partial Ape1 deficiency (∼30% of normal levels) sensitized cells more dramatically to BLM than to IR cytotoxicity. In both cases, expression of the unrelated yeast AP endonuclease, Apn1, largely restored resistance. Ape1 deficiency increased DNA AP site accumulation due to IR treatment but reduced the number of DSB. In contrast, for BLM, there were more DSB under Ape1 deficiency, with little change in the accumulation of AP sites. Although the role of Ape1 in generating DSB was greater for IR, the enzyme facilitated removal of AP sites, which may mitigate the cytotoxic effects of IR. In contrast, BLM generates scattered AP sites, and the DSB have 3′-phosphoglycolate termini that require Ape1 processing. These DSB persist under Ape1 deficiency. Apoptosis induced by BLM (but not by IR) under Ape1 deficiency was partially p53-dependent, more dramatically in TK6 than HCT116 cells. Thus, Ape1 suppression or inhibition may be a more efficacious adjuvant for BLM than for IR cancer therapy, particularly for tumors with a functional p53 pathway. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Ramirez-Fort M.K.,University of Pittsburgh | Case E.C.,Sloan Kettering Cancer Center | Rosen A.C.,Sloan Kettering Cancer Center | Cerci F.B.,Hospital Santa Casa Of Misericordia Of Curitiba Puc Pr | And 2 more authors.
American Journal of Clinical Oncology: Cancer Clinical Trials | Year: 2014

Background: Everolimus is a mammalian target of rapamycin (mTOR) inhibitor approved for treatment of renal cell carcinoma, subependymal giant cell astrocytoma, breast cancer, and progressive neuroendocrine tumors of pancreatic origin. Its use may be hindered because of adverse events, including rash. The reported incidence and risk of a rash to everolimus varies widely and has not been closely investigated. Therefore, we conducted a systematic review and meta-analysis of the literature to determine the incidence and risk of developing a rash. Methods: We searched PubMed and Web of Science databases and abstracts presented at the American Society of Clinical Oncology from 1998 to December 2011 using the keyword "everolimus" to identify relevant clinical trials. Eligible studies included prospective phase II and III clinical trials of cancer patients on 10 mg of everolimus daily with available data on incidence of rash. The summary incidence and relative risk (RR) of rash were calculated using either the randomeffects or fixed-effects model, depending on the heterogeneity of the constituent studies. Results: A total of 2242 patients with various malignancies from 13 clinical trials were included in the analysis. The summary incidences of all-grade and high-grade rash in patients on everolimus were 28.6% [95% confidence interval (CI), 20.8-38.0] and 1.0% (95% CI, 0.6-1.8), respectively. Everolimus was associated with a statistically significant increased risk of all-grade rash (RR = 3.853, 95% CI, 2.470-6.013, P = 0.000), but the RR for high-grade rash (RR = 2.997, 95% CI, 0.633- 14.185) was not statistically significant, with a P value of 0.166. Conclusions: Everolimus is associated with a significant risk of developing a rash. Management of rash to everolimus is critical to prevent dose modifications and decreased quality of life, both of which can negatively affect overall clinical outcomes.

Hari S.B.,University of Washington | Perera B.G.K.,University of Washington | Ranjitkar P.,University of Washington | Seeliger M.A.,Stony Brook University Medical School | Maly D.J.,University of Washington
ACS Chemical Biology | Year: 2013

Over the past decade, an increasingly diverse array of potent and selective inhibitors that target the ATP-binding sites of protein kinases have been developed. Many of these inhibitors, like the clinically approved drug imatinib (Gleevec), stabilize a specific catalytically inactive ATP-binding site conformation of their kinases targets. Imatinib is notable in that it is highly selective for its kinase target, Abl, over other closely related tyrosine kinases, such as Src. In addition, imatinib is highly sensitive to the phosphorylation state of Abl's activation loop, which is believed to be a general characteristic of all inhibitors that stabilize a similar inactive ATP-binding site conformation. In this report, we perform a systematic analysis of a diverse series of ATP-competitive inhibitors that stabilize a similar inactive ATP-binding site conformation as imatinib with the tyrosine kinases Src and Abl. In contrast to imatinib, many of these inhibitors have very similar potencies against Src and Abl. Furthermore, only a subset of this class of inhibitors is sensitive to the phosphorylation state of the activation loop of these kinases. In attempting to explain this observation, we have uncovered an unexpected correlation between Abl's activation loop and another flexible active site feature, called the phosphate-binding loop (p-loop). These studies shed light on how imatinib is able to obtain its high target selectivity and reveal how the conformational preference of flexible active site regions can vary between closely related kinases. © 2013 American Chemical Society.

Morim A.,Winthrop University | Shah R.,Winthrop University | Jimenez E.,Winthrop University | Schmidt A.,Stony Brook University Medical School
Applied Radiology | Year: 2015

A 30-year-old asymptomatic female presented for IUD placement 5 months after an uncomplicated C-section. Ultrasound confirmed correct IUD placement but revealed a “complex pelvic mass” in the posterior cul-de-sac. Rectovaginal exam revealed a nontender soft tissue mass, 6-7cm in size, just to the right of the rectum and vaginal apex. Pelvic MRI showed a 7 cm mass deep in the right hemipelvis, felt to possibly represent an endometrioma, which remained unchanged on a 3-month follow-up study. Colonoscopy revealed extrinsic bowel compression but no mucosal changes. Due to recent pelvic surgery, the imaging characteristics of the mass, and the normal appearance of both ovaries, a gossypiboma was considered. Exploratory laparotomy revealed a right perirectal retroperitoneal mass containing copious amounts of keratin. The mass was excised and the patient had an uneventful recovery.

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