News Article | February 22, 2017
Pre-B acute lymphoblastic leukaemia (ALL) cells were obtained from patients who gave informed consent in compliance with the guidelines of the Internal Review Board of the University of California San Francisco (Supplementary Table 2). Leukaemia cells from bone marrow biopsy of patients with ALL were xenografted into sublethally irradiated NOD/SCID (non-obese diabetic/severe combined immunodeficient) mice via tail vein injection. After passaging, leukaemia cells were collected. Cells were cultured on OP9 stroma cells in minimum essential medium-α (MEMα; Invitrogen), supplemented with 20% fetal bovine serum (FBS), 2 mM l-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 100 μg/ml streptomycin. Primary chronic myeloid leukaemia (CML) cases were obtained with informed consent from the University Hospital Jena in compliance with institutional internal review boards (including the IRB of the University of California San Francisco; Supplementary Table 3). Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM; Invitrogen) supplemented with 20% BIT serum substitute (StemCell Technologies); 100 IU/ml penicillin and 100 μg/ml streptomycin; 25 μmol/l β-mercaptoethanol; 100 ng/ml SCF; 100 ng/ml G-CSF; 20 ng/ml FLT3; 20 ng/ml IL-3; and 20 ng/ml IL-6. Human cell lines (Supplementary Table 2) were obtained from DSMZ and were cultured in Roswell Park Memorial Institute medium (RPMI-1640; Invitrogen) supplemented with GlutaMAX containing 20% FBS, 100 IU/ml penicillin and 100 μg/ml streptomycin. Cell cultures were kept at 37 °C in a humidified incubator in a 5% CO atmosphere. None of the cell lines used was found in the database of commonly misidentified cell lines maintained by ICLAC and NCBI Biosample. All cell lines were authenticated by STR profiles and tested negative for mycoplasma. BML275 (water-soluble) and imatinib were obtained from Santa Cruz Biotechnology and LC Laboratories, respectively. Stock solutions were prepared in DMSO or sterile water at 10 mmol/l and stored at −20 °C. Prednisolone and dexamethasone (water-soluble) were purchased from Sigma-Aldrich and were resuspended in ethanol or sterile water, respectively, at 10 mmol/l. Stock solutions were stored at −20 °C. Fresh solutions (pH-adjusted) of methyl pyruvate, OAA, 3-OMG (an agonist of TXNIP), d-allose (an agonist of TXNIP) and recombinant insulin (Sigma-Aldrich) were prepared for each experiment. DMS was obtained from Acros Organics, and fresh solutions (pH-adjusted) were prepared before each experiment. For competitive-growth assays, 5 mmol/l methyl pyruvate, 5 mmol/l dimethyl succinate (DMS) and 5 mmol/l OAA were used. The CNR2 agonist HU308 was obtained from Cayman Chemical. To avoid inflammation-related effects in mice, bone marrow cells were extracted from mice (Supplementary Table 4) younger than 6 weeks of age without signs of inflammation. All mouse experiments were conducted in compliance with institutional approval by the University of California, San Francisco Institutional Animal Care and Use Committee. Bone marrow cells were obtained by flushing cavities of femur and tibia with PBS. After filtration through a 70-μm filter and depletion of erythrocytes using a lysis buffer (BD PharmLyse, BD Biosciences), washed cells were either frozen for storage or subjected to further experiments. Bone marrow cells were cultured in IMDM (Invitrogen) with GlutaMAX containing 20% fetal bovine serum, 100 IU/ml penicillin, 100 μg/ml streptomycin and 50 μM β-mercaptoethanol. To generate pre-B ALL (Ph+ ALL-like) cells, bone marrow cells were cultured in 10 ng/ml recombinant mouse IL-7 (PeproTech) and retrovirally transformed by BCR–ABL1. BCR–ABL1-transformed pre-B ALL cells were propagated only for short periods of time and usually not for longer than 2 months to avoid acquisition of additional genetic lesions during long-term cell culture. To generate myeloid leukaemia (CML-like) cells, the myeloid-restricted protocol described previously30 was used. Bone marrow cells were cultured in 10 ng/ml recombinant mouse IL-3, 25 ng/ml recombinant mouse IL-6, and 50 ng/ml recombinant mouse SCF (PeproTech) and retrovirally transformed by BCR–ABL1. Immunophenotypic characterization was performed by flow cytometry. For conditional deletion, a 4-OHT-inducible, Cre-mediated deletion system was used. For retroviral constructs used, see Supplementary Table 5. Transfection of retroviral constructs (Supplementary Table 5) was performed using Lipofectamine 2000 (Invitrogen) with Opti-MEM medium (Invitrogen). Retroviral supernatant was produced by co-transfecting HEK 293FT cells with the plasmids pHIT60 (gag-pol) and pHIT123 (ecotropic env). Lentiviral supernatant was produced by co-transfecting HEK 293FT cells with the plasmids pCDNL-BH and VSV-G or EM140. 293FT cells were cultured in high glucose Dulbecco’s modified Eagle’s medium (DMEM, Invitrogen) with GlutaMAX containing 10% fetal bovine serum, 100 IU/ml penicillin, 100 μg/ml streptomycin, 25 mmol/l HEPES, 1 mmol/l sodium pyruvate and 0.1 mmol/l non-essential amino acids. Regular medium was replaced after 16 h by growth medium containing 10 mmol /l sodium butyrate. After incubation for 8 h, the medium was changed back to regular growth medium. After 24 h, retroviral supernatant was collected, filtered through a 0.45-μm filter and loaded by centrifugation (2,000g, 90 min at 32 °C) onto 50 μg/ml RetroNectin- (Takara) coated non-tissue 6-well plates. Lentiviral supernatant produced with VSV-G was concentrated using Lenti-X Concentrator (Clontech), loaded onto RetroNectin-coated plates and incubated for 15 min at room temperature. Lentiviral supernatant produced with EM140 was collected, loaded onto RetroNectin-coated plates and incubated for 30 min at room temperature. Per well, 2–3 × 106 cells were transduced by centrifugation at 600g for 30 min and maintained for 48 h at 37 °C with 5% CO before transferring into culture flasks. For cells transduced with lentiviral supernatant produced with EM140, supernatant was removed the day after transduction and replaced with fresh culture medium. Cells transduced with oestrogen-receptor fusion proteins were induced with 4-OHT (1 μmol/l). Cells transduced with constructs carrying an antibiotic-resistance marker were selected with its respective antibiotic. For loss-of-function studies, dominant-negative variants of IKZF1 (DN-IKZF1, lacking the IKZF1 zinc fingers 1–4) and PAX5 (DN-PAX5; PAX5–ETV6 fusion) were cloned from patient samples. Expression of DN-IKZF1 was induced by doxycycline (1 μg/ml), while activation of DN-PAX5 was induced by 4-OHT (1 μg/ml) in patient-derived pre-B ALL cells carrying IKZF1 and PAX5 wild-type alleles, respectively. Inducible reconstitution of wild-type IKZF1 and PAX5 in haploinsufficient pre-B ALL cells carrying deletions of either IKZF1 (IKZF1∆) or PAX5 (PAX5∆) were also studied. Lentiviral constructs used are listed in Supplementary Table 5. A doxycycline-inducible TetOn vector system was used for inducible expression of PAX5 in mouse BCR–ABL1 pre-B ALL. The retroviral constructs used are listed in Supplementary Table 5. To study the effects of B-cell- versus myeloid-lineage identity in genetically identical mouse leukaemia cells, a doxycycline-inducible TetOn-CEBPα vector system31 was used to reprogram B cells. Mouse BCR–ABL1 pre-B ALL cells expressing doxycycline-inducible CEBPα or an empty vector were induced with doxycycline (1 μg/ml). Conversion from the B-cell lineage (CD19+Mac1−) to the myeloid lineage (CD19−Mac1+) was monitored by flow cytometry. For western blots, B-lineage cells (CD19+Mac1−) and CEBPα-reprogrammed cells (CD19−Mac1+) were sorted from cells expressing an empty vector or CEBPα, respectively, following doxycycline induction. For metabolic assays, sorted B-lineage cells and CEBPα-reprogrammed cells were cultured (with doxycycline) for 2 days following sorting, and were then seeded in fresh medium for measurement of glucose consumption (normalized to cell numbers) and total ATP levels (normalized to total protein). To study Lkb1 deletion in the context of CEBPα-mediated reprogramming, BCR–ABL1-transformed Lkb1fl/fl pre-B ALL cells expressing doxycycline-inducible CEBPα were transduced with 4-OHT(1 μg/ml) inducible Cre-GFP (Cre-ERT2-GFP). Without sorting for GFP+ cells, cells were induced with doxycycline and 4-OHT. Viability (expressed as relative change of GFP+ cells) was measured separately in B-lineage (gated on CD19+ Mac1−) and myeloid lineage (gated on CD19− Mac1+) populations. To study whether Lkb1 deletion causes CEBPα-dependent effects on metabolism and signalling, Lkb1fl/fl BCR–ABL1 B-lineage ALL cells expressing doxycycline-inducible CEBPα or an empty vector were transduced with 4-OHT-inducible Cre-GFP. After sorting for GFP+ populations, cells were induced with doxycycline. B-lineage cells (CD19+ Mac1−) and CEBPα-reprogrammed cells (CD19− Mac1+) were sorted from cells expressing an empty vector or CEBPα, respectively. Sorted cells were cultured with doxycycline and induced with 4-OHT. Protein lysates were collected on day 2 following 4-OHT induction. For metabolomics, sorted cells were re-seeded in fresh medium on day 2 following 4-OHT induction and collected for metabolite extraction. For CRISPR/Cas9-mediated deletion of target genes, all constructs including lentiviral vectors expressing gRNA and Cas9 nuclease were purchased from Transomic Technologies (Supplementary Table 5; see Supplementary Table 6 for gRNA sequences). In brief, patient-derived pre-B ALL cells transduced with GFP-tagged, 4-OHT-inducible PAX5 or an empty vector were transduced with pCLIP-hCMV-Cas9-Nuclease-Blast. Blasticidin-resistant cells were subsequently transduced with pCLIP-hCMV-gRNA-RFP. Non-targeting gRNA was used as control. Constructs including lentiviral vectors expressing gRNA and dCas9-VPR used for CRISPR/dCas9-mediated activation of gene expression are listed in Supplementary Table 5. Nuclease-null Cas9 (dCas9) fused with VP64-p65-Rta (VPR) was cloned from SP-dCas9-VPR (a gift from G. Church; Addgene plasmid #63798) and then subcloned into pCL6 vector with a blasticidin-resistant marker. gRNA sequences (Supplementary Table 6) targeting the transcriptional start site of each specific gene were obtained from public databases (http://sam.genome-engineering.org/ and http://www.genscript.com/gRNA-database.html)32. gBlocks Gene Fragments were used to generate single-guide RNAs (sgRNAs) and were purchased from Integrated DNA Technologies, Inc. Each gRNA was subcloned into pCL6 vector with a dsRed reporter. Patient-derived pre-B ALL cells transduced with either GFP-tagged inducible PAX5 or an empty vector were transduced with pCL6-hCMV-dCas9-VPR-Blast. Blasticidin-resistant cells were used for subsequent transduction with pCL6-hCMV-gRNA-dsRed, and dsRed+ cells were further analysed by flow cytometry. For each target gene, 2–3 sgRNA clones were pooled together to generate lentiviruses. Non-targeting gRNA was used as control. To elucidate the mechanistic contribution of PAX5 targets, the percentage of GFP+ cells carrying gRNA(s) for each target gene was monitored by flow cytometry upon inducible activation of GFP-tagged PAX5 or an empty vector in patient-derived pre-B ALL cells in competitive-growth assays. Cells were lysed in CelLytic buffer (Sigma-Aldrich) supplemented with a 1% protease inhibitor cocktail (Thermo Fisher Scientific). A total of 20 μg of protein mixture per sample was separated on NuPAGE (Invitrogen) 4–12% Bis-Tris gradient gels or 4–20% Mini-PROTEAN TGX precast gels, and transferred onto nitrocellulose membranes (Bio-Rad). The primary antibodies used are listed in Supplementary Table 7. For protein detection, the WesternBreeze Immunodetection System (Invitrogen) was used, and light emission was detected by either film exposure or the BioSpectrum Imaging system (UPV). Approximately 106 cells per sample were resuspended in PBS blocked using Fc blocker for 10 min on ice, followed by staining with the appropriate dilution of the antibodies or their respective isotype controls for 15 min on ice. Cells were washed and resuspended in PBS with propidium iodide (0.2 μg/ml) or DAPI (0.75 μg/ml) as a dead-cell marker. The antibodies used for flow cytometry are listed in Supplementary Table 7. For competitive-growth assays, the percentage of GFP+ cells was monitored by flow cytometry. For annexin V staining, annexin V binding buffer (BD Bioscience) was used instead of PBS and 7-aminoactinomycin D (7AAD; BD Bioscience) instead of propidium iodide. Phycoerythrin-labelled annexin V was purchased from BD Bioscience. For BrdU staining, the BrdU Flow Kit was purchased from BD Bioscience and used according to the manufacturer’s protocol. Methylcellulose colony-forming assays were performed with 10,000 BCR–ABL1 pre-B ALL cells. Cells were resuspended in mouse MethoCult medium (StemCell Technologies) and cultured on 3-cm dishes, with an extra water supply dish to prevent evaporation. Images were taken and colony numbers were counted after 14 days. Cell viability upon the genetic loss of function of target genes and/or inducible expression of PAX5 was monitored by flow cytometry using propidium iodide (0.2 μg/ml) as a dead-cell marker. To study the effects of an AMPK inhibitor (BML275), glucocorticoids (dexamethasone and prednisolone), CNR2 agonist (HU308), or TXNIP agonists (3-OMG and d-allose), 40,000 human or mouse leukaemia cells were seeded in a volume of 80 μl in complete growth medium on opaque-walled, white 96-well plates (BD Biosciences). Compounds were added at the indicated concentrations giving a total volume of 100 μl per well. After culturing for 3 days, cells were subjected to CellTiter-Glo Luminescent Cell Viability Assay (Promega). Relative viability was calculated using baseline values of cells treated with vehicle control as a reference. Combination index (CI) was calculated using the CalcuSyn software to determine interaction (synergistic, CI < 1; additive, CI = 1; or antagonistic, CI > 1) between the two agents. Constant ratio combination design was used. Concentrations of BML275, d-allose, 3-OMG and HU308 used are indicated in the figures. Concentrations of Dex used were tenfold lower than those of BML275. Concentrations of prednisolone used were twofold lower than those of BML275. To determine the number of viable cells, the trypan blue exclusion method was applied, using the Vi-CELL Cell Counter (Beckman Coulter). ChIP was performed as described previously33. Chromatin from fixed patient-derived Ph+ ALL cells (ICN1) was isolated and sonicated to 100–500-bp DNA fragments. Chromatin fragments were immunoprecipitated with either IgG (as a control) or anti-Pax5 antibody (see Supplementary Table 7). Following reversal of crosslinking by formaldehyde, specific DNA sequences were analysed by quantitative real-time PCR (see Supplementary Table 8 for primers). Primers were designed according to ChIP–seq tracks for PAX5 antibodies in B lymphocytes (ENCODE, Encyclopedia of DNA Elements, GM12878). ChIP–seq tracks for PAX5, IKZF1, EBF1 and TCF3 antibodies in a normal B-cell sample (ENCODE GM12878, UCSC genome browser) on INSR, GLUT1, GLUT3, GLUT6, HK2, G6PD, NR3C1, TXNIP, CNR2 and LKB1 gene promoter regions are shown. CD19 and ACTA1 served as a positive and a negative control gene, respectively. The y axis represents the normalized number of reads per million reads for peak summit for each track. The ChIP–seq peaks were called by the MACS peak-caller by comparing read density in the ChIP experiment relative to the input chromatin control reads, and are shown as bars under each wiggle track. Gene models are shown in UCSC genome browser hg19. Extracellular glucose levels were measured using the Amplex Red Glucose/Glucose Oxidase Assay Kit (Invitrogen), according to the manufacturer’s protocol. Glucose concentrations were measured in fresh and spent medium. Total ATP levels were measured using the ATP Bioluminescence Assay Kit CLS II (Roche) according to the manufacturer’s protocol. In fresh medium, 1 × 106 cells per ml were seeded and treated as indicated in the figure legends. Relative levels of glucose consumed and total ATP are shown. All values were normalized to cell numbers (Figs 1b, c, 2c (glucose uptake), 3a and Extended Data Figs 2c, 4f, 6d) or total protein (Fig. 2c, ATP levels). Numbers of viable cells were determined by applying trypan blue dye exclusion, using the Vi-CELL Cell Counter (Beckman Coulter). Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) were measured using a Seahorse XFe24 Flux Analyzer with an XF Cell Mito Stress Test Kit and XF Glycolysis Stress Test Kit (Seahorse Bioscience) according to the manufacturer’s instructions. All compounds and materials were obtained from Seahorse Bioscience. In brief, 1.5 × 105 cells per well were plated using Cell-Tak (BD Biosciences). Following incubation in XF-Base medium supplemented with glucose and GlutaMAX for 1 h at 37 °C (non-CO incubator) for pH stabilization, OCR was measured at the resting stage (basal respiration in XF Base medium supplemented with GlutaMax and glucose) and in response to oligomycin (1 μmol/l; mitochondrial ATP production), mitochondrial uncoupler FCCP (5 μmol/l; maximal respiration), and respiratory chain inhibitor antimycin and rotenone (1 μmol/l). Spare respiratory capacity is the difference between maximal respiration and basal respiration. ECAR was measured under specific conditions to generate glycolytic profiles. Following incubation in glucose-free XF Base medium supplemented with GlutaMAX for 1 h at 37 °C (non-CO incubator) for pH stabilization, basal ECAR was measured. Following measurement of the glucose-deprived, basal ECAR, changes in ECAR upon the sequential addition of glucose (10 mmol/l; glycolysis), oligomycin (1 μmol/l; glycolytic capacity), and 2-deoxyglucose (0.1 mol/l) were measured. Glycolytic reserve was determined as the difference between oligomycin-stimulated glycolytic capacity and glucose-stimulated glycolysis. All values were normalized to cell numbers (Extended Data Fig. 2c) or total protein (Extended Data Figs 3a, 7a, b 8f) and are shown as the fold change relative to basal ECAR or OCR. Metabolite extraction and mass-spectrometry-based analysis were performed as described previously34. Metabolites were extracted from 2 × 105 cells per sample using the methanol/water/chloroform method. After incubation at 37 °C for the indicated time, cells were rinsed with 150 mM ammonium acetate (pH 7.3), and 400 μl cold 100% methanol (Optima* LC/MS, Fisher) and then 400 μl cold water (HPLC-Grade, Fisher) was added to cells. A total of 10 nmol norvaline (Sigma) was added as internal control, followed by 400 μl cold chloroform (HPLC-Grade, Fisher). Samples were vortexed three times over 15 min and spun down at top speed for 5 min at 4 °C. The top layer (aqueous phase) was transferred to a new Eppendorf tube, and samples were dried on Vacufuge Plus (Eppendorf) at 30 °C. Extracted metabolites were stored at −80 °C. For mass spectrometry-based analysis, the metabolites were resuspended in 70% acetonitrile and 5 μl used for analysis with a mass spectrometer. The mass spectrometer (Q Exactive, Thermo Scientific) was coupled to an UltiMate3000 RSLCnano HPLC. The chromatography was performed with 5 mM NH AcO (pH 9.9) and acetonitrile at a flow rate of 300 μl/min starting at 85% acetonitrile, going to 5% acetonitrile at 18 min, followed by an isocratic step to 27 min and re-equilibration to 34 min. The separation was achieved on a Luna 3u NH2 100A (150 × 2 mm) (Phenomenex). The Q Exactive was run in polarity switching mode (+3 kV/−2.25 kV). Metabolites were detected based on retention time (t ) and on accurate mass (± 3 p.p.m.). Metabolite quantification was performed as area-under-the-curve (AUC) with TraceFinder 3.1 (Thermo Scientific). Data analysis was performed in R (https://www.r-project.org/), and data were normalized to the number of cells. Relative amounts were log -transformed, median-centred and are shown as a heat map. To generate a model for pre-leukaemic B cell precursors expressing BCR–ABL1, BCR–ABL1 knock-in mice were crossed with Mb1-Cre deleter strain (Mb1-Cre; Bcr+/LSL-BCR/ABL) for excision of a stop-cassette in early pre-B cells. Bone marrow cells collected from Mb1-Cre; Bcr+/LSL-BCR/ABL mice cultured in the presence of IL-7 were primed with vehicle control or a combination of OAA (8 mmol/l), DMS (8 mmol/l) and insulin (210 pmol/l). Following a week of priming, cells were maintained and expanded in the presence of IL-7, supplemented with vehicle control or a combination of OAA (0.8 mmol/l) and DMS (0.8 mmol/l) for 4 weeks. Pre-B cells from Mb1-Cre; Bcr+/LSL-BCR/ABL mice expressed low levels of BCR–ABL1 tagged to GFP, and were analysed by flow cytometry for surface expression of GFP and CD19. The methylcellulose colony-forming assays were performed with 10,000 cells treated with vehicle control or metabolites. Cells were resuspended in mouse MethoCult medium (StemCell Technologies) and cultured on 3-cm diameter dishes, with an extra water supply dish to prevent evaporation. Images were taken and colony numbers counted after 14 days. For in vivo transplantation experiments, cells were treated with vehicle control or metabolites (OAA/DMS) for 6 weeks. One million cells were intravenously injected into sublethally irradiated (250 cGy) 6–8-week-old female NSG mice (n = 7 per group). Mice were randomly allocated into each group, and the minimal number of mice in each group was calculated by using the ‘cpower’ function in R/Hmisc package. No blinding was used. Each mouse was killed when it became terminally sick and showed signs of leukaemia burden (hunched back, weight loss and inability to move). The bone marrow and spleen were collected for flow cytometry analyses for leukaemia infiltration (CD19, B220). After 63 days, all remaining mice were killed and bone marrow and spleens from all mice were analysed by flow cytometry. Statistical analysis was performed using the Mantel–Cox log-rank test. All mouse experiments were in compliance with institutional approval by the University of California, San Francisco Institutional Animal Care and Use Committee. Following cytokine-independent proliferation, BCR–ABL1-transformed Lkb1fl/fl or AMPKa2fl/fl pre-B ALL cells were transduced with 4-OHT-inducible Cre or an empty vector control. For ex vivo deletion, deletion was induced 24 h before injection. For in vivo deletion, deletion was induced by 4-OHT (0.4 mg per mouse; intraperitoneal injection). Approximately 106 cells were injected into each sublethally irradiated (250 cGy) NOD/SCID mouse. Seven mice per group were injected via the tail vein. We randomly allocated 6–8-week-old female NOD/SCID or NSG mice into each group. The minimal number of mice in each group was calculated using the ‘cpower’ function in R/Hmisc package. No blinding was used. When a mouse became terminally sick and showed signs of leukaemia burden (hunched back, weight loss and inability to move), it was killed and the bone marrow and/or spleen were collected for flow cytometry analyses for leukaemia infiltration. Statistical analysis was performed by Mantel–Cox log-rank test. In vivo expansion and leukaemia burden were monitored by luciferase bioimaging. Bioimaging of leukaemia progression in mice was performed at the indicated time points using an in vivo IVIS 100 bioluminescence/optical imaging system (Xenogen). d-luciferin (Promega) dissolved in PBS was injected intraperitoneally at a dose of 2.5 mg per mouse 15 min before measuring the luminescence signal. General anaesthesia was induced with 5% isoflurane and continued during the procedure with 2% isoflurane introduced through a nose cone. All mouse experiments were in compliance with institutional approval by the University of California, San Francisco Institutional Animal Care and Use Committee. Data are shown as mean ± s.d. unless stated. Statistical significance was analysed by using Grahpad Prism software or R software (https://www.r-project.org/) by using two-tailed t-test, two-way ANOVA, or log-rank test as indicated in figure legends. Significance was considered at P < 0.05. For in vitro experiments, no statistical methods were used to predetermine the sample size. For in vivo transplantation experiments, the minimal number of mice in each group was calculated through use of the ‘cpower’ function in the R/Hmisc package. No animals were excluded. Overall survival and relapse-free survival data were obtained from GEO accession number GSE11877 (refs 35, 36) and TCGA. Kaplan–Meier survival analysis was used to estimate overall survival and relapse-free survival. Patients with high risk pre-B ALL (COG clinical trial, P9906, n = 207; Supplementary Table 10) were segregated into two groups on the basis of high or low mRNA levels with respect to the median mRNA values of the probe sets for the gene of interest. A log-rank test was used to compare survival differences between patient groups. R package ‘survival’ Version 2.35-8 was used for the survival analysis and Cox proportional hazards regression model in R package for the multivariate analysis (https://www.r-project.org/). The investigators were not blinded to allocation during experiments and outcome assessment. Experiments were repeated to ensure reproducibility of the observations. Gel scans are provided in Supplementary Fig. 1. Gene expression data were obtained from the GEO database accession numbers GSE32330 (ref. 12), GSE52870 (ref. 37), and GSE38463 (ref. 38). Patient-outcome data were derived from the National Cancer Institute TARGET Data Matrix of the Children’s Oncology Group (COG) Clinical Trial P9906 (GSE11877)35, 36 and from TCGA (the Cancer Genome Atlas). GEO accession details are provided in Supplementary Tables 9 and 10. ChIP–seq tracks for PAX5, IKZF1, EBF1 and TCF3 antibodies in a normal B-cell sample (ENCODE GM12878, UCSC genome browser) on INSR, GLUT1, GLUT3, GLUT6, HK2, G6PD, NR3C1, TXNIP, CNR2 and LKB1 gene promoter regions are shown in UCSC genome browser hg19. All other data are available from the corresponding author upon reasonable request.
News Article | February 15, 2017
DETROIT, MI--(Marketwired - February 13, 2017) - SmithGroupJJR, one of the nation's leading architecture, engineering and planning firms, is pleased to announce that Tom Butcavage, Sam D'Amico, Mark Kranz and David Varner have been elevated to the American Institute of Architects (AIA) College of Fellows. The recognition reflects their significant contributions to architecture and society and achievement of a standard of excellence in the profession. The four from SmithGroupJJR will be among the 178 new Fellows recognized at an investiture ceremony at the AIA Conference on Architecture 2017, to be held April 27-29 in Orlando, Florida. Tom Butcavage, FAIA, LEED AP BD+C, is a SmithGroupJJR vice president and leader of the Higher Education Studio at the firm's Washington, DC office. He has spent the past 20 years as a pioneer in the programming, planning and design of award-winning and nationally significant higher education facilities across the U.S., ranging from instructional facilities and student centers to libraries and professional schools. Butcavage is widely recognized for his unparalleled expertise in law school design. He has led more than 20 law school projects, each containing a variety of spaces for specialized instruction, research and legal skills development. Among his most recently completed law schools are the University of Utah S.J. Quinney College of Law, American University Washington College of Law, George State University College of Law, and New York Law School - all which exemplify cutting-edge environments for modern legal education. Presently, he is leading the design of a number of new professional education facilities at the University of South Carolina, University of North Carolina at Chapel Hill, and Georgetown University. A frequent presenter at national academic conferences such as the Society for College and University Planning, American Bar Association and Association of College Unions International, Butcavage speaks on topics including the design of student spaces and maximizing student engagement through new facilities. He has served as a critic and lecturer at the Corcoran College of Art + Design and Catholic University of America School of Architecture and Planning. Butcavage is a graduate of Columbia University with a Master of Architecture, preceded by a BA in art history at Swarthmore College. His is a resident of Washington, DC's Shepherd Park neighborhood. Sam D'Amico, FAIA, LEED AP BD+C, is a SmithGroupJJR vice president and design leader for the firm's Health Practice. Based at its San Francisco office, he is now commencing his 35th year practicing architecture throughout the U.S. as well as parts of Asia. D'Amico approaches every project with a specific architectural response that integrates the client's culture, context and place. His design tenets include the integration of daylight, nature and art into the healthcare environment to improve the healing process. D'Amico has designed for world-class teaching institutions and national leaders in healthcare such as the University of California San Francisco Medical Center, Kaiser Permanente, and Barnes Jewish Hospital. Currently, D'Amico is design principal for a new medical office building and bed tower, part of a multi-year expansion program for Community Regional Medical Center in Fresno, California. His design of the new Robley Rex Veteran Administration Medical Center, a 1.2 million-square-foot replacement hospital to be constructed in Louisville, Kentucky, led to SmithGroupJJR's award of a prestigious AIA Academy of Architecture National Health Design Award, Unbuilt Category. Another D'Amico design, for the Fuwai Huazhong Cardiovascular and Heart Hospital, Zhenghou, Henan Province, China, was the recipient of an AIA San Francisco Citation Award for unbuilt design. At SmithGroupJJR, D'Amico is a member of the firm's National Design Committee. In 2016, he served as a featured panelist at firm's public forum on design, Perspectives, for a program titled, "The Fusion of Art and Architecture." A graduate from the University of Houston with a Bachelor of Architecture with Honors, the Houston, Texas native now resides in Lafayette, California, where he is on the Board of the city's Improvement Association. Mark Kranz, FAIA, LEED AP BD+C, vice president and design director at SmithGroupJJR, is known for his elegant and synthesized solutions for research and higher education environments across the U.S. As the designer of projects recognized by a total of 27 AIA design awards to-date, he believes that each has the potential for excellence, regardless of budget or constraints. Kranz, who is based at the firm's Phoenix office, is an advocate of pushing the boundaries of innovation and sustainability. He designed the LEED Platinum Energy Systems Integration Facility at the National Renewable Energy Lab in Golden, Colorado, leading a complex team and design vision for a high performance/ultra-low energy building later honored as R&D Magazine's "Lab of the Year." His design of the Defense POW/MIA Accounting Agency Center for Excellence, located at Joint Base Pearl Harbor Hickam, Oahu, Hawaii, was the recipient of the Naval Facilities Engineering Command (NAVFAC) 2015 Commander's Award for Design Excellence. Among Kranz's projects currently underway is the $82 million Engineering Building, now under construction at the University of Texas at Dallas. Scheduled for completion in 2018, the new, 208,000-square-foot building will house the university's rapidly growing mechanical engineering program. He is also serving design principal for the new $60 million San Diego County Crime Laboratory, slated to be completed in 2019. Kranz was elected to the SmithGroupJJR Board of Directors in 2015 and is a member of the firm's National Design Committee and Science & Technology Practice. He is a graduate of the University of Nebraska in Lincoln with a Bachelor of Science in architectural studies, followed by a Master of Architecture from Arizona State University. He now resides in Phoenix. David Varner, FAIA, LEED AP BD+C, is vice president and director of the firm's 200-person office in Washington, DC, located in the 1700 New York Avenue building in the heart of DC's monumental core. Varner is known for his talent in discovering and celebrating hidden environmental, economic and design opportunities in existing buildings. His special expertise and success in creating new value for owners, communities and cities through such building transformation is well demonstrated with the complete transformation of the 2.1 million-square-foot, Constitution Center, a repositioning of a 1960's property into the largest, privately-owned office building in Washington, DC. Certified LEED Gold, the building today is not only highly energy-efficient, but secure, elegant and fully leased. Varner is currently serving as SmithGroupJJR's principal-in-charge for one of the District's most exciting new buildings now under construction: the $60 million, 150,000-square-foot, DC Water Headquarters. When completed in late 2017 along the waterfront of the Anacostia River, the new building will set a new standard for low-energy, high-performance and resilient waterfront development. As a result of his expertise in existing buildings, transformation, planning and mixed-use development, Varner is frequently invited to join interdisciplinary panels of some of the nation's most significant leadership groups. In 2015 he was elected a Trustee of the Federal City Council, a position that catalyzes the collaboration of key business leaders in Washington, DC to solve challenging problems across the city. He is a long-time member of the Urban Land Institute and currently on its exclusive Redevelopment and Reuse Council. Varner has been a member of the SmithGroupJJR Board of Directors since 2011. He is graduate of Rice University with dual degrees: a Bachelor of Arts degree in architecture and art/art history and a Bachelor of Architecture. A native of Houston, Texas, Varner now lives in Arlington, Virginia. The American Institute of Architects Fellowship program was developed to elevate those architects who have made a significant contribution to architecture and society and who have achieved a standard of excellence in the profession. Election to fellowship not only recognizes the achievements of architects as individuals, but also their significant contribution to architecture and society on a national level. SmithGroupJJR (www.smithgroupjjr.com) is an integrated architecture, engineering and planning firm, employing more than 1,100 across 10 offices. In May 2016, SmithGroupJJR was ranked as one of the nation's top architecture firms by Architect magazine's Architect 50. A national leader in sustainable design, SmithGroupJJR has 420 LEED professionals and 160 LEED certified projects.
News Article | March 1, 2017
SAN FRANCISCO--(BUSINESS WIRE)--Freenome, the health technology company reinventing disease management through systematized early detection and intervention, announced today that it has raised $65 million USD in Series A funding led by Andreessen Horowitz. Seed investors Andreessen Horowitz, Data Collective (DCVC), and Founders Fund also contributed to this Series A round, and are joined by GV (Google Ventures), Polaris Partners, Innovation Endeavors, Asset Management Ventures, Charles River Ventures and Spectrum 28. Andreessen Horowitz General Partner Vijay Pande will also be joining Freenome’s Board. Since 2014, Freenome has been using a combination of machine learning, biology and computer science to create simple and effective disease screenings. To date, the company has collaborated with 25 research partners around the world - including Moores Cancer Center at UC San Diego Health (UCSD), University of California San Francisco (UCSF) and Massachusetts General Hospital (MGH) - and have gathered and processed thousands of samples through their active clinical trials. Freenome has also partnered with five pharmaceutical companies to assess generalizability of their software to other questions in oncology such as pre-treatment drug response prediction. “Our goal is to bringing accurate, accessible and non-invasive disease screenings to doctors to proactively treat cancer and other diseases at their most manageable stages,“ said Freenome co-founder Gabe Otte. “This funding will allow us to increase the number of clinical trials in collaboration with top researchers and clinicians around the world, enabling us to bring our product to market more quickly and equip people with knowledge and tools to live healthier lives.” Freenome raised $5.5M USD in 2016 to prove the potential of its technology. Through machine learning, the team discovered signatures independent of traditional mutation calling, such as immunological and metabolic changes in cell-free DNA and other analytes, that are more robust for early cancer detection and allow for a cost-effective assay. Freenome is currently focused on scaling technology and accuracy of screenings for four types of cancer - lung, colorectal, breast and prostate - with plans to address other forms of cancer and diseases. This Series A funding will be used to expand clinical trials, accelerate research and bring their disease screenings to market. "There are many drugs and surgical techniques to cure patients of cancer –– if the cancer is caught early. While tests to detect cancer early exist, they are not sufficiently accurate, and are riddled with false positives and false negatives," said Andreessen Horowitz General Partner and Freenome Board member, Vijay Pande. “Freenome's machine learning-driven approach and impressively accurate results from blinded trials make them the right team to swing the pendulum toward a new era of prevention.” Headquartered in South San Francisco, Freenome is a health technology company bringing accurate, accessible and non-invasive disease screenings to you and your doctor to proactively treat cancer and other diseases at their most manageable stages. Freenome aims to reinvent disease management through systematized early detection and intervention. Freenome has raised $71.2M USD since launching in 2014, and is funded by Andreessen Horowitz, GV (Google Ventures), Polaris Partners, Innovation Endeavors, Spectrum 28, Asset Management Ventures, Charles River Ventures, Data Collective (DCVC), Third Kind Ventures, AME Cloud Ventures, Allen and Company and Founders Fund.
News Article | February 15, 2017
WASHINGTON - Clinical trials for genome editing of the human germline - adding, removing, or replacing DNA base pairs in gametes or early embryos - could be permitted in the future, but only for serious conditions under stringent oversight, says a new report from the National Academy of Sciences and the National Academy of Medicine. The report outlines several criteria that should be met before allowing germline editing clinical trials to go forward. Genome editing has already entered clinical trials for non-heritable applications, but should be allowed only for treating or preventing diseases or disabilities at this time. Genome editing is not new. But new powerful, precise, and less costly genome editing tools, such as CRISPR/Cas9, have led to an explosion of new research opportunities and potential clinical applications, both heritable and non-heritable, to address a wide range of human health issues. Recognizing the promise and the concerns related to this technology, NAS and NAM appointed a study committee of international experts to examine the scientific, ethical, and governance issues surrounding human genome editing. Human genome editing is already widely used in basic research and is in the early stages of development and trials for clinical applications that involve non-heritable (somatic) cells. These therapies affect only the patient, not any offspring, and should continue for treatment and prevention of disease and disability, using the existing ethical norms and regulatory framework for development of gene therapy. Oversight authorities should evaluate safety and efficacy of proposed somatic applications in the context of the risks and benefits of intended use. However, there is significant public concern about the prospect of using these same techniques for so-called "enhancement" of human traits and capacities such as physical strength, or even for uses that are not possible, such as improving intelligence. The report recommends that genome editing for enhancement should not be allowed at this time, and that broad public input and discussion should be solicited before allowing clinical trials for somatic genome editing for any purpose other than treating or preventing disease or disability. "Human genome editing holds tremendous promise for understanding, treating, or preventing many devastating genetic diseases, and for improving treatment of many other illnesses," said Alta Charo, co-chair of the study committee and Sheldon B. Lubar Distinguished Chair and Warren P. Knowles Professor of Law and Bioethics, University of Wisconsin-Madison. "However, genome editing to enhance traits or abilities beyond ordinary health raises concerns about whether the benefits can outweigh the risks, and about fairness if available only to some people." Germline genome editing, in contrast, is contentious because genetic changes would be inherited by the next generation. Many view germline editing as crossing an "ethically inviolable" line, the report says. Concerns raised include spiritual objections to interfering with human reproduction to speculation about effects on social attitudes toward people with disabilities to possible risks to the health and safety of future children. But germline genome editing could provide some parents who are carriers of genetic diseases with their best or most acceptable option for having genetically related children who are born free of these diseases. Heritable germline editing is not ready to be tried in humans. Much more research is needed before it could meet the appropriate risk and benefit standards for clinical trials. The technology is advancing very rapidly, though, making heritable genome editing of early embryos, eggs, sperm, or precursor cells in the foreseeable future "a realistic possibility that deserves serious consideration," the report says. Although heritable germline genome editing trials must be approached with caution, the committee said, caution does not mean prohibition. At present, heritable germline editing is not permissible in the United States, due to an ongoing prohibition on the U.S. Food and Drug Administration's ability to use federal funds to review "research in which a human embryo is intentionally created or modified to include a heritable genetic modification." A number of other countries have signed an international convention that prohibits germline modification. If current restrictions are removed, and for countries where germline editing would already be permitted, the committee recommended stringent criteria that would need to be met before going forward with clinical trials. They include: (1) absence of reasonable alternatives; (2) restriction to editing genes that have been convincingly demonstrated to cause or strongly predispose to a serious disease or condition; (3) credible pre-clinical and/or clinical data on risks and potential health benefits; (4) ongoing, rigorous oversight during clinical trials; (5) comprehensive plans for long-term multigenerational follow-up; and (6) continued reassessment of both health and societal benefits and risks, with wide-ranging, ongoing input from the public. Policymaking surrounding human genome editing applications should incorporate public participation, and funding of genome editing research should include support to study the socio-political, ethical, and legal aspects and evaluate efforts to build public communication and engagement on these issues. "Genome editing research is very much an international endeavor, and all nations should ensure that any potential clinical applications reflect societal values and be subject to appropriate oversight and regulation," said committee co-chair Richard Hynes, Howard Hughes Medical Institute Investigator and Daniel K. Ludwig Professor for Cancer Research, Massachusetts Institute of Technology. "These overarching principles and the responsibilities that flow from them should be reflected in each nation's scientific community and regulatory processes. Such international coordination would enhance consistency of regulation." The study was funded by the Defense Advanced Research Projects Agency, the Greenwall Foundation, the John D. and Catherine T. MacArthur Foundation, U.S. Department of Health and Human Services, U.S. Food and Drug Administration, and the Wellcome Trust, with additional support from the National Academies' Presidents' Circle Fund and the National Academy of Sciences W.K. Kellogg Foundation Fund. The National Academy of Sciences and the National Academy of Medicine are private, nonprofit institutions that, along with the National Academy of Engineering, provide independent, objective analysis and advice to the nation to solve complex problems and inform public policy decisions related to science, technology, and medicine. The Academies operate under an 1863 congressional charter to the National Academy of Sciences, signed by President Lincoln. For more information, visit http://www. . Copies of Human Genome Editing: Science, Ethics, and Governance are available at http://www. or by calling 202-334-3313 or 1-800-624-6242. Reporters may obtain a copy from the Office of News and Public Information (contacts listed above). R. Alta Charo1 (co-chair) Sheldon B. Lubar Distinguished Chair and Warren P. Knowles Professor of Law and Bioethics University of Wisconsin Madison Richard O. Hynes1,2 (co-chair) Investigator Howard Hughes Medical Institute, and Daniel K. Ludwig Professor for Cancer Research Massachusetts Institute of Technology Cambridge Ellen Wright Clayton1 Craig Weaver Professor of Pediatrics, and Professor of Law Vanderbilt University Nashville, Tenn. Barry S. Coller1,2 David Rockefeller Professor of Medicine, Physician in Chief, and Head Allen and Frances Adler Laboratory of Blood and Vascular Biology Rockefeller University New York City Ephrat Levy-Lahad Director Fuld Family Department of Medical Genetics Shaare Zedek Medical Center Faculty of Medicine Hebrew University of Jerusalem Jerusalem Luigi Naldini Professor of Cell and Tissue Biology and of Gene and Cell Therapy San Raffaele University, and Director San Raffaele Telethon Institute for Gene Therapy Milan Duanqing Pei Professor and Director General Guangzhou Institute of Biomedicine and Health Chinese Academy of Sciences Guangzhou, China Janet Rossant2 Senior Scientist and Chief of Research Emeritus Hospital for Sick Children University of Toronto Toronto Dietram A. Scheufele John E. Ross Professor in Science Communication and Vilas Distinguished Achievement Professor University of Wisconsin Madison Jonathan Weissman2 Professor Department of Cellular and Molecular Pharmacology University of California San Francisco Keith R. Yamamoto1,2 Vice Chancellor for Science Policy and Strategy University of California San Francisco
News Article | February 17, 2017
SUMMIT, N.J.--(BUSINESS WIRE)--Celgene Corporation (NASDAQ: CELG) today announced that its phase III SUNBEAM trial, evaluating the efficacy and safety of ozanimod, an investigational oral, selective S1P 1 and 5 receptor modulator, in patients with relapsing multiple sclerosis (RMS), met the primary endpoint in reducing annualized relapse rate (ARR), compared to weekly interferon (IFN) β-1a (Avonex®). SUNBEAM evaluated two orally administered treatment doses (0.5 mg and 1 mg) of ozanimod, with patients treated for at least one year. The randomized phase III trial enrolled 1,346 RMS patients in 20 countries. Top-line data show that both the ozanimod 1 mg and 0.5 mg treatment arms demonstrated statistically significant and clinically meaningful improvements compared to Avonex® for the primary endpoint of ARR and the measured secondary endpoints of the number of gadolinium-enhancing MRI lesions and the number of new or enlarging T2 MRI lesions at month 12. As agreed to in the Special Protocol Assessment (SPA) with the U.S. Food and Drug Administration, a pre-specified analysis on the time to onset of disability progression will be conducted using pooled results from both the SUNBEAM and RADIANCE phase III trials. The overall safety and tolerability profile was consistent with results from previously reported phase II RMS (RADIANCE) and phase II ulcerative colitis (TOUCHSTONE) trials. “The safety and efficacy results from SUNBEAM are consistent with the long-term results from the phase II trial (RADIANCE). These data add to the growing body of evidence supporting the use of ozanimod as a disease modifying therapy for relapsing forms of multiple sclerosis,” said Bruce Cree, Associate Professor of Neurology, Multiple Sclerosis Center, Department of Neurology, University of California San Francisco. “We look forward to the continued study of ozanimod as well as presentation of the full results of the phase III trial at an upcoming international scientific meeting.” “People living with multiple sclerosis need additional therapies and we are pleased that oral ozanimod showed meaningful improvements across primary and measured secondary endpoints in this study,” said Scott Smith, President of Celgene Inflammation and Immunology. “We look forward to data from the confirmatory phase III RADIANCE trial in the second quarter as we advance toward planned regulatory submissions by year-end.” SUNBEAM is a phase III multicenter, randomized, double-blind, double-dummy, active-controlled study assessing the efficacy, safety and tolerability of two orally administered doses of ozanimod (0.5 mg and 1 mg) against weekly intramuscular interferon beta-1a (Avonex®) over a minimum of a 12-month treatment period. The study included 1,346 RMS patients across 152 sites in 20 countries. The primary endpoint of the active comparator trial is ARR during the treatment period. The measured secondary endpoints are: the number of new or enlarging hyperintense T2-weighted brain MRI lesions over 12 months and the number of GdE brain MRI lesions at month 12. The time to onset of disability progression as defined by a sustained worsening in EDSS of 1.0 points or more, confirmed after 3 months and 6 months, will be analyzed as part of a pre-specified pooled analysis of SUNBEAM and RADIANCE data. Ozanimod is a novel, oral, selective, sphingosine 1-phosphate 1 (S1PR1) and 5 (S1PR5) receptor modulator in development for immune-inflammatory indications including relapsing multiple sclerosis, ulcerative colitis and Crohn’s disease. Selective binding with S1PR1 receptors is believed to inhibit a specific sub set of activated lymphocytes from migrating to sites of inflammation. The result is a reduction of circulating T and B lymphocytes that leads to anti-inflammatory activity. Importantly, immune surveillance is maintained. Selective binding with S1PR5 receptors is believed to activate specific cells within the CNS. This has the potential to enhance remyelination and prevent synaptic defects. Ultimately, neurological damage may be prevented. Ozanimod is an investigational compound that is not approved for any use in any country. Multiple sclerosis is a disease in which the immune system attacks the protective myelin sheath that covers the nerves. The myelin damage disrupts communication between the brain and the rest of the body. Ultimately, the nerves themselves may deteriorate — a process that's currently irreversible. Signs and symptoms vary widely, depending on the amount of damage and the nerves affected. Some people with severe multiple sclerosis may lose the ability to walk independently, while others experience long periods of remission during which they develop no new symptoms. Multiple sclerosis affects approximately 400,000 people in the U.S. and approximately 2.5 million people worldwide. RMS is characterized by clearly defined attacks of worsening neurologic function. These attacks — often called relapses, flare-ups or exacerbations — are followed by partial or complete recovery periods (remissions), during which symptoms improve partially or completely, and there is no apparent progression of disease. RMS is the most common disease course at the time of diagnosis. Approximately 85 percent of people are initially diagnosed with relapsing multiple sclerosis, compared with 10-15 percent with progressive forms of the disease. Celgene Corporation, headquartered in Summit, New Jersey, is an integrated global biopharmaceutical company engaged primarily in the discovery, development and commercialization of innovative therapies for the treatment of cancer and inflammatory diseases through next-generation solutions in protein homeostasis, immuno-oncology, epigenetics, immunology and neuro-inflammation. For more information, please visit www.celgene.com. For more information, please visit www.celgene.com. Follow Celgene on Social Media: @Celgene, Pinterest, LinkedIn, Facebook and YouTube. This press release contains forward-looking statements, which are generally statements that are not historical facts. Forward-looking statements can be identified by the words “expects,” “anticipates,” “believes,” “intends,” “estimates,” “plans,” “will,” “outlook” and similar expressions. Forward-looking statements are based on management’s current plans, estimates, assumptions and projections, and speak only as of the date they are made. Celgene Corporation undertakes no obligation to update any forward-looking statement in light of new information or future events, except as otherwise required by law. Forward-looking statements involve inherent risks and uncertainties, most of which are difficult to predict and are generally beyond Celgene’s control. Actual results or outcomes may differ materially from those implied by the forward-looking statements as a result of the impact of a number of factors, many of which are discussed in more detail in Celgene’s Annual Report on Form 10-K and other reports filed with the U.S. Securities and Exchange Commission.
News Article | February 22, 2017
EVANSTON, Ill. --- Though an estimated two billion people drink unsafe water around the globe, there are currently no methods to precisely measure how many people are affected by not having enough water for all aspects of their daily lives. This lack of measurement makes it difficult to pinpoint effective interventions to improve water insecurity and water-related illnesses. To better measure water insecurity, researchers need to assess whether people have reliable access to water in sufficient quality and quantity for all activities. Under a new £250,000 (approximately $310,000) grant from the U.K.-funded Innovative Metrics and Methods for Agriculture and Nutrition Actions (IMMANA) research initiative, Northwestern University anthropologist Sera Young, a fellow in the University's Institute for Policy Research, and an international team of researchers seek to develop a cross-cultural scale of perceived household water insecurity. IMMANA is supported by UK Aid from the British government's Department for International Development. "We are so excited to be working towards the creation of a scale that can finally measure how water insecurity affects people at the household level -- that is, the food people grow, their economic well-being, and, of course, their health," Young said. Additional investigators include Wendy Jepson, a human geographer at Texas A&M University; Amber Wutich, an anthropologist at Arizona State University's (ASU) School of Human Evolution and Social Change; Phelgona Otieno, a pediatrician at Kenya Medical Research Institute; Sheri Weiser and Craig Cohen, physician researchers at the University of California San Francisco; and Lisa Butler, an epidemiologist at the University of Connecticut. The grant is administered by the London School of Hygiene & Tropical Medicine. Young and her co-investigators posit household water insecurity leads to poorer mental and physical health and lower economic productivity, but in ways distinct from food insecurity -- including increased anxiety, stress, and time/energy expenditure, as well as decreased agricultural production. Though water insecurity likely contributes to adverse consequences for all household members, it often disproportionately affects women, as they bear the burden of water collection and water -- intensive chores in developing countries. For instance, because women in water-insecure communities often need to walk long distances to collect water, they might not have time to care for their children. Preliminary data have shown that many women worry about their physical safety while fetching water, and that anxiety about how they will obtain all the water needed for their daily activities is common. Infectious diseases are another possible effect of water insecurity. In Young's work in Kenya, about 31 percent of women reported being unable to wash their hands after contact with feces, and one-third said they drank unsafe water "sometimes" or "often." The researchers will refine the household water-insecurity scale, using cross-cultural research conducted in at least six countries. ASU faculty and students will lead projects in Bangladesh, Guatemala, Nepal, and Tajikistan, and Texas A&M University faculty and students will do the same in Brazil and Costa Rica. After completing the first round of data collection research, the experts will meet in August at Northwestern University to work on refining an open-access manual that will describe the scale and methods. "This scale will be an important first step in pinpointing how water insecurity impacts some of the most vulnerable populations, including pregnant women, mothers with young children and HIV-infected adults," Young said. The research team hopes this will result in a better understanding of household water insecurity and point to new strategies for intervention. They also aim to help direct limited resources to targeting the causes of water insecurity and the people at greatest risk of adverse effects --especially women and their young children.
News Article | February 27, 2017
La Jolla, Calif., Feb. 27, 2016 -- Scientists at Sanford Burnham Prebys Medical Discovery Institute (SBP) have identified a new regulator of the innate immune response--the immediate, natural immune response to foreign invaders. The study, published recently in Nature Microbiology, suggests that therapeutics that modulate the regulator--an immune checkpoint--may represent the next generation of antiviral drugs, vaccine adjuvants, cancer immunotherapies, and treatments for autoimmune disease. "We discovered that a protein called K-homology splicing regulatory protein (KHSRP) weakens the immune response to viral RNA," says Sumit Chanda, Ph.D., director of the Immunity and Pathogenesis Program at SBP, and senior author of the study. "Depleting KHSRP improved immune signaling and reduced viral replication in cell culture and in vivo, suggesting that drugs inhibiting the protein may have therapeutic value." The innate immune response is the first line of defense against pathogens--a one-size-fits-all attack on viruses, bacteria, and pretty much anything that looks like an invader. But innate immunity must be carefully regulated. If the response is too slow or too weak, infections can run rampant, and if the trigger is too sensitive or the response is too strong, excessive inflammation or autoimmune diseases can arise. "That's where KHSRP comes in," explains Chanda. "It physically interacts with a protein called retinoic acid-inducible gene I (RIG-I) to apply the brakes to the innate immune response." RIG-I receptors initiate antiviral immunity by detecting viral RNA in the cytoplasm of cells. When they bind viral RNA, they turn on signaling that leads to the production of interferon, a strong inflammatory signal that helps kill viruses, as well as the induction of other antiviral responses. RIG-I receptors also coordinate signaling with other immune factors to modulate the adaptive immune response--the acquired, specialized response that develops after the innate response and provides long-term immunity. "We identified KHSRP by systematically testing every human proteins to identify those that impact RIG-I signaling," says Stephen Soonthornvacharin, a recent Ph.D. graduate from the Chanda lab. "We found about 240 proteins, but we focused on KHSRP because it was the only one of the 240 that was found to inhibit the very early steps of RIG-I signaling." "Molecules that block KHSRP's actions could serve as adjuvants--components that heighten the immune response--to vaccines against influenza or hepatitis C, as antiviral drugs, or even next-generation cancer immunotherapies," Soonthornvacharin adds. "Also, among the 240 RIG-I regulators we identified, 125 appear to activate RIG-I, so finding drugs that inhibit these proteins may be a way to treat autoimmune conditions involving too much interferon, like type 1 diabetes or lupus. Figuring out which ones are promising requires further investigation." "We think KHSRP protects against autoimmunity," adds Chanda. "RIG-I normally recognizes RNA molecules that arise during viral infections, but it can also mistakenly sense RNA present in normal cells. Without KHSRP, the innate immune response could be erroneously turned on when there's no virus. Increasing the activity of KHSRP might therefore be a way to treat autoimmunity." "Next, we plan to figure out more of the details of how KHSRP regulates RIG-I," says Sunnie Yoh, Ph.D., staff scientist in the Chanda lab and a key contributor to the research. "That's the information that will move us in the direction of developing therapies." This research was performed in collaboration with scientists at the Novartis Research Foundation, the Icahn School of Medicine at Mount Sinai, Oregon State University Corvallis, the Paul Ehrlich Institute in Langen, Germany, and the University of California San Francisco. Financial support was provided by the National Institutes of Health and the James B. Pendleton Charitable Trust. Sanford Burnham Prebys Medical Discovery Institute (SBP) is an independent nonprofit medical research organization that conducts world-class, collaborative, biological research and translates its discoveries for the benefit of patients. SBP focuses its research on cancer, immunity, neurodegeneration, metabolic disorders and rare children's diseases. The Institute invests in talent, technology and partnerships to accelerate the translation of laboratory discoveries that will have the greatest impact on patients. Recognized for its world-class NCI-designated Cancer Center and the Conrad Prebys Center for Chemical Genomics, SBP employs about 1,100 scientists and staff in San Diego (La Jolla), Calif., and Orlando (Lake Nona), Fla. For more information, visit us at SBPdiscovery.org or on Facebook at facebook.com/SBPdiscovery and on Twitter @SBPdiscovery.
News Article | February 21, 2017
A reporter who ignores a whistleblower might miss an astonishing but true story. That’s one of the many lessons I learned from Andrew Schneider. The investigative public health journalist died on February 17 from heart failure due to a respiratory disease. Schneider was respected by co-workers for his dogged search for the truth. Others, including myself, are also remembering him for his significant contributions to public health. My colleague, Bob Harrison, MD, MPH at University of California San Francisco told me Harrison was recalling Schneider’s reporting for the Baltimore Sun in 2006 about individuals with severe lung disease. They’d worked with the butter-flavoring agent diacetyl and were gravely ill. I first met Schneider while he was reporting for the Seattle Post-Intelligencer on the man-made asbestos disaster in Libby, Montana. The W.R. Grace caused disaster in that town—-including hundreds of deaths–seemed that it might be repeating itself in Louisa County, Virginia. I was working at the Mine Safety and Health Administration at the time and a whistleblower had come forward who was familiar with what was happening at Louisa County mine. (It too had previously been owned by W.R. Grace.) The whistleblower’s story was mind boggling, but I was inclined to believe it. MSHA inspectors later confirmed some of what the whistleblower reported. That’s when Schneider told me that he doesn’t ignore what he hears from a whistleblower. The story may not be precisely what the whistleblower asserts, but there’s usually something to their story—and potentially something quite remarkable. In a 2009 interview with fellow journalist William Heisel, I see Schneider offered a similar sentiment: “I very rarely ignore whistle blowers, no matter how crazy they sound. I’ve learned too many times over the years that if they are that passionate about something, there’s probably something going on. It may not be what they suspect, but there is something going on. I have never had an emotionally passionate source be completely wrong.” David McCumber, who worked with Schneider at the Seattle Post-Intelligencer and co-author of their book: An Air That Kills: How the Asbestos Poisoning of Libby, Montana Uncovered a National Scandal, wrote a wonderful tribute to his friend. McCumber’s piece includes touching recollections from Schneider’s colleagues. Mary Pat Flaherty reported with Schneider on one of his two Pulitzer Prize winning stories. She told McCumber: Indeed he did and the world is a better place because of him. Andrew, you will be missed. P.S. My colleague Jennifer Sass has her own wonderful remembrance about Andrew. It made me smile to remember the story of his puppy named Libby.
News Article | February 15, 2017
San Francisco dentist, Dr. Ben Amini, the founder at CitiDent, announces the incorporation of iTero Element, the latest in 3-D scanning device which is capable of taking digital impressions of teeth and gums. Conventional bite impressions have lagged behind some of the latest advances in dentistry, such as CAD CAM restorations, in terms of speed, efficiency and patient comfort. Increasingly, digital impressions are being used to capture images of the teeth and gums from all angles to use for planning treatments from creating restorations to Invisalign aligners. iTero Element, a small wand that is inserted into the mouth, creates detailed digital 3D images of the teeth and gums that can then be used to design and modify a treatment plan that best suits the patient. At the same time, patients benefit from the improved accuracy of treatment results, including greater comfort and aesthetic appeal. Several treatments benefit from iTero Element, from Invisalign, which relies on personalized esthetic aligners, to CAD/CAM restorations, which are milled on site in a single visit. More patients are choosing same-day restorations produced this way. With the combination of digital bite impressions and CAD/CAM milling, eligible patients can get veneers, dental implants, crowns, inlays, and onlays in a single appointment. The iTero Element wand combines optical imaging with a laser to produce precise images, allowing for comfortable lifelike restorations. The entire process is also easier for patients who do not wish to endure inconvenient conventional bite impressions. About Dr. Ben Amini Dr. Amini attended University of California San Francisco School of Dentistry, where he graduated in 1996 and obtained his DDS degree. An assistant clinical professor at his alma mater and a reputable member of many local and international organizations in his profession, Dr. Amini offers a complete range of treatments at CitiDent, including general, cosmetic, and implant dentistry, periodontics, emergency dentistry, and tooth replacements. A full selection of orthodontics is also available thru a team orthodontist at CitiDent. They include Invisalign, esthetic metallic braces, lingual braces, and others. Alongside his personally trained associate dentists, Dr. Amini focuses on giving patients of all ages the latest choices in dental technologies.
News Article | February 21, 2017
SAN FRANCISCO, Feb. 21, 2017 (GLOBE NEWSWIRE) -- World-renowned brain scientist Dr. Michael Merzenich will deliver a keynote address at the “I Can Change My Brain” conference at Deakin University in Melbourne, Australia on Sunday, February 26, 2017. Dr. Merzenich is Chief Scientific Officer at Posit Science and Professor Emeritus at University of California San Francisco (UCSF). Dr. Merzenich will speak on how breakthroughs in brain plasticity in his lab (and in the labs of colleagues across the globe) have now entered the final stage of translational research – resulting in strategies and products that people can engage with today to monitor and improve brain performance and brain health. Three decades ago, Dr. Merzenich forever changed the way scientists look at the brain with his seminal experiments showing that the adult brain remains plastic – capable of changing chemically, physically and functionally, throughout life, based on sensory and other inputs. Previously, scientists believed that the brain was plastic only in childhood. Dr. Merzenich realized that plasticity could be harnessed to create tools to benefit humanity. He first applied plasticity in the co-invention of the cochlear implant, which has restored hearing to hundreds of thousands of people living with deafness. With the wide adoption of personal computers and, then, mobile devices, Dr. Merzenich focused on how to create online (and in app) assessments and exercises that continuously adapt and personalize to monitor and improve individual health and performance. The exercises in the BrainHQ brain-training platform from Posit Science have been shown to improve performance across a wide range of populations in more than 140 peer-reviewed journal articles. Studies in healthy mature adults have shown gains in standard and real world measures of cognition (e.g., brain speed, attention, memory and executive function); quality of life (mood, confidence, self-rated health, functional independence); and everyday activities (balance, movement, driving). Last year, Dr. Merzenich was awarded the Kavli Prize, the highest honor in neuroscience. The prior year, he was awarded the Russ Prize, the highest honor in bio-engineering. He has been elected by his peers to both the National Academy of Sciences and to the National Academy of Medicine in the USA. He also is a member of the Norwegian Academy of Sciences and Letters. Dr. Merzenich frequently appears on television and in the press. He may be best known to Australian audiences for his role in the award-winning television series “Redesign My Brain.” Dr. Merzenich is the author of several books, including Soft-Wired: How the New Science of Brain Plasticity Can Change Your Life. More information about the conference can be found at http://changemybrain.businessbrainmapping.com.