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Atkins SLP, Greer YE, Jenkins S, Gatti-Mays ME, Houston N, Lee S, Lee MJ, Rastogi S, Sato N, Burks C, Annunziata CM, Lee JM, Nagashima K, Trepel JB, Lipkowitz S, Zimmer AS. A Single-Arm, Open-Label Phase II Study of ONC201 in Recurrent/Refractory Metastatic Breast Cancer and Advanced Endometrial Carcinoma. Oncologist 2023; 28:919-e972. [PMID: 37279797 PMCID: PMC10546825 DOI: 10.1093/oncolo/oyad164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 05/11/2023] [Indexed: 06/08/2023] Open
Abstract
BACKGROUND ONC201 is a small molecule that can cause nonapoptotic cell death through loss of mitochondrial function. Results from the phase I/II trials of ONC201 in patients with refractory solid tumors demonstrated tumor responses and prolonged stable disease in some patients. METHODS This single-arm, open-label, phase II clinical trial evaluated the efficacy of ONC201 at the recommended phase II dose (RP2D) in patients with recurrent or refractory metastatic breast or endometrial cancer. Fresh tissue biopsies and blood were collected at baseline and at cycle 2 day 2 for correlative studies. RESULTS Twenty-two patients were enrolled; 10 patients with endometrial cancer, 7 patients with hormone receptor-positive breast cancer, and 5 patients with triple-negative breast cancer. The overall response rate was 0%, and the clinical benefit rate, defined by complete response (CR) + partial response (PR) + stable disease (SD), was 27% (n = 3/11). All patients experienced an adverse event (AE), which was primarily low grade. Grade 3 AEs occurred in 4 patients; no grade 4 AEs occurred. Tumor biopsies did not show that ONC201 consistently induced mitochondrial damage or alterations in tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) or the TRAIL death receptors. ONC201 treatment caused alterations in peripheral immune cell subsets. CONCLUSION ONC201 monotherapy did not induce objective responses in recurrent or refractory metastatic breast or endometrial cancer at the RP2D dose of 625 mg weekly but had an acceptable safety profile (ClinicalTrials.gov Identifier: NCT03394027).
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Affiliation(s)
- Sarah L P Atkins
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Yoshimi Endo Greer
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Sarah Jenkins
- University of Tennessee Medical Center, Knoxville, TN, USA
| | - Margaret E Gatti-Mays
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
- Division of Hematology/Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Nicole Houston
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Sunmin Lee
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Min-Jung Lee
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Shraddha Rastogi
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Nahoko Sato
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Christina Burks
- Electron Microscopy Laboratory, NCI, NIH, Frederick, MD, USA
| | - Christina M Annunziata
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Kunio Nagashima
- Electron Microscopy Laboratory, NCI, NIH, Frederick, MD, USA
| | - Jane B Trepel
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Stanley Lipkowitz
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
| | - Alexandra S Zimmer
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute , National Institutes of Health, Bethesda, MD, USA
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2
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Lita A, Pliss A, Kuzmin A, Yamasaki T, Zhang L, Dowdy T, Burks C, de Val N, Celiku O, Ruiz-Rodado V, Nicoli ER, Kruhlak M, Andresson T, Das S, Yang C, Schmitt R, Herold-Mende C, Gilbert MR, Prasad PN, Larion M. IDH1 mutations induce organelle defects via dysregulated phospholipids. Nat Commun 2021; 12:614. [PMID: 33504762 PMCID: PMC7840755 DOI: 10.1038/s41467-020-20752-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 12/11/2020] [Indexed: 01/25/2023] Open
Abstract
Infiltrating gliomas are devastating and incurable tumors. Amongst all gliomas, those harboring a mutation in isocitrate dehydrogenase 1 mutation (IDH1mut) acquire a different tumor biology and clinical manifestation from those that are IDH1WT. Understanding the unique metabolic profile reprogrammed by IDH1 mutation has the potential to identify new molecular targets for glioma therapy. Herein, we uncover increased monounsaturated fatty acids (MUFA) and their phospholipids in endoplasmic reticulum (ER), generated by IDH1 mutation, that are responsible for Golgi and ER dilation. We demonstrate a direct link between the IDH1 mutation and this organelle morphology via D-2HG-induced stearyl-CoA desaturase (SCD) overexpression, the rate-limiting enzyme in MUFA biosynthesis. Inhibition of IDH1 mutation or SCD silencing restores ER and Golgi morphology, while D-2HG and oleic acid induces morphological defects in these organelles. Moreover, addition of oleic acid, which tilts the balance towards elevated levels of MUFA, produces IDH1mut-specific cellular apoptosis. Collectively, these results suggest that IDH1mut-induced SCD overexpression can rearrange the distribution of lipids in the organelles of glioma cells, providing new insight into the link between lipid metabolism and organelle morphology in these cells, with potential and unique therapeutic implications. The understanding of altered lipid metabolism by isocitrate dehydrogenase 1 (IDH1) mutations in gliomas at a compartment-specific level is limited. Here, the authors use Raman spectroscopy to monitor organelle-specific metabolic changes and report that IDH1 mutations induce phospholipid imbalances which lead to ER and Golgi dilation.
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Affiliation(s)
- Adrian Lita
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Artem Pliss
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Andrey Kuzmin
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA.,Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Tomohiro Yamasaki
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Lumin Zhang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Tyrone Dowdy
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Christina Burks
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA
| | - Natalia de Val
- Electron Microscopy Laboratory, Frederick National Laboratory for Cancer Research, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, 21701, USA
| | - Orieta Celiku
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Victor Ruiz-Rodado
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Elena-Raluca Nicoli
- Undiagnosed Diseases Program, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Michael Kruhlak
- Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD, 20892, USA
| | - Thorkell Andresson
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Sudipto Das
- Protein Characterization Laboratory of the Cancer Research Technology Program (CRTP), National Cancer Institute, Frederick, MD, 21702, USA
| | - Chunzhang Yang
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Rebecca Schmitt
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Christel Herold-Mende
- Division of Neurosurgical Research, Department of Neurosurgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA
| | - Paras N Prasad
- Institute for Lasers, Photonics and Biophotonics, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA.,Advanced Cytometry Instrumentation Systems, LLC, Buffalo, NY, 14260, USA
| | - Mioara Larion
- Neuro-Oncology Branch, National Cancer Institute, Center for Cancer Research, National Institutes of Health, Bethesda, MD, USA.
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3
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Burks C, Van Heertum K, Purdue-Smithe A, Mumford S, Weinerman R. SIMILAR SUCCESS RATES WITH FRESH AND FROZEN DONOR OOCYTES IN GESTATIONAL CARRIERS: A SART ANALYSIS. Fertil Steril 2020. [DOI: 10.1016/j.fertnstert.2020.02.091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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4
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Kwon S, Burks C, Freed J, Novo J, El-Neemany D, Kocjancic E. 29: Ovotesticular disorder of sexual development: a case report. Am J Obstet Gynecol 2019. [DOI: 10.1016/j.ajog.2019.01.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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5
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Belanger A, Hollyfield J, Yacovone G, Seppe A, Akulian J, Burks C, Rivera P, Dodd L, Long J, Haithcock B, Pecot C. P1.05-01 Incidence and Clinical Relevance of NSCLC Lymph Node Micro-Metastasis Detected by Staging EBUS-TBNA. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Begonia GB, Miller GS, Begonia MFT, Burks C. Chelate-enhanced phytoextraction of lead-contaminated soils using coffeeweed (Sesbania exaltata Raf.). Bull Environ Contam Toxicol 2002; 69:624-631. [PMID: 12375108 DOI: 10.1007/s00128-002-0106-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Affiliation(s)
- G B Begonia
- Department of Biology, Jackson State University, MS 39217, USA
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7
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Burks C. Careers-perspective interview. Trends Cell Biol 2000; 10:123. [PMID: 10675907 DOI: 10.1016/s0962-8924(99)01593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Abstract
Genetic studies have identified an unusual transvection process in the Abdominal-B (Abd-B) locus of Drosophila. In some cases distal infraabdominal (iab) regulatory domains continue to activate the Abd-B promoter even when translocated onto different chromosomes. Transvection depends on an approx. 10 kb genomic DNA sequence, termed the transvection mediating region (tmr), located immediately downstream of the Abd-B transcription unit. Here we report a detailed analysis of this region. Different DNA fragments from the tmr were inserted into a variety of P-transformation vectors. Analyses of reporter gene expression in transgenic embryos and adults identify at least three cis-regulatory elements, including two enhancers (IAB7 and IAB8) and a new insulator DNA (Frontabdominal-8, Fab-8). Evidence is also presented for a Polycomb Response Element (PRE) linked to the IAB8 enhancer, and an internal promoter in the iab-8 domain, which transcribes the iab-7 and iab-8 cis-regulatory DNA, including the Fab-8 insulator. We discuss the significance of these findings with regard to Abd-B transvection and long-range enhancer-promoter interactions in mammalian globin loci.
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Affiliation(s)
- J Zhou
- Dept Mol. Cell Biol., Division of Genetics, University of California, Berkeley, CA 94720, USA.
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9
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Abstract
Molecular Biology Database List (MBDL) includes brief descriptions and pointers to Web sites for the various databases described in this issue as well as other Web sites presenting data sets relevant to molecular biology. This information is compiled into a list (http://www.oup.co.uk/nar/Volume_27/Issue_01/summary/ gkc105_gml.html) which includes links both to source Web sites and to on-line versions of articles describing the databases.
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Affiliation(s)
- C Burks
- Exelixis Pharmaceuticals, Inc., 260 Littlefield Avenue, South San Francisco, CA 94080, USA.
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10
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Lai EC, Burks C, Posakony JW. The K box, a conserved 3′ UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts. Development 1998; 125:4077-88. [PMID: 9735368 DOI: 10.1242/dev.125.20.4077] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Cell-cell interactions mediated by the Notch receptor play an essential role in the development of the Drosophila adult peripheral nervous system (PNS). Transcriptional activation of multiple genes of the Enhancer of split Complex [E(spl)-C] is a key intracellular response to Notch receptor activity. Here we report that most E(spl)-C genes contain a novel sequence motif, the K box (TGTGAT), in their 3′ untranslated regions (3′ UTRs). We present three lines of evidence that demonstrate the importance of this element in the post-transcriptional regulation of E(spl)-C genes. First, K box sequences are specifically conserved in the orthologs of two structurally distinct E(spl)-C genes (m4 and m8) from a distantly related Drosophila species. Second, the wild-type m8 3′ UTR strongly reduces accumulation of heterologous transcripts in vivo, an activity that requires its K box sequences. Finally, m8 genomic DNA transgenes lacking these motifs cause mild gain-of-function PNS defects and can partially phenocopy the genetic interaction of E(spl)D with Notchspl. Although E(spl)-C genes are expressed in temporally and spatially specific patterns, we find that K box-mediated regulation is ubiquitous, implying that other targets of this activity may exist. In support of this, we present sequence analyses that implicate genes of the iroquois Complex (Iro-C) and engrailed as additional targets of K box-mediated regulation.
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Affiliation(s)
- E C Lai
- Department of Biology and Center for Molecular Genetics, University of California San Diego, La Jolla, CA 92093-0349, USA
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11
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Abstract
There is no clear picture to date of the mechanisms determining nucleosome positioning. Generally, local DNA sequence signals (sequence-dependent positioning) or non-local signals (e.g. boundary effects) are possible. We have analyzed the DNA sequences of a series of positioned and mapped nucleosome cores in a systematic search for local sequence signals. The data set consists of 113 mapped nucleosome cores, mapped in vivo, in situ, or in reconstituted chromatin. The analysis focuses on the periodic distribution of sequence elements implied by each of six different published DNA structural models. We have also investigated the periodic distribution of all mono-, di-, and trinucleotides. An identical analysis was performed on a set of isolated chicken nucleosome cores (nucleosome data from the literature) that are presumably positioned due to local sequence signals. The results show that the sequences of the isolated nucleosome cores have a number of characteristic features that distinguish them clearly from randomly chosen reference DNA. This confirms that the positioning of these nucleosomes is mainly sequence-dependent (i.e., dependent on local octamer-DNA interactions) and that our algorithms are able to detect these patterns. Using the same algorithms, the sequences of the mapped nucleosome cores, however, are on average very similar to randomly chosen reference DNA. This suggests that the position of the majority of these nucleosomes can not be attributed to the sequence patterns implemented in our algorithms. The arrangement of positioned nucleosomes seems to be the result of a dynamic interplay of octamer-DNA interactions, nucleosome-nucleosome interactions and other positioning signals with varying relative contributions along the DNA.
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Affiliation(s)
- H Staffelbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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12
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Affiliation(s)
- M L Engle
- Los Alamos National Laboratory, NM 87545
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13
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Abstract
GRAM (Genomic Restriction map AsseMbly) takes as input single-digest restriction fragments for a set of overlapping clones and outputs one or more plausible partially ordered restriction maps. For each restriction map, GRAM shows the corresponding alignment of the input clone fragments. Due to the error and uncertainty in experimental data, this problem is computationally difficult to solve; therefore, the principle objective in the design of GRAM is to facilitate man-machine collaborative problem solving. GRAM quickly approximates a solution, as follows. (i) A clustering algorithm determines a probable set of restriction fragments. (ii) An assembly algorithm permutes the set of restriction fragments such that the maximal number of clone fragments are contiguous. The output of the GRAM algorithm is displayed for the user to query and edit. This paper describes the stochastic assembly algorithm and shows how it works with the interactive graphics to support man-machine problem solving. In order to test and verify the performance of GRAM, we have developed a program called genfragII to simulate the digestion of clones and fragments; this program is described and results are presented. GRAM is also being used for a number of genome mapping projects.
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Affiliation(s)
- C Soderlund
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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14
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Abstract
Using data currently available from transcriptional element (TE) databases, we have analyzed the density of these elements in both promoter and non-promoter sequences obtained from the GenBank sequence database. The density of putative TEs in non-promoter sequences was about 16% higher than that seen in pseudo-random DNA sequences. Promoter TE density from the transcription startsite to 100 basepairs upstream was found to be about 42% higher than in non-promoter sequences. However, the extensive overlap of putative TE densities between promoters and non-promoters confounds an attempt to use TE density as a simple discriminator.
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Affiliation(s)
- D S Prestridge
- Theoretical Biology and Biophysics Group, Los Alamos National Labatory, NM 87545
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15
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Abstract
We have developed a set of tools, genfrag, to fragment and optionally mutate a DNA sequence to generate benchmark data sets for testing DNA sequence assembly algorithms. Data parameters can be systematically and independently varied to explore the range of data--and corresponding performance of assembly tools--encountered on large-scale random, or "shot-gun," sequencing projects.
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Affiliation(s)
- M L Engle
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, New Mexico 87545
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16
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Mount SM, Burks C, Hertz G, Stormo GD, White O, Fields C. Splicing signals in Drosophila: intron size, information content, and consensus sequences. Nucleic Acids Res 1992; 20:4255-62. [PMID: 1508718 PMCID: PMC334133 DOI: 10.1093/nar/20.16.4255] [Citation(s) in RCA: 309] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A database of 209 Drosophila introns was extracted from Genbank (release number 64.0) and examined by a number of methods in order to characterize features that might serve as signals for messenger RNA splicing. A tight distribution of sizes was observed: while the smallest introns in the database are 51 nucleotides, more than half are less than 80 nucleotides in length, and most of these have lengths in the range of 59-67 nucleotides. Drosophila splice sites found in large and small introns differ in only minor ways from each other and from those found in vertebrate introns. However, larger introns have greater pyrimidine-richness in the region between 11 and 21 nucleotides upstream of 3' splice sites. The Drosophila branchpoint consensus matrix resembles C T A A T (in which branch formation occurs at the underlined A), and differs from the corresponding mammalian signal in the absence of G at the position immediately preceding the branchpoint. The distribution of occurrences of this sequence suggests a minimum distance between 5' splice sites and branchpoints of about 38 nucleotides, and a minimum distance between 3' splice sites and branchpoints of 15 nucleotides. The methods we have used detect no information in exon sequences other than in the few nucleotides immediately adjacent to the splice sites. However, Drosophila resembles many other species in that there is a discontinuity in A + T content between exons and introns, which are A + T rich.
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Affiliation(s)
- S M Mount
- Department of Biological Sciences, Columbia University, New York, NY 10027
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17
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18
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Abstract
The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 85,000,000 nucleotides in 67,000 entries from a total of 3,000 organisms. The input stream of data coming into the database is primarily as direct submissions from the scientific community on electronic media, with little or no data being keyboarded from the printed page by the databank staff. The data are maintained in a relational database management system and are made available in flatfile form through on-line access, and through various network and off-line computer-readable media. The data are also distributed in relational form through satellite copies at a number of institutions in the U.S. and elsewhere. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.
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Affiliation(s)
- C Burks
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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19
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Abstract
We have developed an algorithm that automatically and reproducibly identifies potential tRNA genes in genomic DNA sequences, and we present a general strategy for testing the sensitivity of such algorithms. This algorithm is useful for the flagging and characterization of long genomic sequences that have not been experimentally analyzed for identification of functional regions, and for the scanning of nucleotide sequence databases for errors in the sequences and the functional assignments associated with them. In an exhaustive scan of the GenBank database, 97.5% of the 744 known tRNA genes were correctly identified (true-positives), and 42 previously unidentified sequences were predicted to be tRNAs. A detailed analysis of these latter predictions reveals that 16 of the 42 are very similar to known tRNA genes, and we predict that they do, in fact, code for tRNA, yielding a false-positive rate for the algorithm of 0.003%. The new algorithm and testing strategy are a considerable improvement over any previously described strategies for recognizing tRNA genes, and they allow detections of genes (including introns) embedded in long genomic sequences.
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Affiliation(s)
- G A Fichant
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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20
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Cannon TM, Koskela RJ, Burks C, Stallings RL, Ford AA, Hempfner PE, Brown HT, Fickett JW. A program for computer-assisted scoring of Southern blots. Biotechniques 1991; 10:764-7. [PMID: 1878210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
SCORE, a program for computer-assisted scoring of Southern blots of clone DNA, retains the use of expert human judgment while taking over much of the drudgery of the scoring task. The primary functions of the program are to help make an aligned overlay of the fluorescence gel image and the autoradiogram blot image, to keep track of band and lane locations and to store the resulting data directly into a database. Use of SCORE has resulted in greatly increased efficiency and accuracy.
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Affiliation(s)
- T M Cannon
- Los Alamos National Laboratory, NM 87545
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21
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Abstract
GenBank, the national repository for nucleotide sequence data, has implemented a new model of scientific data management, which we term electronic data publishing. In traditional publishing, both scientific conclusions and supporting data are communicated via the printed page, and in electronic journal publishing, both types of information are communicated via electronic media. In electronic data publishing, by contrast, conclusions are published in a journal while data are published via a network-accessible, electronic database.
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Affiliation(s)
- M J Cinkosky
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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22
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Abstract
The GenBank nucleotide sequence database now contains sequence data and associated annotation corresponding to 56,000,000 nucleotides in 45,000 entries. The input stream of data coming into the database has largely been shifted to direct submissions from the scientific community on electronic media. The data have been installed in a relational database management system and are made available in this form through on-line access, and through various network and off-line computer-readable media. In addition, GenBank provides the U.S. distribution center for the BIOSCI electronic bulletin board service.
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Affiliation(s)
- C Burks
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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23
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Burks C, Cinkosky MJ, Gilna P, Hayden JE, Abe Y, Atencio EJ, Barnhouse S, Benton D, Buenafe CA, Cumella KE. GenBank: current status and future directions. Methods Enzymol 1990; 183:3-22. [PMID: 2314279 DOI: 10.1016/0076-6879(90)83003-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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24
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Abstract
The rapidly increasing number of databases relevant to molecular biology has given rise to a need for a coordinated effort to identify, characterize, and link them. The LiMB database, which contains information about molecular biology and related databases, is a step in that direction. It serves molecular biologists seeking data sets containing information relevant to their research, and is also intended to anticipate the needs of database designers and managers building software links for related data sets. We present an abbreviated version of the database here; the full database is available free of charge as described below.
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Affiliation(s)
- J R Lawton
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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25
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Affiliation(s)
- P Gilna
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, NM 87545
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26
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Abstract
The lipid state hypothesis proposes that liquid crystalline states of cholesteryl esters play a role in the development and persistence of the fatty streak lesions characteristic of atherosclerosis. We have tested several corollaries suggested by this hypothesis and find that the ensemble of droplets in atherosclerotic tissue are predominantly in the isotropic (fluid) state at 37.0 degrees C. Furthermore, the liquid-crystalline state transition behavior of these droplets is not influenced significantly by the distribution of component cholesteryl ester species. There are no significant correlations between the transition behavior of the droplets and the age, sex, or race of the subjects from which tissue samples were taken. These results show that the lipid state hypothesis is weak, and that the origin and persistence of fatty streak lesions in humans is probably dominated by other factors.
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Affiliation(s)
- C Burks
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511
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Moyzis RK, Torney DC, Meyne J, Buckingham JM, Wu JR, Burks C, Sirotkin KM, Goad WB. The distribution of interspersed repetitive DNA sequences in the human genome. Genomics 1989; 4:273-89. [PMID: 2714792 DOI: 10.1016/0888-7543(89)90331-5] [Citation(s) in RCA: 147] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The distribution of interspersed repetitive DNA sequences in the human genome has been investigated, using a combination of biochemical, cytological, computational, and recombinant DNA approaches. "Low-resolution" biochemical experiments indicate that the general distribution of repetitive sequences in human DNA can be adequately described by models that assume a random spacing, with an average distance of 3 kb. A detailed "high-resolution" map of the repetitive sequence organization along 400 kb of cloned human DNA, including 150 kb of DNA fragments isolated for this study, is consistent with this general distribution pattern. However, a higher frequency of spacing distances greater than 9.5 kb was observed in this genomic DNA sample. While the overall repetitive sequence distribution is best described by models that assume a random distribution, an analysis of the distribution of Alu repetitive sequences appearing in the GenBank sequence database indicates that there are local domains with varying Alu placement densities. In situ hybridization to human metaphase chromosomes indicates that local density domains for Alu placement can be observed cytologically. Centric heterochromatin regions, in particular, are at least 50-fold underrepresented in Alu sequences. The observed distribution for repetitive sequences in human DNA is the expected result for sequences that transpose throughout the genome, with local regions of "preference" or "exclusion" for integration.
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Affiliation(s)
- R K Moyzis
- Genetics Group, Los Alamos National Laboratory, University of California, New Mexico 87545
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Affiliation(s)
- C Burks
- Theoretical Biology and Biophysics Group T-10, Los Alamos National Laboratory, NM 87545
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Abstract
The GenBank Genetic Sequence Data Bank contains nearly 15,000 entries for DNA and RNA sequences that have been reported since 1967. This paper briefly describes the contents of the database, the forms in which the data are distributed, and the services available to scientists using the GenBank database.
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Affiliation(s)
- H S Bilofsky
- Life Sciences/Research Systems Department, BBN Laboratories Incorporated, Cambridge, MA 02238
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Burks C. The GenBank database and the flow of sequence data for the human genome. Basic Life Sci 1988; 46:51-6. [PMID: 3223871 DOI: 10.1007/978-1-4684-5547-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- C Burks
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, CA 87545
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Abstract
We report 3 cases of penile curvature deformity and fibrosis of the tunica albuginea after long-term self-injection with papaverine hydrochloride and phentolamine mesylate. To our knowledge this complication has not been reported previously. The clinical presentation and possible etiology are discussed.
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Abstract
A growing body of data indicates that the equilibrium structures of some DNA fragments are curved and that curvature is sequence-directed. We describe a quantitative measure of DNA curvature that can be used for evaluating and comparing current proposed models for the molecular basis of DNA curvature. We demonstrate that this measure, in conjunction with any given prediction model, enables both the comparison of experimental data to predictions and the scanning of nucleotide sequence databases for potential curved regions.
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Affiliation(s)
- C S Tung
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, University of California, New Mexico 87545
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Burks C, Fickett J, Goad W. GenBank status report. Science 1987; 235:267-8. [PMID: 3798110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Burks C, Fickett J, Goad W. GenBank status report. Science 1987. [DOI: 10.1126/science.3798110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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Tung CS, Burks C. Characterization of the distribution of potential short restriction fragments in nucleic acid sequence databases. Implications for an alternative to chemical synthesis of oligonucleotides. FEBS Lett 1986; 205:299-302. [PMID: 3017763 DOI: 10.1016/0014-5793(86)80916-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have searched the GenBank nucleic acid sequence database for potential short restriction fragments. All possible oligonucleotides up to length five are found at least once flanked by known restriction recognition patterns. Thus, searches in the database for a specific sequence corresponding to a desired oligonucleotide would often point to one or more sources of short, retrievable fragments containing that sequence. These results underscore the potential of nucleic acid sequence databases in planning experiments.
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Bilofsky HS, Burks C, Fickett JW, Goad WB, Lewitter FI, Rindone WP, Swindell CD, Tung CS. The GenBank genetic sequence databank. Nucleic Acids Res 1986; 14:1-4. [PMID: 3945546 PMCID: PMC339347 DOI: 10.1093/nar/14.1.1] [Citation(s) in RCA: 200] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The GenBank Genetic Sequence Data Bank contains over 5700 entries for DNA and RNA sequences that have been reported since 1967. This paper briefly describes the contents of the database, the forms in which the database is distributed, and the services we offer to scientists who use the GenBank database.
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Burks C, Fickett JW, Goad WB, Kanehisa M, Lewitter FI, Rindone WP, Swindell CD, Tung CS, Bilofsky HS. The GenBank nucleic acid sequence database. Comput Appl Biosci 1985; 1:225-33. [PMID: 3880345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The GenBank nucleic acid sequence database is a computer-based collection of all published DNA and RNA sequences; it contains over five million bases in close to six thousand sequence entries drawn from four thousand five hundred published articles. Each sequence is accompanied by relevant biological annotation. The database is available either on magnetic tape, on floppy diskettes, on-line or in hardcopy form. We discuss the structure of the database, the extent of the data and the implications of the database for research on nucleic acids.
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Affiliation(s)
- C Burks
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, University of California, NM 87545
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Abstract
All pairs of a large set of known vertebrate DNA sequences were searched by computer for most similar segments. Analysis of this data shows that the computed similarity scores are distributed proportionally to the logarithm of the product of the lengths of the sequences involved. This distribution is closely related to recent results of Erdos and others on the longest run of heads in coin tossing. A simple rule is derived for determination of statistical significance of the similarity scores and to assist in relating statistical and biological significance.
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Dean GE, Macnab RM, Stader J, Matsumura P, Burks C. Gene sequence and predicted amino acid sequence of the motA protein, a membrane-associated protein required for flagellar rotation in Escherichia coli. J Bacteriol 1984; 159:991-9. [PMID: 6090403 PMCID: PMC215758 DOI: 10.1128/jb.159.3.991-999.1984] [Citation(s) in RCA: 145] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The motA and motB gene products of Escherichia coli are integral membrane proteins necessary for flagellar rotation. We determined the DNA sequence of the region containing the motA gene and its promoter. Within this sequence, there is an open reading frame of 885 nucleotides, which with high probability (98% confidence level) meets criteria for a coding sequence. The 295-residue amino acid translation product had a molecular weight of 31,974, in good agreement with the value determined experimentally by gel electrophoresis. The amino acid sequence, which was quite hydrophobic, was subjected to a theoretical analysis designed to predict membrane-spanning alpha-helical segments of integral membrane proteins; four such hydrophobic helices were predicted by this treatment. Additional amphipathic helices may also be present. A remarkable feature of the sequence is the existence of two segments of high uncompensated charge density, one positive and the other negative. Possible organization of the protein in the membrane is discussed. Asymmetry in the amino acid composition of translated DNA sequences was used to distinguish between two possible initiation codons. The use of this method as a criterion for authentication of coding regions is described briefly in an Appendix.
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Burks C, Engelman DM. Cholesteryl myristate conformation in liquid crystalline mesophases determined by neutron scattering. Proc Natl Acad Sci U S A 1981; 78:6863-7. [PMID: 6947261 PMCID: PMC349152 DOI: 10.1073/pnas.78.11.6863] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The possible involvement of cholesteryl ester states in the development and persistence of atherosclerosis and the transport and storage of cholesteryl esters has led to questions concerning the organization and conformation of cholesteryl ester molecules in both pure phases and membranes. The experiments we report here were designed to measure the distance between the center of mass of the fatty acyl terminal methyl group and the center of mass of the three-carbon branched terminus of the cholesterol moiety at the opposite end of the molecule. The distance obtained is thus a gauge of cholesteryl ester conformation through the conformational range from a completely extended conformation to a U-shaped conformation. Neutron scattering experiments on partially deuterated samples of pure cholesteryl myristate in the crystalline, smectic, cholesteric, and isotropic phases indicate that the molecule is extended in each of these states. A discussion of specific molecular models consistent with these results and extension of these conclusions to other cholesteryl esters is included.
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Cleveland WH, Bowles B, Hicks W, Burks C, Rogers KD. Outcomes of methadone treatment of 300 innercity addicts. Public Health Rep 1974; 89:563-8. [PMID: 4218906 PMCID: PMC1434685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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