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Keeney JG, Gulzar N, Baker JB, Klempir O, Hannigan GD, Bitton DA, Maritz JM, King CHS, Patel JA, Duncan P, Mazumder R. Communicating computational workflows in a regulatory environment. Drug Discov Today 2024; 29:103884. [PMID: 38219969 DOI: 10.1016/j.drudis.2024.103884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 12/14/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines.
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Affiliation(s)
- Jonathon G Keeney
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA.
| | - Naila Gulzar
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Ondrej Klempir
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | | | - Danny A Bitton
- R&D Informatics Solutions, MSD Czech Republic, Prague, Czech Republic
| | - Julia M Maritz
- Exploratory Science Center, Merck & Co., Cambridge, MA, USA
| | - Charles H S King
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | - Janisha A Patel
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
| | | | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, School of Medicine and Health Sciences, The George Washington University, Washington, DC, USA
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2
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Sobitan A, Gebremedhin B, Yao Q, Xie G, Gu X, Li J, Teng S. A Computational Approach: The Functional Effects of Thyroid Peroxidase Variants in Thyroid Cancer and Genetic Disorders. JCO Clin Cancer Inform 2024; 8:e2300140. [PMID: 38295322 PMCID: PMC10843385 DOI: 10.1200/cci.23.00140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/16/2023] [Accepted: 10/18/2023] [Indexed: 02/02/2024] Open
Abstract
PURPOSE Thyroid peroxidase (TPO) is essential for the synthesis of thyroid hormones. However, specific mutations render TPO antigenic and prone to autoimmune attacks leading to thyroid cancer, TPO deficiency, and congenital hypothyroidism (CH). Despite technological advancement, most experimental procedures cannot quickly identify the genetic causes of CH nor detect thyroid cancer in the early stages. METHODS We performed saturated computational mutagenesis to calculate the folding energy changes (∆∆G) caused by missense mutations and analyzed the mutations involved in post-translational modifications (PTMs). RESULTS Our results showed that the functional important missense mutations occurred in the heme peroxidase domain. Through computational saturation mutagenesis, we identified the TPO mutations in G393 and G348 affecting protein stability and PTMs. Our folding energy calculations revealed that seven of nine somatic thyroid cancer mutations destabilized TPO. CONCLUSION These findings highlight the impact of these specific mutations on TPO stability, linking them to thyroid cancer and other genetic thyroid-related disorders. Our results show that computational mutagenesis of proteins provides a quick insight into rare mutations causing Mendelian disorders and cancers in humans.
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Affiliation(s)
| | | | - Qiaobin Yao
- Department of Biology, Howard University, Washington, DC
| | - Guiqin Xie
- Department of Oral Pathology, Howard University, Washington, DC
| | - Xinbin Gu
- Department of Oral Pathology, Howard University, Washington, DC
| | - Jiang Li
- Department of Electrical Engineering and Computer Science, Howard University, Washington, DC
| | - Shaolei Teng
- Department of Biology, Howard University, Washington, DC
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Epidemiology of Type 3 Poliovirus AFP Cases in Israel between 1973 and 1988: Whole Genome Sequencing of RNA Extracted Directly from Archived Stocks to Avoid Re-Culturing Neurovirulent Wild Poliovirus. Vaccines (Basel) 2022; 10:vaccines10122154. [PMID: 36560563 PMCID: PMC9781118 DOI: 10.3390/vaccines10122154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/05/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Poliovirus post-eradication containment of wild-type 2 poliovirus (PV2) requires the destruction of all materials containing, or potentially containing, PV2. Acute flaccid paralysis (AFP) cases in Israel between 1973 and 1988 were caused by all three serotypes; thus, isolates from cases and case-contacts were either PV2 or potentially contaminated with PV2. AIMS To provide a proof-of-concept that whole genome sequences (WGS) of wild-type 3 poliovirus (PV3s) could be salvaged from the RNA extracted directly from archived poliovirus stocks avoiding re-amplification of neurovirulent viruses, we link WGSs to case histories and determine the phylogenetic relationships among the PV3s. METHODS Data retrieved from 427 poliovirus-positive cases reported between 1973 and 1988 identified 85 PV3-associated cases. A total of 71 archived PV3 isolates were available from PV3-positive cases and contacts. WGSs were obtained by NGS from cDNA libraries constructed from RNA extracted directly from archived viral stocks. Sequences were subjected to phylogenetic analysis and linked to case data. RESULTS WGSs were successfully constructed for 55 isolates. Phylogenetic analysis revealed the circulation of seven lineages of PV3. One lineage, with 23 isolates, presented as an outbreak of six-year duration. Isolates from six other lineages were consistent with subsequent separate introductions, sporadic cases, and limited transmission. Recombinant vaccine-like PV3 recombinants were isolated from some cases. CONCLUSIONS Whole or near-whole genome sequence information, obtained from RNA extracted directly from the archived material, safely provided detailed genetic information linked to patient data from a time when limited sequence information was previously available and revealed the pattern of transmission of wild PV3 in Israel.
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Abe T, Kinsella I, Saxena S, Buchanan EK, Couto J, Briggs J, Kitt SL, Glassman R, Zhou J, Paninski L, Cunningham JP. Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis. Neuron 2022; 110:2771-2789.e7. [PMID: 35870448 PMCID: PMC9464703 DOI: 10.1016/j.neuron.2022.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 05/06/2022] [Accepted: 06/22/2022] [Indexed: 10/17/2022]
Abstract
A key aspect of neuroscience research is the development of powerful, general-purpose data analyses that process large datasets. Unfortunately, modern data analyses have a hidden dependence upon complex computing infrastructure (e.g., software and hardware), which acts as an unaddressed deterrent to analysis users. Although existing analyses are increasingly shared as open-source software, the infrastructure and knowledge needed to deploy these analyses efficiently still pose significant barriers to use. In this work, we develop Neuroscience Cloud Analysis As a Service (NeuroCAAS): a fully automated open-source analysis platform offering automatic infrastructure reproducibility for any data analysis. We show how NeuroCAAS supports the design of simpler, more powerful data analyses and that many popular data analysis tools offered through NeuroCAAS outperform counterparts on typical infrastructure. Pairing rigorous infrastructure management with cloud resources, NeuroCAAS dramatically accelerates the dissemination and use of new data analyses for neuroscientific discovery.
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Affiliation(s)
- Taiga Abe
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University Medical Center, Columbia University, New York, NY 10027, USA
| | - Ian Kinsella
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Department of Statistics, Columbia University, New York, NY 10027, USA
| | - Shreya Saxena
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Statistics, Columbia University, New York, NY 10027, USA; Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL 32607, USA
| | - E Kelly Buchanan
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University Medical Center, Columbia University, New York, NY 10027, USA
| | - Joao Couto
- Department of Neurobiology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - John Briggs
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA
| | - Sian Lee Kitt
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Ryan Glassman
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - John Zhou
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Liam Paninski
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Neuroscience, Columbia University Medical Center, Columbia University, New York, NY 10027, USA; Department of Statistics, Columbia University, New York, NY 10027, USA
| | - John P Cunningham
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Neuroscience, Columbia University, New York, NY 10027, USA; Center for Theoretical Neuroscience, Columbia University, New York, NY 10027, USA; Grossman Center for the Statistics of Mind, Columbia University, New York, NY 10027, USA; Department of Statistics, Columbia University, New York, NY 10027, USA.
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Manukyan H, Wahid R, Ansari A, Tritama E, Macadam A, Konz J, Chumakov K, Laassri M. Quantitative RT-PCR Assays for Quantification of Undesirable Mutants in the Novel Type 2 Oral Poliovirus Vaccine. Vaccines (Basel) 2022; 10:vaccines10091394. [PMID: 36146473 PMCID: PMC9502871 DOI: 10.3390/vaccines10091394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 01/09/2023] Open
Abstract
Emergence of mutations is an inherent property of RNA viruses with several implications for their replication, pathogenesis, and evolutionary adaptation. Oral poliovirus vaccine (OPV), developed by Albert Sabin, is composed of live attenuated polioviruses of three serotypes that can revert to neurovirulence during replication in cell culture and in vaccine recipients. Recently, a new modified variant of Sabin 2 virus was developed by introducing changes in its genome, making it more genetically stable to prevent the reversion. The new strain was used to manufacture novel OPV2 (nOPV2), which was approved by the World Health Organization for emergency use to stop outbreaks caused by circulating vaccine-derived poliovirus (cVDPV2). Manufacture of this improved vaccine requires close attention to the genetic heterogenicity to ensure that the levels of the undesirable mutations are limited. Preliminary studies using whole-genome Illumina sequencing (NGS) identified several genomic sites where mutations tend to occur with regularity. They include VP1-I143T amino acid change at the secondary attenuation site; VP1-N171D, a substitution that modestly increases neurovirulence in mice; and VP1-E295K, which may reduce the immunogenicity of the nOPV2. Therefore, to ensure the molecular consistency of vaccine batches, the content of these mutants must be quantified and kept within specifications. To do this, we have developed quantitative, multiplex, one-step reverse-transcriptase polymerase chain reactions (qmosRT-PCRs) as simple methods for quantification of these mutations. Each method uses specific short TaqMan probes with different dyes for the analysis of both mutants and non-mutants in the same sample. The quantification is done using calibration curves developed using validated reference materials. To evaluate the sensitivity and the linearity of the qmosRT-PCR method, the mutant viruses were spiked in non-mutant viruses, and nOPV2 batches were used to validate the method. The spiked samples and the nOPV2 batches were analyzed by qmosRT-PCR and NGS assays. The results showed that qmosRT-PCR is sensitive enough to detect around 1% of mutants. The percentages of mutants determined by qmosRT-PCR correlate well with the results of the NGS. Further, the analysis of the nOPV2 batches showed that the results of qmosRT-PCR correlated well with the results of NGS. In conclusion, the qmosRT-PCR is a specific, sensitive, and linear method. It could be used for quality control of the nOPV2 batches.
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Affiliation(s)
- Hasmik Manukyan
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Azeem Ansari
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Erman Tritama
- Research and Development Division, PT. Bio Farma, Bandung, West Java 40161, Indonesia
| | - Andrew Macadam
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire EN6 3QG, UK
| | - John Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA 98121, USA
| | - Konstantin Chumakov
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
- Correspondence: ; Tel.: +1-(240)-402-9656; Fax: +1-3015951440
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Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet. EBioMedicine 2022; 80:104061. [PMID: 35598439 PMCID: PMC9126955 DOI: 10.1016/j.ebiom.2022.104061] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/22/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
Background Recently, studies have suggested a role for the gut microbiota in epilepsy. Gut microbial changes during ketogenic diet (KD) treatment of drug-resistant epilepsy have been described. Inflammation is associated with certain types of epilepsy and specific inflammation markers decrease during KD. The gut microbiota plays an important role in the regulation of the immune system and inflammation. Methods 28 children with drug-resistant epilepsy treated with the ketogenic diet were followed in this observational study. Fecal and serum samples were collected at baseline and three months after dietary intervention. Findings We identified both gut microbial and inflammatory changes during treatment. KD had a general anti-inflammatory effect. Novel bioinformatics and machine learning approaches identified signatures of specific Bifidobacteria and TNF (tumor necrosis factor) associated with responders before starting KD. During KD, taxonomic and inflammatory profiles between responders and non-responders were more similar than at baseline. Interpretation Our results suggest that children with drug-resistant epilepsy are more likely to benefit from KD treatment when specific Bifidobacteria and TNF are elevated. We here present a novel signature of interaction of the gut microbiota and the immune system associated with anti-epileptic response to KD treatment. This signature could be used as a prognostic biomarker to identify potential responders to KD before starting treatment. Our findings may also contribute to the development of new anti-seizure therapies by targeting specific components of the gut microbiota. Funding This study was supported by the Swedish Brain Foundation, Margarethahemmet Society, Stiftelsen Sunnerdahls Handikappfond, Linnea & Josef Carlssons Foundation, and The McCormick Genomic & Proteomic Center.
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Communicating regulatory high-throughput sequencing data using BioCompute Objects. Drug Discov Today 2022; 27:1108-1114. [DOI: 10.1016/j.drudis.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 08/20/2021] [Accepted: 01/18/2022] [Indexed: 11/23/2022]
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Edwards V, Smith DL, Meylan F, Tiffany L, Poncet S, Wu WW, Phue JN, Santana-Quintero L, Clouse KA, Gabay O. Analyzing the Role of Gut Microbiota on the Onset of Autoimmune Diseases Using TNF ΔARE Murine Model. Microorganisms 2021; 10:73. [PMID: 35056521 PMCID: PMC8779571 DOI: 10.3390/microorganisms10010073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 12/13/2021] [Accepted: 12/21/2021] [Indexed: 12/24/2022] Open
Abstract
Very little is known about disease transmission via the gut microbiome. We hypothesized that certain inflammatory features could be transmitted via the gut microbiome and tested this hypothesis using an animal model of inflammatory diseases. Twelve-week-old healthy C57 Bl/6 and Germ-Free (GF) female and male mice were fecal matter transplanted (FMT) under anaerobic conditions with TNFΔARE-/+ donors exhibiting spontaneous Rheumatoid Arthritis (RA) and Inflammatory Bowel Disease (IBD) or with conventional healthy mice control donors. The gut microbiome analysis was performed using 16S rRNA sequencing amplification and bioinformatics analysis with the HIVE bioinformatics platform. Histology, immunohistochemistry, ELISA Multiplex analysis, and flow cytometry were conducted to confirm the inflammatory transmission status. We observed RA and IBD features transmitted in the GF mice cohort, with gut tissue disruption, cartilage alteration, elevated inflammatory mediators in the tissues, activation of CD4/CD8+ T cells, and colonization and transmission of the gut microbiome similar to the donors' profile. We did not observe a change or transmission when conventional healthy mice were FMT with TNFΔARE-/+ donors, suggesting that a healthy microbiome might withstand an unhealthy transplant. These findings show the potential involvement of the gut microbiome in inflammatory diseases. We identified a cluster of bacteria playing a role in this mechanism.
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Affiliation(s)
- Vivienne Edwards
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
| | - Dylan L. Smith
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
| | - Francoise Meylan
- Translational Immunology Section, NIH, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892, USA;
| | - Linda Tiffany
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
| | - Sarah Poncet
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (W.W.W.); (J.-N.P.)
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Center for Biologicals Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA; (W.W.W.); (J.-N.P.)
| | - Luis Santana-Quintero
- U.S. Food and Drug Administration, Center for Biologics Evaluation & Research, Office of Biostatistics and Epidemiology, HIVE, Silver Spring, MD 20993, USA;
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of New Drugs, Office of Hematology and Oncology Products, Silver Spring, MD 20993, USA
| | - Kathleen A. Clouse
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
| | - Odile Gabay
- Division of Biotechnology Review and Research I, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Office of Biotechnology Products, Office of Pharmaceutical Quality, Silver Spring, MD 20993, USA; (V.E.); (D.L.S.); (L.T.); (S.P.); (K.A.C.)
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Li W, Lückstädt W, Wöhner B, Bub S, Schulz A, Socher E, Arnold P. Structural and functional properties of meprin β metalloproteinase with regard to cell signaling. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119136. [PMID: 34626678 DOI: 10.1016/j.bbamcr.2021.119136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/05/2021] [Accepted: 09/06/2021] [Indexed: 10/20/2022]
Abstract
The metalloproteinase meprin β plays an important role during collagen I deposition in the skin, mucus detachment in the small intestine and also regulates the abundance of different cell surface proteins such as the interleukin-6 receptor (IL-6R), the triggering receptor expressed on myeloid cells 2 (TREM2), the cluster of differentiation 99 (CD99), the amyloid precursor protein (APP) and the cluster of differentiation 109 (CD109). With that, regulatory mechanisms that control meprin β activity and regulate its release from the cell surface to enable access to distant substrates are increasingly important. Here, we will summarize factors that alternate meprin β activity and thereby regulate its proteolytic activity on the cell surface or in the supernatant. We will also discuss cleavage of the IL-6R and TREM2 on the cell surface and compare it to CD109. CD109, as a substrate of meprin β, is cleaved within the protein core, thereby releasing defined fragments from the cell surface. At last, we will also summarize the role of proteases in general and meprin β in particular in substrate release on extracellular vesicles.
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Affiliation(s)
- Wenjia Li
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Wiebke Lückstädt
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Birte Wöhner
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Simon Bub
- Department of Molecular-Neurology, University Hospital Erlangen, Erlangen, Germany
| | - Antonia Schulz
- Institute of Anatomy, Christian-Albrechts-Universität zu Kiel (CAU), Kiel, Germany
| | - Eileen Socher
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Philipp Arnold
- Institute of Functional and Clinical Anatomy, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
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Development of a Quantitative One-Step RT-PCR Method for the Detection of Sabin 2 Virus Contamination in a Novel Oral Poliovirus Vaccine Type 2. Vaccines (Basel) 2021; 9:vaccines9070688. [PMID: 34201447 PMCID: PMC8310199 DOI: 10.3390/vaccines9070688] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 06/14/2021] [Accepted: 06/16/2021] [Indexed: 11/26/2022] Open
Abstract
To control circulating vaccine-derived type 2 poliovirus outbreaks, a more genetically stable novel Oral Poliovirus Vaccine type 2 (nOPV2) was developed by targeted modifications of Sabin 2 genome. Since the use of OPV2 made of Sabin 2 strain has been stopped, it is important to exclude the possibility that batches of nOPV2 are contaminated with Sabin 2 virus. Here, we report the development of a simple quantitative one-step reverse-transcription polymerase chain reaction assay for the detection and quantitation of Sabin 2 virus in the presence of overwhelming amounts of nOPV2 strain. The method is specific and linear within 8 log10 range even in the presence of relevant amounts of nOPV2 virus. It is sensitive, with a lower limit of detection of 0.2 CCID50/mL (an equivalent of 198 genome copies per mL), and generates reproducible results. This assay can be used for quality control and lot release of the nOPV2.
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Wang Z, Hopson LM, Singleton SS, Yang X, Jogunoori W, Mazumder R, Obias V, Lin P, Nguyen BN, Yao M, Miller L, White J, Rao S, Mishra L. Mice with dysfunctional TGF-β signaling develop altered intestinal microbiome and colorectal cancer resistant to 5FU. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166179. [PMID: 34082069 DOI: 10.1016/j.bbadis.2021.166179] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 05/13/2021] [Accepted: 05/17/2021] [Indexed: 12/20/2022]
Abstract
Emerging data show a rise in colorectal cancer (CRC) incidence in young men and women that is often chemoresistant. One potential risk factor is an alteration in the microbiome. Here, we investigated the role of TGF-β signaling on the intestinal microbiome and the efficacy of chemotherapy for CRC induced by azoxymethane and dextran sodium sulfate in mice. We used two genotypes of TGF-β-signaling-deficient mice (Smad4+/- and Smad4+/-Sptbn1+/-), which developed CRC with similar phenotypes and had similar alterations in the intestinal microbiome. Using these mice, we evaluated the intestinal microbiome and determined the effect of dysfunctional TGF-β signaling on the response to the chemotherapeutic agent 5-Fluoro-uracil (5FU) after induction of CRC. Using shotgun metagenomic sequencing, we determined gut microbiota composition in mice with CRC and found reduced amounts of beneficial species of Bacteroides and Parabacteroides in the mutants compared to the wild-type (WT) mice. Furthermore, the mutant mice with CRC were resistant to 5FU. Whereas the abundances of E. boltae, B.dorei, Lachnoclostridium sp., and Mordavella sp. were significantly reduced in mice with CRC, these species only recovered to basal amounts after 5FU treatment in WT mice, suggesting that the alterations in the intestinal microbiome resulting from compromised TGF-β signaling impaired the response to 5FU. These findings could have implications for inhibiting the TGF-β pathway in the treatment of CRC or other cancers.
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Affiliation(s)
- Zhuanhuai Wang
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; Department of Colorectal Surgery and Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Lindsay M Hopson
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Stephanie S Singleton
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Xiaochun Yang
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA
| | - Wilma Jogunoori
- Research and Development, Veterans Affairs Medical Center, Washington, DC, USA
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, The George Washington University, Washington, DC, USA
| | - Vincent Obias
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Paul Lin
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Bao-Ngoc Nguyen
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA
| | - Michael Yao
- Department of Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Larry Miller
- Department of Medicine, Division of Gastroenterology, Zucker School of Medicine at Hofstra/Northwell Health System, New Hyde Park, NY, USA
| | - Jon White
- Department of Surgery, The George Washington University, Washington, DC, USA
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA.
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, The George Washington University, Washington, DC, USA; The Institute for Bioelectronic Medicine, Feinstein Institutes for Medical Research & Cold Spring Harbor Laboratory, Department of Medicine, Division of Gastroenterology and Hepatology, Northwell Health, NY, USA.
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12
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Patel JA, Dean DA, King CH, Xiao N, Koc S, Minina E, Golikov A, Brooks P, Kahsay R, Navelkar R, Ray M, Roberson D, Armstrong C, Mazumder R, Keeney J. Bioinformatics tools developed to support BioCompute Objects. Database (Oxford) 2021; 2021:baab008. [PMID: 33784373 PMCID: PMC8009203 DOI: 10.1093/database/baab008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/10/2021] [Accepted: 03/06/2021] [Indexed: 11/17/2022]
Abstract
Developments in high-throughput sequencing (HTS) result in an exponential increase in the amount of data generated by sequencing experiments, an increase in the complexity of bioinformatics analysis reporting and an increase in the types of data generated. These increases in volume, diversity and complexity of the data generated and their analysis expose the necessity of a structured and standardized reporting template. BioCompute Objects (BCOs) provide the requisite support for communication of HTS data analysis that includes support for workflow, as well as data, curation, accessibility and reproducibility of communication. BCOs standardize how researchers report provenance and the established verification and validation protocols used in workflows while also being robust enough to convey content integration or curation in knowledge bases. BCOs that encapsulate tools, platforms, datasets and workflows are FAIR (findable, accessible, interoperable and reusable) compliant. Providing operational workflow and data information facilitates interoperability between platforms and incorporation of future dataset within an HTS analysis for use within industrial, academic and regulatory settings. Cloud-based platforms, including High-performance Integrated Virtual Environment (HIVE), Cancer Genomics Cloud (CGC) and Galaxy, support BCO generation for users. Given the 100K+ userbase between these platforms, BioCompute can be leveraged for workflow documentation. In this paper, we report the availability of platform-dependent and platform-independent BCO tools: HIVE BCO App, CGC BCO App, Galaxy BCO API Extension and BCO Portal. Community engagement was utilized to evaluate tool efficacy. We demonstrate that these tools further advance BCO creation from text editing approaches used in earlier releases of the standard. Moreover, we demonstrate that integrating BCO generation within existing analysis platforms greatly streamlines BCO creation while capturing granular workflow details. We also demonstrate that the BCO tools described in the paper provide an approach to solve the long-standing challenge of standardizing workflow descriptions that are both human and machine readable while accommodating manual and automated curation with evidence tagging. Database URL: https://www.biocomputeobject.org/resources.
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Affiliation(s)
- Janisha A Patel
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | | | - Charles Hadley King
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Nan Xiao
- Seven Bridges, Charlestown, MA 02129, USA
| | - Soner Koc
- Seven Bridges, Charlestown, MA 02129, USA
| | - Ekaterina Minina
- CBER-HIVE, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Anton Golikov
- CBER-HIVE, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA
| | | | - Robel Kahsay
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Rahi Navelkar
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | | | | | - Chris Armstrong
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
- The McCormick Genomic and Proteomic Center, The George Washington University, Washington, DC 20037, USA
| | - Jonathon Keeney
- The Department of Biochemistry & Molecular Medicine, The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
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13
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Molecular basis for ubiquitin ligase CRL2 FEM1C-mediated recognition of C-degron. Nat Chem Biol 2021; 17:263-271. [PMID: 33398170 DOI: 10.1038/s41589-020-00703-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 10/30/2020] [Indexed: 01/28/2023]
Abstract
Proteome integrity depends on the ubiquitin-proteasome system to degrade unwanted or abnormal proteins. In addition to the N-degrons, C-terminal residues of proteins can also serve as degradation signals (C-degrons) that are recognized by specific cullin-RING ubiquitin ligases (CRLs) for proteasomal degradation. FEM1C is a CRL2 substrate receptor that targets the C-terminal arginine degron (Arg/C-degron), but the molecular mechanism of substrate recognition remains largely elusive. Here, we present crystal structures of FEM1C in complex with Arg/C-degron and show that FEM1C utilizes a semi-open binding pocket to capture the C-terminal arginine and that the extreme C-terminal arginine is the major structural determinant in recognition by FEM1C. Together with biochemical and mutagenesis studies, we provide a framework for understanding molecular recognition of the Arg/C-degron by the FEM family of proteins.
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14
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Liang H, Lin Z, Ye Y, Luo R, Zeng L. ARRB2 promotes colorectal cancer growth through triggering WTAP. Acta Biochim Biophys Sin (Shanghai) 2021; 53:85-93. [PMID: 33367479 DOI: 10.1093/abbs/gmaa151] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most lethal cancers worldwide. The expression of β-arrestin2 (β-Arr2, ARRB2) in CRC has been well investigated; however, its exact mechanism causing the cancer progression remains unclear. In this study, we discovered that the expression level of ARRB2 was significantly upregulated in CRC as compared to the normal tissues by employing the Cancer Genome Atlas (TCGA) data, western blot analysis, and immunohistochemistry. Furthermore, the level of ARRB2 was correlated with the patients' overall survival by Kaplan-Meier analysis. The higher expression of ARRB2 promoted CRC cell growth, enhanced the cell motility, and blocked cell apoptosis, which is crucial for tumor growth. Lastly, the suppression of ARRB2 expression was enough to attenuate the progression of CRC induced by azoxymethane/dextran sodium sulfate. Interestingly, we also found that the knockdown of ARRB2 decreased several cancer pathways mediated by the expression of Wilms tumor 1 associated protein (WTAP), which led to the inhibition of cell proliferation and migration. Altogether, our results demonstrated that ARRB2 promoted the growth and migration of CRC cells by regulating the WTAP expression.
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Affiliation(s)
- Hongguang Liang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Thoracic Surgery, Jinshazhou Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510168, China
| | - Zelong Lin
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
| | - Youqiong Ye
- Department of Biochemistry and Molecular Biology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Rongcheng Luo
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
- Thoracic Surgery, Jinshazhou Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510168, China
| | - Lixian Zeng
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou 510315, China
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15
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Lyu ZJ, Wang Y, Huang JL, Chen M, Wu SY, Yan Q, Zhang Y, Tang Y, Jiang C, Li L, Jia YZ, Liu YC, Mei HB, Wang F, Li RH, Chen YC, Lin X, Cai ZM, Guan XY. Recurrent ZNF83-E293V Mutation Promotes Bladder Cancer Progression through the NF-κB Pathway via Transcriptional Dysregulation of S100A8. Mol Ther 2021; 29:275-290. [PMID: 33002420 PMCID: PMC7791007 DOI: 10.1016/j.ymthe.2020.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 08/07/2020] [Accepted: 09/01/2020] [Indexed: 02/05/2023] Open
Abstract
Urothelial carcinoma (UC) is the predominant form of bladder cancer. Significant molecular heterogeneity caused by diverse molecular alterations brings about large variations in the response to treatment in UC. An improved understanding of the genetic mechanisms underlying the development and progression of UC is essential. Through deep analysis of next-generation sequencing data of 99 UC patients, we found that 18% of cases had recurrent somatic mutations in zinc finger protein gene zinc finger protein 83 (ZNF83). ZNF83 mutations were correlated with poor prognosis of UC. We also found a hotspot mutation, p.E293V, in the evolutionarily well-conserved region of ZNF83. ZNF83-E293V increased tumor growth and reduced the apoptosis of UC cells compared to wild-type ZNF83 both in vitro and in mice xenografted tumors. ZNF83-E293V activated nuclear factor κB (NF-κB) more potently than did the wild-type protein owing to its decreased transcriptional repression for S100A8. The NF-κB inhibitors could pharmacologically block the tumor growth in mice engrafted with ZNF83-E293V-transfected UC cells. These findings provide a mechanistic insight and a potential therapeutic strategy for UC, which established a foundation for using the ZNF83-E293V mutation as a predictive biomarker of therapeutic response from NF-κB inhibitors.
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Affiliation(s)
- Zhao J Lyu
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518029, China; Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Ying Wang
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518029, China; Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China; State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China
| | - Jin L Huang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China
| | - Miao Chen
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Sha Y Wu
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Qian Yan
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Yu Zhang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Ying Tang
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Chen Jiang
- State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China; Department of Pathology, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China
| | - Lei Li
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China
| | - Yi Z Jia
- Core Laboratory, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518029, China
| | - Yu C Liu
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518029, China
| | - Hong B Mei
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518029, China
| | - Feng Wang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518029, China
| | - Ren H Li
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ya C Chen
- Department of Pathology, Shenzhen University General Hospital, Shenzhen 518055, China
| | - Xiang Lin
- School of Chinese Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Zhi M Cai
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen 518029, China; Department of Urology, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, China; Carson International Cancer Center, School of Medicine, Shenzhen University, Shenzhen 518061, China; BGI-Medicine, BGI, Shenzhen 518083, China.
| | - Xin Y Guan
- Department of Clinical Oncology, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518029, China; Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; State Key Laboratory of Oncology in South China, Sun Yat-Sen University Cancer Center, Guangzhou 510030, China.
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16
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Khan AA, Patel K, Patil S, Babu N, Mangalaparthi KK, Solanki HS, Nanjappa V, Kumari A, Manoharan M, Karunakaran C, Murugan S, Nair B, Kumar RV, Biswas M, Sidransky D, Gupta R, Gupta R, Khanna-Gupta A, Kumar P, Chatterjee A, Gowda H. Multi-Omics Analysis to Characterize Cigarette Smoke Induced Molecular Alterations in Esophageal Cells. Front Oncol 2020; 10:1666. [PMID: 33251127 PMCID: PMC7675040 DOI: 10.3389/fonc.2020.01666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 07/28/2020] [Indexed: 12/29/2022] Open
Abstract
Though smoking remains one of the established risk factors of esophageal squamous cell carcinoma, there is limited data on molecular alterations associated with cigarette smoke exposure in esophageal cells. To investigate molecular alterations associated with chronic exposure to cigarette smoke, non-neoplastic human esophageal epithelial cells were treated with cigarette smoke condensate (CSC) for up to 8 months. Chronic treatment with CSC increased cell proliferation and invasive ability of non-neoplastic esophageal cells. Whole exome sequence analysis of CSC treated cells revealed several mutations and copy number variations. This included loss of high mobility group nucleosomal binding domain 2 (HMGN2) and a missense variant in mediator complex subunit 1 (MED1). Both these genes play an important role in DNA repair. Global proteomic and phosphoproteomic profiling of CSC treated cells lead to the identification of 38 differentially expressed and 171 differentially phosphorylated proteins. Bioinformatics analysis of differentially expressed proteins and phosphoproteins revealed that most of these proteins are associated with DNA damage response pathway. Proteomics data revealed decreased expression of HMGN2 and hypophosphorylation of MED1. Exogenous expression of HMGN2 and MED1 lead to decreased proliferative and invasive ability of smoke exposed cells. Immunohistochemical labeling of HMGN2 in primary ESCC tumor tissue sections (from smokers) showed no detectable expression while strong to moderate staining of HMGN2 was observed in normal esophageal tissues. Our data suggests that cigarette smoke perturbs expression of proteins associated with DNA damage response pathways which might play a vital role in development of ESCC.
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Affiliation(s)
- Aafaque Ahmad Khan
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Krishna Patel
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Shankargouda Patil
- Division of Oral Pathology, Department of Maxillofacial Surgery and Diagnostic Sciences, College of Dentistry, Jazan University, Jazan, Saudi Arabia.,Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, Siena, Italy
| | - Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Kiran K Mangalaparthi
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | | | | | | | | | | | | | - Bipin Nair
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam, India
| | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, India
| | - Manjusha Biswas
- Department of Molecular Pathology, Mitra Biotech, Bangalore, India
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ravi Gupta
- Medgenome Labs Pvt. Ltd., Bangalore, India
| | | | | | - Prashant Kumar
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India.,Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
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17
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Streamlined Subpopulation, Subtype, and Recombination Analysis of HIV-1 Half-Genome Sequences Generated by High-Throughput Sequencing. mSphere 2020; 5:5/5/e00551-20. [PMID: 33055255 PMCID: PMC7565892 DOI: 10.1128/msphere.00551-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS). High-throughput sequencing (HTS) has been widely used to characterize HIV-1 genome sequences. There are no algorithms currently that can directly determine genotype and quasispecies population using short HTS reads generated from long genome sequences without additional software. To establish a robust subpopulation, subtype, and recombination analysis workflow, we amplified the HIV-1 3′-half genome from plasma samples of 65 HIV-1-infected individuals and sequenced the entire amplicon (∼4,500 bp) by HTS. With direct analysis of raw reads using HIVE-hexahedron, we showed that 48% of samples harbored 2 to 13 subpopulations. We identified various subtypes (17 A1s, 4 Bs, 27 Cs, 6 CRF02_AGs, and 11 unique recombinant forms) and defined recombinant breakpoints of 10 recombinants. These results were validated with viral genome sequences generated by single genome sequencing (SGS) or the analysis of consensus sequence of the HTS reads. The HIVE-hexahedron workflow is more sensitive and accurate than just evaluating the consensus sequence and also more cost-effective than SGS. IMPORTANCE The highly recombinogenic nature of human immunodeficiency virus type 1 (HIV-1) leads to recombination and emergence of quasispecies. It is important to reliably identify subpopulations to understand the complexity of a viral population for drug resistance surveillance and vaccine development. High-throughput sequencing (HTS) provides improved resolution over Sanger sequencing for the analysis of heterogeneous viral subpopulations. However, current methods of analysis of HTS reads are unable to fully address accurate population reconstruction. Hence, there is a dire need for a more sensitive, accurate, user-friendly, and cost-effective method to analyze viral quasispecies. For this purpose, we have improved the HIVE-hexahedron algorithm that we previously developed with in silico short sequences to analyze raw HTS short reads. The significance of this study is that our standalone algorithm enables a streamlined analysis of quasispecies, subtype, and recombination patterns from long HIV-1 genome regions without the need of additional sequence analysis tools. Distinct viral populations and recombination patterns identified by HIVE-hexahedron are further validated by comparison with sequences obtained by single genome sequencing (SGS).
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18
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Berruien NNA, Smith CL. Emerging roles of melanocortin receptor accessory proteins (MRAP and MRAP2) in physiology and pathophysiology. Gene 2020; 757:144949. [PMID: 32679290 DOI: 10.1016/j.gene.2020.144949] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/07/2023]
Abstract
Melanocortin-2 receptor accessory protein (MRAP) has an unusual dual topology and influences the expression, localisation, signalling and internalisation of the melanocortin receptor 2 (MC2); the adrenocorticotropic hormone (ACTH) receptor. Mutations in MRAP are associated with familial glucocorticoid deficiency type-2 and evidence is emerging of the importance of MRAP in adrenal development and ACTH signalling. Human MRAP has two functional splice variants: MRAP-α and MRAP-β, unlike MRAP-β, MRAP-α has little expression in brain but is highly expressed in ovary. MRAP2, identified through whole human genome sequence analysis, has approximately 40% sequence homology to MRAP. MRAP2 facilitates MC2 localisation to the cell surface but not ACTH signalling. MRAP and MRAP2 have been found to regulate the surface expression and signalling of all melanocortin receptors (MC1-5). Additionally, MRAP2 moderates the signalling of the G-protein coupled receptors (GCPRs): orexin, prokineticin and GHSR1a; the ghrelin receptor. Whilst MRAP appears to be mainly involved in glucocorticoid synthesis, an important role is emerging for MRAP2 in regulating appetite and energy homeostasis. Transgenic models indicate the importance of MRAP in adrenal gland formation. Like MC3R and MC4R knockout mice, MRAP2 knockout mice have an obese phenotype. In vitro studies indicate that MRAP2 enhances the MC3 and MC4 response to the agonist αMSH, which, like ACTH, is produced through precursor polypeptide proopiomelanocortin (POMC) cleavage. Analysis of cohorts of individuals with obesity have revealed several MRAP2 genetic variants with loss of function mutations which are causative of monogenic hyperphagic obesity with hyperglycaemia and hypertension. MRAP2 may also be associated with female infertility. This review summarises current knowledge of MRAP and MRAP2, their influence on GPCR signalling, and focusses on pathophysiology, particularly familial glucocorticoid deficiency type-2 and obesity.
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Affiliation(s)
- Nasrin N A Berruien
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK.
| | - Caroline L Smith
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK.
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19
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Plant EP, Manukyan H, Laassri M, Ye Z. Insights from the comparison of genomic variants from two influenza B viruses grown in the presence of human antibodies in cell culture. PLoS One 2020; 15:e0239015. [PMID: 32925936 PMCID: PMC7489522 DOI: 10.1371/journal.pone.0239015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/27/2020] [Indexed: 12/25/2022] Open
Abstract
Understanding the extent and limitation of viral genome evolution can provide insight about potential drug and vaccine targets. Influenza B Viruses (IBVs) infect humans in a seasonal manner and causes significant morbidity and mortality. IBVs are negative-sense single-stranded RNA viruses with a segmented genome and can be divided into two antigenically distinct lineages. The two lineages have been circulating and further evolving for almost four decades. The immune response to IBV infection can lead to antibodies that target the strain causing the infection. Some antibodies are cross-reactive and are able to bind strains from both lineages but, because of antigenic drift and immunodominance, both lineages continue to evolve and challenge human health. Here we investigate changes in the genomes of an IBVs from each lineage after passage in tissue culture in the presence of human sera containing polyclonal antibodies directed toward antigenically and temporally distinct viruses. Our previous analysis of the fourth segment, which encodes the major surface protein HA, revealed a pattern of change in which signature sequences from one lineage mutated to the signature sequences of the other lineage. Here we analyze genes from the other genomic segments and observe that most of the quasispecies’ heterogeneity occurs at the same loci in each lineage. The nature of the variants at these loci are investigated and possible reasons for this pattern are discussed. This work expands our understanding of the extent and limitations of genomic change in IBV.
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Affiliation(s)
- Ewan P. Plant
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
| | - Hasmik Manukyan
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Majid Laassri
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Zhiping Ye
- Office of Vaccine Research and Review, US Food and Drug Administration, Silver Spring, Maryland, United States of America
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20
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Bae DH, Marino M, Iaffaldano B, Fenstermaker S, Afione S, Argaw T, McCright J, Kwilas A, Chiorini JA, Timmons AE, Reiser J. Design and Testing of Vector-Producing HEK293T Cells Bearing a Genomic Deletion of the SV40 T Antigen Coding Region. Mol Ther Methods Clin Dev 2020; 18:631-638. [PMID: 32775497 PMCID: PMC7397404 DOI: 10.1016/j.omtm.2020.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/06/2020] [Indexed: 12/18/2022]
Abstract
The use of the human embryonic kidney (HEK) 293T cell line to manufacture vectors for in vivo applications raises safety concerns due to the presence of SV40 T antigen-encoding sequences. We used CRISPR-Cas9 genome editing to remove the SV40 T antigen-encoding sequences from HEK293T cells by transfecting them with a recombinant plasmid expressing Cas9 and two distinct single guide RNAs (sgRNAs) corresponding to the beginning and end of the T antigen coding region. Cell clones lacking T antigen-encoding sequences were identified using PCR. Whole-genome (WG) and targeted locus amplification (TLA) sequencing of the parental HEK293T cell line revealed multiple SV40 T antigen-encoding sequences replacing cellular sequences on chromosome 3. The putative T antigen null clones demonstrated a loss of sequence reads mapping to T antigen-encoding sequences. Western blot analysis of cell extracts prepared from the T antigen null clones confirmed that the SV40 large and small T antigen proteins were absent. Lentiviral vectors produced using the T antigen null clones exhibited titers up to 1.5 × 107 transducing units (TU)/mL, while the titers obtained from the parent HEK293T cell line were up to 4 × 107 TU/mL. The capacity of the T antigen-negative cells to produce high titer adeno-associated virus (AAV) vectors was also evaluated. The results obtained revealed that the lack of T antigen sequences did not impact AAV vector titers.
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Affiliation(s)
- Dahae Hailey Bae
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Michael Marino
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Brian Iaffaldano
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Sydney Fenstermaker
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, FDA, Silver Spring, MD, USA
| | - Sandra Afione
- AAV Biology Section, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Takele Argaw
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Jacob McCright
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Anna Kwilas
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - John A. Chiorini
- AAV Biology Section, National Institute of Dental and Craniofacial Research, NIH, Bethesda, MD, USA
| | - Andrew E. Timmons
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
| | - Jakob Reiser
- Division of Cellular and Gene Therapies, Center for Biologics Evaluation and Research, US Food and Drug Administration (FDA), Silver Spring, MD, USA
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21
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Plant EP, Manukyan H, Sanchez JL, Laassri M, Ye Z. Immune Pressure on Polymorphous Influenza B Populations Results in Diverse Hemagglutinin Escape Mutants and Lineage Switching. Vaccines (Basel) 2020; 8:vaccines8010125. [PMID: 32168968 PMCID: PMC7157493 DOI: 10.3390/vaccines8010125] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/27/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations arise in the genomes of progeny viruses during infection. Mutations that occur in epitopes targeted by host antibodies allow the progeny virus to escape the host adaptive, B-cell mediated antibody immune response. Major epitopes have been identified in influenza B virus (IBV) hemagglutinin (HA) protein. However, IBV strains maintain a seasonal presence in the human population and changes in IBV genomes in response to immune pressure are not well characterized. There are two lineages of IBV that have circulated in the human population since the 1980s, B-Victoria and B-Yamagata. It is hypothesized that early exposure to one influenza subtype leads to immunodominance. Subsequent seasonal vaccination or exposure to new subtypes may modify subsequent immune responses, which, in turn, results in selection of escape mutations in the viral genome. Here we show that while some mutations do occur in known epitopes suggesting antibody escape, many mutations occur in other parts of the HA protein. Analysis of mutations outside of the known epitopes revealed that these mutations occurred at the same amino acid position in viruses from each of the two IBV lineages. Interestingly, where the amino acid sequence differed between viruses from each lineage, reciprocal amino acid changes were observed. That is, the virus from the Yamagata lineage become more like the Victoria lineage virus and vice versa. Our results suggest that some IBV HA sequences are constrained to specific amino acid codons when viruses are cultured in the presence of antibodies. Some changes to the known antigenic regions may also be restricted in a lineage-dependent manner. Questions remain regarding the mechanisms underlying these results. The presence of amino acid residues that are constrained within the HA may provide a new target for universal vaccines for IBV.
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Affiliation(s)
- Ewan P. Plant
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
- Correspondence: ; Tel.: +1-240-402-7319
| | - Hasmik Manukyan
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Jose L. Sanchez
- Armed Forces Health Surveillance Branch, Public Health Division, Assistant Director for Combat Support (AD-CS), Defense Health Agency, Silver Spring, MD 20904, USA;
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
| | - Zhiping Ye
- Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD 20993, USA; (H.M.); (M.L.); (Z.Y.)
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22
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Abstract
A crucial step for tumor cell extravasation and metastasis is the migration through the extracellular matrix, which requires proteolytic activity. Hence, proteases, particularly matrix metalloproteases (MMPs), have been discussed as therapeutic targets and their inhibition should diminish tumor growth and metastasis. The metalloproteases meprin α and meprin β are highly abundant on intestinal enterocytes and their expression was associated with different stages of colorectal cancer. Due to their ability to cleave extracellular matrix (ECM) components, they were suggested as pro-tumorigenic enzymes. Additionally, both meprins were shown to have pro-inflammatory activity by cleaving cytokines and their receptors, which correlates with chronic intestinal inflammation and associated conditions. On the other hand, meprin β was identified as an essential enzyme for the detachment and renewal of the intestinal mucus, important to prevent bacterial overgrowth and infection. Considering this, it is hard to estimate whether high activity of meprins is generally detrimental or if these enzymes have also protective functions in certain cancer types. For instance, for colorectal cancer, patients with high meprin β expression in tumor tissue exhibit a better survival prognosis, which is completely different to prostate cancer. This demonstrates that the very same enzyme may have contrary effects on tumor initiation and growth, depending on its tissue and subcellular localization. Hence, precise knowledge about proteolytic enzymes is required to design the most efficient therapeutic options for cancer treatment. In this review, we summarize the current findings on meprins' functions, expression, and cancer-associated variants with possible implications for tumor progression and metastasis.
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23
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ElTanbouly MA, Schaafsma E, Noelle RJ, Lines JL. VISTA: Coming of age as a multi-lineage immune checkpoint. Clin Exp Immunol 2020; 200:120-130. [PMID: 31930484 DOI: 10.1111/cei.13415] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
The immune response is governed by a highly complex set of interactions among cells and mediators. T cells may be rendered dysfunctional by the presence of high levels of antigen in the absence of co-stimulation while myeloid cells may be programmed towards an immunosuppressive state that promotes cancer growth and metastasis while deterring tumor immunity. In addition, inhibitory programs driven by immune checkpoint regulators dampen anti-tumor immunity. The ideal cancer immunotherapy treatment will improve both cross-priming in the tumor microenvironment and relieve suppression by the inhibitory checkpoints. Recently, blockade of programmed cell death 1 (PD-1) and cytotoxic T lymphocyte antigen 4 (CTLA-4) has elicited impressive results, but not in all patients, so additional targets are under investigation. V-set immunoglobulin domain suppressor of T cell activation (VISTA) is a novel immunoregulatory receptor that is broadly expressed on cells of the myeloid and lymphoid lineages, and is frequently implicated as a poor prognostic indicator in multiple cancers. Importantly, antibody targeting of VISTA uniquely engages both innate and adaptive immunity. This, combined with the expression of VISTA and its non-redundant activities compared to other immune checkpoint regulators, qualifies VISTA to be a promising target for improving cancer immunotherapy.
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Affiliation(s)
- M A ElTanbouly
- Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - E Schaafsma
- Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - R J Noelle
- Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - J L Lines
- Department of Microbiology and Immunology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
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24
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PipeMEM: A Framework to Speed Up BWA-MEM in Spark with Low Overhead. Genes (Basel) 2019; 10:genes10110886. [PMID: 31689965 PMCID: PMC6896194 DOI: 10.3390/genes10110886] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/30/2019] [Accepted: 11/01/2019] [Indexed: 02/08/2023] Open
Abstract
(1) Background: DNA sequence alignment process is an essential step in genome analysis. BWA-MEM has been a prevalent single-node tool in genome alignment because of its high speed and accuracy. The exponentially generated genome data requiring a multi-node solution to handle large volumes of data currently remains a challenge. Spark is a ubiquitous big data platform that has been exploited to assist genome alignment in handling this challenge. Nonetheless, existing works that utilize Spark to optimize BWA-MEM suffer from higher overhead. (2) Methods: In this paper, we presented PipeMEM, a framework to accelerate BWA-MEM with lower overhead with the help of the pipe operation in Spark. We additionally proposed to use a pipeline structure and in-memory-computation to accelerate PipeMEM. (3) Results: Our experiments showed that, on paired-end alignment tasks, our framework had low overhead. In a multi-node environment, our framework, on average, was 2.27× faster compared with BWASpark (an alignment tool in Genome Analysis Toolkit (GATK)), and 2.33× faster compared with SparkBWA. (4) Conclusions: PipeMEM could accelerate BWA-MEM in the Spark environment with high performance and low overhead.
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25
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King CH, Desai H, Sylvetsky AC, LoTempio J, Ayanyan S, Carrie J, Crandall KA, Fochtman BC, Gasparyan L, Gulzar N, Howell P, Issa N, Krampis K, Mishra L, Morizono H, Pisegna JR, Rao S, Ren Y, Simonyan V, Smith K, VedBrat S, Yao MD, Mazumder R. Baseline human gut microbiota profile in healthy people and standard reporting template. PLoS One 2019; 14:e0206484. [PMID: 31509535 PMCID: PMC6738582 DOI: 10.1371/journal.pone.0206484] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 08/05/2019] [Indexed: 12/19/2022] Open
Abstract
A comprehensive knowledge of the types and ratios of microbes that inhabit the healthy human gut is necessary before any kind of pre-clinical or clinical study can be performed that attempts to alter the microbiome to treat a condition or improve therapy outcome. To address this need we present an innovative scalable comprehensive analysis workflow, a healthy human reference microbiome list and abundance profile (GutFeelingKB), and a novel Fecal Biome Population Report (FecalBiome) with clinical applicability. GutFeelingKB provides a list of 157 organisms (8 phyla, 18 classes, 23 orders, 38 families, 59 genera and 109 species) that forms the baseline biome and therefore can be used as healthy controls for studies related to dysbiosis. This list can be expanded to 863 organisms if closely related proteomes are considered. The incorporation of microbiome science into routine clinical practice necessitates a standard report for comparison of an individual’s microbiome to the growing knowledgebase of “normal” microbiome data. The FecalBiome and the underlying technology of GutFeelingKB address this need. The knowledgebase can be useful to regulatory agencies for the assessment of fecal transplant and other microbiome products, as it contains a list of organisms from healthy individuals. In addition to the list of organisms and their abundances, this study also generated a collection of assembled contiguous sequences (contigs) of metagenomics dark matter. In this study, metagenomic dark matter represents sequences that cannot be mapped to any known sequence but can be assembled into contigs of 10,000 nucleotides or higher. These sequences can be used to create primers to study potential novel organisms. All data is freely available from https://hive.biochemistry.gwu.edu/gfkb and NCBI’s Short Read Archive.
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Affiliation(s)
- Charles H. King
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
- McCormick Genomic and Proteomic Center, George Washington University, Washington, DC, United States of America
| | - Hiral Desai
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Allison C. Sylvetsky
- The Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Jonathan LoTempio
- The Institute for Biomedical Science, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
- Center for Genetic Medicine, Children’s National Medical Center, George Washington University, Washington, DC, United States of America
| | - Shant Ayanyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Jill Carrie
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Keith A. Crandall
- Computational Biology Institute and The Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Brian C. Fochtman
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Lusine Gasparyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Naila Gulzar
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Paul Howell
- KamTek Inc, Frederick, Maryland, United States of America
| | - Najy Issa
- The Department of Exercise and Nutrition Sciences, Milken Institute School of Public Health, George Washington University, Washington, DC, United States of America
| | - Konstantinos Krampis
- Department of Biological Sciences, Hunter College, City University of New York, New York, New York, United States of America
| | - Lopa Mishra
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America
| | - Hiroki Morizono
- Center for Genetic Medicine, Children’s National Medical Center, George Washington University, Washington, DC, United States of America
| | - Joseph R. Pisegna
- Division of Gastroenterology and Hepatology VA Greater Los Angeles Healthcare System and Department of Medicine and Human Genetics, University of California, Los Angeles, Los Angeles, California, United States of America
| | - Shuyun Rao
- Center for Translational Medicine, Department of Surgery, George Washington University, Washington, DC, United States of America
| | - Yao Ren
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Vahan Simonyan
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | - Krista Smith
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
| | | | - Michael D. Yao
- Washington DC VA Medical Center, Gastroenterology & Hepatology Section, Washington, DC, United States of America
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
| | - Raja Mazumder
- The Department of Biochemistry & Molecular Medicine, School of Medicine and Health Sciences, George Washington University Medical Center, Washington, DC, United States of America
- Department of Medicine, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
- * E-mail:
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26
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Liu S, Wang Z, Liu Z, Shi S, Zhang Z, Zhang J, Lin H. miR-221/222 activate the Wnt/β-catenin signaling to promote triple-negative breast cancer. J Mol Cell Biol 2019; 10:302-315. [PMID: 30053090 DOI: 10.1093/jmcb/mjy041] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/21/2018] [Indexed: 12/19/2022] Open
Abstract
Triple-negative breast cancer (TNBC), characterized by the lack of expression of the estrogen receptor, the progesterone receptor, and the human epidermal growth factor receptor 2, is an aggressive form of cancer that conveys unpredictable and poor prognosis due to limited treatment options and lack of effective targeted therapies. Wnt/β-catenin signaling is hyperactivated in TNBC, which promotes the progression of TNBC. However, the molecular mechanism of Wnt/β-catenin activation in TNBC remains unknown. Here, we report the drastic overexpression of miR-221/222 in all of four TNBC cell lines and TNBC primary tumor samples from patients. Furthermore, we demonstrate by both ex vivo and xenograft experiments that inhibiting miR-221/222 expression in a TNBC cell line (MDA-MB-231) suppresses its proliferation, viability, epithelial-to-mesenchymal transition, and migration; whereas expressing miR-221/222 in a non-TNBC line (MCF7) promotes all of the above cancer properties. miR-221/222 achieve so by directly repressing multiple negative regulators of the Wnt/β-catenin signaling pathway, including WIF1, SFRP2, DKK2, and AXIN2, to activate the pathway. Notably, the level of miR-221/222 expression is inversely correlated whereas that of WIF1, DKK2, SFRP2, and AXIN2 expression is positively correlated with the patient survival. Last, we show that anti-miR-221/222 significantly increases apoptotic cells with tamoxifen/Wnt3a treatment but not with cyclophosphamide/Wnt3a treatment. These results demonstrate that miR-221/222 activate the Wnt/β-catenin signaling to promote the aggressiveness and TNBC properties of breast cancers, and thus reveal a new prospect for TNBC treatment.
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Affiliation(s)
- Sanhong Liu
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Zifeng Wang
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Zukai Liu
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shuo Shi
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Zhaoran Zhang
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Jiawei Zhang
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Haifan Lin
- Shanghai Institute of Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China.,The Yale Stem Cell Center and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
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27
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Schäffler H, Li W, Helm O, Krüger S, Böger C, Peters F, Röcken C, Sebens S, Lucius R, Becker-Pauly C, Arnold P. The cancer-associated meprin β variant G32R provides an additional activation site and promotes cancer cell invasion. J Cell Sci 2019; 132:jcs.220665. [PMID: 31076514 DOI: 10.1242/jcs.220665] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 04/23/2019] [Indexed: 12/13/2022] Open
Abstract
The extracellular metalloprotease meprin β is expressed as a homodimer and is primarily membrane bound. Meprin β can be released from the cell surface by its known sheddases ADAM10 and ADAM17. Activation of pro-meprin β at the cell surface prevents its shedding, thereby stabilizing its proteolytic activity at the plasma membrane. We show that a single amino acid exchange variant (G32R) of meprin β, identified in endometrium cancer, is more active against a peptide substrate and the IL-6 receptor than wild-type meprin β. We demonstrate that the change to an arginine residue at position 32 represents an additional activation site used by furin-like proteases in the Golgi, which consequently leads to reduced shedding by ADAM17. We investigated this meprin β G32R variant to assess cell proliferation, invasion through a collagen IV matrix and outgrowth from tumor spheroids. We found that increased meprin β G32R activity at the cell surface reduces cell proliferation, but increases cell invasion.
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Affiliation(s)
| | - Wenjia Li
- Anatomical Institute, Otto-Hahn Platz 8, 24118 Kiel, Germany
| | - Ole Helm
- Institute for Experimental Cancer Research, Arnold-Heller-Str. 3, 24105 Kiel, Germany
| | - Sandra Krüger
- Dept. of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Arnold-Heller-Str. 3/14, 24105 Kiel, Germany
| | - Christine Böger
- Dept. of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Arnold-Heller-Str. 3/14, 24105 Kiel, Germany
| | - Florian Peters
- Biochemical Institute, Otto-Hahn Platz 9, 24118 Kiel, Germany
| | - Christoph Röcken
- Dept. of Pathology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Arnold-Heller-Str. 3/14, 24105 Kiel, Germany
| | - Susanne Sebens
- Institute for Experimental Cancer Research, Arnold-Heller-Str. 3, 24105 Kiel, Germany
| | - Ralph Lucius
- Anatomical Institute, Otto-Hahn Platz 8, 24118 Kiel, Germany
| | | | - Philipp Arnold
- Anatomical Institute, Otto-Hahn Platz 8, 24118 Kiel, Germany
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28
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Abstract
The use of large datasets has become ubiquitous in biomedical sciences. Researchers in the field of cancer genomics have, in recent years, generated large volumes of data from their experiments. Those responsible for production of this data often analyze a narrow subset of this data based on the research question they are trying to address: this is the case whether or not they are acting independently or in conjunction with a large-scale cancer genomics project. The reality of this situation creates the opportunity for other researchers to repurpose this data for different hypotheses if the data is made easily and freely available. New insights in biology resulting from more researchers having access to data they otherwise would be unable to generate on their own are a boon for the field. The following chapter reviews several cancer genomics-related databases and outlines the type of data they contain, as well as the methods required to access each database. While this list is not comprehensive, it should provide a basis for cancer researchers to begin exploring some of the many large datasets that are available to them.
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29
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Bosma TJ, Karagiannis K, Santana-Quintero L, Ilyushina N, Zagorodnyaya T, Petrovskaya S, Laassri M, Donnelly RP, Rubin S, Simonyan V, Sauder CJ. Identification and quantification of defective virus genomes in high throughput sequencing data using DVG-profiler, a novel post-sequence alignment processing algorithm. PLoS One 2019; 14:e0216944. [PMID: 31100083 PMCID: PMC6524942 DOI: 10.1371/journal.pone.0216944] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 05/01/2019] [Indexed: 12/18/2022] Open
Abstract
Most viruses are known to spontaneously generate defective viral genomes (DVG) due to errors during replication. These DVGs are subgenomic and contain deletions that render them unable to complete a full replication cycle in the absence of a co-infecting, non-defective helper virus. DVGs, especially of the copyback type, frequently observed with paramyxoviruses, have been recognized to be important triggers of the antiviral innate immune response. DVGs have therefore gained interest for their potential to alter the attenuation and immunogenicity of vaccines. To investigate this potential, accurate identification and quantification of DVGs is essential. Conventional methods, such as RT-PCR, are labor intensive and will only detect primer sequence-specific species. High throughput sequencing (HTS) is much better suited for this undertaking. Here, we present an HTS-based algorithm called DVG-profiler to identify and quantify all DVG sequences in an HTS data set generated from a virus preparation. DVG-profiler identifies DVG breakpoints relative to a reference genome and reports the directionality of each segment from within the same read. The specificity and sensitivity of the algorithm was assessed using both in silico data sets as well as HTS data obtained from parainfluenza virus 5, Sendai virus and mumps virus preparations. HTS data from the latter were also compared with conventional RT-PCR data and with data obtained using an alternative algorithm. The data presented here demonstrate the high specificity, sensitivity, and robustness of DVG-profiler. This algorithm was implemented within an open source cloud-based computing environment for analyzing HTS data. DVG-profiler might prove valuable not only in basic virus research but also in monitoring live attenuated vaccines for DVG content and to assure vaccine lot to lot consistency.
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Affiliation(s)
- Trent J. Bosma
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Konstantinos Karagiannis
- Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, Washington, DC, United States of America
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Luis Santana-Quintero
- Office of Hematology and Oncology Products, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Natalia Ilyushina
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Tatiana Zagorodnyaya
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Svetlana Petrovskaya
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Majid Laassri
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Raymond P. Donnelly
- Division of Biotechnology Review and Research II, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Steven Rubin
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Vahan Simonyan
- Office of Biostatistics and Epidemiology, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
| | - Christian J. Sauder
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland, United States of America
- * E-mail:
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30
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Genomics Analyses of GIV and GVI Noroviruses Reveal the Distinct Clustering of Human and Animal Viruses. Viruses 2019; 11:v11030204. [PMID: 30823663 PMCID: PMC6466045 DOI: 10.3390/v11030204] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/23/2019] [Accepted: 02/25/2019] [Indexed: 01/23/2023] Open
Abstract
Noroviruses are highly diverse viruses that are the major viral cause of acute gastroenteritis in humans. Although these viruses can infect multiple mammalian species, their potential for zoonosis is not well understood, especially within Genogroup IV (GIV), which contains viruses that infect humans, canines, and felines. The study of GIV viruses has been, in part, hindered by the limited number of complete genomes. Here, we developed a full-genome amplicon-based platform that facilitated the sequencing of canine noroviruses circulating in the United States. Eight novel nearly full-length canine norovirus genomes and two nearly complete VP1 sequences, including four GIV.2, three GVI.1, and three GVI.2 viruses, were successfully obtained. Only animal strains exhibited GVI/GIV chimeric viruses, demonstrating restrictions in norovirus recombination. Using genomic, phylogenetic, and structural analyses, we show that differences within the major capsid protein and the non-structural proteins of GIV and GVI noroviruses could potentially limit cross-species transmission between humans, canines, and felines.
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31
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Chen Y, Hora B, DeMarco T, Berba R, Register H, Hood S, Carter M, Stone M, Pappas A, Sanchez AM, Busch M, Denny TN, Gao F. Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines. J Gen Virol 2019; 100:511-522. [PMID: 30676308 PMCID: PMC7011713 DOI: 10.1099/jgv.0.001198] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 11/20/2018] [Indexed: 12/28/2022] Open
Abstract
The growth rate of new HIV infections in the Philippines was the fastest of any countries in the Asia-Pacific region between 2010 and 2016. To date, HIV-1 subtyping results in the Philippines have been determined by characterizing only partial viral genome sequences. It is not known whether recombination occurs in the majority of unsequenced genome regions. Near-full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes from plasma samples collected between 2015 and 2017 from 23 newly diagnosed infected individuals in the Philippines. Phylogenetic analysis showed that the newly characterized sequences were CRF01_AE (14), subtype B (3), CRF01/B recombinants (5) and a CRF01/CRF07/B recombinant (1). All 14 CRF01_AE formed a tight cluster, suggesting that they were derived from a single introduction. The time to the most recent common ancestor (tMRCA) for CRF01_AE in the Philippines was 1995 (1992-1998), about 10-15 years later than that of CRF01_AE in China and Thailand. All five CRF01/B recombinants showed distinct recombination patterns, suggesting ongoing recombination between the two predominant circulating viruses. The identification of partial CRF07_BC sequences in one CRF01/CRF07/B recombinant, not reported previously in the Philippines, indicated that CRF07_BC may have been recently introduced into that country from China, where CRF07_BC is prevalent. Our results show that the major epidemic strains may have shifted to an increased predominance of CRF01_AE and its recombinants, and that other genotypes such as CRF07_BC may have been introduced into the Philippines.
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Affiliation(s)
- Yue Chen
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Bhavna Hora
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Todd DeMarco
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Regina Berba
- I-REACT Clinic, Section of Infectious Diseases, Department of Medicine, The Medical City, 1605 Pasig City, Philippines
| | - Heidi Register
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Sylvia Hood
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Meredith Carter
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Andrea Pappas
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Ana M. Sanchez
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Michael Busch
- Blood Systems Research Institute, San Francisco, CA 94118, USA
| | - Thomas N. Denny
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Feng Gao
- Department of Medicine, Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA
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Enabling precision medicine via standard communication of HTS provenance, analysis, and results. PLoS Biol 2018; 16:e3000099. [PMID: 30596645 PMCID: PMC6338479 DOI: 10.1371/journal.pbio.3000099] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/18/2019] [Indexed: 11/30/2022] Open
Abstract
A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews. This Community Page article presents a communication standard for the provenance of high-throughput sequencing data; a BioCompute Object (BCO) can serve as a history of what was computed, be used as part of a validation process, or provide clarity and transparency of an experimental process to collaborators.
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A complete Leishmania donovani reference genome identifies novel genetic variations associated with virulence. Sci Rep 2018; 8:16549. [PMID: 30409989 PMCID: PMC6224596 DOI: 10.1038/s41598-018-34812-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022] Open
Abstract
Leishmania donovani is responsible for visceral leishmaniasis, a neglected and lethal parasitic disease with limited treatment options and no vaccine. The study of L. donovani has been hindered by the lack of a high-quality reference genome and this can impact experimental outcomes including the identification of virulence genes, drug targets and vaccine development. We therefore generated a complete genome assembly by deep sequencing using a combination of second generation (Illumina) and third generation (PacBio) sequencing technologies. Compared to the current L. donovani assembly, the genome assembly reported within resulted in the closure over 2,000 gaps, the extension of several chromosomes up to telomeric repeats and the re-annotation of close to 15% of protein coding genes and the annotation of hundreds of non-coding RNA genes. It was possible to correctly assemble the highly repetitive A2 and Amastin virulence gene clusters. A comparative sequence analysis using the improved reference genome confirmed 70 published and identified 15 novel genomic differences between closely related visceral and atypical cutaneous disease-causing L. donovani strains providing a more complete map of genes associated with virulence and visceral organ tropism. Bioinformatic tools including protein variation effect analyzer and basic local alignment search tool were used to prioritize a list of potential virulence genes based on mutation severity, gene conservation and function. This complete genome assembly and novel information on virulence factors will support the identification of new drug targets and the development of a vaccine for L. donovani.
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Masannat J, Purayil HT, Zhang Y, Russin M, Mahmud I, Kim W, Liao D, Daaka Y. βArrestin2 Mediates Renal Cell Carcinoma Tumor Growth. Sci Rep 2018; 8:4879. [PMID: 29559707 PMCID: PMC5861056 DOI: 10.1038/s41598-018-23212-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/07/2018] [Indexed: 12/16/2022] Open
Abstract
Renal Cell Carcinoma (RCC) is one of the most lethal urological cancers worldwide. The disease does not present early clinical symptoms and is commonly diagnosed at an advanced stage. Limited molecular drivers have been identified for RCC, resulting in the lack of effective treatment for patients with progressive disease. Ubiquitous βArrestin2 (βArr2) is well established for its function in the desensitization and trafficking of G protein-coupled receptors. More recently, βArr2 has been implicated in the regulation of fundamental cellular functions, including proliferation and invasion. We used bioinformatic and genetic approaches to determine role of βArr2 in RCC tumor growth. Analysis of published human datasets shows that ARRB2 (gene encoding βArr2) expression is increased in RCC tumor compared to normal tissue and that high levels of ARRB2 correlate with worse patient survival. Experimentally, we show that knockout of ARRB2 decreases rate of RCC cell proliferation and migration in vitro and xenograft tumor growth in animals. Mechanistically, βArr2 regulates c-Src activity, Cyclin A expression and cell cycle progression that are involved in tumor growth. These results show that βArr2 is a critical regulator of RCC tumor growth and suggest its utility as a potential marker and drug target to treat advanced disease.
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Affiliation(s)
- Jude Masannat
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA.,Moffitt Cancer Center, Tampa, FL, USA
| | - Hamsa Thayele Purayil
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Yushan Zhang
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA.,Stephenson Cancer Center, University of Oklahoma, Oklahoma City, OK, USA
| | - Michelle Russin
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Iqbal Mahmud
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Wanju Kim
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Daiqing Liao
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, 32610, USA.
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Laassri M, Zagorodnyaya T, Hassin-Baer S, Handsher R, Sofer D, Weil M, Karagiannis K, Simonyan V, Chumakov K, Shulman L. Evolution of echovirus 11 in a chronically infected immunodeficient patient. PLoS Pathog 2018; 14:e1006943. [PMID: 29554133 PMCID: PMC5875893 DOI: 10.1371/journal.ppat.1006943] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/29/2018] [Accepted: 02/16/2018] [Indexed: 01/20/2023] Open
Abstract
Deep sequencing was used to determine complete nucleotide sequences of echovirus 11 (EV11) strains isolated from a chronically infected patient with CVID as well as from cases of acute enterovirus infection. Phylogenetic analysis showed that EV11 strains that circulated in Israel in 1980-90s could be divided into four clades. EV11 strains isolated from a chronically infected individual belonged to one of the four clades and over a period of 4 years accumulated mutations at a relatively constant rate. Extrapolation of mutations accumulation curve into the past suggested that the individual was infected with circulating EV11 in the first half of 1990s. Genomic regions coding for individual viral proteins did not appear to be under strong selective pressure except for protease 3C that was remarkably conserved. This may suggest its important role in maintaining persistent infection. We describe evolution of Echovirus 11 genome in chronically infected immunodeficient patient over a period of several years and compare it with the evolution of circulating echoviruses from which it originated. Ratio of silent to missense mutations in protein coding regions suggests that chronic virus was under lower selective pressure than circulating viruses, except for a region coding for viral protease that may participate in neutralizing host cell anti-viral defense mechanisms. This suggests that adaptation to persistence in immunodeficient host may require maintaining functional viral counter-defense mechanisms.
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Affiliation(s)
- Majid Laassri
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Tatiana Zagorodnyaya
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
| | - Sharon Hassin-Baer
- Movement Disorders Institute and Department of Neurology, Sheba Medical Center, Tel Hashomer; and Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Rachel Handsher
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Danit Sofer
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Merav Weil
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
| | - Konstantinos Karagiannis
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Vahan Simonyan
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
| | - Konstantin Chumakov
- FDA Center for Biologics Evaluation and Research, Silver Spring, MD, United States of America
- Department of Biochemistry and Molecular Biology, George Washington University Medical Center, Washington, DC, United States of America
- * E-mail:
| | - Lester Shulman
- Central Virology Laboratory, Public Health Service Laboratories Israel Ministry of Health at Sheba Medical Center, Tel Hashomer, Israel
- Dept. of Epidemiology and Preventive Medicine, School of Public Health, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
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Whole genome sequencing of live attenuated Leishmania donovani parasites reveals novel biomarkers of attenuation and enables product characterization. Sci Rep 2017; 7:4718. [PMID: 28680050 PMCID: PMC5498541 DOI: 10.1038/s41598-017-05088-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 06/06/2017] [Indexed: 01/03/2023] Open
Abstract
No licensed human vaccines are currently available against leishmaniasis. Several anti-leishmanial vaccines are currently undergoing testing, including genetically modified live-attenuated parasite vaccines. Studies with live attenuated Leishmania vaccines such as centrin deleted Leishmania donovani parasites (LdCen−/−) showed protective immunity in animal models. Such studies typically examined the biomarkers of protective immunity however the biomarkers of attenuation in the parasite preparations have not received adequate attention. As several candidate vaccines enter clinical trials, a more complete product characterization to enable maintenance of product quality will help meet regulatory requirements. Towards this goal, we have determined the complete genome sequence of LdCen−/− and its parent strain Ld1S-2D (LdWT) and characterized the LdCen−/− vaccine strain using bioinformatics tools. Results showed that the LdCen−/− parasites, in addition to loss of the centrin gene, have additional deletions ranging from 350 bp to 6900 bp in non-contiguous loci on several chromosomes, most commonly in untranslated regions. We have experimentally verified a subset of these adventitious deletions that had no impact on the attenuation of the LdCen−/− parasites. Our results identified hitherto unknown features of attenuation of virulence that could be used as markers of product quality in production lots and highlight the importance of product characterization in parasitic vaccines.
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Simonyan V, Chumakov K, Donaldson E, Karagiannis K, Lam PV, Dingerdissen H, Voskanian A. HIVE-heptagon: A sensible variant-calling algorithm with post-alignment quality controls. Genomics 2017; 109:131-140. [PMID: 28188908 DOI: 10.1016/j.ygeno.2017.01.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/19/2016] [Accepted: 01/24/2017] [Indexed: 10/20/2022]
Abstract
Advances in high-throughput sequencing (HTS) technologies have greatly increased the availability of genomic data and potential discovery of clinically significant genomic variants. However, numerous issues still exist with the analysis of these data, including data complexity, the absence of formally agreed upon best practices, and inconsistent reproducibility. Toward a more robust and reproducible variant-calling paradigm, we propose a series of selective noise filtrations and post-alignment quality control (QC) techniques that may reduce the rate of false variant calls. We have implemented both novel and refined post-alignment QC mechanisms to augment existing pre-alignment QC measures. These techniques can be used independently or in combination to identify and correct issues caused during data generation or early analysis stages. The adoption of these procedures by the broader scientific community is expected to improve the identification of clinically significant variants both in terms of computational efficiency and in the confidence of the results. AVAILABILITY https://hive.biochemistry.gwu.edu/.
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Affiliation(s)
- Vahan Simonyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Eric Donaldson
- Center for Drug Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, 10993 New Hampshire Ave., United States.
| | - Konstantinos Karagiannis
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States; Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, 2300 Eye St. NW, Washington DC, United States.
| | - Phuc VinhNguyen Lam
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
| | - Hayley Dingerdissen
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States; Department of Biochemistry and Molecular Medicine, George Washington University Medical Center, 2300 Eye St. NW, Washington DC, United States.
| | - Alin Voskanian
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10993 New Hampshire Ave., Silver Spring, MD, United States.
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Chen Y, Hora B, DeMarco T, Shah SA, Ahmed M, Sanchez AM, Su C, Carter M, Stone M, Hasan R, Hasan Z, Busch MP, Denny TN, Gao F. Fast Dissemination of New HIV-1 CRF02/A1 Recombinants in Pakistan. PLoS One 2016; 11:e0167839. [PMID: 27973597 PMCID: PMC5156399 DOI: 10.1371/journal.pone.0167839] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 11/21/2016] [Indexed: 12/21/2022] Open
Abstract
A number of HIV-1 subtypes are identified in Pakistan by characterization of partial viral gene sequences. Little is known whether new recombinants are generated and how they disseminate since whole genome sequences for these viruses have not been characterized. Near full-length genome (NFLG) sequences were obtained by amplifying two overlapping half genomes or next generation sequencing from 34 HIV-1-infected individuals in Pakistan. Phylogenetic tree analysis showed that the newly characterized sequences were 16 subtype As, one subtype C, and 17 A/G recombinants. Further analysis showed that all 16 subtype A1 sequences (47%), together with the vast majority of sequences from Pakistan from other studies, formed a tight subcluster (A1a) within the subtype A1 clade, suggesting that they were derived from a single introduction. More in-depth analysis of 17 A/G NFLG sequences showed that five shared similar recombination breakpoints as in CRF02 (15%) but were phylogenetically distinct from the prototype CRF02 by forming a tight subcluster (CRF02a) while 12 (38%) were new recombinants between CRF02a and A1a or a divergent A1b viruses. Unique recombination patterns among the majority of the newly characterized recombinants indicated ongoing recombination. Interestingly, recombination breakpoints in these CRF02/A1 recombinants were similar to those in prototype CRF02 viruses, indicating that recombination at these sites more likely generate variable recombinant viruses. The dominance and fast dissemination of new CRF02a/A1 recombinants over prototype CRF02 suggest that these recombinant have more adapted and may become major epidemic strains in Pakistan.
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Affiliation(s)
- Yue Chen
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bhavna Hora
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Todd DeMarco
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | | | | | - Ana M. Sanchez
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Chang Su
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Meredith Carter
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Mars Stone
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Rumina Hasan
- Department of Pathology, Aga Khan University, Karachi, Pakistan
- Department of Microbiology, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology, Aga Khan University, Karachi, Pakistan
- Department of Microbiology, Aga Khan University, Karachi, Pakistan
| | - Michael P. Busch
- Blood Systems Research Institute, San Francisco, California, United States of America
| | - Thomas N. Denny
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Feng Gao
- Duke Human Vaccine Institute, Department of Medicine, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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Simonyan V, Goecks J, Mazumder R. Biocompute Objects-A Step towards Evaluation and Validation of Biomedical Scientific Computations. PDA J Pharm Sci Technol 2016; 71:136-146. [PMID: 27974626 DOI: 10.5731/pdajpst.2016.006734] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The unpredictability of actual physical, chemical, and biological experiments due to the multitude of environmental and procedural factors is well documented. What is systematically overlooked, however, is that computational biology algorithms are also affected by multiplicity of parameters and have no lesser volatility. The complexities of computation protocols and interpretation of outcomes is only a part of the challenge: There are also virtually no standardized and industry-accepted metadata schemas for reporting the computational objects that record the parameters used for computations together with the results of computations. Thus, it is often impossible to reproduce the results of a previously performed computation due to missing information on parameters, versions, arguments, conditions, and procedures of application launch. In this article we describe the concept of biocompute objects developed specifically to satisfy regulatory research needs for evaluation, validation, and verification of bioinformatics pipelines. We envision generalized versions of biocompute objects called biocompute templates that support a single class of analyses but can be adapted to meet unique needs. To make these templates widely usable, we outline a simple but powerful cross-platform implementation. We also discuss the reasoning and potential usability for such concept within the larger scientific community through the creation of a biocompute object database initially consisting of records relevant to the U.S. Food and Drug Administration. A biocompute object database record will be similar to a GenBank record in form; the difference being that instead of describing a sequence, the biocompute record will include information related to parameters, dependencies, usage, and other information related to specific computational instance. This mechanism will extend similar efforts and also serve as a collaborative ground to ensure interoperability between different platforms, industries, scientists, regulators, and other stakeholders interested in biocomputing.
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Affiliation(s)
- Vahan Simonyan
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA;
| | - Jeremy Goecks
- Computational Biology Institute, George Washington University, Ashburn, VA, USA; and
| | - Raja Mazumder
- Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC, USA
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Abstract
INTRODUCTION The drug development industry is restructuring worldwide in terms of the research and development process. As with pharmaceuticals in the west, China faces major challenges for drug discovery and development. Areas covered: In this review, the authors discuss anti-cancer, anti-allergy, anti-infectious, and proprietary Chinese Medicines (pCM) for various chronic diseases (such as the allergic diseases: eczema, asthma and allergic rhinitis), which remain the contemporary therapeutic strategies that are being explored and developed. Drug transporters, disease specific biomarkers, pharmacophores, bioactive natural products and pharmacogenetics are some aspects of research technologies. Proprietary Chinese medicine remains one of the most popular strategies. There is however the issue of good research documentation of efficacy versus adverse effects. China has a complex healthcare system involving a large patient pool. Expert opinion: Various factors can impact drug development in China including the concurrent use of both western and Chinese medicines, pharmacogenetic variances, lack of multidisciplinary team impact on disease management and drug safety. China may adopt the current development of big data analysis in other countries such as UK and US to build and centralize a nationwide database for better monitoring and clinical evaluation to provide more efficient care at a lower cost.
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Affiliation(s)
- Kam Lun Hon
- a Department of Pediatrics , The Chinese University of Hong Kong , Prince of Wales Hospital, Shatin , Hong Kong
| | - Vivian W Y Lee
- b School of Pharmacy , The Chinese University of Hong Kong , Shatin , Hong Kong
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Novatt H, Theisen TC, Massie T, Massie T, Simonyan V, Voskanian-Kordi A, Renn LA, Rabin RL. Distinct Patterns of Expression of Transcription Factors in Response to Interferonβ and Interferonλ1. J Interferon Cytokine Res 2016; 36:589-598. [PMID: 27447339 DOI: 10.1089/jir.2016.0031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
After viral infection, type I and III interferons (IFNs) are coexpressed by respiratory epithelial cells (RECs) and activate the ISGF3 transcription factor (TF) complex to induce expression of a cell-specific set of interferon-stimulated genes (ISGs). Type I and III IFNs share a canonical signaling pathway, suggesting that they are redundant. Animal and in vitro models, however, have shown that they are not redundant. Because TFs dictate cellular phenotype and function, we hypothesized that focusing on TF-ISG will reveal critical combinatorial and nonredundant functions of type I or III IFN. We treated BEAS-2B human RECs with increasing doses of IFNβ or IFNλ1 and measured expression of TF-ISG. ISGs were expressed in a dose-dependent manner with a nonlinear jump at intermediate doses. At subsaturating combinations of IFNβ and IFNλ1, many ISGs were expressed in a pattern that we modeled with a cubic equation that mathematically defines this threshold effect. Uniquely, IFNβ alone induced early and transient IRF1 transcript and protein expression, while IFNλ1 alone induced IRF1 protein expression at low levels that were sustained through 24 h. In combination, saturating doses of these 2 IFNs together enhanced and sustained IRF1 expression. We conclude that the cubic model quantitates combinatorial effects of IFNβ and IFNλ1 and that IRF1 may mediate nonredundancy of type I or III IFN in RECs.
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Affiliation(s)
- Hilary Novatt
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Terence C Theisen
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Tammy Massie
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Tristan Massie
- 2 Drugs Evaluation and Research, USFDA, Silver Spring, Maryland
| | - Vahan Simonyan
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Alin Voskanian-Kordi
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Lynnsey A Renn
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
| | - Ronald L Rabin
- 1 Center for Biologics Evaluation and Research , US Food and Drug Administration, Silver Spring, Maryland
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Kautz TF, Díaz-González EE, Erasmus JH, Malo-García IR, Langsjoen RM, Patterson EI, Auguste DI, Forrester NL, Sanchez-Casas RM, Hernández-Ávila M, Alpuche-Aranda CM, Weaver SC, Fernández-Salas I. Chikungunya Virus as Cause of Febrile Illness Outbreak, Chiapas, Mexico, 2014. Emerg Infect Dis 2016; 21:2070-3. [PMID: 26488312 PMCID: PMC4622247 DOI: 10.3201/eid2111.150546] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Since chikungunya virus (CHIKV) was introduced into the Americas in 2013, its geographic distribution has rapidly expanded. Of 119 serum samples collected in 2014 from febrile patients in southern Mexico, 79% were positive for CHIKV or IgM against CHIKV. Sequencing results confirmed CHIKV strains closely related to Caribbean isolates.
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Xiao W, Wu L, Yavas G, Simonyan V, Ning B, Hong H. Challenges, Solutions, and Quality Metrics of Personal Genome Assembly in Advancing Precision Medicine. Pharmaceutics 2016; 8:E15. [PMID: 27110816 PMCID: PMC4932478 DOI: 10.3390/pharmaceutics8020015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 03/11/2016] [Accepted: 04/06/2016] [Indexed: 01/15/2023] Open
Abstract
Even though each of us shares more than 99% of the DNA sequences in our genome, there are millions of sequence codes or structure in small regions that differ between individuals, giving us different characteristics of appearance or responsiveness to medical treatments. Currently, genetic variants in diseased tissues, such as tumors, are uncovered by exploring the differences between the reference genome and the sequences detected in the diseased tissue. However, the public reference genome was derived with the DNA from multiple individuals. As a result of this, the reference genome is incomplete and may misrepresent the sequence variants of the general population. The more reliable solution is to compare sequences of diseased tissue with its own genome sequence derived from tissue in a normal state. As the price to sequence the human genome has dropped dramatically to around $1000, it shows a promising future of documenting the personal genome for every individual. However, de novo assembly of individual genomes at an affordable cost is still challenging. Thus, till now, only a few human genomes have been fully assembled. In this review, we introduce the history of human genome sequencing and the evolution of sequencing platforms, from Sanger sequencing to emerging "third generation sequencing" technologies. We present the currently available de novo assembly and post-assembly software packages for human genome assembly and their requirements for computational infrastructures. We recommend that a combined hybrid assembly with long and short reads would be a promising way to generate good quality human genome assemblies and specify parameters for the quality assessment of assembly outcomes. We provide a perspective view of the benefit of using personal genomes as references and suggestions for obtaining a quality personal genome. Finally, we discuss the usage of the personal genome in aiding vaccine design and development, monitoring host immune-response, tailoring drug therapy and detecting tumors. We believe the precision medicine would largely benefit from bioinformatics solutions, particularly for personal genome assembly.
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Affiliation(s)
- Wenming Xiao
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Leihong Wu
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Gokhan Yavas
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Vahan Simonyan
- Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD 20993, USA.
| | - Baitang Ning
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
| | - Huixiao Hong
- National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA.
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Evidence that a polyhexameric genome length is preferred, but not strictly required, for efficient mumps virus replication. Virology 2016; 493:173-88. [PMID: 27058764 DOI: 10.1016/j.virol.2016.03.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/22/2016] [Accepted: 03/24/2016] [Indexed: 11/22/2022]
Abstract
Mumps virus (MuV) is postulated to adhere to the "rule of six" for efficient replication. To examine the requirement for MuV, minigenomes of nonpolyhexameric length (6n-1 and 6n+1) were analyzed. Expression of the reporter gene CAT was significantly reduced with minigenomes of nonpolyhexameric length compared to the wild type 6n genome, and reduction was more pronounced for the 6n-1 than for the 6n+1 minigenome. That 6n-1 genomes are impacted by nonconformance with the rule of six to a greater degree as compared to 6n+1 genomes was also suggested with MuV derived from cDNA coding for 6n+1 or 6n-1 genomes. While viruses recovered from 6n+1 cDNAs maintained a nonpolyhexameric genome length over multiple replication cycles, viruses rescued from the 6n-1 cDNAs acquired length correcting mutations rapidly following rescue. Our data indicate that polyhexameric genomes are the preferred template for the MuV RNA polymerase, but that this requirement is not absolute.
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Sauder CJ, Ngo L, Simonyan V, Cong Y, Zhang C, Link M, Malik T, Rubin SA. Generation and propagation of recombinant mumps viruses exhibiting an additional U residue in the homopolymeric U tract of the F gene-end signal. Virus Genes 2015; 51:12-24. [DOI: 10.1007/s11262-015-1204-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/27/2015] [Indexed: 11/28/2022]
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Big Data Literature Search. BIG DATA 2014; 2:230-232. [PMID: 27442757 DOI: 10.1089/big.2014.1526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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