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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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Wang X, Li W, Feng X, Li J, Liu GE, Fang L, Yu Y. Harnessing male germline epigenomics for the genetic improvement in cattle. J Anim Sci Biotechnol 2023; 14:76. [PMID: 37277852 PMCID: PMC10242889 DOI: 10.1186/s40104-023-00874-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 04/02/2023] [Indexed: 06/07/2023] Open
Abstract
Sperm is essential for successful artificial insemination in dairy cattle, and its quality can be influenced by both epigenetic modification and epigenetic inheritance. The bovine germline differentiation is characterized by epigenetic reprogramming, while intergenerational and transgenerational epigenetic inheritance can influence the offspring's development through the transmission of epigenetic features to the offspring via the germline. Therefore, the selection of bulls with superior sperm quality for the production and fertility traits requires a better understanding of the epigenetic mechanism and more accurate identifications of epigenetic biomarkers. We have comprehensively reviewed the current progress in the studies of bovine sperm epigenome in terms of both resources and biological discovery in order to provide perspectives on how to harness this valuable information for genetic improvement in the cattle breeding industry.
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Affiliation(s)
- Xiao Wang
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
- Konge Larsen ApS, Kongens Lyngby, 2800, Denmark
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Wenlong Li
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xia Feng
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jianbing Li
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, Henry A. Wallace Beltsville Agricultural Research Center, USDA, Beltsville, MD, 20705, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, Denmark.
| | - Ying Yu
- Laboratory of Animal Genetics and Breeding, Ministry of Agriculture and Rural Affairs of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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HIV-1 Drug Resistance Assay Using Ion Torrent Next Generation Sequencing and On-Instrument End-to-End Analysis Software. J Clin Microbiol 2022; 60:e0025322. [PMID: 35699434 DOI: 10.1128/jcm.00253-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
HIV-1 antiretroviral therapy management requires sequencing the protease, reverse transcriptase, and integrase portions of the HIV-1 pol gene. Most resistance testing is performed with Sanger sequencing, which has limited ability to detect minor variants. Next generation sequencing (NGS) platforms enable variant detection at frequencies as low as 1% allowing for earlier detection of resistance and modification of therapy. Implementation of NGS assays in the clinical laboratory is hindered by complicated assay design, cumbersome wet bench procedures, and the complexity of data analysis and bioinformatics. We developed a complete NGS protocol and companion analysis and reporting pipeline using AmpliSeq multiplex PCR, Ion Torrent S5 XL sequencing, and Stanford's HIVdb resistance algorithm. Implemented as a Torrent Suite software plugin, the pipeline runs automatically after sequencing. An optimum variant frequency threshold of 10% was determined by comparing Sanger sequences of archived samples from ViroSeq testing, resulting in a sensitivity of 98.2% and specificity of 99.0%. The majority (91%) of drug resistance mutations were detected by both Sanger and NGS, with 1.7% only by Sanger and 7.3% only by NGS. Variant calls were highly reproducible and there was no cross-reactivity to VZV, HBV, CMV, EBV, and HCV. The limit of detection was 500 copies/mL. The NGS assay performance was comparable to ViroSeq Sanger sequencing and has several advantages, including a publicly available end-to-end analysis and reporting plugin. The assay provides a straightforward path for implementation of NGS for HIV drug resistance testing in the laboratory setting without additional investment in bioinformatics infrastructure and resources.
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Manuela J, David ZJ, Nicole S, Nicole C, Paul B, Erich K, Lisa SP, Claudia M, Marcel L, Stefan K. Optimization of the TeraTox assay for preclinical teratogenicity assessment. Toxicol Sci 2022; 188:17-33. [PMID: 35485993 PMCID: PMC9237991 DOI: 10.1093/toxsci/kfac046] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Current animal-free methods to assess teratogenicity of drugs under development still deliver high numbers of false negatives. To improve the sensitivity of human teratogenicity prediction, we characterized the TeraTox test, a newly developed multilineage differentiation assay using 3D human-induced pluripotent stem cells. TeraTox produces primary output concentration-dependent cytotoxicity and altered gene expression induced by each test compound. These data are fed into an interpretable machine-learning model to perform prediction, which relates to the concentration-dependent human teratogenicity potential of drug candidates. We applied TeraTox to profile 33 approved pharmaceuticals and 12 proprietary drug candidates with known in vivo data. Comparing TeraTox predictions with known human or animal toxicity, we report an accuracy of 69% (specificity: 53%, sensitivity: 79%). TeraTox performed better than 2 quantitative structure-activity relationship models and had a higher sensitivity than the murine embryonic stem cell test (accuracy: 58%, specificity: 76%, and sensitivity: 46%) run in the same laboratory. The overall prediction accuracy could be further improved by combining TeraTox and mouse embryonic stem cell test results. Furthermore, patterns of altered gene expression revealed by TeraTox may help grouping toxicologically similar compounds and possibly deducing common modes of action. The TeraTox assay and the dataset described here therefore represent a new tool and a valuable resource for drug teratogenicity assessment.
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Affiliation(s)
- Jaklin Manuela
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland.,Department for In Vitro Toxicology and Biomedicine Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Germany
| | - Zhang Jitao David
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | - Schäfer Nicole
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | - Clemann Nicole
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | - Barrow Paul
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | - Küng Erich
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | - Sach-Peltason Lisa
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
| | | | - Leist Marcel
- Department for In Vitro Toxicology and Biomedicine Inaugurated by the Doerenkamp-Zbinden Foundation, University of Konstanz, Germany
| | - Kustermann Stefan
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Switzerland
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Aires V, Coulon-Bainier C, Pavlovic A, Ebeling M, Schmucki R, Schweitzer C, Kueng E, Gutbier S, Harde E. CD22 Blockage Restores Age-Related Impairments of Microglia Surveillance Capacity. Front Immunol 2021; 12:684430. [PMID: 34140954 PMCID: PMC8204252 DOI: 10.3389/fimmu.2021.684430] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
Microglia, the innate immune cells of the brain, are essential for maintaining homeostasis by their ramified, highly motile processes and for orchestrating the immune response to pathological stimuli. They are implicated in several neurodegenerative diseases like Alzheimer's and Parkinson's disease. One commonality of these diseases is their strong correlation with aging as the highest risk factor and studying age-related alterations in microglia physiology and associated signaling mechanism is indispensable for a better understanding of age-related pathomechanisms. CD22 has been identified as a modifier of microglia phagocytosis in a recent study, but not much is known about the function of CD22 in microglia. Here we show that CD22 surface levels are upregulated in aged versus adult microglia. Furthermore, in the amyloid mouse model PS2APP, Aβ-containing microglia also exhibit increased CD22 signal. To assess the impact of CD22 blockage on microglia morphology and dynamics, we have established a protocol to image microglia process motility in acutely prepared brain slices from CX3CR1-GFP reporter mice. We observed a significant reduction of microglial ramification and surveillance capacity in brain slices from aged versus adult mice. The age-related decrease in surveillance can be restored by antibody-mediated CD22 blockage in aged mice, whereas surveillance in adult mice is not affected by CD22 inhibition. Moreover to complement the results obtained in mice, we show that human iPSC-derived macrophages exhibit an increased phagocytic capacity upon CD22 blockage. Downstream analysis of antibody-mediated CD22 inhibition revealed an influence on BMP and TGFβ associated gene networks. Our results demonstrate CD22 as a broad age-associated modulator of microglia functionality with potential implications for neurodegenerative disorders.
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Affiliation(s)
- Vanessa Aires
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland.,Department of Neurology, Medical Center - University of Freiburg, Freiburg, Germany.,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Claire Coulon-Bainier
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Anto Pavlovic
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Martin Ebeling
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Roland Schmucki
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Christophe Schweitzer
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Erich Kueng
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Simon Gutbier
- Roche Pharma Research and Early Development, Therapeutic Modalities, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eva Harde
- Roche Pharma Research and Early Development, Neuroscience and Rare Diseases Discovery and Translational Area, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Basel, Switzerland
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Narasimhan A, Zhong X, Au EP, Ceppa EP, Nakeeb A, House MG, Zyromski NJ, Schmidt CM, Schloss KNH, Schloss DEI, Liu Y, Jiang G, Hancock BA, Radovich M, Kays JK, Shahda S, Couch ME, Koniaris LG, Zimmers TA. Profiling of Adipose and Skeletal Muscle in Human Pancreatic Cancer Cachexia Reveals Distinct Gene Profiles with Convergent Pathways. Cancers (Basel) 2021; 13:1975. [PMID: 33923976 PMCID: PMC8073275 DOI: 10.3390/cancers13081975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/06/2023] Open
Abstract
The vast majority of patients with pancreatic ductal adenocarcinoma (PDAC) suffer cachexia. Although cachexia results from concurrent loss of adipose and muscle tissue, most studies focus on muscle alone. Emerging data demonstrate the prognostic value of fat loss in cachexia. Here we sought to identify the muscle and adipose gene profiles and pathways regulated in cachexia. Matched rectus abdominis muscle and subcutaneous adipose tissue were obtained at surgery from patients with benign conditions (n = 11) and patients with PDAC (n = 24). Self-reported weight loss and body composition measurements defined cachexia status. Gene profiling was done using ion proton sequencing. Results were queried against external datasets for validation. 961 DE genes were identified from muscle and 2000 from adipose tissue, demonstrating greater response of adipose than muscle. In addition to known cachexia genes such as FOXO1, novel genes from muscle, including PPP1R8 and AEN correlated with cancer weight loss. All the adipose correlated genes including SCGN and EDR17 are novel for PDAC cachexia. Pathway analysis demonstrated shared pathways but largely non-overlapping genes in both tissues. Age related muscle loss predominantly had a distinct gene profiles compared to cachexia. This analysis of matched, externally validate gene expression points to novel targets in cachexia.
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Affiliation(s)
- Ashok Narasimhan
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Xiaoling Zhong
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
| | - Ernie P. Au
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Eugene P. Ceppa
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Atilla Nakeeb
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Michael G. House
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Nicholas J. Zyromski
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - C. Max Schmidt
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Katheryn N. H. Schloss
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Daniel E. I. Schloss
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Yunlong Liu
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Center for Musculoskeletal Health, Indianapolis, IN 46202, USA
| | - Guanglong Jiang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Bradley A. Hancock
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Milan Radovich
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
| | - Joshua K. Kays
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
| | - Safi Shahda
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Marion E. Couch
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
- Department of Otolaryngology—Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Leonidas G. Koniaris
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
- Indiana Center for Musculoskeletal Health, Indianapolis, IN 46202, USA
| | - Teresa A. Zimmers
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA; (A.N.); (X.Z.); (E.P.A.); (E.P.C.); (A.N.); (M.G.H.); (N.J.Z.); (C.M.S.); (K.N.H.S.); (D.E.I.S.); (B.A.H.); (M.R.); (J.K.K.); (L.G.K.)
- IUPUI Center for Cachexia Research Innovation and Therapy, Indianapolis, IN 46202, USA; (Y.L.); (S.S.); (M.E.C.)
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana University Simon Cancer Center, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Indiana Center for Musculoskeletal Health, Indianapolis, IN 46202, USA
- Department of Otolaryngology—Head & Neck Surgery, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Department of Anatomy, Cell Biology & Physiology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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7
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Gut microorganisms and their metabolites modulate the severity of acute colitis in a tryptophan metabolism-dependent manner. Eur J Nutr 2020; 59:3591-3601. [PMID: 32055962 DOI: 10.1007/s00394-020-02194-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2019] [Accepted: 01/28/2020] [Indexed: 12/13/2022]
Abstract
PURPOSE Growing evidence shows that nutrient metabolism affects inflammatory bowel diseases (IBD) development. Previously, we showed that deficiency of indoleamine 2,3-dioxygenase 1 (Ido1), a tryptophan-catabolizing enzyme, reduced the severity of dextran sulfate sodium (DSS)-induced colitis in mice. However, the roles played by intestinal microbiota in generating the differences in disease progression between Ido1+/+ and Ido1-/- mice are unknown. Therefore, we aimed to investigate the interactions between the intestinal microbiome and host IDO1 in governing intestinal inflammatory responses. METHODS Microbial 16s rRNA sequencing was conducted in Ido1+/+ and Ido1-/- mice after DSS treatment. Bacteria-derived tryptophan metabolites were measured in urine. Transcriptome analysis revealed the effects of the metabolite and IDO1 expression in HCT116 cells. Colitis severity of Ido1+/+ was compared to Ido1-/- mice following fecal microbiota transplantation (FMT). RESULTS Microbiome analysis through 16S-rRNA gene sequencing showed that IDO1 deficiency increased intestinal bacteria that use tryptophan preferentially to produce indolic compounds. Urinary excretion of 3-indoxyl sulfate, a metabolized form of gut bacteria-derived indole, was significantly higher in Ido1-/- than in Ido1+/+ mice. Transcriptome analysis showed that tight junction transcripts were significantly increased by indole treatment in HCT116 cells; however, the effects were diminished by IDO1 overexpression. Using FMT experiments, we demonstrated that bacteria from Ido1-/- mice could directly attenuate the severity of DSS-induced colitis. CONCLUSIONS Our results provide evidence that a genetic defect in utilizing tryptophan affects intestinal microbiota profiles, altering microbial metabolites, and colitis development. This suggests that the host and intestinal microbiota communicate through shared nutrient metabolic networks.
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Dehghani M, Rosenblatt KP, Li L, Rakhade M, Amato RJ. Validation and Clinical Applications of a Comprehensive Next Generation Sequencing System for Molecular Characterization of Solid Cancer Tissues. Front Mol Biosci 2019; 6:82. [PMID: 31681791 PMCID: PMC6798036 DOI: 10.3389/fmolb.2019.00082] [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: 05/06/2019] [Accepted: 08/23/2019] [Indexed: 12/18/2022] Open
Abstract
Identification of somatic molecular alterations in primary and metastatic solid tumor specimens can provide critical information regarding tumor biology and its heterogeneity, and enables the detection of molecular markers for clinical personalized treatment assignment. However, the optimal methods and target genes for clinical use are still being in development. Toward this end, we validated a targeted amplification-based NGS panel (Oncomine comprehensive assay v1) on a personal genome machine sequencer for molecular profiling of solid tumors. This panel covers 143 genes, and requires low amounts of DNA (20 ng) and RNA (10 ng). We used 27 FFPE tissue specimens, 10 cell lines, and 24 commercial reference materials to evaluate the performance characteristics of this assay. We also evaluated the performance of the assay on 26 OCT-embedded fresh frozen specimens (OEFF). The assay was found to be highly specific (>99%) and sensitive (>99%), with low false-positive and false-negative rates for single-nucleotide variants, indels, copy number alterations, and gene fusions. Our results indicate that this is a reliable method to determine molecular alterations in both fixed and fresh frozen solid tumor samples, including core needle biopsies.
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Affiliation(s)
- Mehdi Dehghani
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Kevin P Rosenblatt
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States.,NX Prenatal, Inc., Bellaire, TX, United States.,Consultative Genomics, PLLC, Bellaire, TX, United States
| | - Lei Li
- Principle Health Systems, Houston, TX, United States
| | - Mrudula Rakhade
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
| | - Robert J Amato
- Division of Oncology, Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, United States
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9
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Nourbakhsh M, Mansoor A, Koro K, Zhang Q, Minoo P. Expression Profiling Reveals Involvement of WNT Pathway in the Malignant Progression of Sessile Serrated Adenomas. THE AMERICAN JOURNAL OF PATHOLOGY 2019; 189:1732-1743. [PMID: 31199922 DOI: 10.1016/j.ajpath.2019.05.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 02/07/2023]
Abstract
Approximately 15% to 20% of colorectal cancers are developed through the serrated pathway of tumorigenesis, which is associated with BRAF mutation, CpG island methylation phenotype, and MLH1 methylation. However, the detailed process of progression from sessile serrated adenoma (SSA) to dysplasia and carcinoma has not been elucidated. To further characterize mechanisms involved in the dysplastic progression of SSA, we investigated differential expressions of mRNAs between areas with and without dysplasia within the same SSA polyps. Significantly dysregulated genes in paired samples were applied for functional annotation and biological significance. The same lysates from a subset of matched samples were subjected for miRNA expression profiling. Differentially expressed miRNAs were determined, and their targeted mRNAs were compared in parallel to the list of differentially expressed mRNAs from an RNA sequencing study. Fourteen common mRNA targets were identified, which include AXIN2, a known indicator of WNT/β-catenin pathway activation. Together, in this study, different genes, pathways, and biological processes involved in the initiation and progression of dysplasia in the serrated pathway are documented. One of the most significant findings is the involvement of the WNT/β-catenin pathway in the dysplastic progression of SSAs with different genes being targeted in early versus advanced dysplasia.
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Affiliation(s)
- Mahra Nourbakhsh
- Department of Pathology, Cumming School of Medicine and Alberta Public Laboratories, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Adnan Mansoor
- Department of Pathology, Cumming School of Medicine and Alberta Public Laboratories, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Konstantin Koro
- Department of Pathology, Cumming School of Medicine and Alberta Public Laboratories, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Qingrun Zhang
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada
| | - Parham Minoo
- Department of Pathology, Cumming School of Medicine and Alberta Public Laboratories, University of Calgary, Calgary, Alberta, Canada; Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta, Canada.
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10
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Aulner N, Danckaert A, Ihm J, Shum D, Shorte SL. Next-Generation Phenotypic Screening in Early Drug Discovery for Infectious Diseases. Trends Parasitol 2019; 35:559-570. [PMID: 31176583 DOI: 10.1016/j.pt.2019.05.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/08/2019] [Accepted: 05/08/2019] [Indexed: 12/30/2022]
Abstract
Cell-based phenotypic screening has proven to be valuable, notably in recapitulating relevant biological conditions, for example, the host cell/pathogen niche. However, the corresponding methodological complexity is not readily compatible with high-throughput pipelines, and fails to inform either molecular target or mechanism of action, which frustrates conventional drug-discovery roadmaps. We review the state-of-the-art and emerging technologies that suggest new strategies for harnessing value from the complexity of phenotypic screening and augmenting powerful utility for translational drug discovery. Advances in cellular, molecular, and bioinformatics technologies are converging at a cutting edge where the complexity of phenotypic screening may no longer be considered a hinderance but rather a catalyst to chemotherapeutic discovery for infectious diseases.
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Affiliation(s)
- Nathalie Aulner
- Institut Pasteur Paris, UTechS-PBI/Imagopole, 25-28 rue du Docteur Roux, 75015, France
| | - Anne Danckaert
- Institut Pasteur Paris, UTechS-PBI/Imagopole, 25-28 rue du Docteur Roux, 75015, France
| | - JongEun Ihm
- Institut Pasteur Paris, UTechS-PBI/Imagopole, 25-28 rue du Docteur Roux, 75015, France
| | - David Shum
- Institut Pasteur Korea, 16 Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea
| | - Spencer L Shorte
- Institut Pasteur Paris, UTechS-PBI/Imagopole, 25-28 rue du Docteur Roux, 75015, France; Institut Pasteur Korea, 16 Daewangpangyo-ro 712 beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 13488, Republic of Korea.
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11
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Brown RA, Henderlight M, Do T, Yasin S, Grom AA, DeLay M, Thornton S, Schulert GS. Neutrophils From Children With Systemic Juvenile Idiopathic Arthritis Exhibit Persistent Proinflammatory Activation Despite Long-Standing Clinically Inactive Disease. Front Immunol 2018; 9:2995. [PMID: 30619348 PMCID: PMC6305285 DOI: 10.3389/fimmu.2018.02995] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 12/04/2018] [Indexed: 01/09/2023] Open
Abstract
Background: Systemic juvenile idiopathic arthritis (SJIA) is a chronic childhood arthropathy with features of autoinflammation. Early inflammatory SJIA is associated with expansion and activation of neutrophils with a sepsis-like phenotype, but neutrophil phenotypes present in longstanding and clinically inactive disease (CID) are unknown. The objective of this study was to examine activated neutrophil subsets, S100 alarmin release, and gene expression signatures in children with a spectrum of SJIA disease activity. Methods: Highly-purified neutrophils were isolated using a two-step procedure of density-gradient centrifugation followed by magnetic-bead based negative selection prior to flow cytometry or cell culture to quantify S100 protein release. Whole transcriptome gene expression profiles were compared in neutrophils from children with both active SJIA and CID. Results: Patients with SJIA and active systemic features demonstrated a higher proportion of CD16+CD62Llo neutrophil population compared to controls. This neutrophil subset was not seen in patients with CID or patients with active arthritis not exhibiting systemic features. Using imaging flow cytometry, CD16+CD62Llo neutrophils from patients with active SJIA and features of macrophage activation syndrome (MAS) had increased nuclear hypersegmentation compared to CD16+CD62L+ neutrophils. Serum levels of S100A8/A9 and S100A12 were strongly correlated with peripheral blood neutrophil counts. Neutrophils from active SJIA patients did not show enhanced resting S100 protein release; however, regardless of disease activity, neutrophils from SJIA patients did show enhanced S100A8/A9 release upon PMA stimulation compared to control neutrophils. Furthermore, whole transcriptome analysis of highly purified neutrophils from children with active SJIA identified 214 differentially expressed genes (DEG) compared to neutrophils from healthy controls. The most significantly upregulated gene pathway was Immune System Process, including AIM2, IL18RAP, and NLRC4. Interestingly, this gene set showed intermediate levels of expression in neutrophils from patients with long-standing CID yet persistent serum IL-18 elevation. Indeed, all patient samples regardless of disease activity demonstrated elevated inflammatory gene expression, including inflammasome components and S100A8. Conclusion: We identify features of neutrophil activation in SJIA patients with both active disease and CID, including a proinflammatory gene expression signature, reflecting persistent innate immune activation. Taken together, these studies expand understanding of neutrophil function in chronic autoinflammatory disorders such as SJIA.
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Affiliation(s)
- Rachel A Brown
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Maggie Henderlight
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Thuy Do
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Shima Yasin
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Alexei A Grom
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Monica DeLay
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Sherry Thornton
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Grant S Schulert
- Division of Rheumatology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States
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12
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DeSena AD, Do T, Schulert GS. Systemic autoinflammation with intractable epilepsy managed with interleukin-1 blockade. J Neuroinflammation 2018; 15:38. [PMID: 29426321 PMCID: PMC5807745 DOI: 10.1186/s12974-018-1063-2] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/11/2018] [Indexed: 12/13/2022] Open
Abstract
Background Autoinflammatory disorders are distinguished by seemingly random episodes of systemic hyperinflammation, driven in particular by IL-1. Recent pre-clinical work has shown a key role for IL-1 in epilepsy in animal models, and therapies for autoinflammation including IL-1 blockade are proposed for refractory epilepsy. Case presentation Here, we report an adolescent female with signs of persistent systemic inflammation and epilepsy unresponsive to multiple anti-epileptic drugs (AED). She was diagnosed with generalized epilepsy with a normal brain MRI and an electroencephalogram (EEG) showing occasional generalized spike and slow wave discharges. Her diagnostic evaluation showed no signs of autoimmunity or genetic causes of epilepsy or periodic fever syndromes but persistently elevated serum inflammatory markers including S100 alarmin proteins. She experienced prompt clinical response to IL-1 blockade with first anakinra and then canakinumab, with near complete resolution of clinical seizures. Additionally, she displayed marked improvements in quality of life and social/academic functioning. Baseline gene expression studies on peripheral blood mononuclear cells (PBMC) from this patient showed significantly activated gene pathways suggesting systemic immune activation, including focal adhesion, platelet activation, and Rap1 signaling, which is an upstream regulator of IL-1β production by the NLRP3 inflammasome. It also showed activation of genes that characterize inflammasome-mediated autoinflammatory disorders and no signs of interferon activation. This gene expression signature was largely extinguished after anakinra treatment. Conclusions Together, these findings suggest that patients with epilepsy responsive to immune modulation may have distinct autoinflammatory features supporting IL-1 blockade. As such, IL-1 blockade may be highly efficacious adjunctive medication for certain refractory epilepsy syndromes. Electronic supplementary material The online version of this article (10.1186/s12974-018-1063-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allen D DeSena
- Division of Neurology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, MLC 2015, Cincinnati, OH, 45229, USA.
| | - Thuy Do
- Division of Rheumatology, Department of Pediatrics, Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, MLC 4010, Cincinnati, OH, 45229, USA
| | - Grant S Schulert
- Division of Rheumatology, Department of Pediatrics, Children's Hospital Medical Center, University of Cincinnati College of Medicine, 3333 Burnet Ave, MLC 4010, Cincinnati, OH, 45229, USA.
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13
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Wang P, Xia P, Yang J, Wang Z, Peng Y, Shi W, Villeneuve DL, Yu H, Zhang X. A Reduced Transcriptome Approach to Assess Environmental Toxicants Using Zebrafish Embryo Test. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:821-830. [PMID: 29224359 PMCID: PMC5839301 DOI: 10.1021/acs.est.7b04073] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Omics approaches can monitor responses and alterations of biological pathways at genome-scale, which are useful to predict potential adverse effects by environmental toxicants. However, high throughput application of transcriptomics in chemical assessment is limited due to the high cost and lack of "standardized" toxicogenomic methods. Here, a reduced zebrafish transcriptome (RZT) approach was developed to represent the whole transcriptome and to profile bioactivity of chemical and environmental mixtures in zebrafish embryo. RZT gene set of 1637 zebrafish Entrez genes was designed to cover a wide range of biological processes, and to faithfully capture gene-level and pathway-level changes by toxicants compared with the whole transcriptome. Concentration-response modeling was used to calculate the effect concentrations (ECs) of DEGs and corresponding molecular pathways. To validate the RZT approach, quantitative analysis of gene expression by RNA-ampliseq technology was used to identify differentially expressed genes (DEGs) at 32 hpf following exposure to seven serial dilutions of reference chemical BPA (10-10E-5μM) or each of four water samples ranging from wastewater to drinking water (relative enrichment factors 10-6.4 × 10-4). The RZT-ampliseq-embryo approach was both sensitive and able to identify a wide spectrum of biological activities associated with BPA exposure. Water quality was benchmarked based on the sensitivity distribution curve of biological pathways detected using RZT-ampliseq-embryo. Finally, the most sensitive biological pathways were identified, including those linked with adverse reproductive outcomes, genotoxicity and development outcomes. RZT-ampliseq-embryo approach provides an efficient and cost-effective tool to prioritize toxicants based on responsiveness of biological pathways.
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Affiliation(s)
- Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Jianghua Yang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Zhihao Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Ying Peng
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Wei Shi
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Daniel L. Villeneuve
- United States Environmental Protection Agency, Mid-Continent Ecology Division, Duluth, MN, USA
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University, Nanjing, P. R. China, 210023
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14
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Moffat JG, Vincent F, Lee JA, Eder J, Prunotto M. Opportunities and challenges in phenotypic drug discovery: an industry perspective. Nat Rev Drug Discov 2017; 16:531-543. [PMID: 28685762 DOI: 10.1038/nrd.2017.111] [Citation(s) in RCA: 506] [Impact Index Per Article: 72.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Phenotypic drug discovery (PDD) approaches do not rely on knowledge of the identity of a specific drug target or a hypothesis about its role in disease, in contrast to the target-based strategies that have been widely used in the pharmaceutical industry in the past three decades. However, in recent years, there has been a resurgence in interest in PDD approaches based on their potential to address the incompletely understood complexity of diseases and their promise of delivering first-in-class drugs, as well as major advances in the tools for cell-based phenotypic screening. Nevertheless, PDD approaches also have considerable challenges, such as hit validation and target deconvolution. This article focuses on the lessons learned by researchers engaged in PDD in the pharmaceutical industry and considers the impact of 'omics' knowledge in defining a cellular disease phenotype in the era of precision medicine, introducing the concept of a chain of translatability. We particularly aim to identify features and areas in which PDD can best deliver value to drug discovery portfolios and can contribute to the identification and the development of novel medicines, and to illustrate the challenges and uncertainties that are associated with PDD in order to help set realistic expectations with regard to its benefits and costs.
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Affiliation(s)
- John G Moffat
- Biochemical &Cellular Pharmacology, Genentech, South San Francisco, California 94080, USA
| | - Fabien Vincent
- Discovery Sciences, Primary Pharmacology Group, Pfizer, Groton, Connecticut 06340, USA
| | - Jonathan A Lee
- Department of Quantitative Biology, Eli Lilly and Company, Indianapolis, Indiana 46285, USA
| | - Jörg Eder
- Novartis Institutes for Biomedical Research, 4002 Basel, Switzerland
| | - Marco Prunotto
- Phenotype and Target ID, Chemical Biology, pRED, Roche, 4070 Basel, Switzerland. Present address: Office of Innovation, Immunology, Infectious Diseases &Ophthalmology (I2O), Roche Late Stage Development, 124 Grenzacherstrasse, 4070 Basel, Switzerland
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15
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Drawnel FM, Zhang JD, Küng E, Aoyama N, Benmansour F, Araujo Del Rosario A, Jensen Zoffmann S, Delobel F, Prummer M, Weibel F, Carlson C, Anson B, Iacone R, Certa U, Singer T, Ebeling M, Prunotto M. Molecular Phenotyping Combines Molecular Information, Biological Relevance, and Patient Data to Improve Productivity of Early Drug Discovery. Cell Chem Biol 2017; 24:624-634.e3. [DOI: 10.1016/j.chembiol.2017.03.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 02/22/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022]
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16
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Inhibition of EGF Uptake by Nephrotoxic Antisense Drugs In Vitro and Implications for Preclinical Safety Profiling. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 6:89-105. [PMID: 28325303 PMCID: PMC5363415 DOI: 10.1016/j.omtn.2016.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2016] [Revised: 10/30/2016] [Accepted: 11/21/2016] [Indexed: 12/12/2022]
Abstract
Antisense oligonucleotide (AON) therapeutics offer new avenues to pursue clinically relevant targets inaccessible with other technologies. Advances in improving AON affinity and stability by incorporation of high affinity nucleotides, such as locked nucleic acids (LNA), have sometimes been stifled by safety liabilities related to their accumulation in the kidney tubule. In an attempt to predict and understand the mechanisms of LNA-AON-induced renal tubular toxicity, we established human cell models that recapitulate in vivo behavior of pre-clinically and clinically unfavorable LNA-AON drug candidates. We identified elevation of extracellular epidermal growth factor (EGF) as a robust and sensitive in vitro biomarker of LNA-AON-induced cytotoxicity in human kidney tubule epithelial cells. We report the time-dependent negative regulation of EGF uptake and EGF receptor (EGFR) signaling by toxic but not innocuous LNA-AONs and revealed the importance of EGFR signaling in LNA-AON-mediated decrease in cellular activity. The robust EGF-based in vitro safety profiling of LNA-AON drug candidates presented here, together with a better understanding of the underlying molecular mechanisms, constitutes a significant step toward developing safer antisense therapeutics.
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17
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Affiliation(s)
| | - Tanya Kanigan
- COO, Genomic Expression, 54 West 40th Street, NY, USA
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18
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Beadling C, Wald AI, Warrick A, Neff TL, Zhong S, Nikiforov YE, Corless CL, Nikiforova MN. A Multiplexed Amplicon Approach for Detecting Gene Fusions by Next-Generation Sequencing. J Mol Diagn 2016; 18:165-75. [DOI: 10.1016/j.jmoldx.2015.10.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 10/25/2015] [Accepted: 10/30/2015] [Indexed: 01/05/2023] Open
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19
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Li W, Turner A, Aggarwal P, Matter A, Storvick E, Arnett DK, Broeckel U. Comprehensive evaluation of AmpliSeq transcriptome, a novel targeted whole transcriptome RNA sequencing methodology for global gene expression analysis. BMC Genomics 2015; 16:1069. [PMID: 26673413 PMCID: PMC4681149 DOI: 10.1186/s12864-015-2270-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 12/03/2015] [Indexed: 12/29/2022] Open
Abstract
Background Whole transcriptome sequencing (RNA-seq) represents a powerful approach for whole transcriptome gene expression analysis. However, RNA-seq carries a few limitations, e.g., the requirement of a significant amount of input RNA and complications led by non-specific mapping of short reads. The Ion AmpliSeq™ Transcriptome Human Gene Expression Kit (AmpliSeq) was recently introduced by Life Technologies as a whole-transcriptome, targeted gene quantification kit to overcome these limitations of RNA-seq. To assess the performance of this new methodology, we performed a comprehensive comparison of AmpliSeq with RNA-seq using two well-established next-generation sequencing platforms (Illumina HiSeq and Ion Torrent Proton). We analyzed standard reference RNA samples and RNA samples obtained from human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs). Results Using published data from two standard RNA reference samples, we observed a strong concordance of log2 fold change for all genes when comparing AmpliSeq to Illumina HiSeq (Pearson’s r = 0.92) and Ion Torrent Proton (Pearson’s r = 0.92). We used ROC, Matthew’s correlation coefficient and RMSD to determine the overall performance characteristics. All three statistical methods demonstrate AmpliSeq as a highly accurate method for differential gene expression analysis. Additionally, for genes with high abundance, AmpliSeq outperforms the two RNA-seq methods. When analyzing four closely related hiPSC-CM lines, we show that both AmpliSeq and RNA-seq capture similar global gene expression patterns consistent with known sources of variations. Conclusions Our study indicates that AmpliSeq excels in the limiting areas of RNA-seq for gene expression quantification analysis. Thus, AmpliSeq stands as a very sensitive and cost-effective approach for very large scale gene expression analysis and mRNA marker screening with high accuracy. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2270-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenli Li
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Amy Turner
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Praful Aggarwal
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Andrea Matter
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Erin Storvick
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Donna K Arnett
- Department of Epidemiology, University of Alabama at Birmingham, 1530 3rd Avenue South, Birmingham, AL, 35294, USA.
| | - Ulrich Broeckel
- Department of Pediatrics, Section of Genomic Pediatrics, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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20
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Shooter C, Rooks H, Thein SL, Clark B. Next generation sequencing identifies a novel rearrangement in the HBB cluster permitting to-the-base characterization. Hum Mutat 2015; 36:142-50. [PMID: 25331561 DOI: 10.1002/humu.22707] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Accepted: 09/16/2014] [Indexed: 12/29/2022]
Abstract
Genetic testing for hemoglobinopathies is required for prenatal diagnosis, understanding complex cases where multiple pathogenic variants may be present or investigating cases of unexplained anemia. Characterization of disease causing variants that range from single base changes to large rearrangements may require several different labor-intensive methodologies. Multiplex ligation probe amplification analysis is the current method used to detect indels, but the technique does not characterize the breakpoints or detect balanced translocations. Here, we describe a next-generation sequencing (NGS) method that is able to identify and characterize a novel rearrangement of the HBB cluster responsible for εγδβ thalassemia in an English family. The structural variant involved a 59.0 kb inversion encompassing HBG2 exon 3, HBG1, HBD, HBB, and OR51V1, juxtaposed by a deletion of 122.6 kb including 82 bp of the inverted sequence, HBG2 exon 1 and 2, HBE, and the β-locus control region. Identification of reads spanning the breakpoints provided to-the-base resolution of the rearrangement, subsequently confirmed by gap-PCR and Sanger sequence analysis. The same rearrangement, termed Inv-Del English V εγδβ thalassemia (HbVar 2935), was identified in two other unrelated English individuals with a similar hematological phenotype. Our NGS approach should be applicable as a diagnostic tool for other disorders.
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Affiliation(s)
- Claire Shooter
- King's College London, Faculty of Life Sciences and Medicine, Molecular Haematology, London, UK
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21
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Osman A, Hitzler WE, Ameur A, Provost P. Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems. PLoS One 2015; 10:e0133070. [PMID: 26172280 PMCID: PMC4501785 DOI: 10.1371/journal.pone.0133070] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/23/2015] [Indexed: 11/18/2022] Open
Abstract
Platelet concentrates (PCs) are prepared at blood banks for transfusion to patients in certain clinical conditions associated with a low platelet count. To prevent transfusion-transmitted infections via PCs, different pathogen reduction (PR) systems have been developed that inactivate the nucleic acids of contaminating pathogens by chemical cross-linking, a mechanism that may also affect platelets' nucleic acids. We previously reported that treatment of stored platelets with the PR system Intercept significantly reduced the level of half of the microRNAs that were monitored, induced platelet activation and compromised the platelet response to physiological agonists. Using genome-wide differential expression (DE) RNA sequencing (RNA-Seq), we now report that Intercept markedly perturbs the mRNA transcriptome of human platelets and alters the expression level of >800 mRNAs (P<0.05) compared to other PR systems and control platelets. Of these, 400 genes were deregulated with DE corresponding to fold changes (FC) ≥ 2. At the p-value < 0.001, as many as 147 genes were deregulated by ≥ 2-fold in Intercept-treated platelets, compared to none in the other groups. Finally, integrated analysis combining expression data for microRNA (miRNA) and mRNA, and involving prediction of miRNA-mRNA interactions, disclosed several positive and inverse correlations between miRNAs and mRNAs in stored platelets. In conclusion, this study demonstrates that Intercept markedly deregulates the platelet mRNA transcriptome, concomitant with reduced levels of mRNA-regulatory miRNAs. These findings should enlighten authorities worldwide when considering the implementation of PR systems, that target nucleic acids and are not specific to pathogens, for the management of blood products.
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Affiliation(s)
- Abdimajid Osman
- Department of Clinical Chemistry, Region Östergötland, Ingång 64, Linköping, Sweden
- Department of Clinical and Experimental Medicine, University of Linköping, Linköping, Sweden
| | - Walter E. Hitzler
- Transfusion Center, University Medical Center of the Johannes Gutenberg University Mainz, Hochhaus Augustusplatz, Mainz, Germany
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala, Uppsala University, Uppsala, Sweden
| | - Patrick Provost
- Université Laval CHUQ Research Center / CHUL 2705 Blvd Laurier, Quebec, QC, Canada
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22
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Antiviral Innate Immune Activation in HIV-Infected Adults Negatively Affects H1/IC31-Induced Vaccine-Specific Memory CD4+ T Cells. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2015; 22:688-96. [PMID: 25924764 DOI: 10.1128/cvi.00092-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/19/2015] [Indexed: 12/16/2022]
Abstract
Tuberculosis (TB) remains a global health problem, with vaccination being a necessary strategy for disease containment and elimination. A TB vaccine should be safe and immunogenic as well as efficacious in all affected populations, including HIV-infected individuals. We investigated the induction and maintenance of vaccine-induced memory CD4(+) T cells following vaccination with the subunit vaccine H1/IC31. H1/IC31 was inoculated twice on study days 0 and 56 among HIV-infected adults with CD4(+) lymphocyte counts of >350 cells/mm(3). Whole venous blood stimulation was conducted with the H1 protein, and memory CD4(+) T cells were analyzed using intracellular cytokine staining and polychromatic flow cytometry. We identified high responders, intermediate responders, and nonresponders based on detection of interleukin-2 (IL-2), tumor necrosis factor alpha (TNF-α), and gamma interferon (IFN-γ) expressing central (TCM) and effector memory CD4(+) T cells (TEM) 182 days after the first immunization. Amplicon-based transcript quantification using next-generation sequencing was performed to identify differentially expressed genes that correlated with vaccine-induced immune responses. Genes implicated in resolution of inflammation discriminated the responders from the nonresponders 3 days after the first inoculation. The volunteers with higher expression levels of genes involved in antiviral innate immunity at baseline showed impaired H1-specific TCM and TEM maintenance 6 months after vaccination. Our study showed that in HIV-infected volunteers, expression levels of genes involved in the antiviral innate immune response affected long-term maintenance of H1/IC31 vaccine-induced cellular immunity. (The clinical trial was registered in the Pan African Clinical Trials Registry [PACTR] with the identifier PACTR201105000289276.).
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23
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Zhang JD, Küng E, Boess F, Certa U, Ebeling M. Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics 2015; 16:342. [PMID: 25903797 PMCID: PMC4415216 DOI: 10.1186/s12864-015-1532-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/13/2015] [Indexed: 12/21/2022] Open
Abstract
Background The phenotype of a living cell is determined by its pattern of active signaling networks, giving rise to a “molecular phenotype” associated with differential gene expression. Digital amplicon based RNA quantification by sequencing is a useful technology for molecular phenotyping as a novel tool to characterize the state of biological systems. Results We show here that the activity of signaling networks can be assessed based on a set of established key regulators and expression targets rather than the entire transcriptome. We compiled a panel of 917 human pathway reporter genes, representing 154 human signaling and metabolic networks for integrated knowledge- and data-driven understanding of biological processes. The reporter genes are significantly enriched for regulators and effectors covering a wide range of biological processes, and faithfully capture gene-level and pathway-level changes. We apply the approach to iPSC derived cardiomyocytes and primary human hepatocytes to describe changes in molecular phenotype during development or drug response. The reporter genes deliver an accurate pathway-centric view of the biological system under study, and identify known and novel modulation of signaling networks consistent with literature or experimental data. Conclusions A panel of 917 pathway reporter genes is sufficient to describe changes in the molecular phenotype defined by 154 signaling cascades in various human cell types. AmpliSeq-RNA based digital transcript imaging enables simultaneous monitoring of the entire pathway reporter gene panel in up to 150 samples. We propose molecular phenotyping as a useful approach to understand diseases and drug action at the network level. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1532-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jitao David Zhang
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Erich Küng
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Franziska Boess
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Ulrich Certa
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland
| | - Martin Ebeling
- Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
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24
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Weis A, Liang F, Gao J, Barnard RT, Corrie S. RNA and DNA Diagnostics on Microspheres: Current and Emerging Methods. RNA TECHNOLOGIES 2015. [DOI: 10.1007/978-3-319-17305-4_10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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