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Frunze O, Kim H, Kim BJ, Lee JH, Bilal M, Kwon HW. Monitoring Immune Modulation in Season Population: Identifying Effects and Markers Related to Apis mellifera ligustica Honey Bee Health. Biomolecules 2023; 14:19. [PMID: 38254619 PMCID: PMC10813216 DOI: 10.3390/biom14010019] [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: 11/13/2023] [Revised: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Honey bees play a significant role in ecology, producing biologically active substances used to promote human health. However, unlike humans, the molecular markers indicating honey bee health remain unknown. Unfortunately, numerous reports of honey bee collapse have been documented. To identify health markers, we analyzed ten defense system genes in Apis mellifera ligustica honey bees from winter (Owb) and spring (Fb for foragers and Nb for newly emerged) populations sampled in February and late April 2023, respectively. We focused on colonies free from SBV and DWV viruses. Molecular profiling revealed five molecular markers of honey bee health. Of these, two seasonal molecular markers-domeless and spz genes-were significantly downregulated in Owb compared to Nb and Fb honey bees. One task-related marker gene, apid-1, was identified as being downregulated in Owb and Nb compared to Fb honey bees. Two recommended general health markers, SOD and defensin-2, were upregulated in honey bees. These markers require further testing across various honey bee subspecies in different climatic regions. They can diagnose bee health without colony intervention, especially during low-temperature months like winter. Beekeepers can use this information to make timely adjustments to nutrients or heating to prevent seasonal losses.
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Affiliation(s)
- Olga Frunze
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Hyunjee Kim
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Byung-ju Kim
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Jeong-Hyeon Lee
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Mustafa Bilal
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
| | - Hyung-Wook Kwon
- Department of Life Sciences, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; (O.F.); (H.K.); (B.-j.K.); (J.-H.L.)
- Convergence Research Center for Insect Vectors (CRCIV), Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea
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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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Is the reductionist paradox an Achilles Heel of drug discovery? J Comput Aided Mol Des 2022; 36:329-338. [PMID: 35861913 DOI: 10.1007/s10822-022-00457-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 05/02/2022] [Indexed: 10/17/2022]
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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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Liu W, Gu R, Lou Y, He C, Zhang Q, Li D. Emodin-induced autophagic cell death hinders epithelial-mesenchymal transition via regulation of BMP-7/TGF-β1 in renal fibrosis. J Pharmacol Sci 2021; 146:216-225. [PMID: 34116735 DOI: 10.1016/j.jphs.2021.03.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 12/28/2022] Open
Abstract
We aim to explore the effects of emodin and its mechanisms on renal fibrosis (RF). We firstly modeled adriamycin-induced rat RF with unilateral nephrectomy. In vivo and in vitro pharmacological experiments were performed in this study. The presence of collagen deposition was detected by Masson staining. To verify whether emodin attenuates RF by monitoring autophagy, the immunohistochemistry staining for autophagy protein LC3B was performed. We conducted western blot to detect the expression of the autophagy-related proteins in EMT in vitro model after treating with emotin and BMP-7. In vivo, we demonstrated that emodin could improve renal dysfunction and decrease pathological damage of the kidney by activation of autophagy and inhibition of EMT. Upregulation of BMP-7 was recorded in the RF rats subjected to emodin treatment. In vitro studies, emodin has the capacity of reversing EMT and activating autophagy, and emodin could regulate the expression of BMP-7. The results revealed that the attenuation of EMT by emodin could be blocked after the inhibition of BMP-7 and suppression of autophagy. Our findings demonstrated that emodin alleviates EMT during RF by actuating autophagy through BMP-7, suggesting a role of BMP-7 in RF treatment and prevention.
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Affiliation(s)
- Wei Liu
- Department of Urology Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, PR China
| | - Renze Gu
- Department of Urology Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, PR China
| | - Yujiao Lou
- Department of Urology Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, PR China
| | - Chunfeng He
- Department of Urology Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, PR China
| | - Qingchuan Zhang
- Department of Urology Surgery, PuTuo Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, 200062, PR China.
| | - Dongmei Li
- Department of Pediatrics, Shanghai 9th People's Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai, 200011, PR China.
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7
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Ferguson LR. Inflammatory bowel disease: why this provides a useful example of the evolving science of nutrigenomics. J R Soc N Z 2020. [DOI: 10.1080/03036758.2020.1728345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Lynnette R. Ferguson
- Auckland Cancer Society Research Centre and Discipline of Nutrition and Dietetics, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
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8
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Reyes-Caballero H, Park B, Loube J, Sanchez I, Vinayachandran V, Choi Y, Woo J, Edwards J, Brinkman MC, Sussan T, Mitzner W, Biswal S. Immune modulation by chronic exposure to waterpipe smoke and immediate-early gene regulation in murine lungs. Tob Control 2019; 29:s80-s89. [PMID: 31852817 DOI: 10.1136/tobaccocontrol-2019-054965] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 08/22/2019] [Accepted: 08/24/2019] [Indexed: 01/02/2023]
Abstract
OBJECTIVE We investigated the effects of chronic waterpipe (WP) smoke on pulmonary function and immune response in a murine model using a research-grade WP and the effects of acute exposure on the regulation of immediate-early genes (IEGs). METHODS WP smoke was generated using three WP smoke puffing regimens based on the Beirut regimen. WP smoke samples generated under these puffing regimens were quantified for nicotine concentration. Mice were chronically exposed for 6 months followed by assessment of pulmonary function and airway inflammation. Transcriptomic analysis using RNAseq was conducted after acute exposure to characterise the IEG response. These biomarkers were then compared with those generated after exposure to dry smoke (without water added to the WP bowl). RESULTS We determined that nicotine composition in WP smoke ranged from 0.4 to 2.5 mg per puffing session. The lung immune response was sensitive to the incremental severity of chronic exposure, with modest decreases in airway inflammatory cells and chemokine levels compared with air-exposed controls. Pulmonary function was unmodified by chronic WP exposure. Acute WP exposure was found to activate the immune response and identified known and novel IEG as potential biomarkers of WP exposure. CONCLUSION Chronic exposure to WP smoke leads to immune suppression without significant changes to pulmonary function. Transcriptomic analysis of the lung after acute exposure to WP smoke showed activation of the immune response and revealed IEGs that are common to WP and dry smoke, as well as pools of IEGs unique to each exposure, identifying potential biomarkers specific to WP exposure.
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Affiliation(s)
- Hermes Reyes-Caballero
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bongsoo Park
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jeffrey Loube
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Ian Sanchez
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vinesh Vinayachandran
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Youngshim Choi
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Juhyung Woo
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Justin Edwards
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | | | - Thomas Sussan
- Toxicology Directorate, US Army Public Health Command, Aberdeen Proving Ground, Maryland, USA
| | - Wayne Mitzner
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shyam Biswal
- Environmental Health and Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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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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Zhang K, Zhao Y. Reduced Zebrafish Transcriptome Atlas toward Understanding Environmental Neurotoxicants. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7120-7130. [PMID: 29782159 DOI: 10.1021/acs.est.8b01350] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Transcriptomic approaches monitoring gene responses at genome-scale are increasingly used in toxicological research and help to clarify the molecular mechanisms of adverse effects caused by environmental toxicants. However, their applications for chemical assessment are hampered due to high expenses required and more importantly the lack of in-depth data mining and mechanistic perspectives. Here, we described a reduced transcriptome atlas (RTA) approach which integrates transcriptomic data sets and a comprehensive panel of genes generated to represent neurogenesis and the early neuronal development of zebrafish, to determine the potential neurodevelopmental toxicities of environmental chemicals. Transcriptomic data sets of 74 chemicals and 736 related gene expression profiles were integrated resulting in 135 exposure signatures. Chemical prioritization demonstrated four sets of hits to be neurotoxic: neuro-active chemicals (representatively, Valproic acid, VPA and Carbamazepine, CAR), xenoestrogens (Bisphenol A, BPA; Genistein, GEN; 17-α ethinylestradiol, EE2), microcystins (cyanopeptolin, CP1020; microcystin-LR, MCLR) and heavy metals (AgNO3, AgNPs). The enriched biological pathways and processes were distinct among the four sets, while the overlapping functional enrichments were observed within each set, for example, over 25% differentially expressed genes and four of top five KEGG pathways were shared between VPA and CAR. Furthermore, gene expression index (GEI) analysis demonstrated that a gene panel with 300 genes was sufficient to effectively characterize and cluster chemicals and therefore offer an efficient and cost-effective tool for the prioritization of neurotoxicants. Thus, the RTA approach provides novel insights into the understanding of the in-depth molecular mechanisms of environmental neurotoxicants and can be used as an indication for potential adverse outcomes.
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Affiliation(s)
- Kun Zhang
- School of Environmental Science and Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
- Brigham and Women's Hospital , Harvard Medical School , 60 Fenwood Road , Boston , Massachusetts 02115 , United States
| | - Yanbin Zhao
- School of Environmental Science and Engineering , Shanghai Jiao Tong University , 800 Dongchuan Road , Shanghai 200240 , China
- Brigham and Women's Hospital , Harvard Medical School , 60 Fenwood Road , Boston , Massachusetts 02115 , United States
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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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Complete sequence-based pathway analysis by differential on-chip DNA and RNA extraction from a single cell. Sci Rep 2017; 7:11030. [PMID: 28887473 PMCID: PMC5591254 DOI: 10.1038/s41598-017-10704-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/11/2017] [Indexed: 02/07/2023] Open
Abstract
We demonstrate on-chip, differential DNA and RNA extraction from a single cell using a microfluidic chip and a two-stage lysis protocol. This method enables direct use of the whole extract, without additional washing steps, reducing sample loss. Using this method, the tumor driving pathway in individual cells from a colorectal cancer cell line was determined by applying a Bayesian computational pathway model to sequences obtained from the RNA fraction of a single cell and, the mutations driving the pathway were determined by analyzing sequences obtained from the DNA fraction of the same single cell. This combined functional and mutational pathway assessment of a single cell could be of significant value for dissecting cellular heterogeneity in tumors and analyzing single circulating tumor cells.
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Xia P, Zhang X, Zhang H, Wang P, Tian M, Yu H. Benchmarking Water Quality from Wastewater to Drinking Waters Using Reduced Transcriptome of Human Cells. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:9318-9326. [PMID: 28696678 DOI: 10.1021/acs.est.7b02648] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
One of the major challenges in environmental science is monitoring and assessing the risk of complex environmental mixtures. In vitro bioassays with limited key toxicological end points have been shown to be suitable to evaluate mixtures of organic pollutants in wastewater and recycled water. Omics approaches such as transcriptomics can monitor biological effects at the genome scale. However, few studies have applied omics approach in the assessment of mixtures of organic micropollutants. Here, an omics approach was developed for profiling bioactivity of 10 water samples ranging from wastewater to drinking water in human cells by a reduced human transcriptome (RHT) approach and dose-response modeling. Transcriptional expression of 1200 selected genes were measured by an Ampliseq technology in two cell lines, HepG2 and MCF7, that were exposed to eight serial dilutions of each sample. Concentration-effect models were used to identify differentially expressed genes (DEGs) and to calculate effect concentrations (ECs) of DEGs, which could be ranked to investigate low dose response. Furthermore, molecular pathways disrupted by different samples were evaluated by Gene Ontology (GO) enrichment analysis. The ability of RHT for representing bioactivity utilizing both HepG2 and MCF7 was shown to be comparable to the results of previous in vitro bioassays. Finally, the relative potencies of the mixtures indicated by RHT analysis were consistent with the chemical profiles of the samples. RHT analysis with human cells provides an efficient and cost-effective approach to benchmarking mixture of micropollutants and may offer novel insight into the assessment of mixture toxicity in water.
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Affiliation(s)
- Pu Xia
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Hanxin Zhang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Pingping Wang
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Mingming Tian
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control & Resource Reuse, School of the Environment, Nanjing University , Nanjing 210023, PR China
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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: 499] [Impact Index Per Article: 71.3] [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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Abstract
In this issue, Drawnel et al. (2017) introduce the concept of a "molecular phenotype" and demonstrate how "big data" coming from gene expression profiling, combined with signaling pathway information, small-molecule chemical information, preclinical animal models, and clinical samples can empower phenotypic discovery at several critical levels.
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Affiliation(s)
- John G Moffat
- Department of Biochemical and Cellular Pharmacology, Genentech Research and Early Development, South San Francisco, CA 94112, USA.
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16
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Zhang JD, Küng E, Boess F, Certa U, Ebeling M. Erratum to: Pathway reporter genes define molecular phenotypes of human cells. BMC Genomics 2017; 18:337. [PMID: 28464836 PMCID: PMC5412029 DOI: 10.1186/s12864-017-3730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 04/26/2017] [Indexed: 11/23/2022] Open
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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17
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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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18
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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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Maryanoff BE. Phenotypic Assessment and the Discovery of Topiramate. ACS Med Chem Lett 2016; 7:662-5. [PMID: 27437073 PMCID: PMC4948003 DOI: 10.1021/acsmedchemlett.6b00176] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 06/13/2016] [Indexed: 12/25/2022] Open
Abstract
![]()
The
role of phenotypic assessment in drug discovery is discussed,
along with the discovery and development of TOPAMAX (topiramate),
a billion-dollar molecule for the treatment of epilepsy and migraine.
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Affiliation(s)
- Bruce E. Maryanoff
- Baruch S. Blumberg Institute, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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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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