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Gladow N, Hollmann C, Weirather J, Ding X, Burkard M, Uehlein S, Bharti R, Förstner K, Kerkau T, Beyersdorf N, Frantz S, Ramos G, Hofmann U. Role of CD4 + T-cells for regulating splenic myelopoiesis and monocyte differentiation after experimental myocardial infarction. Basic Res Cardiol 2024; 119:261-275. [PMID: 38436707 PMCID: PMC11008073 DOI: 10.1007/s00395-024-01035-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/10/2024] [Accepted: 01/27/2024] [Indexed: 03/05/2024]
Abstract
Myocardial infarction (MI) induces the generation of proinflammatory Ly6Chigh monocytes in the spleen and the recruitment of these cells to the myocardium. CD4+ Foxp3+ CD25+ T-cells (Tregs) promote the healing process after myocardial infarction by engendering a pro-healing differentiation state in myocardial monocyte-derived macrophages. We aimed to study the effects of CD4+ T-cells on splenic myelopoiesis and monocyte differentiation. We instigated MI in mice and found that MI-induced splenic myelopoiesis is abrogated in CD4+ T-cell deficient animals. Conventional CD4+ T-cells promoted myelopoiesis in vitro by cell-cell-contact and paracrine mechanisms, including interferon-gamma (IFN-γ) signalling. Depletion of regulatory T-cells enhanced myelopoiesis in vivo, as evidenced by increases in progenitor cell numbers and proliferative activity in the spleen 5 days after MI. The frequency of CD4+ T-cells-producing factors that promote myelopoiesis increased within the spleen of Treg-depleted mice. Moreover, depletion of Tregs caused a proinflammatory bias in splenic Ly6Chigh monocytes, which showed predominantly upregulated expression of IFN-γ responsive genes after MI. Our results indicate that conventional CD4+ T-cells promote and Tregs attenuate splenic myelopoiesis and proinflammatory differentiation of monocytes.
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Affiliation(s)
- Nadine Gladow
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany.
- Comprehensive Heart Failure Centre, University Clinic Würzburg, Würzburg, Germany.
| | - Claudia Hollmann
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | | | - Xin Ding
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Centre, University Clinic Würzburg, Würzburg, Germany
| | - Matthias Burkard
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany
| | - Sabrina Uehlein
- Department of Cardiology and Angiology, Hannover Medical School, Hannover, Germany
| | - Richa Bharti
- TUM Campus, Straubing for Biotechnology and Sustainability, Weihenstephan-Triesdorf University of Applied Sciences, Straubing, Germany
| | - Konrad Förstner
- ZB MED-Information Centre for Life Sciences, Cologne, Germany
- Faculty of Information Science and Communication Studies, Cologne University of Applied Sciences, Cologne, Germany
| | - Thomas Kerkau
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Niklas Beyersdorf
- Institute for Virology and Immunobiology, University of Würzburg, Würzburg, Germany
| | - Stefan Frantz
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Centre, University Clinic Würzburg, Würzburg, Germany
| | - Gustavo Ramos
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Centre, University Clinic Würzburg, Würzburg, Germany
| | - Ulrich Hofmann
- Department of Internal Medicine I, University Clinic Würzburg, Würzburg, Germany
- Comprehensive Heart Failure Centre, University Clinic Würzburg, Würzburg, Germany
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Gupta J, Taneja S, Bharti R, Bhalla V, Jain A. Effect of laser bleaching, ultrasonic scaling and powered tooth brushing on surface roughness and bacterial adherence of class V composite restorations. J Oral Biol Craniofac Res 2023; 13:429-435. [PMID: 37274090 PMCID: PMC10233206 DOI: 10.1016/j.jobcr.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/25/2023] [Indexed: 06/06/2023] Open
Abstract
Objective To evaluate and compare the effect of diode laser assisted bleaching, ultrasonic scaling and powered tooth brushing on surface roughness and bacterial adherence on class V cavities restored with composites. Materials and methods A total of one hundred and twenty samples (40 samples each of Brilliant Everglow, Beautifil II and Heytec-N) were prepared in standardized stainless steel molds. The samples were further subdivided into four subgroups i.e. one control group (without any intervention) and three experimental groups - diode laser assisted bleaching, ultrasonic scaling and powered tooth brushing consisting of 10 sample each. Surface roughness was measured quantitatively with the help of 3D Optical Profilometer. For bacterial adherence analysis S. mutans strain (ATCC 25175) was cultured in BHI medium and samples were evaluated for the presence of viable bacteria using the Colony Forming Unit (CFU) count. Results obtained were then tabulated and subjected to statistical analysis. Results Diode laser bleaching caused a significant increase in surface roughness and bacterial adherence with lowest mean change exhibited by Heytec-N followed by Beautifil II and highest by Brilliant Everglow group. Similarly, Ultrasonic scaling increased the surface roughness of all the three tested samples with significant difference between the groups. Powered tooth brushing had no effect on the surface roughness and bacterial adherence of the tested composites. Conclusion Diode assisted laser bleaching and ultrasonic caused significantly higher surface roughness and bacterial adherence values for all the tested composites. It may therefore be recommended to do finishing and polishing of restorations after such procedures.
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Affiliation(s)
| | - S. Taneja
- Department of Conservative Dentistry and Endodontics, ITS Centre for Dental Studies and Research, Ghaziabad, Uttar Pradesh, India
| | - R. Bharti
- Department of Conservative Dentistry and Endodontics, Faculty of Dental Sciences, King George's Medical University, Lucknow, India
| | - V.K. Bhalla
- Department of Conservative Dentistry and Endodontics, ITS Centre for Dental Studies and Research, Ghaziabad, Uttar Pradesh, India
| | - A. Jain
- Department of Oral Pathology, ITS Centre for Dental Studies and Research, Ghaziabad, Uttar Pradesh, India
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Bharti R, Siebert D, Blombach B, Grimm DG. Systematic analysis of the underlying genomic architecture for transcriptional-translational coupling in prokaryotes. NAR Genom Bioinform 2022; 4:lqac074. [PMID: 36186922 PMCID: PMC9514032 DOI: 10.1093/nargab/lqac074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/12/2022] Open
Abstract
Transcriptional-translational coupling is accepted to be a fundamental mechanism of gene expression in prokaryotes and therefore has been analyzed in detail. However, the underlying genomic architecture of the expression machinery has not been well investigated so far. In this study, we established a bioinformatics pipeline to systematically investigated >1800 bacterial genomes for the abundance of transcriptional and translational associated genes clustered in distinct gene cassettes. We identified three highly frequent cassettes containing transcriptional and translational genes, i.e. rplk-nusG (gene cassette 1; in 553 genomes), rpoA-rplQ-rpsD-rpsK-rpsM (gene cassette 2; in 656 genomes) and nusA-infB (gene cassette 3; in 877 genomes). Interestingly, each of the three cassettes harbors a gene (nusG, rpsD and nusA) encoding a protein which links transcription and translation in bacteria. The analyses suggest an enrichment of these cassettes in pathogenic bacterial phyla with >70% for cassette 3 (i.e. Neisseria, Salmonella and Escherichia) and >50% for cassette 1 (i.e. Treponema, Prevotella, Leptospira and Fusobacterium) and cassette 2 (i.e. Helicobacter, Campylobacter, Treponema and Prevotella). These insights form the basis to analyze the transcriptional regulatory mechanisms orchestrating transcriptional-translational coupling and might open novel avenues for future biotechnological approaches.
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Affiliation(s)
- Richa Bharti
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315 Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
| | - Daniel Siebert
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Microbial Biotechnology, Uferstraße 53, 94315 Straubing, Germany
| | - Bastian Blombach
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Microbial Biotechnology, Uferstraße 53, 94315 Straubing, Germany
| | - Dominik G Grimm
- Technical University of Munich, Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Petersgasse 18, 94315 Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315 Straubing, Germany
- SynBiofoundry@TUM, Technical University of Munich, Schulgasse 22, 94315 Straubing, Germany
- Technical University of Munich, Department of Informatics, Boltzmannstr. 3, 85748 Garching, Germany
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Rao ES, Yadav R, Rizwana R, Lalmuanpuia C, Marwaha A, Bharti R, Meena PL. Impact of Nutrition Education on Whole Grains Consumption amongst Primary and Middle School Children in Delhi. fst 2022. [DOI: 10.13189/fst.2022.100202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Madan J, Blonquist T, Rao E, Marwaha A, Mehra J, Bharti R, Sharma N, Samaddar R, Pandey S, Mah E, Shete V, Chu Y, Chen O. Effect of COVID-19 Pandemic-Induced Dietary and Lifestyle Changes and Their Associations with Perceived Health Status and Self-Reported Body Weight Changes in India: A Cross-Sectional Survey. Nutrients 2021; 13:nu13113682. [PMID: 34835938 PMCID: PMC8620355 DOI: 10.3390/nu13113682] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/01/2021] [Accepted: 10/13/2021] [Indexed: 02/07/2023] Open
Abstract
Home confinement during the COVID-19 pandemic is accompanied by dramatic changes in lifestyle and dietary behaviors that can significantly influence health. We conducted an online cross-sectional survey to assess COVID-19 pandemic-induced dietary and lifestyle changes and their association with perceived health status and self-reported body weight changes among 1000 Indian adults in early 2021. Positive improvements in dietary habits, e.g., eating more nutritious (85% of participants) and home-cooked food (89%) and an increase in overall nutrition intake (79%), were observed. Sixty-five percent of participants self-reported increased oat consumption to support immunity. There were some negative changes, e.g., more binge eating (69%), eating more in between meals (67%), and increasing meal portion size (72%). Two-thirds of participants reported no change in lifestyles, whereas 21 and 23% reported an increase, and 13 and 10% reported a decrease in physical activity and sleep, respectively. Overall, 64 and 65% of participants reported an improvement in perceived health and an increase in body weight during the COVID-19 period compared to pre-COVID-19, respectively. The top motivations for improving dietary habits included improving physical and mental health and building immunity. In conclusion, the overall perceived health was improved and there was an increase in self-reported body weight in most participants during COVID-19. Diet emerged as the most crucial determinant for these changes.
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Affiliation(s)
- Jagmeet Madan
- Sir Vithaldas Thackersey College of Home Science (Autonomous), Shreemati Nathibai Damodar Thackersey Women’s University, Mumbai 400049, India;
| | - Traci Blonquist
- Biofortis Research, Merieux NutriSciences, Addison, IL 60101, USA; (T.B.); (E.M.)
| | - Eram Rao
- Department of Food Technology, Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi 110075, India;
| | - Ankita Marwaha
- PepsiCo, Inc., Gurugram 122022, India; (J.M.); (R.B.); (N.S.)
- Correspondence: (A.M.); (O.C.)
| | - Joshya Mehra
- PepsiCo, Inc., Gurugram 122022, India; (J.M.); (R.B.); (N.S.)
| | - Richa Bharti
- PepsiCo, Inc., Gurugram 122022, India; (J.M.); (R.B.); (N.S.)
| | - Nishi Sharma
- PepsiCo, Inc., Gurugram 122022, India; (J.M.); (R.B.); (N.S.)
| | | | | | - Eunice Mah
- Biofortis Research, Merieux NutriSciences, Addison, IL 60101, USA; (T.B.); (E.M.)
| | - Varsha Shete
- PepsiCo, Inc., Barrington, IL 60010, USA; (V.S.); (Y.C.)
| | - YiFang Chu
- PepsiCo, Inc., Barrington, IL 60010, USA; (V.S.); (Y.C.)
| | - Oliver Chen
- Biofortis Research, Merieux NutriSciences, Addison, IL 60101, USA; (T.B.); (E.M.)
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA 02111, USA
- Correspondence: (A.M.); (O.C.)
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Bharti R, Marwaha A, Badshah T, Sengupta R, Barmi B, Rao E, Madan J, Bhatia B. Effectiveness of a Nutritional Education Intervention Focussed on Iron among School Children in National Capital Region and Mumbai. J Clin Diagn Res 2021. [DOI: 10.7860/jcdr/2021/46024.14806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Introduction: Anaemia is a major health problem in India. Various studies mention poor nutrition knowledge and education as main factors of malnutrition. Aim: This study aims at assessing the effect of nutritional education on iron among school children. Materials and Methods: A cross-sectional interventional study to improve nutrition literacy in schools was undertaken from April 2018 to February 2019. The outreach platform used was Eat Right School program by Food Safety and Standards Authority of India (FSSAI). A study tool employed was data collection using self-developed questionnaire for pre and post-intervention knowledge assessment. School children from Delhi NCR and Mumbai participated in this study. Knowledge intervention was done on 5 key elements related to iron including role, sources, iron deficiency anaemia, iron absorption and knowledge of fortification. Chi-squared test (α=0.05) was applied for comparison. Results: It was found that 54% (n=18,626) of school children studied were in the age group 11-14 years. From 27355 participants who reported the gender, 58.1% (n=15899) were boys and 41.9% (n=11456) girls. Comparison of pre and post-intervention assessment revealed that percentage of students knowing importance/role of iron increased from 27.30% to 59.50%, iron deficiency anaemia from 34.03% to 59.85%, sources of iron from 25.20% to 51.70%, iron absorption from 36.00% to 61.2% and knowledge of fortification from 55.4% to 76.9%. Thus, significant shift (p≤0.001) in all the parameters was observed; improvement in scores ranged from 21.5% to 32.20% with highest increase seen in understanding the role of iron. Conclusion: Results of the study reject the null hypothesis leading to acceptance of alternate hypothesis. The alternate hypothesis highlights the role of nutrition education in improving the nutritional literacy of school children in the area of iron and iron deficiency anaemia. Results of the current study increased the knowledge of children on all parameters related to iron education module. Thus, nutritional literacy is imperative in improving nutritional status and adolescent age-group is the window of opportunity to correct it.
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Genze N, Bharti R, Grieb M, Schultheiss SJ, Grimm DG. Accurate machine learning-based germination detection, prediction and quality assessment of three grain crops. Plant Methods 2020; 16:157. [PMID: 33353559 PMCID: PMC7754596 DOI: 10.1186/s13007-020-00699-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/11/2020] [Indexed: 05/03/2023]
Abstract
BACKGROUND Assessment of seed germination is an essential task for seed researchers to measure the quality and performance of seeds. Usually, seed assessments are done manually, which is a cumbersome, time consuming and error-prone process. Classical image analyses methods are not well suited for large-scale germination experiments, because they often rely on manual adjustments of color-based thresholds. We here propose a machine learning approach using modern artificial neural networks with region proposals for accurate seed germination detection and high-throughput seed germination experiments. RESULTS We generated labeled imaging data of the germination process of more than 2400 seeds for three different crops, Zea mays (maize), Secale cereale (rye) and Pennisetum glaucum (pearl millet), with a total of more than 23,000 images. Different state-of-the-art convolutional neural network (CNN) architectures with region proposals have been trained using transfer learning to automatically identify seeds within petri dishes and to predict whether the seeds germinated or not. Our proposed models achieved a high mean average precision (mAP) on a hold-out test data set of approximately 97.9%, 94.2% and 94.3% for Zea mays, Secale cereale and Pennisetum glaucum respectively. Further, various single-value germination indices, such as Mean Germination Time and Germination Uncertainty, can be computed more accurately with the predictions of our proposed model compared to manual countings. CONCLUSION Our proposed machine learning-based method can help to speed up the assessment of seed germination experiments for different seed cultivars. It has lower error rates and a higher performance compared to conventional and manual methods, leading to more accurate germination indices and quality assessments of seeds.
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Affiliation(s)
- Nikita Genze
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Schulgasse 22, 94315, Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315, Straubing, Germany
| | - Richa Bharti
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Schulgasse 22, 94315, Straubing, Germany
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315, Straubing, Germany
| | - Michael Grieb
- Technology and Support Centre in the Centre of Excellence for Renewable Resources (TFZ), Schulgasse 20, 94315, Straubing, Germany
| | | | - Dominik G Grimm
- Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Bioinformatics, Schulgasse 22, 94315, Straubing, Germany.
- Weihenstephan-Triesdorf University of Applied Sciences, Petersgasse 18, 94315, Straubing, Germany.
- Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748, Garching, Germany.
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Melms H, Herrmann M, Förstner K, Bharti R, Schneider D, Mentrup B, Rudert M, Schlagenhauf U, Jakob F, Graser S. Novel molecular cues for dental defects in hypophosphatasia. Exp Cell Res 2020; 392:112026. [PMID: 32333908 DOI: 10.1016/j.yexcr.2020.112026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 01/09/2023]
Abstract
Mineralization disorders with a broad range of etiological factors represent a huge challenge in dental diagnosis and therapy. Hypophosphatasia (HPP) belongs to the rare diseases affecting predominantly mineralized tissues, bones and teeth, and occurs due to mutations in the ALPL gene, which encodes tissue-nonspecific alkaline phosphatase (TNAP). Here we analyzed stem cells from bone marrow (BMSCs), dental pulp (DPSCs) and periodontal ligament (PDLSCs) in the absence and presence of efficient TNAP inhibitors. The differentiation capacity, expression of surface markers, and gene expression patterns of donor-matched dental cells were compared during this in vitro study. Differentiation assays showed efficient osteogenic but low adipogenic differentiation (aD) capacity of PDLSCs and DPSCs. TNAP inhibitor treatment completely abolished the mineralization process during osteogenic differentiation (oD). RNA-seq analysis in PDLSCs, comparing oD with and without TNAP inhibitor levamisole, showed clustered regulation of candidate molecular mechanisms that putatively impaired osteogenesis and mineralization, disequilibrated ECM production and turnover, and propagated inflammation. Combined alteration of cementum formation, mineralization, and elastic attachment of teeth to cementum via elastic fibers may explain dental key problems in HPP. Using this in vitro model of TNAP deficiency in DPSCs and PDLSCs, we provide novel putative target areas for research on molecular cues for specific dental problems in HPP.
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Affiliation(s)
- Hannah Melms
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany; Department of Conservative Dentistry, School of Dental Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Marietta Herrmann
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany; IZKF Research Group Tissue Regeneration in Musculoskeletal Diseases, University Hospital Würzburg, Würzburg, Germany
| | - Konrad Förstner
- Core Unit SysMed, University of Würzburg, Würzburg, Germany; Institute for Information Sciences, University of Applied Sciences, Cologne, Germany; ZB MED - Information Centre for Life Science, Cologne, Germany
| | - Richa Bharti
- Core Unit SysMed, University of Würzburg, Würzburg, Germany; Department for Bioinformatics, Weihenstephan-Triesdorf University of Applied Sciences, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
| | - Doris Schneider
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany
| | - Birgit Mentrup
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany; Department for Regenerative Musculoskeletal Medicine, University of Münster, Germany
| | - Maximilian Rudert
- Department of Orthopaedics, Orthopedic Department König-Ludwig-Haus, University of Würzburg, Würzburg, Germany
| | - Ulrich Schlagenhauf
- Department of Periodontology, University Clinics Würzburg, Würzburg, Germany
| | - Franz Jakob
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany
| | - Stephanie Graser
- Bernhard-Heine-Center for Locomotion Research, University of Würzburg, Würzburg, Germany.
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Moltzau Anderson J, Lipinski S, Sommer F, Pan WH, Boulard O, Rehman A, Falk-Paulsen M, Stengel ST, Aden K, Häsler R, Bharti R, Künzel S, Baines JF, Chamaillard M, Rosenstiel P. NOD2 Influences Trajectories of Intestinal Microbiota Recovery After Antibiotic Perturbation. Cell Mol Gastroenterol Hepatol 2020; 10:365-389. [PMID: 32289499 PMCID: PMC7327897 DOI: 10.1016/j.jcmgh.2020.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Loss-of-function variants in nucleotide-binding oligomerization domain-containing protein 2 (NOD2) impair the recognition of the bacterial cell wall component muramyl-dipeptide and are associated with an increased risk for developing Crohn's disease. Likewise, exposure to antibiotics increases the individual risk for developing inflammatory bowel disease. Here, we studied the long-term impact of NOD2 on the ability of the gut bacterial and fungal microbiota to recover after antibiotic treatment. METHODS Two cohorts of 20-week-old and 52-week-old wild-type (WT) C57BL/6J and NOD2 knockout (Nod2-KO) mice were treated with broad-spectrum antibiotics and fecal samples were collected to investigate temporal dynamics of the intestinal microbiota (bacteria and fungi) using 16S ribosomal RNA and internal transcribed spacer 1 sequencing. In addition, 2 sets of germ-free WT mice were colonized with either WT or Nod2-KO after antibiotic donor microbiota and the severity of intestinal inflammation was monitored in the colonized mice. RESULTS Antibiotic exposure caused long-term shifts in the bacterial and fungal community composition. Genetic ablation of NOD2 was associated with delayed body weight gain after antibiotic treatment and an impaired recovery of the bacterial gut microbiota. Transfer of the postantibiotic fecal microbiota of Nod2-KO mice induced an intestinal inflammatory response in the colons of germ-free recipient mice compared with respective microbiota from WT controls based on histopathology and gene expression analyses. CONCLUSIONS Our data show that the bacterial sensor NOD2 contributes to intestinal microbial community composition after antibiotic treatment and may add to the explanation of how defects in the NOD2 signaling pathway are involved in the etiology of Crohn's disease.
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Affiliation(s)
| | | | - Felix Sommer
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Wei-Hung Pan
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Olivier Boulard
- University of Lille, Centre national de la recherche scientifique, Inserm, Centre Hospitalier Universitaire de Lille Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | | | | | | | - Konrad Aden
- Institute of Clinical Molecular Biology, Kiel, Germany,First Medical Department, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Kiel, Germany
| | - Sven Künzel
- Evolutionary Genomics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - John F. Baines
- Institute for Experimental Medicine, Christian-Albrechts-University, Kiel, Germany,Evolutionary Genomics, Max-Planck-Institute for Evolutionary Biology, Plön, Germany
| | - Mathias Chamaillard
- University of Lille, Centre national de la recherche scientifique, Inserm, Centre Hospitalier Universitaire de Lille Lille, Institut Pasteur de Lille, Centre d'Infection et d'Immunité de Lille, Lille, France
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Kiel, Germany,Correspondence Address correspondence to: Philip Rosenstiel, MD, Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Rosalind-Franklin-Str. 12, Kiel D-24105, Germany. fax: (49) 4315971842.
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Bharti R, Grimm DG. Current challenges and best-practice protocols for microbiome analysis. Brief Bioinform 2019; 22:178-193. [PMID: 31848574 PMCID: PMC7820839 DOI: 10.1093/bib/bbz155] [Citation(s) in RCA: 209] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 10/23/2019] [Accepted: 11/06/2019] [Indexed: 12/15/2022] Open
Abstract
Analyzing the microbiome of diverse species and environments using next-generation sequencing techniques has significantly enhanced our understanding on metabolic, physiological and ecological roles of environmental microorganisms. However, the analysis of the microbiome is affected by experimental conditions (e.g. sequencing errors and genomic repeats) and computationally intensive and cumbersome downstream analysis (e.g. quality control, assembly, binning and statistical analyses). Moreover, the introduction of new sequencing technologies and protocols led to a flood of new methodologies, which also have an immediate effect on the results of the analyses. The aim of this work is to review the most important workflows for 16S rRNA sequencing and shotgun and long-read metagenomics, as well as to provide best-practice protocols on experimental design, sample processing, sequencing, assembly, binning, annotation and visualization. To simplify and standardize the computational analysis, we provide a set of best-practice workflows for 16S rRNA and metagenomic sequencing data (available at https://github.com/grimmlab/MicrobiomeBestPracticeReview).
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Affiliation(s)
- Richa Bharti
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
| | - Dominik G Grimm
- Weihenstephan-Triesdorf University of Applied Sciences and Technical University of Munich, TUM Campus Straubing for Biotechnology and Sustainability, Straubing, Germany
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11
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Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, Schulte B, Schulte D, Franke A, Nikolaus S, Schroeder JO, Vandeputte D, Raes J, Szymczak S, Waetzig GH, Zeuner R, Schmitt-Kopplin P, Kaleta C, Schreiber S, Rosenstiel P. Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases. Gastroenterology 2019; 157:1279-1292.e11. [PMID: 31326413 DOI: 10.1053/j.gastro.2019.07.025] [Citation(s) in RCA: 148] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Altered interactions between the mucosal immune system and intestinal microbiota contribute to pathogenesis of inflammatory bowel diseases (IBD). It is not clear how inhibitors of cytokines, such as antagonists of tumor necrosis factor (anti-TNF), affect the intestinal microbiome. We investigated the effects of anti-TNF agents on gut microbe community structure and function in a longitudinal 2-step study of patients with IBD. We correlated our findings with outcomes of treatment and investigated patterns of metabolites in fecal samples before and after anti-TNF therapy. METHODS We performed a prospective study of 2 cohorts of patients in Germany; the discovery cohort comprised 12 patients with IBD, 17 patients with rheumatic disease, and 19 healthy individuals (controls); fecal samples were collected at baseline and 2, 6, and 30 weeks after induction of anti-TNF therapy. The validation cohort comprised 23 patients with IBD treated with anti-TNF or vedolizumab (anti-α4β7 integrin) and 99 healthy controls; fecal samples were collected at baseline and at weeks 2, 6, and 14. Fecal microbiota were analyzed by V3-V4 16S ribosomal RNA gene amplicon sequencing. Clinical response and remission were determined by clinical disease activity scores. Metabolic network reconstruction and associated fecal metabolite level inference was performed in silico using the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. Metabolomic analyses of fecal samples from a subset of patients were performed to validate metabolites associated with treatment outcomes. RESULTS Anti-TNF therapy shifted the diversity of fecal microbiota in patients with IBD, but not with rheumatic disease, toward that of controls. Across timepoints, diversity indices did not vary significantly between patients with IBD who did or did not achieve clinical remission after therapy. In contrast, in silico modeling of metabolic interactions between gut microbes found metabolite exchange to be significantly reduced at baseline in fecal samples from patients with IBD and to be associated with later clinical remission. Predicted levels of butyrate and substrates involved in butyrate synthesis (ethanol or acetaldehyde) were significantly associated with clinical remission following anti-TNF therapy, verified by fecal metabolomic analyses. CONCLUSIONS Metabolic network reconstruction and assessment of metabolic profiles of fecal samples might be used to identify patients with IBD likely to achieve clinical remission following anti-TNF therapy and increase our understanding of the heterogeneity of IBD.
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Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Silvio Waschina
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wei-Hung Pan
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Alejandro Mena Nunez
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Zimmerman
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Bethge
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Berenice Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dominik Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johann Oltmann Schroeder
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Doris Vandeputte
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Jeroen Raes
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, University of Kiel, Kiel, Germany
| | | | - Rainald Zeuner
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
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12
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Schropp V, Rohde J, Rovituso DM, Jabari S, Bharti R, Kuerten S. Contribution of LTi and T H17 cells to B cell aggregate formation in the central nervous system in a mouse model of multiple sclerosis. J Neuroinflammation 2019; 16:111. [PMID: 31138214 PMCID: PMC6540524 DOI: 10.1186/s12974-019-1500-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/06/2019] [Indexed: 01/26/2023] Open
Abstract
Background In a subgroup of patients suffering from progressive multiple sclerosis (MS), which is an inflammation-mediated neurodegenerative disease of the central nervous system (CNS), B cell aggregates were discovered within the meninges. Occurrence of these structures was associated with a more severe disease course and cortical histopathology. We have developed the B cell-dependent MP4-induced experimental autoimmune encephalomyelitis (EAE) as a mouse model to mimic this trait of the human disease. The aim of this study was to determine a potential role of lymphoid tissue inducer (LTi) and TH17 cells in the process of B cell aggregate formation in the MP4 model. Methods We performed flow cytometry of cerebellar and splenic tissue of MP4-immunized mice in the acute and chronic stage of the disease to analyze the presence of CD3−CD5−CD4+RORγt+ LTi and CD3+CD5+CD4+RORγt+ TH17 cells. Myelin oligodendrocyte glycoprotein (MOG):35–55-induced EAE was used as B cell-independent control model. We further determined the gene expression profile of B cell aggregates using laser capture microdissection, followed by RNA sequencing. Results While we were able to detect LTi cells in the embryonic spleen and adult intestine, which served as positive controls, there was no evidence for the existence of such a population in acute or chronic EAE in neither of the two models. Yet, we detected CD3−CD5−CD4−RORγt+ innate lymphoid cells (ILCs) and TH17 cells in the CNS, the latter especially in the chronic stage of MP4-induced EAE. Moreover, we observed a unique gene signature in CNS B cell aggregates compared to draining lymph nodes of MP4-immunized mice and to cerebellum as well as draining lymph nodes of mice with MOG:35–55-induced EAE. Conclusion The absence of LTi cells in the cerebellum suggests that other cells might take over the function as an initiator of lymphoid tissue formation in the CNS. Overall, the development of ectopic lymphoid organs is a complex process based on an interplay between several molecules and signals. Here, we propose some potential candidates, which might be involved in the formation of B cell aggregates in the CNS of MP4-immunized mice.
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Affiliation(s)
- Verena Schropp
- Institute of Anatomy, Chair of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jörn Rohde
- Institute of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Damiano M Rovituso
- Institute of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Samir Jabari
- Institute of Anatomy, Chair of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany
| | - Stefanie Kuerten
- Institute of Anatomy, Chair of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg (FAU), Erlangen, Germany.
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13
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Tanwar G, Mazumder AG, Bhardwaj V, Kumari S, Bharti R, Yamini, Singh D, Das P, Purohit R. Target identification, screening and in vivo evaluation of pyrrolone-fused benzosuberene compounds against human epilepsy using Zebrafish model of pentylenetetrazol-induced seizures. Sci Rep 2019; 9:7904. [PMID: 31133639 PMCID: PMC6536720 DOI: 10.1038/s41598-019-44264-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/14/2019] [Indexed: 11/22/2022] Open
Abstract
Pyrrolone-fused benzosuberene (PBS) compounds were semi-synthesized from α,β,γ-Himachalenes extracted from the essential oil of Cedrus deodara following amino-vinyl-bromide substituted benzosuberenes as intermediates. These PBSs compounds classified as an attractive source of therapeutics. The α-isoform of PI3K which is a pivotal modulator of PI3K/AKT/mTOR signaling pathway, responsible for neurological disorders like epilepsy, found as a potential target molecule against these 17 semi-synthesized PBS compounds using in silico ligand-based pharmacophore mapping and target screening. The compounds screened using binding affinities, ADMET properties, and toxicity that were accessed by in silico docking simulations and pharmacokinetics profiling. Ultimately two compounds viz., PBS-8 and PBS-9 were selected for further in vivo evaluation using a zebrafish (Danio rerio) model of pentylenetetrazol (PTZ)-induced clonic convulsions. Additionally, gene expression studies performed for the genes of the PI3K/AKT/mTOR pathway which further validated our results. In conclusion, these findings suggested that PBS-8 is a promising candidate that could bedeveloped as a potential antiepileptic.
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Affiliation(s)
- Garima Tanwar
- Structural Bioinformatics Laboratory, Biotechnology division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
| | - Arindam Ghosh Mazumder
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Vijay Bhardwaj
- Structural Bioinformatics Laboratory, Biotechnology division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India
| | - Savita Kumari
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Richa Bharti
- Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Yamini
- Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Damanpreet Singh
- Pharmacology and Toxicology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Pralay Das
- Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Rituraj Purohit
- Structural Bioinformatics Laboratory, Biotechnology division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India.
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14
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Bal Reddy C, Ram S, Kumar A, Bharti R, Das P. Supported Palladium Nanoparticles that Catalyze Aminocarbonylation of Aryl Halides with Amines using Oxalic Acid as a Sustainable CO Source. Chemistry 2019; 25:4067-4071. [PMID: 30730074 DOI: 10.1002/chem.201900271] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/06/2019] [Indexed: 01/13/2023]
Abstract
Polystyrene-supported palladium (Pd@PS) nanoparticles (NPs) have been used to catalyze the aminocarbonylation of aryl halides with amines using oxalic acid as a CO source for the first-time for the synthesis of amides. Furthermore, o-iodoacetophenones participated in amidation and cyclization reactions to give isoindolinones in a single step following a concerted approach. Oxalic acid has been used as a safe, environmentally benign and operationally simple ex situ sustainable CO source under double-layer-vial (DLV) system for different aminocarbonylation reactions. Catalyst stability under a CO environment is a challenging task, however, Pd@PS was found to be recyclable and applicable for a vast substrate scope avoiding regeneration steps. Easy handling of oxalic acid, additive and base-free CO generation, catalyst stability and effortless catalyst separation from the reaction mixture by filtration and introduce of DLV are the added advantages to make the overall process a sustainable approach.
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Affiliation(s)
- C Bal Reddy
- Natural Product Chemistry & Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.,Academy of Scientific & Innovative Research, New Delhi, 110025, India
| | - Shankar Ram
- Natural Product Chemistry & Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.,Academy of Scientific & Innovative Research, New Delhi, 110025, India
| | - Ajay Kumar
- Natural Product Chemistry & Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India
| | - Richa Bharti
- Natural Product Chemistry & Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.,Academy of Scientific & Innovative Research, New Delhi, 110025, India
| | - Pralay Das
- Natural Product Chemistry & Process Development Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, HP, India.,Academy of Scientific & Innovative Research, New Delhi, 110025, India
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15
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Balasubramanian S, Skaf J, Holzgrabe U, Bharti R, Förstner KU, Ziebuhr W, Humeida UH, Abdelmohsen UR, Oelschlaeger TA. A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. Front Microbiol 2018; 9:1473. [PMID: 30050506 PMCID: PMC6050364 DOI: 10.3389/fmicb.2018.01473] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 06/13/2018] [Indexed: 01/09/2023] Open
Abstract
Staphylococcus epidermidis, the common inhabitant of human skin and mucosal surfaces has emerged as an important pathogen in patients carrying surgical implants and medical devices. Entering the body via surgical sites and colonizing the medical devices through formation of multi-layered biofilms leads to refractory and persistent device-related infections (DRIs). Staphylococci organized in biofilms are more tolerant to antibiotics and immune responses, and thus are difficult-to-treat. The consequent morbidity and mortality, and economic losses in health care systems has strongly necessitated the need for development of new anti-bacterial and anti-biofilm-based therapeutics. In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal, and silicone surfaces. A bioassay-guided fractionation was performed to isolate the active compound (SKC3) from the crude SBT348 extract. Our results demonstrated that SKC3 effectively inhibits the growth (MIC: 31.25 μg/ml) and biofilm formation (sub-MIC range: 1.95–<31.25 μg/ml) of S. epidermidis RP62A in vitro. Chemical characterization of SKC3 by heat and enzyme treatments, and mass spectrometry (HRMS) revealed its heat-stable and non-proteinaceous nature, and high molecular weight (1258.3 Da). Cytotoxicity profiling of SKC3 in vitro on mouse fibroblast (NIH/3T3) and macrophage (J774.1) cell lines, and in vivo on the greater wax moth larvae Galleria mellonella revealed its non-toxic nature at the effective dose. Transcriptome analysis of SKC3 treated S. epidermidis RP62A has further unmasked its negative effect on central metabolism such as carbon flux as well as, amino acid, lipid, and energy metabolism. Taken together, these findings suggest a potential of SKC3 as a putative drug to prevent staphylococcal DRIs.
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Affiliation(s)
| | - Joseph Skaf
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Ulrike Holzgrabe
- Institute of Pharmacy and Food Chemistry, University of Würzburg, Würzburg, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Konrad U Förstner
- Core Unit Systems Medicine, University of Würzburg, Würzburg, Germany
| | - Wilma Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Ute H Humeida
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Usama R Abdelmohsen
- Department of Pharmacognosy, Faculty of Pharmacy, Minia University, Minia, Egypt
| | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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16
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Bury S, Soundararajan M, Bharti R, von Bünau R, Förstner KU, Oelschlaeger TA. The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ. Front Microbiol 2018; 9:929. [PMID: 29896160 PMCID: PMC5987069 DOI: 10.3389/fmicb.2018.00929] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/20/2018] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin (Stx) producing E. coli (STEC) such as Enterohemorrhagic E. coli (EHEC) are the major cause of foodborne illness in humans. In vitro studies showed the probiotic Escherichia coli strain Nissle 1917 (EcN) to efficiently inhibit the production of Stx. Life threatening EHEC strains as for example the serotype O104:H4, responsible for the great outbreak in 2011 in Germany, evolutionary developed from certain E. coli strains which got infected by stx2-encoding lambdoid phages turning the E. coli into lysogenic and subsequently Stx producing strains. Since antibiotics induce stx genes and Stx production, EHEC infected persons are not recommended to be treated with antibiotics. Therefore, EcN might be an alternative medication. However, because even commensal E. coli strains might be converted into Stx-producers after becoming host to a stx encoding prophage, we tested EcN for stx-phage genome integration. Our experiments revealed the resistance of EcN toward not only stx-phages but also against lambda-phages. This resistance was not based on the lack of or by mutated phage receptors. Rather it involved the expression of a phage repressor (pr) gene of a defective prophage in EcN which was able to partially protect E. coli K-12 strain MG1655 against stx and lambda phage infection. Furthermore, we observed EcN to inactivate phages and thereby to protect E. coli K-12 strains against infection by stx- as well as lambda-phages. Inactivation of lambda-phages was due to binding of lambda-phages to LamB of EcN whereas inactivation of stx-phages was caused by a thermostable protein of EcN. These properties together with its ability to inhibit Stx production make EcN a good candidate for the prevention of illness caused by EHEC and probably for the treatment of already infected people.
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Affiliation(s)
- Susanne Bury
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | | | - Richa Bharti
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | | | - Konrad U Förstner
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Tobias A Oelschlaeger
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
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17
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Bail K, Notz Q, Rovituso DM, Schampel A, Wunsch M, Koeniger T, Schropp V, Bharti R, Scholz CJ, Foerstner KU, Kleinschnitz C, Kuerten S. Differential effects of FTY720 on the B cell compartment in a mouse model of multiple sclerosis. J Neuroinflammation 2017; 14:148. [PMID: 28738885 PMCID: PMC5525315 DOI: 10.1186/s12974-017-0924-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/14/2017] [Indexed: 12/11/2022] Open
Abstract
Background MP4-induced experimental autoimmune encephalomyelitis (EAE) is a mouse model of multiple sclerosis (MS), which enables targeted research on B cells, currently much discussed protagonists in MS pathogenesis. Here, we used this model to study the impact of the S1P1 receptor modulator FTY720 (fingolimod) on the autoreactive B cell and antibody response both in the periphery and the central nervous system (CNS). Methods MP4-immunized mice were treated orally with FTY720 for 30 days at the peak of disease or 50 days after EAE onset. The subsequent disease course was monitored and the MP4-specific B cell/antibody response was measured by ELISPOT and ELISA. RNA sequencing was performed to determine any effects on B cell-relevant gene expression. S1P1 receptor expression by peripheral T and B cells, B cell subset distribution in the spleen and B cell infiltration into the CNS were studied by flow cytometry. The formation of B cell aggregates and of tertiary lymphoid organs (TLOs) was evaluated by histology and immunohistochemistry. Potential direct effects of FTY720 on B cell aggregation were studied in vitro. Results FTY720 significantly attenuated clinical EAE when treatment was initiated at the peak of EAE. While there was a significant reduction in the number of T cells in the blood after FTY720 treatment, B cells were only slightly diminished. Yet, there was evidence for the modulation of B cell receptor-mediated signaling upon FTY720 treatment. In addition, we detected a significant increase in the percentage of B220+ B cells in the spleen both in acute and chronic EAE. Whereas acute treatment completely abrogated B cell aggregate formation in the CNS, the numbers of infiltrating B cells and plasma cells were comparable between vehicle- and FTY720-treated mice. In addition, there was no effect on already developed aggregates in chronic EAE. In vitro B cell aggregation assays suggested the absence of a direct effect of FTY720 on B cell aggregation. However, FTY720 impacted the evolution of B cell aggregates into TLOs. Conclusions The data suggest differential effects of FTY720 on the B cell compartment in MP4-induced EAE. Electronic supplementary material The online version of this article (doi:10.1186/s12974-017-0924-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kathrin Bail
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Quirin Notz
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Damiano M Rovituso
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Andrea Schampel
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Marie Wunsch
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Tobias Koeniger
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany
| | - Verena Schropp
- Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Richa Bharti
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany
| | - Claus-Juergen Scholz
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany.,LIMES Institute, University of Bonn, Bonn, Germany
| | - Konrad U Foerstner
- Core Unit Systems Medicine, University Hospitals of Würzburg, Würzburg, Germany
| | - Christoph Kleinschnitz
- Department of Neurology, University Hospital Würzburg, Würzburg, Germany.,Department of Neurology, University Hospital Essen, Essen, Germany
| | - Stefanie Kuerten
- Department of Anatomy and Cell Biology, University of Würzburg, Würzburg, Germany. .,Institute of Anatomy and Cell Biology, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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18
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Sommer F, Anderson JM, Bharti R, Raes J, Rosenstiel P. The resilience of the intestinal microbiota influences health and disease. Nat Rev Microbiol 2017. [DOI: 10.1038/nrmicro.2017.58] [Citation(s) in RCA: 460] [Impact Index Per Article: 65.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Bharti R, Reddy CB, Das P. Oxalic Acid as Sustainable CO Source for Pyrrolone-Fused Benzosuberenes Synthesis through Palladium Catalyzed Carbonylative Cyclization. ChemistrySelect 2017. [DOI: 10.1002/slct.201700592] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Richa Bharti
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - C. Bal Reddy
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - Pralay Das
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
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Bhattacherjee D, Thakur V, Sharma S, Kumar S, Bharti R, Reddy CB, Das P. Iodine(III)-Promoted Ring Contractive Cyanation of Exocyclic β-Enaminones for the Synthesis of Cyanocyclopentanones. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201601208] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dhananjay Bhattacherjee
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Vandna Thakur
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Saurabh Sharma
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Sandeep Kumar
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Richa Bharti
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - C. Bal Reddy
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
| | - Pralay Das
- Natural Product Chemistry and Process Development Division; CSIR-Institute of Himalayan Bioresource Technology; Palampur 176061, H.P India
- Academy of Scientific and Innovative Research, New Delhi, India
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21
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Bharti R, Bal Reddy C, Kumar S, Das P. Supported palladium nanoparticle‐catalysed Suzuki–Miyaura cross‐coupling approach for synthesis of aminoarylbenzosuberene analogues from natural precursor. Appl Organomet Chem 2017. [DOI: 10.1002/aoc.3749] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Richa Bharti
- Natural Product Chemistry and Process Development DivisionCSIR‐Institute of Himalayan Bioresource Technology Palampur 176061 HP India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi India
| | - C. Bal Reddy
- Natural Product Chemistry and Process Development DivisionCSIR‐Institute of Himalayan Bioresource Technology Palampur 176061 HP India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi India
| | - Sandeep Kumar
- Natural Product Chemistry and Process Development DivisionCSIR‐Institute of Himalayan Bioresource Technology Palampur 176061 HP India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi India
| | - Pralay Das
- Natural Product Chemistry and Process Development DivisionCSIR‐Institute of Himalayan Bioresource Technology Palampur 176061 HP India
- Academy of Scientific and Innovative Research (AcSIR) New Delhi India
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22
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Ott SJ, Waetzig GH, Rehman A, Moltzau-Anderson J, Bharti R, Grasis JA, Cassidy L, Tholey A, Fickenscher H, Seegert D, Rosenstiel P, Schreiber S. Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection. Gastroenterology 2017; 152:799-811.e7. [PMID: 27866880 DOI: 10.1053/j.gastro.2016.11.010] [Citation(s) in RCA: 393] [Impact Index Per Article: 56.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/03/2016] [Accepted: 11/11/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND & AIMS Fecal microbiota transplantation (FMT) is a highly effective therapy for recurrent Clostridium difficile infection (CDI). However, transferring undefined living bacteria entails uncontrollable risks for infectious and metabolic or malignant diseases, particularly in immunocompromised patients. We investigated whether sterile fecal filtrates (containing bacterial debris, proteins, antimicrobial compounds, metabolic products, and oligonucleotides/DNA), rather than intact microorganisms, are effective in patients with CDI. METHODS We performed a clinical case series to investigate the effects of fecal filtrate transfer (FFT) in 5 patients with symptomatic chronic-relapsing CDI at the Department of Internal Medicine I at the University Hospital Schleswig-Holstein (Kiel, Germany). Patients were followed up for at least 6 months and for up to 33 months. Stool was collected from 5 donors selected by the patients, and fully characterized according to FMT standards. Stool was sterile-filtered to remove small particles and bacteria; the filtrate was transferred to patients in a single administration via nasojejunal tube. Fecal samples were collected from patients before and at 1 week and 6 weeks after FFT. Microbiome, virome, and proteome profiles of donors and patients were compared. RESULTS In all 5 patients, FFT restored normal stool habits and eliminated symptoms of CDI for a minimum period of 6 months. Proteome analyses of selected FFT filtrates showed no obvious protein candidates associated with therapeutic efficacy. 16S ribosomal RNA gene sequencing detected diverse bacterial DNA signatures in the filtrates. Analysis of virus-like particles from a filtrate found to reduce symptoms of CDI showed a complex signature of bacteriophages. Bacterial phylogeny and virome profile analyses of fecal samples from recipients indicated longitudinal changes in microbial and viral community structures after FFT. CONCLUSIONS A preliminary investigation of 5 patients with CDI shows that transfer of sterile filtrates from donor stool (FFT), rather than fecal microbiota, can be sufficient to restore normal stool habits and eliminate symptoms. This finding indicates that bacterial components, metabolites, or bacteriophages mediate many of the effects of FMT, and that FFT might be an alternative approach, particularly for immunocompromised patients.
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Affiliation(s)
- Stephan J Ott
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Ateequr Rehman
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Jacqueline Moltzau-Anderson
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany; Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Juris A Grasis
- Department of Biology, San Diego State University, San Diego, California
| | - Liam Cassidy
- Institute of Experimental Medicine, University of Kiel, Kiel, Germany
| | - Andreas Tholey
- Institute of Experimental Medicine, University of Kiel, Kiel, Germany
| | - Helmut Fickenscher
- Institute for Infection Medicine, University of Kiel and University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany
| | - Stefan Schreiber
- Department of Internal Medicine I, University Hospital Schleswig-Holstein, Kiel, Germany; Institute of Clinical Molecular Biology, University of Kiel, Kiel, Germany.
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23
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Tschurtschenthaler M, Adolph TE, Ashcroft JW, Niederreiter L, Bharti R, Saveljeva S, Bhattacharyya J, Flak MB, Shih DQ, Fuhler GM, Parkes M, Kohno K, Iwawaki T, Janneke van der Woude C, Harding HP, Smith AM, Peppelenbosch MP, Targan SR, Ron D, Rosenstiel P, Blumberg RS, Kaser A. Defective ATG16L1-mediated removal of IRE1α drives Crohn's disease-like ileitis. J Exp Med 2017; 214:401-422. [PMID: 28082357 PMCID: PMC5294857 DOI: 10.1084/jem.20160791] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 10/02/2016] [Accepted: 12/07/2016] [Indexed: 02/02/2023] Open
Abstract
ATG16L1T300A, a major risk polymorphism in Crohn's disease (CD), causes impaired autophagy, but it has remained unclear how this predisposes to CD. In this study, we report that mice with Atg16l1 deletion in intestinal epithelial cells (IECs) spontaneously develop transmural ileitis phenocopying ileal CD in an age-dependent manner, driven by the endoplasmic reticulum (ER) stress sensor IRE1α. IRE1α accumulates in Paneth cells of Atg16l1ΔIEC mice, and humans homozygous for ATG16L1T300A exhibit a corresponding increase of IRE1α in intestinal epithelial crypts. In contrast to a protective role of the IRE1β isoform, hyperactivated IRE1α also drives a similar ileitis developing earlier in life in Atg16l1;Xbp1ΔIEC mice, in which ER stress is induced by deletion of the unfolded protein response transcription factor XBP1. The selective autophagy receptor optineurin interacts with IRE1α, and optineurin deficiency amplifies IRE1α levels during ER stress. Furthermore, although dysbiosis of the ileal microbiota is present in Atg16l1;Xbp1ΔIEC mice as predicted from impaired Paneth cell antimicrobial function, such structural alteration of the microbiota does not trigger ileitis but, rather, aggravates dextran sodium sulfate-induced colitis. Hence, we conclude that defective autophagy in IECs may predispose to CD ileitis via impaired clearance of IRE1α aggregates during ER stress at this site.
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Affiliation(s)
- Markus Tschurtschenthaler
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Timon E. Adolph
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Jonathan W. Ashcroft
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Lukas Niederreiter
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Richa Bharti
- Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany
| | - Svetlana Saveljeva
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Joya Bhattacharyya
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Magdalena B. Flak
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - David Q. Shih
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Gwenny M. Fuhler
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, 3015 CE Rotterdam, Netherlands
| | - Miles Parkes
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Kenji Kohno
- Laboratory of Molecular and Cell Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Takao Iwawaki
- Division of Cell Medicine, Department of Life Science, Medical Research Institute, Kanazawa Medical University, Kahoku, Ishikawa 920-0293, Japan
| | - C. Janneke van der Woude
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, 3015 CE Rotterdam, Netherlands
| | - Heather P. Harding
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Andrew M. Smith
- Eastman Dental Institute, University College London, London WC1E 6BT, England, UK
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center Rotterdam, 3015 CE Rotterdam, Netherlands
| | - Stephan R. Targan
- Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - David Ron
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Philip Rosenstiel
- Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, D-24105 Kiel, Germany
| | - Richard S. Blumberg
- Division of Gastroenterology, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, England, UK
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Guha NR, Thakur V, Bhattacherjee D, Bharti R, Das P. Supported Rhodium Nanoparticle-Catalyzed Intermolecular Regioselective Carbonylative Cyclization of Terminal Alkynes using Oxalic Acid as Sustainable C1Source. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600451] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Nitul Ranjan Guha
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - Vandna Thakur
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - Dhananjay Bhattacherjee
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - Richa Bharti
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
| | - Pralay Das
- Natural Product Chemistry & Process Development; CSIR-Institute of Himalayan Bioresource Technology; Palampur - 176061, H.P. India
- Academy of Scientific & Innovative Research (AcSIR); New Delhi India
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25
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Aden K, Rehman A, Falk-Paulsen M, Secher T, Kuiper J, Tran F, Pfeuffer S, Sheibani-Tezerji R, Breuer A, Luzius A, Jentzsch M, Häsler R, Billmann-Born S, Will O, Lipinski S, Bharti R, Adolph T, Iovanna JL, Kempster SL, Blumberg RS, Schreiber S, Becher B, Chamaillard M, Kaser A, Rosenstiel P. Epithelial IL-23R Signaling Licenses Protective IL-22 Responses in Intestinal Inflammation. Cell Rep 2016; 16:2208-2218. [PMID: 27524624 PMCID: PMC5443566 DOI: 10.1016/j.celrep.2016.07.054] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 02/16/2016] [Accepted: 07/20/2016] [Indexed: 12/28/2022] Open
Abstract
A plethora of functional and genetic studies have suggested a key role for the IL-23 pathway in chronic intestinal inflammation. Currently, pathogenic actions of IL-23 have been ascribed to specific effects on immune cells. Herein, we unveil a protective role of IL-23R signaling. Mice deficient in IL-23R expression in intestinal epithelial cells (Il23R(ΔIEC)) have reduced Reg3b expression, show a disturbed colonic microflora with an expansion of flagellated bacteria, and succumb to DSS colitis. Surprisingly, Il23R(ΔIEC) mice show impaired mucosal IL-22 induction in response to IL-23. αThy-1 treatment significantly deteriorates colitis in Il23R(ΔIEC) animals, which can be rescued by IL-22 application. Importantly, exogenous Reg3b administration rescues DSS-treated Il23R(ΔIEC) mice by recruiting neutrophils as IL-22-producing cells, thereby restoring mucosal IL-22 levels. The study identifies a critical barrier-protective immune pathway that originates from, and is orchestrated by, IL-23R signaling in intestinal epithelial cells.
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Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; First Medical Department, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Maren Falk-Paulsen
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Thomas Secher
- University Toulouse, CNRS, Inserm, CHU Toulouse, UMR 1043-UMR 5282, Centre de Physiopathologie Toulouse Purpan, 31024 Toulouse, France
| | - Jan Kuiper
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Florian Tran
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Steffen Pfeuffer
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Raheleh Sheibani-Tezerji
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Alexandra Breuer
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Anne Luzius
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Marlene Jentzsch
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Robert Häsler
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Susanne Billmann-Born
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Olga Will
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Simone Lipinski
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Timon Adolph
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Juan L Iovanna
- Aix-Marseille University, Institut Paoli-Calmettes, CNRS, Inserm, UMR 1068-UMR 7258, Centre de Recherche en Carcérologie de Marseille, 13273 Marseille, France
| | - Sarah L Kempster
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Richard S Blumberg
- Gastroenterology Division, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany; First Medical Department, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany
| | - Burkhard Becher
- Institute of Experimental Immunology, University of Zurich, 8057 Zurich, Switzerland
| | - Mathias Chamaillard
- University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL, Centre d'Infection et d'Immunité de Lille, 59000 Lille, France
| | - Arthur Kaser
- Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, England, UK
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian Albrechts University and University Hospital Schleswig-Holstein, Campus Kiel, 24105 Kiel, Germany.
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Panja S, Dey G, Bharti R, Kumari K, Maiti TK, Mandal M, Chattopadhyay S. Tailor-Made Temperature-Sensitive Micelle for Targeted and On-Demand Release of Anticancer Drugs. ACS Appl Mater Interfaces 2016; 8:12063-12074. [PMID: 27128684 DOI: 10.1021/acsami.6b03820] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The design of nanomedicines from the tuned architecture polymer is a leading object of immense research in recent years. Here, smart thermoresponsive micelles were prepared from novel architecture four-arm star block copolymers, namely, pentaerythritol polycaprolactone-b-poly(N-isopropylacrylamide) and pentaerythritol polycaprolactone-b-poly(N-vinylcaprolactam). The polymers were synthesized and tagged with folic acid (FA) to render them as efficient cancer cell targeting cargos. FA-conjugated block copolymers were self-assembled to a nearly spherical (ranging from 15 to 170 nm) polymeric micelle (FA-PM) with a sufficiently lower range of critical micelle concentration (0.59 × 10(-2) to 1.52 × 10(-2) mg/mL) suitable for performing as an efficient drug carrier. The blocks show lower critical solution temperature (LCST) ranging from 30 to 39 °C with high DOX-loading content (24.3%, w/w) as compared to that reported for a linear polymer in the contemporary literature. The temperature-induced reduction in size (57%) of the FA-PM enables a high rate of DOX release (78.57% after 24 h) at a temperature above LCST. The DOX release rate has also been tuned by on-demand administration of temperature. The in vitro biocompatibilities of the blank and DOX-loaded FA-PMs have been studied by the MTT assay. The cellular uptake study proves selective internalization of the FA-PM into cancerous cells (C6 glioma) compared that into normal cells (HaCaT). In vivo administration of the DOX-loaded FA-PMs into the C6 glioma rat tumor model resulted in significant accumulation in tumor sites, which drastically inhibited the tumor volume by ∼83.9% with respect to control without any significant systemic toxicity.
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Affiliation(s)
- S Panja
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - G Dey
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - R Bharti
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - K Kumari
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - T K Maiti
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - M Mandal
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
| | - S Chattopadhyay
- Rubber Technology Centre, ‡School of Medical Science and Technology, and §Department of Biotechnology, Indian Institute of Technology , Kharagpur 721302, India
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27
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Parida S, Pal I, Parekh A, Thakur B, Bharti R, Das S, Mandal M. GW627368X inhibits proliferation and induces apoptosis in cervical cancer by interfering with EP4/EGFR interactive signaling. Cell Death Dis 2016; 7:e2154. [PMID: 27010855 PMCID: PMC4823960 DOI: 10.1038/cddis.2016.61] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 02/07/2016] [Accepted: 02/19/2016] [Indexed: 12/25/2022]
Abstract
PGE2, the major product of cyclooxygenases implicated in carcinogenesis, is significantly upregulated in cervical cancer. PGE2 via prostanoid receptor EP4 stimulates proliferation and motility while inhibiting apoptosis and immune surveillance. It promotes angiogenesis by stimulating the production of pro-angiogenic factors. The present study demonstrates GW627368X, a highly selective competitive EP4 antagonist, which hinders cervical cancer progression by inhibiting EP4/epithelial growth factor receptor (EGFR) interactive signaling. GW627368X reduced protein kinase A (PKA) phosphorylation which in turn leads to decreased cAMP response element-binding protein (CREB) activation. Decreased PKA phosphorylation also directly enhanced Bax activity and in part reduced glycogen synthase kinase 3 (GSK3)β phosphorylation. Owing to the interactive signaling between EP4 and EGFR, GW627368X lowered EGFR phosphorylation in turn reducing Akt, mitogen-activated protein kinase (MAPK) and GSK3β activity significantly. Sublethal dose of GW627368X was found to reduce the nuclear translocation of β-catenin in a time dependent manner along with time-dependent decrease in cytoplasmic as well as whole-cell β-catenin. Decreased CREB and β-catenin transcriptional activity restricts the aberrant transcription of key genes like EP4, cyclooxygenase (COX)-2, vascular endothelial growth factor and c-myc, which ultimately control cell survival, proliferation and angiogenesis. Reduced activity of EGFR resulted in enhanced expression of 15-hydroxyprostaglandin dehydrogenase increasing PGE2 degradation thereby blocking a positive feedback loop. In xenograft model, dose-dependent decrease in cancer proliferation was observed characterized by reduction in tumor mass and volume and a marked decrease in Ki67 expression. A diminished CD31 specific staining signified decreased tumor angiogenesis. Reduced expression of pAkt, pMAPK, pEGFR and COX-2 validated in vitro results. GW627368X therefore effectively inhibits tumor survival, motility, proliferation and angiogenesis by blocking EP4/EGFR interactive signaling. EP4 is a potent therapeutic target in cervical cancer and can be explored in combination with conventional therapies to attain superior outcomes and to overcome complications associated with organ toxicities, therapeutic resistance and disease relapse.
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Affiliation(s)
- S Parida
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - I Pal
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - A Parekh
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - B Thakur
- National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beleghata, Kolkata, West Bengal 700010, India
| | - R Bharti
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
| | - S Das
- National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme XM, Beleghata, Kolkata, West Bengal 700010, India
| | - M Mandal
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal 721302, India
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28
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Reddy CB, Bharti R, Kumar S, Das P. Supported palladium nanoparticles-catalyzed decarboxylative coupling approaches to aryl alkynes, indoles and pyrrolines synthesis. RSC Adv 2016. [DOI: 10.1039/c6ra12046f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The polystyrene supported palladium (Pd@PS) nanoparticles catalyzed decarboxylative coupling of arylhalides and alkynyl carboxylic acids was developed for the synthesis of diaryl alkynes, indoles and pyrrolines.
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Affiliation(s)
- C. Bal Reddy
- Natural Product Chemistry and Process Development Division
- CSIR-Institute of Himalayan Bioresource Technology
- Palampur-176061
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Richa Bharti
- Natural Product Chemistry and Process Development Division
- CSIR-Institute of Himalayan Bioresource Technology
- Palampur-176061
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Sandeep Kumar
- Natural Product Chemistry and Process Development Division
- CSIR-Institute of Himalayan Bioresource Technology
- Palampur-176061
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Pralay Das
- Natural Product Chemistry and Process Development Division
- CSIR-Institute of Himalayan Bioresource Technology
- Palampur-176061
- India
- Academy of Scientific and Innovative Research (AcSIR)
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Bharti R, Dey G, Ojha PK, Rajput S, Jaganathan SK, Sen R, Mandal M. Diacerein-mediated inhibition of IL-6/IL-6R signaling induces apoptotic effects on breast cancer. Oncogene 2015; 35:3965-75. [PMID: 26616855 DOI: 10.1038/onc.2015.466] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 09/29/2015] [Accepted: 10/05/2015] [Indexed: 02/08/2023]
Abstract
Interleukin-6 (IL-6) signaling network has been implicated in oncogenic transformations making it attractive target for the discovery of novel cancer therapeutics. In this study, potent antiproliferative and apoptotic effect of diacerein were observed against breast cancer. In vitro apoptosis was induced by this drug in breast cancer cells as verified by increased sub-G1 population, LIVE/DEAD assay, cell cytotoxicity and presence of terminal deoxynucleotidyl transferase dUTP nick end labeling (TUNEL)-positive cells, as well as downregulation of antiapoptotic proteins Bcl-2 and Bcl-xL and upregulation of apoptotic protein Bax. In addition, apoptosis induction was found to be caspase dependent. Further molecular investigations indicated that diacerein instigated apoptosis was associated with inhibition of IL-6/IL-6R autocrine signaling axis. Suppression of STAT3, MAPK and Akt pathways were also observed as a consequence of diacerein-mediated upstream inhibition of IL-6/IL-6R. Fluorescence study and western blot analysis revealed cytosolic accumulation of STAT3 in diacerein-treated cells. The docking study showed diacerein/IL-6R interaction that was further validated by competitive binding assay and isothermal titration calorimetry. Most interestingly, it was found that diacerein considerably suppressed tumor growth in MDA-MB-231 xenograft model. The in vivo antitumor effect was correlated with decreased proliferation (Ki-67), increased apoptosis (TUNEL) and inhibition of IL-6/IL-6R-mediated STAT3, MAPK and Akt pathway in tumor remnants. Taken together, diacerein offered a novel blueprint for cancer therapy by hampering IL-6/IL-6R/STAT3/MAPK/Akt network.
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Affiliation(s)
- R Bharti
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - G Dey
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - P K Ojha
- Drug Theoretics and Cheminformatics Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S Rajput
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - S K Jaganathan
- IJN-UTM Cardiovascular Engineering Centre, Faculty of Biosciences and Medical Engineering, Universiti Teknologi, Malaysia
| | - R Sen
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - M Mandal
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur, India
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30
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Adolph TE, Tomczak MF, Niederreiter L, Ko HJ, Böck J, Martinez-Naves E, Glickman JN, Tschurtschenthaler M, Hartwig J, Hosomi S, Flak MB, Cusick JL, Kohno K, Iwawaki T, Billmann-Born S, Raine T, Bharti R, Lucius R, Kweon MN, Marciniak SJ, Choi A, Hagen SJ, Schreiber S, Rosenstiel P, Kaser A, Blumberg RS. Paneth cells as a site of origin for intestinal inflammation. Nature 2013; 503:272-6. [PMID: 24089213 PMCID: PMC3862182 DOI: 10.1038/nature12599] [Citation(s) in RCA: 535] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/22/2013] [Indexed: 02/06/2023]
Abstract
The recognition of autophagy related 16-like 1 (ATG16L1) as a genetic risk factor has exposed the critical role of autophagy in Crohn's disease. Homozygosity for the highly prevalent ATG16L1 risk allele, or murine hypomorphic (HM) activity, causes Paneth cell dysfunction. As Atg16l1(HM) mice do not develop spontaneous intestinal inflammation, the mechanism(s) by which ATG16L1 contributes to disease remains obscure. Deletion of the unfolded protein response (UPR) transcription factor X-box binding protein-1 (Xbp1) in intestinal epithelial cells, the human orthologue of which harbours rare inflammatory bowel disease risk variants, results in endoplasmic reticulum (ER) stress, Paneth cell impairment and spontaneous enteritis. Unresolved ER stress is a common feature of inflammatory bowel disease epithelium, and several genetic risk factors of Crohn's disease affect Paneth cells. Here we show that impairment in either UPR (Xbp1(ΔIEC)) or autophagy function (Atg16l1(ΔIEC) or Atg7(ΔIEC)) in intestinal epithelial cells results in each other's compensatory engagement, and severe spontaneous Crohn's-disease-like transmural ileitis if both mechanisms are compromised. Xbp1(ΔIEC) mice show autophagosome formation in hypomorphic Paneth cells, which is linked to ER stress via protein kinase RNA-like endoplasmic reticulum kinase (PERK), elongation initiation factor 2α (eIF2α) and activating transcription factor 4 (ATF4). Ileitis is dependent on commensal microbiota and derives from increased intestinal epithelial cell death, inositol requiring enzyme 1α (IRE1α)-regulated NF-κB activation and tumour-necrosis factor signalling, which are synergistically increased when autophagy is deficient. ATG16L1 restrains IRE1α activity, and augmentation of autophagy in intestinal epithelial cells ameliorates ER stress-induced intestinal inflammation and eases NF-κB overactivation and intestinal epithelial cell death. ER stress, autophagy induction and spontaneous ileitis emerge from Paneth-cell-specific deletion of Xbp1. Genetically and environmentally controlled UPR function within Paneth cells may therefore set the threshold for the development of intestinal inflammation upon hypomorphic ATG16L1 function and implicate ileal Crohn's disease as a specific disorder of Paneth cells.
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Affiliation(s)
- Timon E Adolph
- 1] Division of Gastroenterology and Hepatology, Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge CB2 0QQ, UK [2]
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31
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Vaz C, Ahmad HM, Bharti R, Pandey P, Kumar L, Kulshreshtha R, Bhattacharya A. Analysis of the microRNA transcriptome and expression of different isomiRs in human peripheral blood mononuclear cells. BMC Res Notes 2013; 6:390. [PMID: 24073671 PMCID: PMC3851811 DOI: 10.1186/1756-0500-6-390] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 09/17/2013] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) have been recognized as one of the key regulatory non-coding RNAs that are involved in a number of basic cellular processes. miRNA expression profiling helps to identify miRNAs that could serve as biomarkers. Next generation sequencing (NGS) platforms provide the most effective way of miRNA profiling, particularly as expression of different isoforms of miRNA (IsomiRs) can be estimated by NGS. Therefore, it is now possible to discern the overall complexity of miRNA populations that participate in gene regulatory networks. It is thus important to consider different isoforms of miRNA as part of total profiling in order to understand all aspects of the biology of miRNAs. RESULTS Here next generation sequencing data of small RNAs derived from normal peripheral blood mononuclear cells (PBMC) and Chronic myeloid leukemia (CML) patients has been used to generate miRNA profiles using a computation pipeline which can identify isomiRs that are natural variants of mature miRNAs. IsomiR profiles have been generated for all the 5p and 3p miRNAs (previously known as major mature miRNA and minor or miRNA*) and the data has been presented as a composite total miRNA transcriptome. The results indicated that the most abundant isomiR sequence of about 68% miRNAs, did not match the reference miRNA sequence as entered in the miRBase and that there is a definite pattern in relative concentration of different isomiRs derived from same precursors. Finally, a total of 17 potential novel miRNA sequences were identified suggesting that there are still some new miRNAs yet to be discovered. CONCLUSIONS Inclusion of different isoforms provides a detailed miRnome of a cell type or tissues. Availability of miRnome will be useful for finding biomarkers of different cell types and disease states. Our results also indicate that the relative expression levels of different isoforms of a miRNA are likely to be dynamic and may change with respect to changes in the cell or differentiation status.
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Affiliation(s)
- Candida Vaz
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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32
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Shard A, Sharma N, Bharti R, Dadhwal S, Kumar R, Sinha AK. Tandem Heck/Decarboxylation/Heck Strategy: Protecting-Group-Free Synthesis of Symmetric and Unsymmetric Hydroxylated Stilbenoids. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206346] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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33
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Shard A, Sharma N, Bharti R, Dadhwal S, Kumar R, Sinha AK. Tandem Heck/Decarboxylation/Heck Strategy: Protecting-Group-Free Synthesis of Symmetric and Unsymmetric Hydroxylated Stilbenoids. Angew Chem Int Ed Engl 2012; 51:12250-3. [DOI: 10.1002/anie.201206346] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/09/2012] [Indexed: 01/08/2023]
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34
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Rajput S, Dey KK, Ipsita P, Sen K, Dey G, Bharti R, Parida S, Parekh A, Mandal M. 201 Combinatorial Effect of ZD6474 and Thymoquinone Inhibits Src Mediated ERK-1/2/STAT3 Signalling and Renders Antimetastasis in Breast Cancer. Eur J Cancer 2012. [DOI: 10.1016/s0959-8049(12)71999-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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35
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Gupta R, Dewan I, Bharti R, Bhattacharya A. Differential Expression Analysis for RNA-Seq Data. ISRN Bioinform 2012; 2012:817508. [PMID: 25937942 PMCID: PMC4393055 DOI: 10.5402/2012/817508] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/09/2012] [Indexed: 02/05/2023]
Abstract
RNA-Seq is increasingly being used for gene expression profiling. In this approach, next-generation sequencing (NGS) platforms are used for sequencing. Due to highly parallel nature, millions of reads are generated in a short time and at low cost. Therefore analysis of the data is a major challenge and development of statistical and computational methods is essential for drawing meaningful conclusions from this huge data. In here, we assessed three different types of normalization (transcript parts per million, trimmed mean of M values, quantile normalization) and evaluated if normalized data reduces technical variability across replicates. In addition, we also proposed two novel methods for detecting differentially expressed genes between two biological conditions: (i) likelihood ratio method, and (ii) Bayesian method. Our proposed methods for finding differentially expressed genes were tested on three real datasets. Our methods performed at least as well as, and often better than, the existing methods for analysis of differential expression.
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Affiliation(s)
- Rashi Gupta
- School of Computational and Integrative Sciences, JNU, New Delhi 110067, India ; CorrZ Technosolutions Pvt. Ltd., Noida 201304, India
| | - Isha Dewan
- Indian Statistical Institute, New Delhi 110016, India
| | - Richa Bharti
- School of Computational and Integrative Sciences, JNU, New Delhi 110067, India
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36
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Kumar R, Shard A, Bharti R, Thopate Y, Sinha AK. Palladium-Catalyzed Dehydrative Heck Olefination of Secondary Aryl Alcohols in Ionic Liquids: Towards a Waste-Free Strategy for Tandem Synthesis of Stilbenoids. Angew Chem Int Ed Engl 2012; 51:2636-9. [DOI: 10.1002/anie.201107261] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Indexed: 11/06/2022]
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37
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Kumar R, Shard A, Bharti R, Thopate Y, Sinha AK. Palladium-Catalyzed Dehydrative Heck Olefination of Secondary Aryl Alcohols in Ionic Liquids: Towards a Waste-Free Strategy for Tandem Synthesis of Stilbenoids. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201107261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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38
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Bharti R, Das R, Sharma P, Katoch K, Bhattacharya A. MTCID: a database of genetic polymorphisms in clinical isolates of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2011; 92:166-72. [PMID: 22209237 DOI: 10.1016/j.tube.2011.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2011] [Revised: 11/28/2011] [Accepted: 12/02/2011] [Indexed: 01/15/2023]
Abstract
Tuberculosis (TB) is a major cause of morbidity and mortality throughout the world, particularly in developing countries. The response of the patients and treatment outcome depends, in addition to diagnosis, appropriate and timely treatment and host factors, on the virulence of Mycobacterium tuberculosis and genetic polymorphism prevalent in clinical isolates of the bacterium. A number of studies have been carried out to characterize clinical isolates of M. tuberculosis obtained from TB patients. However, the data is scattered in a large number of publications. Though attempts have been made to catalog the observed variations, there is no database that has been developed for cataloging, storing and dissemination of genetic polymorphism information. MTCID (M. tuberculosis clinical isolate genetic polymorphism database) is an attempt to provide a comprehensive repository to store, access and disseminate single nucleotide polymorphism (SNPs) and spoligotyping profiles of M. tuberculosis. It can be used to automatically upload the information available with a user that adds to the existing database at the backend. Besides it may also aid in maintaining clinical profiles of TB and treatment of patients. The database has 'search' features and is available at http://ccbb.jnu.ac.in/Tb.
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Affiliation(s)
- Richa Bharti
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
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39
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Batra A, Bharti R, Batra A. P334 Pregnancy with cirrhosis and portal hypertension. Int J Gynaecol Obstet 2009. [DOI: 10.1016/s0020-7292(09)61826-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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40
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Sharma M, Bharti R, Yadav P, Salhan S. O851 Maternal and foetal outcome in pregnancy with congenital heart disease. Int J Gynaecol Obstet 2009. [DOI: 10.1016/s0020-7292(09)61224-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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41
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Kaur M, Bharti R. Leprosy among circus workers. Indian J Lepr 1996; 68:363-6. [PMID: 9001904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Seven (2.31%) circus workers of two circus companies visiting Amritsar were detected to be suffering from leprosy. Whether or not they acquired the disease during their stay in circus is not so important, but it is necessary to detect and treat these itinerant persons. Our experience clearly underlines the necessity for undertaking surveys of various workers living in crowded conditions (like circus), because of their occupation.
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Affiliation(s)
- M Kaur
- MLTU, Civil Hospital, Amritsar, Punjab
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42
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Bharti R. Mesalazine in treatment of psoriasis. Indian J Dermatol Venereol Leprol 1996; 62:231-232. [PMID: 20948062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Mesalazine- a 5 lipoxygenase inhibitor was tried in this open trial on 20 psoriatics. Whereas 50% patients (10) had complete clearance in 4 weeks, by 12 weeks 85% (17) patients had good response and 15% (3) patients had no relief at all. No side effects were observed. Further longitudinal double-blind trials of this drug, which has an advantage of not causing bone marrow depression and oligospermia over sulfasalazine, another 5 lipoxygenase inhibitor, are advocated.
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Affiliation(s)
- R Bharti
- Sri Guru Ram Das and Civil Hosptials, Amritsar, India
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43
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Bharti R, Girgla PS. Sulfasalazine in treatment of psoriasis. Indian J Dermatol Venereol Leprol 1996; 62:87-88. [PMID: 20947988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A 5-lipoxygenase inhibitor-sulfasalazine was compared to a known effective drug-methotrexate in psoriasis. Fifteen patients each were put on sulfasalazine (1500 mg/day) and methotrexate (7.5 mg/week). Assessment was made on the basis of EST (Erythema, Scaling and Thickness) scale, initially and then weekly upto 4 weeks followed by 4 weekly upto 12 weeks. Efficacy was comparable for the 2 drugs: decrease in mean EST in patients on methotrexate and sulfasalazine therapy was 86.55% and 83.64% at 4 weeks; and 92.86% and 92.13% at 12 weeks respectively. Nine patients on sulfasalazine therapy and 10 patients on methotrexate therapy had complete clearance at the end of 12 weeks.
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Affiliation(s)
- R Bharti
- Department of Skin and STD, Sri Guru Ram Das Hospital, Amritsar-143001, India
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44
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Bharti R. Incontinentia pigmenti. Indian J Dermatol Venereol Leprol 1996; 62:58. [PMID: 20947976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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45
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Bharti R. Relapse, reinfection or inadequate MDT ? Indian J Dermatol Venereol Leprol 1996; 62:45-46. [PMID: 20947969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Relapse by all standard definitions is reported in a middle aged woman after PB MDT. Since she belonged to a family of treated leprosy sufferers (husband and his elder brother) and her daughter has now developed infectious type of leprosy, the possibility of reinfection can also not be ruled out.
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46
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Bharti R, Bal MS. Incontinentia pigmenti. Indian J Dermatol Venereol Leprol 1995; 61:166-167. [PMID: 20952938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
A case of incontinentia pigmenti, a rare genodermatosis, is being presented.
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Affiliation(s)
- R Bharti
- From the Civil Hospital, Amritsar, India
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47
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Bharti R, Malhotra SK, Bal MS, Sharma K. Chromoblastomycosis. Indian J Dermatol Venereol Leprol 1995; 61:54-55. [PMID: 20952879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
This is an account of twenty eight years of sufferings of a young sikh agriculturist, who ultimately succumbed to chromoblastomycosis- a not so uncommon mycotic infection, despite the use of toxic (amphoterecin-B) and newer antimycotic drugs (ketoconazole). Involvement of face, small and large gut, larynx and trachea are the other highlights of this case.
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48
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Bharti R. Pefloxacin in leprosy. Indian J Lepr 1994; 66:443-8. [PMID: 7714353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Fluoroquinolones, a new class of compounds characterised by broad antimicrobial spectrum including mycobacteria together with limited toxicity, have recently been introduced in the chemotherapy of various human infectious diseases. Pefloxacin, one of the members of this class, was recently demonstrated to be bactericidal against M.leprae in the mouse foot-pad model and clinically beneficial in lepromatous leprosy patients. Clinical response to standard MDT with added pefloxacin in ten previously untreated (both PB and MB) was compared with that in ten similar patients on MDT alone in the present trial. The results of chemotherapy were quantified by a method of clinical scoring. This pilot study showed that addition of pefloxacin led to significant and rapid clinical improvement. There were no side effects attributable to pefloxacin.
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49
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Bharti R, Saini R. Improving NLEP performance in a low endemic area. Indian J Lepr 1993; 65:327-32. [PMID: 8283069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
New innovative strategies of the medical officer of an upgraded urban leprosy centre of a low endemic state (Punjab) resulted in an increase in new case detection by seventy-four percent. Indigenous patients were much more regular than immigrant patients in colonies. The number of new indigenous punjabi patients has not shown any decline in last one decade, probably because of deficiencies in the functioning of NLEP. It is suggested that improved case detection by adopting strategies used by the authors and restricting free migration of untreated and partially treated patients would help in achieving the goals of NLEP.
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50
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Bharti R. National strategy for elimination of leprosy in India. Indian J Lepr 1993; 65:103-104. [PMID: 8463714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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