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Reygner J, Delannoy J, Barba-Goudiaby MT, Gasc C, Levast B, Gaschet E, Ferraris L, Paul S, Kapel N, Waligora-Dupriet AJ, Barbut F, Thomas M, Schwintner C, Laperrousaz B, Corvaïa N. Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models. Appl Environ Microbiol 2024:e0001624. [PMID: 38651930 DOI: 10.1128/aem.00016-24] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.
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Affiliation(s)
| | | | | | | | | | | | | | - Stéphane Paul
- Team GIMAP, Centre International de Recherche en Infectiologie, Université Jean Monnet, Saint-Etienne, France
- Inserm, Université Claude Bernard Lyon, Lyon, France
- CIC 1408 Inserm Vaccinology, University Hospital of Saint-Etienne, Saint-Etienne, France
- Immunology Department, iBiothera Reference Center, University Hospital of Saint-Etienne, Saint-Etienne, France
| | - Nathalie Kapel
- UMR-S 1139, INSERM, Université Paris Cite, Paris, France
- Service de Coprologie fonctionnelle, Hôpital de la Pitié-Salpêtrière-Charles Foix, AP-HP, Paris, France
| | | | - Frederic Barbut
- UMR-S 1139, INSERM, Université Paris Cite, Paris, France
- National Reference Laboratory for Clostridioides difficile, Saint-Antoine Hospital, Assistance Publique-Hôpitaux de Paris, Paris, France
- The European Society of Clinical Microbiology and Infectious Diseases Study Group for Clostridioides difficile, Basel, Switzerland
| | - Muriel Thomas
- UMR1319, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
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Sun H, Yang K, Zhang X, Fu Y, Yarbro J, Wu Z, Chen PC, Chen T, Peng J. Evaluation of a Pooling Chemoproteomics Strategy with an FDA-Approved Drug Library. Biochemistry 2023; 62:624-632. [PMID: 35969671 PMCID: PMC9905291 DOI: 10.1021/acs.biochem.2c00256] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Chemoproteomics is a key platform for characterizing the mode of action for compounds, especially for targeted protein degraders such as proteolysis targeting chimeras (PROTACs) and molecular glues. With deep proteome coverage, multiplexed tandem mass tag-mass spectrometry (TMT-MS) can tackle up to 18 samples in a single experiment. Here, we present a pooling strategy for further enhancing the throughput and apply the strategy to an FDA-approved drug library (95 best-in-class compounds). The TMT-MS-based pooling strategy was evaluated in the following steps. First, we demonstrated the capability of TMT-MS by analyzing more than 15 000 unique proteins (> 12 000 gene products) in HEK293 cells treated with five PROTACs (two BRD/BET degraders and three degraders for FAK, ALK, and BTK kinases). We then introduced a rationalized pooling strategy to separate structurally similar compounds in different pools and identified the proteomic response to 14 pools from the drug library. Finally, we validated the proteomic response from one pool by reprofiling the cells via treatment with individual drugs with sufficient replicates. Interestingly, numerous proteins were found to change upon drug treatment, including AMD1, ODC1, PRKX, PRKY, EXO1, AEN, and LRRC58 with 7-hydroxystaurosporine; C6orf64, HMGCR, and RRM2 with Sorafenib; SYS1 and ALAS1 with Venetoclax; and ATF3, CLK1, and CLK4 with Palbocilib. Thus, pooling chemoproteomics screening provides an efficient method for dissecting the molecular targets of compound libraries.
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Affiliation(s)
- Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Equal Contribution
| | - Xue Zhang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Yingxue Fu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jay Yarbro
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Taosheng Chen
- Chemical Biology & Therapeutics Department, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA, Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA,Correspondence:
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Sahajpal NS, Mondal AK, Ananth S, Njau A, Fulzele S, Ahaluwalia P, Chaubey A, Hegde M, Rojiani AM, Kolhe R. Making a Difference: Adaptation of the Clinical Laboratory in Response to the Rapidly Evolving COVID-19 Pandemic. Acad Pathol 2021; 8:23742895211023948. [PMID: 34263025 PMCID: PMC8246561 DOI: 10.1177/23742895211023948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 12/23/2020] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 11/30/2022] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2, led to unprecedented demands assigned to clinical diagnostic laboratories worldwide, forcing them to make significant changes to their regular workflow as they adapted to new diagnostic tests and sample volumes. Herein, we summarize the modifications/adaptation the laboratory had to exercise to cope with rapidly evolving situations in the current pandemic. In the first phase of the pandemic, the laboratory validated 2 reverse transcription polymerase chain reaction–based assays to test ∼1000 samples/day and rapidly modified procedures and validated various preanalytical and analytical steps to overcome the supply chain constraints that would have otherwise derailed testing efforts. Further, the pooling strategy was validated for wide-scale population screening using nasopharyngeal swab samples and saliva samples. The translational research arm of the laboratory pursued several initiatives to understand the variable clinical manifestations that this virus presented in the population. The phylogenetic evolution of the virus was investigated using next-generation sequencing technology. The laboratory has initiated the formation of a consortium that includes groups investigating genomes at the level of large structural variants, using genome optical mapping via this collaborative global effort. This article summarizes our journey as the laboratory has sought to adapt and continue to positively contribute to the unprecedented demands and challenges of this rapidly evolving pandemic.
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Affiliation(s)
- Nikhil S Sahajpal
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Ashis K Mondal
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Sudha Ananth
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Allan Njau
- Department of Pathology, Aga Khan University Hospital, Nairobi, Kenya
| | - Sadanand Fulzele
- Center for Healthy Aging, Medical College of Georgia, Augusta University, GA, USA
| | - Pankaj Ahaluwalia
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Alka Chaubey
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Madhuri Hegde
- Global Laboratory Services, PerkinElmer Inc, Waltham, GA, USA
| | - Amyn M Rojiani
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, GA, USA
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Abstract
In practice, it is common to evaluate biomarkers in binary classification settings (e.g. non-cancer vs. cancer) where one or both main classes involve multiple subclasses. For example, non-cancer class might consist of healthy subjects and benign cases, while cancer class might consist of subjects at early and late stages. The standard practice is pooling within each main class, i.e. all non-cancer subclasses are pooled together to create a control group, and all cancer subclasses are pooled together to create a case group. Based on the pooled data, the area under ROC curve (AUC) and other characteristics are estimated under binary classification for the purpose of biomarker evaluation. Despite the popularity of this pooling strategy in practice, its validity and implication in biomarker evaluation have never been carefully inspected. This paper aims to demonstrate that pooling strategy can be seriously misleading in biomarker evaluation. Furthermore, we present a new diagnostic framework as well as new accuracy measures appropriate for biomaker evaluation under such settings. In the end, an ovarian cancer data set is analyzed.
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Affiliation(s)
- Yingdong Feng
- Department of Biostatistics, University at Buffalo, Buffalo, NY, USA
| | - Lili Tian
- Department of Biostatistics, University at Buffalo, Buffalo, NY, USA
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Petrovan V, Vrajmasu V, Bucur AC, Soare DS, Radu E, Dimon P, Zaulet M. Evaluation of Commercial qPCR Kits for Detection of SARS-CoV-2 in Pooled Samples. Diagnostics (Basel) 2020; 10:E472. [PMID: 32664511 PMCID: PMC7400658 DOI: 10.3390/diagnostics10070472] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/27/2020] [Revised: 07/08/2020] [Accepted: 07/09/2020] [Indexed: 01/14/2023] Open
Abstract
Due to the current pandemic, a global shortage of reagents has drawn interest in developing alternatives to increase the number of coronavirus tests. One such alternative is sample pooling. We compared commercial kits that are used in COVID-19 diagnostics in terms of their sensitivity and feasibility for use in pooling. In this preliminary study, we showed that pooling of up to 80 samples did not affect the efficacy of the kits. Additionally, the RNA-dependent RNA polymerase (RdRp) gene is a more suitable target in pooled samples than the envelope (E) gene. This approach could provide an easy method of screening a large number of samples and help adjust different governmental regulations.
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Affiliation(s)
- Vlad Petrovan
- The Pirbright Institute, Woking, Surrey GU24 0NF, UK
| | | | - Ana Cristina Bucur
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Dan Sebastian Soare
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Eugen Radu
- Emergency Hospital Bucharest, Molecular Pathology Laboratory, 050098 Bucharest, Romania; (A.C.B.); (D.S.S.); (E.R.)
| | - Paula Dimon
- Personal Genetics, 010987 Bucharest, Romania;
| | - Mihaela Zaulet
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095 Bucharest, Romania;
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Nyunt MH, Kyaw MP, Thant KZ, Shein T, Han SS, Zaw NN, Han JH, Lee SK, Muh F, Kim JY, Cho SH, Lee SE, Yang EJ, Chang CL, Han ET. Effective High-Throughput Blood Pooling Strategy before DNA Extraction for Detection of Malaria in Low-Transmission Settings. Korean J Parasitol 2016; 54:253-9. [PMID: 27417078 PMCID: PMC4977795 DOI: 10.3347/kjp.2016.54.3.253] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 05/26/2016] [Accepted: 05/27/2016] [Indexed: 11/26/2022]
Abstract
In the era of (pre) elimination setting, the prevalence of malaria has been decreasing in most of the previously endemic areas. Therefore, effective cost- and time-saving validated pooling strategy is needed for detection of malaria in low transmission settings. In this study, optimal pooling numbers and lowest detection limit were assessed using known density samples prepared systematically, followed by genomic DNA extraction and nested PCR. Pooling strategy that composed of 10 samples in 1 pool, 20 µl in 1 sample, was optimal, and the parasite density as low as 2 p/µl for both falciparum and vivax infection was enough for detection of malaria. This pooling method showed effectiveness for handling of a huge number of samples in low transmission settings (<9% positive rate). The results indicated that pooling of the blood samples before DNA extraction followed by usual nested PCR is useful and effective for detection of malaria in screening of hidden cases in low-transmission settings.
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Affiliation(s)
- Myat Htut Nyunt
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea.,Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Myat Phone Kyaw
- Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Kyaw Zin Thant
- Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Thinzer Shein
- Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Soe Soe Han
- Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Ni Ni Zaw
- Department of Medical Research, Yangon, Republic of the Union of Myanmar
| | - Jin-Hee Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
| | - Fauzi Muh
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
| | - Jung-Yeon Kim
- Division of Malaria and Parasitic Diseases, National Institute of Health, Centers for Disease Control and Prevention, Osong 28159, Korea
| | - Shin-Hyeong Cho
- Division of Malaria and Parasitic Diseases, National Institute of Health, Centers for Disease Control and Prevention, Osong 28159, Korea
| | - Sang-Eun Lee
- Division of Malaria and Parasitic Diseases, National Institute of Health, Centers for Disease Control and Prevention, Osong 28159, Korea
| | - Eun-Jeong Yang
- Division of Malaria and Parasitic Diseases, National Institute of Health, Centers for Disease Control and Prevention, Osong 28159, Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yansan 50612, Korea
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon 24341, Korea
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