2
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Ling W, Lu J, Zhao N, Lulla A, Plantinga AM, Fu W, Zhang A, Liu H, Song H, Li Z, Chen J, Randolph TW, Koay WLA, White JR, Launer LJ, Fodor AA, Meyer KA, Wu MC. Batch effects removal for microbiome data via conditional quantile regression. Nat Commun 2022; 13:5418. [PMID: 36109499 PMCID: PMC9477887 DOI: 10.1038/s41467-022-33071-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
Batch effects in microbiome data arise from differential processing of specimens and can lead to spurious findings and obscure true signals. Strategies designed for genomic data to mitigate batch effects usually fail to address the zero-inflated and over-dispersed microbiome data. Most strategies tailored for microbiome data are restricted to association testing or specialized study designs, failing to allow other analytic goals or general designs. Here, we develop the Conditional Quantile Regression (ConQuR) approach to remove microbiome batch effects using a two-part quantile regression model. ConQuR is a comprehensive method that accommodates the complex distributions of microbial read counts by non-parametric modeling, and it generates batch-removed zero-inflated read counts that can be used in and benefit usual subsequent analyses. We apply ConQuR to simulated and real microbiome datasets and demonstrate its advantages in removing batch effects while preserving the signals of interest.
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Affiliation(s)
- Wodan Ling
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA
| | - Jiuyao Lu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, 21205, Baltimore, USA
| | - Ni Zhao
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, 615 N Wolfe St, 21205, Baltimore, USA.
| | - Anju Lulla
- Nutrition Research Institute and Department of Nutrition, University of North Carolina, 500 Laureate Way, 28081, Kannapolis, USA
| | - Anna M Plantinga
- Department of Mathematics and Statistics, Williams College, 18 Hoxsey St, 01267, Williamstown, USA
| | - Weijia Fu
- Department of Biostatistics, School of Public Health, University of Washington, 1705 NE Pacific St, 98195, Seattle, USA
| | - Angela Zhang
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA
- Department of Biostatistics, School of Public Health, University of Washington, 1705 NE Pacific St, 98195, Seattle, USA
| | - Hongjiao Liu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA
- Department of Biostatistics, School of Public Health, University of Washington, 1705 NE Pacific St, 98195, Seattle, USA
| | - Hoseung Song
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA
| | - Zhigang Li
- Department of Biostatistics, College of Public Health & Health Professions, College of Medicine, University of Florida, 2004 Mowry Rd, 32611, Gainesville, USA
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, 200 First St SW, 55905, Rochester, USA
| | - Timothy W Randolph
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA
| | - Wei Li A Koay
- Children's National Hospital, 111 Michigan Ave NW, 20010, Washington DC, USA
- Department of Pediatrics, George Washington University, Ross Hall 2300 Eye St NW, 20037, Washington DC, USA
| | - James R White
- Resphera Biosciences, 1529 Lancaster St, 21231, Baltimore, USA
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, NIA, NIH, 7201 Wisconsin Ave, 20814, Bethesda, USA
| | - Anthony A Fodor
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, 28223, Charlotte, USA
| | - Katie A Meyer
- Nutrition Research Institute and Department of Nutrition, University of North Carolina, 500 Laureate Way, 28081, Kannapolis, USA
| | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, 98109, Seattle, USA.
- Department of Biostatistics, School of Public Health, University of Washington, 1705 NE Pacific St, 98195, Seattle, USA.
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5
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Perrino C, Schiattarella GG, Sannino A, Pironti G, Petretta MP, Cannavo A, Gargiulo G, Ilardi F, Magliulo F, Franzone A, Carotenuto G, Serino F, Altobelli GG, Cimini V, Cuocolo A, Lombardi A, Goglia F, Indolfi C, Trimarco B, Esposito G. Genetic deletion of uncoupling protein 3 exaggerates apoptotic cell death in the ischemic heart leading to heart failure. J Am Heart Assoc 2013; 2:e000086. [PMID: 23688674 PMCID: PMC3698767 DOI: 10.1161/jaha.113.000086] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND Uncoupling protein 3 (ucp3) is a member of the mitochondrial anion carrier superfamily of proteins uncoupling mitochondrial respiration. In this study, we investigated the effects of ucp3 genetic deletion on mitochondrial function and cell survival under low oxygen conditions in vitro and in vivo. METHODS AND RESULTS To test the effects of ucp3 deletion in vitro, murine embryonic fibroblasts and adult cardiomyocytes were isolated from wild-type (WT, n=67) and ucp3 knockout mice (ucp3(-/-), n=70). To test the effects of ucp3 genetic deletion in vivo, myocardial infarction (MI) was induced by permanent coronary artery ligation in WT and ucp3(-/-) mice. Compared with WT, ucp3(-/-) murine embryonic fibroblasts and cardiomyocytes exhibited mitochondrial dysfunction and increased mitochondrial reactive oxygen species generation and apoptotic cell death under hypoxic conditions in vitro (terminal deoxynucleotidyl transferase-dUTP nick end labeling-positive nuclei: WT hypoxia, 70.3 ± 1.2%; ucp3(-/-) hypoxia, 85.3 ± 0.9%; P<0.05). After MI, despite similar areas at risk in the 2 groups, ucp3(-/-) hearts demonstrated a significantly larger infarct size compared with WT (infarct area/area at risk: WT, 48.2 ± 3.7%; ucp3(-/-), 65.0 ± 2.9%; P<0.05). Eight weeks after MI, cardiac function was significantly decreased in ucp3(-/-) mice compared with WT (fractional shortening: WT MI, 42.7 ± 3.1%; ucp3(-/-) MI, 24.4 ± 2.9; P<0.05), and this was associated with heightened apoptotic cell death (terminal deoxynucleotidyl transferase-dUTP nick end labeling-positive nuclei: WT MI, 0.7 ± 0.04%; ucp3(-/-) MI, 1.1 ± 0.09%, P<0.05). CONCLUSIONS Our data indicate that ucp3 levels regulate reactive oxygen species levels and cell survival during hypoxia, modulating infarct size in the ischemic heart.
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Affiliation(s)
- Cinzia Perrino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Gabriele G. Schiattarella
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Anna Sannino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Gianluigi Pironti
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Maria Piera Petretta
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Alessandro Cannavo
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Giuseppe Gargiulo
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Federica Ilardi
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Fabio Magliulo
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Anna Franzone
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Giuseppe Carotenuto
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Federica Serino
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Giovanna G. Altobelli
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Vincenzo Cimini
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Alberto Cuocolo
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Assunta Lombardi
- Department of Biology, Federico II University, Naples, Italy (A.L.)
| | - Fernando Goglia
- Department of Biology Sciences, Geology and Environment, Sannio University, Benevento, Italy (F.G.)
| | - Ciro Indolfi
- Department of Cardiology, Magna Graecia University, Catanzaro, Italy (C.I.)
| | - Bruno Trimarco
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
| | - Giovanni Esposito
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy (C.P., G.G.S., A.S., G.P., M.P.P., A.C., G.G., F.I., F.M., A.F., G.C., F.S., G.G.A., V.C., A.C., B.T., G.E.)
- Correspondence to: Giovanni Esposito, MD, PhD, or Cinzia Perrino, MD, PhD, Division of Cardiology, Federico II University, Via Pansini 5, 80131 Naples, Italy. E‐mail: ,
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