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Nesline MK, Subbiah V, Previs RA, Strickland KC, Ko H, DePietro P, Biorn MD, Cooper M, Wu N, Conroy J, Pabla S, Zhang S, Wallen ZD, Sathyan P, Saini K, Eisenberg M, Caveney B, Severson EA, Ramkissoon S. The Impact of Prior Single-Gene Testing on Comprehensive Genomic Profiling Results for Patients with Non-Small Cell Lung Cancer. Oncol Ther 2024:10.1007/s40487-024-00270-x. [PMID: 38502426 DOI: 10.1007/s40487-024-00270-x] [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: 12/29/2023] [Accepted: 02/29/2024] [Indexed: 03/21/2024] Open
Abstract
INTRODUCTION Tissue-based broad molecular profiling of guideline-recommended biomarkers is advised for the therapeutic management of patients with non-small cell lung cancer (NSCLC). However, practice variation can affect whether all indicated biomarkers are tested. We aimed to evaluate the impact of common single-gene testing (SGT) on subsequent comprehensive genomic profiling (CGP) test outcomes and results in NSCLC. METHODS Oncologists who ordered SGT for guideline-recommended biomarkers in NSCLC patients were prospectively contacted (May-December 2022) and offered CGP (DNA and RNA sequencing), either following receipt of negative SGT findings, or instead of SGT for each patient. We describe SGT patterns and compare CGP completion rates, turnaround time, and recommended biomarker detection for NSCLC patients with and without prior negative SGT results. RESULTS Oncologists in > 80 community practices ordered CGP for 561 NSCLC patients; 135 patients (27%) first had negative results from 30 different SGT combinations; 84% included ALK, EGFR and PD-L1, while only 3% of orders included all available SGTs for guideline-recommended genes. Among patients with negative SGT results, CGP was attempted using the same tissue specimen 90% of the time. There were also significantly more CGP order cancellations due to tissue insufficiency (17% vs. 7%), DNA sequencing failures (13% vs. 8%), and turnaround time > 14 days (62% vs. 29%) than among patients who only had CGP. Forty-six percent of patients with negative prior SGT had positive CGP results for recommended biomarkers, including targetable genomic variants in genes beyond ALK and EGFR, such as ERBB2, KRAS (non-G12C), MET (exon 14 skipping), NTRK2/3, and RET . CONCLUSION For patients with NSCLC, initial use of SGT increases subsequent CGP test cancellations, turnaround time, and the likelihood of incomplete molecular profiling for guideline-recommended biomarkers due to tissue insufficiency.
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Affiliation(s)
- Mary K Nesline
- Labcorp Oncology, 700 Ellicott Street, Buffalo, NY, 14203, USA.
| | - Vivek Subbiah
- Sarah Cannon Research Institute, Early-Phase Drug Development, Nashville, TN, 37203, USA
| | - Rebecca A Previs
- Labcorp Oncology, Durham, NC, 27560, USA
- Duke Cancer Institute, Department of Obstetrics & Gynecology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Kyle C Strickland
- Labcorp Oncology, Durham, NC, 27560, USA
- Duke Cancer Institute, Department of Pathology, Duke University Medical Center, Durham, NC, 27710, USA
- Department of Gynecologic Oncology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Heidi Ko
- Labcorp Oncology, Durham, NC, 27560, USA
| | - Paul DePietro
- Labcorp Oncology, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | | | - Nini Wu
- Cardinal Health, Dublin, OH, 43017, USA
| | - Jeffrey Conroy
- Labcorp Oncology, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Sarabjot Pabla
- Labcorp Oncology, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | - Shengle Zhang
- Labcorp Oncology, 700 Ellicott Street, Buffalo, NY, 14203, USA
| | | | | | | | | | | | | | - Shakti Ramkissoon
- Labcorp Oncology, Durham, NC, 27560, USA
- Department of Pathology, Wake Forest Comprehensive Cancer Center, Wake Forest School of Medicine, Winston-Salem, NC, 27109, USA
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2
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Payami H, Cohen G, Murchison CF, Sampson TR, Standaert DG, Wallen ZD. Population fraction of Parkinson's disease attributable to preventable risk factors. NPJ Parkinsons Dis 2023; 9:159. [PMID: 38052871 PMCID: PMC10698155 DOI: 10.1038/s41531-023-00603-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/14/2023] [Indexed: 12/07/2023] Open
Abstract
Parkinson's disease is the fastest-growing neurologic disease with seemingly no means of prevention. Intrinsic risk factors (age, sex, and genetics) are inescapable, but environmental factors are not. We identified repeated blows to the head in sports/combat as a potential new risk factor. 23% of PD cases in females were attributable to pesticide/herbicide exposure, and 30% of PD in males were attributable to pesticides/herbicides, military-related chemical exposures, and repeated blows to the head, and therefore could have potentially been prevented.
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Affiliation(s)
- Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
| | - Gwendolyn Cohen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Charles F Murchison
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Timothy R Sampson
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, 30329, USA
| | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
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Payami H, Cohen G, Murchison CF, Sampson TR, Standaert DG, Wallen ZD. Population fraction of Parkinson's disease attributable to preventable risk factors. medRxiv 2023:2023.05.19.23290231. [PMID: 37292848 PMCID: PMC10246145 DOI: 10.1101/2023.05.19.23290231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Parkinson's disease is the fastest growing neurologic disease with seemingly no means for prevention. Intrinsic risk factors (age, sex, genetics) are inescapable, but environmental factors are not. We studied population attributable fraction and estimated fraction of PD that could be reduced if modifiable risk factors were eliminated. Assessing several known risk factors simultaneously in one study, we demonstrate that all were operative and independent, underscoring etiological heterogeneity within a single population. We investigated repeated blows to head in sports or combat as a potential new risk factor, and found it was associated with two-fold increased risk of PD. Considering modifiable risk factors, 23% of PD cases in females were attributable to pesticides/herbicides exposure, and 30% of PD cases in males was attributable to pesticides/herbicides, Agent Orange/chemical warfare, and repeated blows to the head. Thus, one-in-three cases of PD in males, and one-in-four cases in females could have potentially been prevented.
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Affiliation(s)
- Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Gwendolyn Cohen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Charles F Murchison
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Timothy R Sampson
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Department of Cell Biology, Emory University School of Medicine, Atlanta GA 30329, USA
| | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
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Wallen ZD, Demirkan A, Twa G, Cohen G, Dean MN, Standaert DG, Sampson TR, Payami H. Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms. Nat Commun 2022; 13:6958. [PMID: 36376318 PMCID: PMC9663292 DOI: 10.1038/s41467-022-34667-x] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022] Open
Abstract
Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.
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Affiliation(s)
- Zachary D. Wallen
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA ,grid.513948.20000 0005 0380 6410Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815 USA
| | - Ayse Demirkan
- grid.5475.30000 0004 0407 4824Surrey Institute for People-Centred AI, University of Surrey, Guildford, Surrey GU2 7XH UK
| | - Guy Twa
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - Gwendolyn Cohen
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA ,grid.513948.20000 0005 0380 6410Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815 USA
| | - Marissa N. Dean
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - David G. Standaert
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA
| | - Timothy R. Sampson
- grid.513948.20000 0005 0380 6410Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815 USA ,grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA 30329 USA
| | - Haydeh Payami
- grid.265892.20000000106344187Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35233 USA ,grid.513948.20000 0005 0380 6410Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815 USA
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Ilieva NM, Wallen ZD, De Miranda BR. Oral ingestion of the environmental toxicant trichloroethylene in rats induces alterations in the gut microbiome: Relevance to idiopathic Parkinson's disease. Toxicol Appl Pharmacol 2022; 451:116176. [PMID: 35914559 PMCID: PMC10581445 DOI: 10.1016/j.taap.2022.116176] [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] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 07/05/2022] [Accepted: 07/21/2022] [Indexed: 11/22/2022]
Abstract
Microbial alterations within the gut microbiome appear to be a common feature of individuals with Parkinson's disease (PD), providing further evidence for the role of the gut-brain axis in PD development. As a major site of contact with the environment, questions have emerged surrounding the cause and effect of alterations to the gut microbiome by environmental contaminants associated with PD risk, such as pesticides, metals, and organic solvents. Recent data from our lab shows that ingestion of the industrial byproduct and environmental pollutant trichloroethylene (TCE) induces key Parkinsonian pathology within aged rats, including the degeneration of dopaminergic neurons, α-synuclein accumulation, neuroinflammation, and endolysosomal deficits. As TCE is the most common organic contaminant within drinking water, we postulated that ingestion of TCE associated with PD-related neurodegeneration may alter the gut microbiome to a similar extent as observed in persons with PD. To assess this, we collected fecal samples from adult rats treated with 200 mg/kg TCE over 6 weeks via oral gavage - the dose that produced nigrostriatal neurodegeneration - and analyzed the gut microbiome via whole genome shotgun sequencing. Our results showed changes in gut microorganisms reflective of the microbial signatures observed in individuals with idiopathic PD, such as decreased abundance of short-chain fatty acid producing Blautia and elevated lactic-acid producing Bifidobacteria, as well as genera who contain species previously reported as opportunistic pathogens such as Clostridium. From these experimental data, we postulate that TCE exposure within contaminated drinking water could induce alterations of the gut microbiome that contributes to chronic disease risk, including idiopathic PD.
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Affiliation(s)
- Neda M Ilieva
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Zachary D Wallen
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Briana R De Miranda
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
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Wallen ZD, Stone WJ, Factor SA, Molho E, Zabetian CP, Standaert DG, Payami H. Exploring human-genome gut-microbiome interaction in Parkinson's disease. NPJ Parkinsons Dis 2021; 7:74. [PMID: 34408160 PMCID: PMC8373869 DOI: 10.1038/s41531-021-00218-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 07/23/2021] [Indexed: 12/16/2022]
Abstract
The causes of complex diseases remain an enigma despite decades of epidemiologic research on environmental risks and genome-wide studies that have uncovered tens or hundreds of susceptibility loci for each disease. We hypothesize that the microbiome is the missing link. Genetic studies have shown that overexpression of alpha-synuclein, a key pathological protein in Parkinson’s disease (PD), can cause familial PD and variants at alpha-synuclein locus confer risk of idiopathic PD. Recently, dysbiosis of gut microbiome in PD was identified: altered abundances of three microbial clusters were found, one of which was composed of opportunistic pathogens. Using two large datasets, we found evidence that the overabundance of opportunistic pathogens in PD gut is influenced by the host genotype at the alpha-synuclein locus, and that the variants responsible modulate alpha-synuclein expression. Results put forth testable hypotheses on the role of gut microbiome in the pathogenesis of PD, the incomplete penetrance of PD susceptibility genes, and potential triggers of pathology in the gut.
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Affiliation(s)
- Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - William J Stone
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, GA, USA
| | - Eric Molho
- Department of Neurology, Albany Medical College, Albany, NY, USA
| | - Cyrus P Zabetian
- VA Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, WA, USA
| | - David G Standaert
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
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7
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Wallen ZD. Comparison study of differential abundance testing methods using two large Parkinson disease gut microbiome datasets derived from 16S amplicon sequencing. BMC Bioinformatics 2021; 22:265. [PMID: 34034646 PMCID: PMC8147401 DOI: 10.1186/s12859-021-04193-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 03/07/2021] [Accepted: 05/12/2021] [Indexed: 12/30/2022] Open
Abstract
Background Testing for differential abundance of microbes in disease is a common practice in microbiome studies. Numerous differential abundance (DA) testing methods exist and range from traditional statistical tests to methods designed for microbiome data. Comparison studies of DA testing methods have been performed, but none performed on microbiome datasets collected for the study of real, complex disease. Due to this, DA testing was performed here using various DA methods in two large, uniformly collected gut microbiome datasets on Parkinson disease (PD), and their results compared. Results Overall, 78–92% of taxa tested were detected as differentially abundant by at least one method, while 5–22% were called differentially abundant by the majority of methods (depending on dataset and filtering of taxonomic data prior to testing). Concordances between method results ranged from 1 to 100%. Average concordance for datasets 1 and 2 were 24% and 28% respectively, and 27% for replicated DA signatures. Concordances increased when removing rarer taxa before testing, increasing average concordances by 2–32%. Certain methods consistently resulted in higher concordances (e.g. ANCOM-BC, LEfSe), while others consistently resulted in lower (e.g. edgeR, fitZIG). Hierarchical clustering revealed three groups of DA signatures that were (1) replicated by the majority of methods on average and included taxa previously associated with PD, (2) replicated by a subset of methods and included taxa largely enriched in PD, and (3) replicated by few to one method(s). Conclusions Differential abundance tests yielded varied concordances, and amounts of detected DA signatures. Some methods were more concordant than others on both filtered and unfiltered data, therefore, if consistency with other study methodology is a key goal, one might choose among these methods. Even still, using one method on one dataset may find true associations, but may also detect false positives. To help lower false positives, one might analyze data with two or more DA methods to gauge concordance, and use a built-in replication dataset. This study will hopefully serve to complement previously reported DA method comparison studies by implementing and coalescing a large number of both previously and yet to be compared methods on two real gut microbiome datasets. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04193-6.
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Affiliation(s)
- Zachary D Wallen
- Department of Neurology, University of Alabama At Birmingham, Birmingham, AL, 35294, USA.
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Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, Paterson AD, Kraaij R, Raes J, Zhernakova A. Large-scale association analyses identify host factors influencing human gut microbiome composition. Nat Genet 2021; 53:156-165. [PMID: 33462485 PMCID: PMC8515199 DOI: 10.1038/s41588-020-00763-1] [Citation(s) in RCA: 566] [Impact Index Per Article: 188.7] [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: 02/14/2020] [Accepted: 12/14/2020] [Indexed: 01/29/2023]
Abstract
To study the effect of host genetics on gut microbiome composition, the MiBioGen consortium curated and analyzed genome-wide genotypes and 16S fecal microbiome data from 18,340 individuals (24 cohorts). Microbial composition showed high variability across cohorts: only 9 of 410 genera were detected in more than 95% of samples. A genome-wide association study of host genetic variation regarding microbial taxa identified 31 loci affecting the microbiome at a genome-wide significant (P < 5 × 10-8) threshold. One locus, the lactase (LCT) gene locus, reached study-wide significance (genome-wide association study signal: P = 1.28 × 10-20), and it showed an age-dependent association with Bifidobacterium abundance. Other associations were suggestive (1.95 × 10-10 < P < 5 × 10-8) but enriched for taxa showing high heritability and for genes expressed in the intestine and brain. A phenome-wide association study and Mendelian randomization identified enrichment of microbiome trait loci in the metabolic, nutrition and environment domains and suggested the microbiome might have causal effects in ulcerative colitis and rheumatoid arthritis.
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Affiliation(s)
- Alexander Kurilshikov
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
| | - Carolina Medina-Gomez
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Rodrigo Bacigalupe
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Djawad Radjabzadeh
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jun Wang
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ayse Demirkan
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Section of Statistical Multi-Omics, Department of Clinical & Experimental Medicine, School of Biosciences & Medicine, University of Surrey, Guildford, UK
| | - Caroline I Le Roy
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Juan Antonio Raygoza Garay
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Casey T Finnicum
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
| | - Xingrong Liu
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Daria V Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Laboratory of Genomic Diversity, Center for Computer Technologies, ITMO University, St. Petersburg, Russia
| | - Marc Jan Bonder
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tue H Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabian Frost
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Williams Turpin
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Jee-Young Moon
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Han-Na Kim
- Medical Research Institute, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Clinical Research Design and Evaluation, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Kreete Lüll
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Elad Barkan
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiraz A Shah
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Myriam Fornage
- Institute of Molecular Medicine McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genetics Center School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Joanna Szopinska-Tokov
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Dmitrii Borisevich
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Agreus
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Stockholm, Sweden
| | - Anna Andreasson
- Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Corinna Bang
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Larbi Bedrani
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jordana T Bell
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Hans Bisgaard
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Dorret I Boomsma
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Robert D Burk
- Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Microbiology & Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Annique Claringbould
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kenneth Croitoru
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Gastroenterology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Gareth E Davies
- Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Liesbeth Duijts
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gwen Falony
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Jingyuan Fu
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Adriaan van der Graaf
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Richard G Ijzerman
- Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands
| | - Matthew A Jackson
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
| | - Vincent W V Jaddoe
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marie Joossens
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Torben Jørgensen
- Centre for Clinical Research and Prevention, Bispebjerg/Frederiksberg Hospital, Capital Region of Copenhagen and Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel Keszthelyi
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation and Department of Bioengeering, University of California, San Diego, La Jolla, CA, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Matthias Laudes
- Department of Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Science, National Institute on Aging, Bethesda, MD, USA
| | - Wolfgang Lieb
- Institute of Epidemiology, Kiel University, Kiel, Germany
| | - Aldons J Lusis
- Departments of Microbiology, Immunology and Molecular Genetics, and Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ad A M Masclee
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Henriette A Moll
- Department of Pediatrics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Zlatan Mujagic
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Qi Qibin
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daphna Rothschild
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Hocheol Shin
- Department of Family Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Center for Cohort Studies, Total Healthcare Center, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Søren J Sørensen
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Claire J Steves
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | | | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Raul Y Tito
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Henry Völzke
- Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, Bristol, UK
| | - Susanna Walter
- Department of Biomedical and Clinical Sciences, University of Linköping, Linköping, Sweden
- Department of Gastroenterology, County Council of Östergötland, Linköping, Sweden
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University Amsterdam, Amsterdam, the Netherlands
| | - Stefan Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany
| | - Frank U Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Omer Weissbrod
- School of Public Health, Harvard University, Boston, MA, USA
| | - Harm-Jan Westra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gonneke Willemsen
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Daisy M A E Jonkers
- Division of Gastroenterology-Hepatology, Maastricht University Medical Center+, Maastricht, the Netherlands
- NUTRIM School of Nutrition and Translational Research in Metabolism, Maastricht University, Maastricht, the Netherlands
| | - Alejandro Arias Vasquez
- Department of Psychiatry, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
- Department of Human Genetics, Radboudumc, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, the Netherlands
| | - Eco J C de Geus
- Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
- Amsterdam Public Health, Amsterdam UMC, Amsterdam, the Netherlands
| | - Katie A Meyer
- Department of Nutrition, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC, USA
| | - Jakob Stokholm
- COPSAC, Copenhagen University Hospital, Copenhagen, Denmark
| | - Eran Segal
- Department of Computer Science and Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Elin Org
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Hyung-Lae Kim
- Department of Biochemistry, Ewha Womans University School of Medicine, Seoul, Republic of Korea
| | - Robert C Kaplan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London, UK
| | - Andre G Uitterlinden
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
- The Generation R Study, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Serena Sanna
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
- Istituto di Ricerca Genetica e Biomedica, National Research Council, Monserrato, Italy
| | - Mauro D'Amato
- Center for Molecular Medicine and Clinical Epidemiology Division, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
- Department of Gastrointestinal and Liver Diseases, Biodonostia Health Research Institute, San Sebastián, Spain
- Ikerbasque, Basque Science Foundation, Bilbao, Spain
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrew D Paterson
- Genetics and Genome Biology, The Hospital for Sick Children Research Institute, Toronto, Ontario, Canada
| | - Robert Kraaij
- Department of Internal Medicine, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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9
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Abstract
Parkinson's disease (PD) has classically been defined as a movement disorder, in which motor symptoms are explained by the aggregation of alpha-synuclein (α-syn) and subsequent death of dopaminergic neurons of the substantia nigra pars compacta (SNpc). More recently, the multisystem effects of the disease have been investigated, with the immune system being implicated in a number of these processes in the brain, the blood, and the gut. In this review, we highlight the dysfunctional immune system found in both human PD and animal models of the disease, and discuss how genetic risk factors and risk modifiers are associated with pro-inflammatory immune responses. Finally, we emphasize evidence that the immune response drives the pathogenesis and progression of PD, and discuss key questions that remain to be investigated in order to identify immunomodulatory therapies in PD.
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Affiliation(s)
- Aubrey M Schonhoff
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Gregory P Williams
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Zachary D Wallen
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - David G Standaert
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States
| | - Ashley S Harms
- Center for Neurodegeneration and Experimental Therapeutics, Department of Neurology, The University of Alabama at Birmingham, Birmingham, AL, United States.
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10
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Wallen ZD, Chen H, Hill-Burns EM, Factor SA, Zabetian CP, Payami H. Plasticity-related gene 3 ( LPPR1) and age at diagnosis of Parkinson disease. Neurol Genet 2018; 4:e271. [PMID: 30338293 PMCID: PMC6186025 DOI: 10.1212/nxg.0000000000000271] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 06/11/2018] [Indexed: 12/22/2022]
Abstract
Objective To identify modifiers of age at diagnosis of Parkinson disease (PD). Methods Genome-wide association study (GWAS) included 1,950 individuals with PD from the NeuroGenetics Research Consortium (NGRC) study. Replication was conducted in the Parkinson's, Genes and Environment study, including 209 prevalent (PAGEP) and 517 incident (PAGEI) PD cases. Cox regression was used to test association with age at diagnosis. Individuals without neurologic disease were used to rule out confounding. Gene-level analysis and functional annotation were conducted using Functional Mapping and Annotation of GWAS platform (FUMA). Results The GWAS revealed 2 linked but seemingly independent association signals that mapped to LPPR1 on chromosome 9. LPPR1 was significant in gene-based analysis (p = 1E-8). The top signal (rs17763929, hazard ratio [HR] = 1.88, p = 5E-8) replicated in PAGEP (HR = 1.87, p = 0.01) but not in PAGEI. The second signal (rs73656147) was robust with no evidence of heterogeneity (HR = 1.95, p = 3E-6 in NGRC; HR = 2.14, p = 1E-3 in PAGEP + PAGEI, and HR = 2.00, p = 9E-9 in meta-analysis of NGRC + PAGEP + PAGEI). The associations were with age at diagnosis, not confounded by age in patients or in the general population. The PD-associated regions included variants with Combined Annotation Dependent Depletion (CADD) scores = 10–19 (top 1%–10% most deleterious mutations in the genome), a missense with predicted destabilizing effect on LPPR1, an expression quantitative trait locus (eQTL) for GRIN3A (false discovery rate [FDR] = 4E-4), and variants that overlap with enhancers in LPPR1 and interact with promoters of LPPR1 and 9 other brain-expressed genes (Hi-C FDR < 1E-6). Conclusions Through association with age at diagnosis, we uncovered LPPR1 as a modifier gene for PD. LPPR1 expression promotes neuronal regeneration after injury in animal models. Present data provide a strong foundation for mechanistic studies to test LPPR1 as a driver of response to damage and a therapeutic target for enhancing neuroregeneration and slowing disease progression.
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Affiliation(s)
- Zachary D Wallen
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Honglei Chen
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Erin M Hill-Burns
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Stewart A Factor
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Cyrus P Zabetian
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | - Haydeh Payami
- Department of Neurology (Z.D.W., E.M.H.-B., H.P.), University of Alabama at Birmingham, Birmingham, AL; Department of Epidemiology and Biostatistics (H.C.), Michigan State University, East Lansing, MI; Department of Neurology (S.A.F.), Jean & Paul Amos Parkinson's Disease and Movement Disorder Program, Emory University School of Medicine, Atlanta, GA; VA Puget Sound Health Care System and Department of Neurology (C.P.Z.), University of Washington, Seattle, WA; and Center for Genomic Medicine (H.P.), HudsonAlpha Institute for Biotechnology, Huntsville, AL
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11
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Hill-Burns EM, Debelius JW, Morton JT, Wissemann WT, Lewis MR, Wallen ZD, Peddada SD, Factor SA, Molho E, Zabetian CP, Knight R, Payami H. Parkinson's disease and Parkinson's disease medications have distinct signatures of the gut microbiome. Mov Disord 2017; 32:739-749. [PMID: 28195358 DOI: 10.1002/mds.26942] [Citation(s) in RCA: 543] [Impact Index Per Article: 77.6] [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: 09/23/2016] [Revised: 01/06/2017] [Accepted: 01/11/2017] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There is mounting evidence for a connection between the gut and Parkinson's disease (PD). Dysbiosis of gut microbiota could explain several features of PD. OBJECTIVE The objective of this study was to determine if PD involves dysbiosis of gut microbiome, disentangle effects of confounders, and identify candidate taxa and functional pathways to guide research. METHODS A total of 197 PD cases and 130 controls were studied. Microbial composition was determined by 16S rRNA gene sequencing of DNA extracted from stool. Metadata were collected on 39 potential confounders including medications, diet, gastrointestinal symptoms, and demographics. Statistical analyses were conducted while controlling for potential confounders and correcting for multiple testing. We tested differences in the overall microbial composition, taxa abundance, and functional pathways. RESULTS Independent microbial signatures were detected for PD (P = 4E-5), participants' region of residence within the United States (P = 3E-3), age (P = 0.03), sex (P = 1E-3), and dietary fruits/vegetables (P = 0.01). Among patients, independent signals were detected for catechol-O-methyltransferase-inhibitors (P = 4E-4), anticholinergics (P = 5E-3), and possibly carbidopa/levodopa (P = 0.05). We found significantly altered abundances of the Bifidobacteriaceae, Christensenellaceae, [Tissierellaceae], Lachnospiraceae, Lactobacillaceae, Pasteurellaceae, and Verrucomicrobiaceae families. Functional predictions revealed changes in numerous pathways, including the metabolism of plant-derived compounds and xenobiotics degradation. CONCLUSION PD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypotheses on the pathophysiology and treatment of PD. © 2017 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Erin M Hill-Burns
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Justine W Debelius
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA
| | - James T Morton
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA
| | - William T Wissemann
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Matthew R Lewis
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Zachary D Wallen
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Shyamal D Peddada
- Biostatistics and Computational Biology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Stewart A Factor
- Department of Neurology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Eric Molho
- Department of Neurology, Albany Medical College, Albany, New York, USA
| | - Cyrus P Zabetian
- Veterans Affairs Puget Sound Health Care System and Department of Neurology, University of Washington, Seattle, Washington, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, California, USA.,Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Haydeh Payami
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA.,Center for Genomic Medicine, HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, USA
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