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      Causal association between gut microbiota and intrahepatic cholestasis of pregnancy: mendelian randomization study

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          Abstract

          Background

          Previous observational cohort studies have shown that the composition of the gut microbiota is related to the risk of intrahepatic cholestasis of pregnancy (ICP), although it is unclear if the association is causative. This study used Mendelian randomization (MR) to systematically examine whether the gut microbiota was causally linked to ICP.

          Methods

          We obtained the genome-wide association study (GWAS) summary statistics of gut microbiota and ICP from published GWASs. Maximum likelihood (ML), MR-Egger regression, weighted median, inverse variance weighted (IVW), and weighted model were used to investigate the causal association between gut microbiota and ICP. We further conducted a series of sensitivity analyses to confirm the robustness of the primary results of the MR analyses. Reverse MR analysis was performed on the bacterial taxa that were reported to be causally linked to ICP risk in forwarding MR analysis to evaluate the possibility of reverse causation.

          Results

          MR analysis revealed that phylum Tenericutes (OR: 1.670, 95%CI: 1.073–2.598, P = 0.023), class Bacteroidia (OR: 1.644, 95%CI: 1.031–2.622, P = 0.037), class Mollicutes (OR: 1.670, 95%CI: 1.073–2.598, P = 0.023), and order Bacteroidales (OR: 1.644, 95%CI: 1.031–2.622, P = 0.037), and were positively associated with the risk of ICP. And we identified that the relative abundance of genus Dialister (OR: 0.562, 95%CI: 0.323–0.977, P = 0.041), genus Erysipelatoclostridium (OR: 0.695, 95%CI: 0.490–0.987, P = 0.042), genus Eubacterium ( brachy group) (OR: 0.661, 95%CI: 0.497–0.880, P = 0.005), genus Eubacterium ( hallii group) (OR: 0.664, 95%CI: 0.451–0.977, P = 0.037), genus Holdemania (OR: 0.590, 95%CI: 0.414–0.840, P = 0.003), genus Ruminococcus ( torques group) (OR: 0.448, 95%CI: 0.235–0.854, P = 0.015), and genus Veillonella (OR: 0.513, 95%CI: 0.294–0.893, P = 0.018) were related to a lower risk of ICP. Additional sensitivity analyses confirmed the robustness of the association between specific gut microbiota composition and ICP. No evidence of reverse causality from ICP to identified bacterial taxa was found in the findings of the reverse MR analyses.

          Conclusions

          Under MR assumptions, our findings propose new evidence of the relationship between gut microbiota and ICP risk. Our results show that the gut microbiota may be useful target of intervention for ICP.

          Supplementary Information

          The online version contains supplementary material available at 10.1186/s12884-023-05889-8.

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          Most cited references35

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          Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression

          Background: The number of Mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. This is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. However, some genetic variants may not be valid instrumental variables, in particular due to them having more than one proximal phenotypic correlate (pleiotropy). Methods: We view Mendelian randomization with multiple instruments as a meta-analysis, and show that bias caused by pleiotropy can be regarded as analogous to small study bias. Causal estimates using each instrument can be displayed visually by a funnel plot to assess potential asymmetry. Egger regression, a tool to detect small study bias in meta-analysis, can be adapted to test for bias from pleiotropy, and the slope coefficient from Egger regression provides an estimate of the causal effect. Under the assumption that the association of each genetic variant with the exposure is independent of the pleiotropic effect of the variant (not via the exposure), Egger’s test gives a valid test of the null causal hypothesis and a consistent causal effect estimate even when all the genetic variants are invalid instrumental variables. Results: We illustrate the use of this approach by re-analysing two published Mendelian randomization studies of the causal effect of height on lung function, and the causal effect of blood pressure on coronary artery disease risk. The conservative nature of this approach is illustrated with these examples. Conclusions: An adaption of Egger regression (which we call MR-Egger) can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations. The approach provides a sensitivity analysis for the robustness of the findings from a Mendelian randomization investigation.
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            Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator

            ABSTRACT Developments in genome‐wide association studies and the increasing availability of summary genetic association data have made application of Mendelian randomization relatively straightforward. However, obtaining reliable results from a Mendelian randomization investigation remains problematic, as the conventional inverse‐variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. We present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. This estimator is consistent even when up to 50% of the information comes from invalid instrumental variables. In a simulation analysis, it is shown to have better finite‐sample Type 1 error rates than the inverse‐variance weighted method, and is complementary to the recently proposed MR‐Egger (Mendelian randomization‐Egger) regression method. In analyses of the causal effects of low‐density lipoprotein cholesterol and high‐density lipoprotein cholesterol on coronary artery disease risk, the inverse‐variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and MR‐Egger regression methods suggest a null effect of high‐density lipoprotein cholesterol that corresponds with the experimental evidence. Both median‐based and MR‐Egger regression methods should be considered as sensitivity analyses for Mendelian randomization investigations with multiple genetic variants.
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              Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases

              Horizontal pleiotropy occurs when the variant has an effect on disease outside of its effect on the exposure in Mendelian randomization (MR). Violation of the ‘no horizontal pleiotropy’ assumption can cause severe bias in MR. We developed the Mendelian Randomization Pleiotropy RESidual Sum and Outlier (MR-PRESSO) test to identify horizontal pleiotropic outliers in multi-instrument summary-level MR testing. We showed using simulations that MR-PRESSO is best suited when horizontal pleiotropy occurs in <50% of instruments. Next, we applied MR-PRESSO, along with several other MR tests to complex traits and diseases, and found that horizontal pleiotropy: (i) was detectable in over 48% of significant causal relationships in MR; (ii) introduced distortions in the causal estimates in MR that ranged on average from −131% to 201%; (iii) induced false positive causal relationships in up to 10% of relationships; and (iv) can be corrected in some but not all instances.
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                Author and article information

                Contributors
                yinsw1984@163.com
                Journal
                BMC Pregnancy Childbirth
                BMC Pregnancy Childbirth
                BMC Pregnancy and Childbirth
                BioMed Central (London )
                1471-2393
                5 August 2023
                5 August 2023
                2023
                : 23
                : 568
                Affiliations
                [1 ]GRID grid.412467.2, ISNI 0000 0004 1806 3501, Department of Obstetrics & Gynecology, , Shengjing Hospital of China Medical University, ; Shenyang, Liaoning Province 110004 China
                [2 ]GRID grid.412467.2, ISNI 0000 0004 1806 3501, Liaoning Key Laboratory of Maternal-Fetal Medicine, , Shengjing Hospital of China Medical University, ; Shenyang, Liaoning Province 110004 China
                Article
                5889
                10.1186/s12884-023-05889-8
                10403878
                37543573
                33dce7b8-d6c8-42e9-8c31-34a3c6d9a315
                © BioMed Central Ltd., part of Springer Nature 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

                History
                : 30 January 2023
                : 1 August 2023
                Funding
                Funded by: FundRef http://dx.doi.org/10.13039/501100005047, Natural Science Foundation of Liaoning Province;
                Award ID: 2022-MS-13
                Categories
                Research
                Custom metadata
                © BioMed Central Ltd., part of Springer Nature 2023

                Obstetrics & Gynecology
                intrahepatic cholestasis of pregnancy,gut microbiota,causal relationship,mendelian randomization,single nucleotide polymorphism,instrumental variable

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