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Mikó E, Sipos A, Tóth E, Lehoczki A, Fekete M, Sebő É, Kardos G, Bai P. Guideline for designing microbiome studies in neoplastic diseases. GeroScience 2024:10.1007/s11357-024-01255-4. [PMID: 38922379 DOI: 10.1007/s11357-024-01255-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/12/2024] [Indexed: 06/27/2024] Open
Abstract
Oncobiosis has emerged as a key contributor to the development, and modulator of the treatment efficacy of cancer. Hereby, we review the modalities through which the oncobiome can support the progression of tumors, and the emerging therapeutic opportunities they present. The review highlights the inherent challenges and limitations faced in sampling and accurately characterizing oncobiome. Additionally, the review underscores the critical need for the standardization of microbial analysis techniques and the consistent reporting of microbiome data. We provide a suggested metadata set that should accompany microbiome datasets from oncological settings so that studies remain comparable and decipherable.
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Affiliation(s)
- Edit Mikó
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
| | - Adrienn Sipos
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
| | - Emese Tóth
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary
- HUN-REN-DE Cell Biology and Signaling Research Group, 4032, Debrecen, Hungary
| | - Andrea Lehoczki
- Department of Hematology and Stem Cell Transplantation, South Pest Central Hospital-National Institute for Hematology and Infectious Diseases, Budapest, Hungary
- Doctoral College, Health Sciences Program, Semmelweis University, Budapest, Hungary
- Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Monika Fekete
- Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Éva Sebő
- Breast Center, Kenézy Gyula Hospital, University of Debrecen, 4032, Debrecen, Hungary
| | - Gábor Kardos
- Department of Metagenomics, University of Debrecen, 4032, Debrecen, Hungary
- Faculty of Health Sciences, One Health Institute, University of Debrecen, 4032, Debrecen, Hungary
| | - Péter Bai
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem Tér 1., 4032, Debrecen, Hungary.
- HUN-REN-DE Cell Biology and Signaling Research Group, 4032, Debrecen, Hungary.
- MTA-DE Lendület Laboratory of Cellular Metabolism, 4032, Debrecen, Hungary.
- Research Center for Molecular Medicine, Faculty of Medicine, University of Debrecen, 4032, Debrecen, Hungary.
- Center of Excellence, The Hungarian Academy of Sciences, Budapest, Hungary.
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Liu Y, Yu J, Yang Y, Han B, Wang Q, Du S. Investigating the causal relationship of gut microbiota with GERD and BE: a bidirectional mendelian randomization. BMC Genomics 2024; 25:471. [PMID: 38745153 PMCID: PMC11092028 DOI: 10.1186/s12864-024-10377-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Gut microbiota(GM) have been proven associated with lots of gastrointestinal diseases, but its causal relationship with Gastroesophageal reflux disease(GERD) and Barrett's esophagus(BE) hasn't been explored. We aimed to uncover the causal relation between GM and GERD/BE and potential mediators by utilizing Mendelian Randomization(MR) analysis. METHODS Summary statistics of GM(comprising 301 bacteria taxa and 205 metabolism pathways) were extracted from MiBioGen Consortium(N = 18,340) and Dutch Microbiome Project(N = 7,738), GERD and BE from a multitrait meta-analysis(NGERD=602,604, NBE=56,429). Bidirectional two-sample MR analysis and linkage disequilibrium score regression(LDSC) were used to explore the genetic correlation between GM and GERD/BE. Mediation MR analysis was performed for the risk factors of GERD/BE, including Body mass index(BMI), weight, type 2 diabetes, major depressive disorder(MDD), smoking initiation, alcohol consumption, and dietary intake(including carbohydrate, sugar, fat, protein intake), to detect the potential mediators between GM and GERD/BE. RESULTS 11 bacterial taxa and 13 metabolism pathways were found associated with GERD, and 18 taxa and 5 pathways exhibited causal relationship with BE. Mediation MR analysis suggested weight and BMI played a crucial role in these relationships. LDSC identified 1 taxon and 4 metabolism pathways related to GERD, and 1 taxon related to BE. Specie Faecalibacterium prausnitzii had a suggestive impact on both GERD(OR = 1.087, 95%CI = 1.01-1.17) and BE(OR = 1.388, 95%CI = 1.03-1.86) and LDSC had determined their correlation. Reverse MR indicated that BE impacted 10 taxa and 4 pathways. CONCLUSIONS This study established a causal link between gut microbiota and GERD/BE, and identified the probable mediators. It offers new insights into the role of gut microbiota in the development and progression of GERD and BE in the host.
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Affiliation(s)
- Yuan Liu
- Graduate School of Beijing, University of Chinese Medicine, Beijing, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Jiali Yu
- Department of Gastroenterology, Chinese Academy of Medical Sciences & Peking Union Medical College, China-Japan Friendship Hospital(Institute of Clinical Medical Sciences), Beijing, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Yuxiao Yang
- Department of Gastroenterology, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Bingyu Han
- Graduate School of Beijing, University of Chinese Medicine, Beijing, China
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China
| | - Qiao Wang
- Graduate School of Beijing, University of Chinese Medicine, Beijing, China
- Department of Traditional Chinese Medicine for Pulmonary Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Shiyu Du
- Department of Gastroenterology, China-Japan Friendship Hospital, Beijing, China.
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Tang Y, Lin TC, Yang H, Zhou Y, Sibeko L, Liu Z. High-fat diet during early life reshapes the gut microbiome and is associated with the disrupted mammary microenvironment in later life in mice. Nutr Res 2024; 127:1-12. [PMID: 38763113 DOI: 10.1016/j.nutres.2024.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/22/2024] [Accepted: 04/27/2024] [Indexed: 05/21/2024]
Abstract
The influence of gut microbiota on gut health is well-documented, but it remains obscure for extraintestinal diseases such as breast cancer. Moreover, it is entirely unknown how gut dysbiosis during early life contributes to breast tumorigenesis later in life. In this study, we hypothesized that a high-fat diet during early life leads to alterations in the gut microbiome and is associated with disruptions in the mammary microenvironment. Female C57BL/6 mice were fed a low-fat diet (10% kcal fat) or a high-fat diet (HF, 60% kcal fat) for 8 weeks from the age of 4 to 12 weeks, which is equivalent to human childhood and adolescence. Twelve mice were sacrificed immediately after the 8-week feeding, the remainder were euthanized after switching to a normal lifecycle-supporting diet for an additional 12 weeks; the gut microbiome was then sequenced. The 8-week HF diet feeding altered the beta-diversity (Bray & Jaccard P < .01), and the difference remained significant after switching the diet (Bray & Jaccard P < .05). Immediately after HF feeding, a greater number of microbial taxa (>50) were altered, and about half of the taxa (25) remained significantly changed after switching the diet. The abundance of Alistipes, Bilophila, and Rikenellaceae stood out as significantly associated with multiple metabolic and inflammatory biomarkers in mammary tissue, including aromatase, Ccl2, and Cox2. In conclusion, an 8-week early-life HF feeding reshaped the gut microbiome, which connected with disrupted mammary microenvironments.
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Affiliation(s)
- Ying Tang
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA; Center for Regenerative Medicine and Skeletal Development, School of Dental Medicine, University of Connecticut Health Center, Farmington, CT, USA
| | - Ting-Chun Lin
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Hong Yang
- Department of Oncology and Pathology, Hunan Provincial People's Hospital, Changsha, China
| | - Yanjiao Zhou
- Department of Medicine, University of Connecticut Health Center, Farmington, CT, USA; Hunan, China
| | - Lindiwe Sibeko
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA
| | - Zhenhua Liu
- School of Public Health and Health Sciences, University of Massachusetts, Amherst, MA, USA; UMass Cancer Center, University of Massachusetts Chan Medical Chan Medical School, Worcester, MA, USA.
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Ding W, Chen L, Xia J, Dong G, Song B, Pei B, Li X. Causal relationships between gut microbrome and digestive system diseases: A two-sample Mendelian randomization study. Medicine (Baltimore) 2024; 103:e37735. [PMID: 38669367 PMCID: PMC11049755 DOI: 10.1097/md.0000000000037735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/06/2024] [Indexed: 04/28/2024] Open
Abstract
Growing evidences of recent studies have shown that gut microbrome are causally related to digestive system diseases (DSDs). However, causal relationships between the gut microbiota and the risk of DSDs still remain unclear. We utilized identified gut microbiota based on class, family, genus, order and phylum information and digestive system diseases genome-wide association study (GWAS) dataset for two-sample Mendelian randomization (MR) analysis. The inverse variance weighted (IVW) method was used to evaluate causal relationships between gut microbiota and 7 DSDs, including chronic gastritis, colorectal cancer, Crohn's disease, gastric cancer, gastric ulcer, irritable bowel syndrome and esophageal cancer. Finally, we verified the robustness of MR results based on heterogeneity and pleiotropy analysis. We discovered 15 causal associations with genetic liabilities in the gut microbiota and DSDs, such as genus Victivallis, genus RuminococcaceaeUCG005, genus Ruminococcusgauvreauiigroup, genus Oxalobacter and so on. Our MR analysis revealed that the gut microbiota is causally associated with DSDs. Further researches of the gut microbiota and the pathogenesis of DSDs are still significant and provide new methods for the prevention and treatment of DSDs.
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Affiliation(s)
- Wenjing Ding
- The Second Clinical Medical School, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Liangliang Chen
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Jianguo Xia
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Gang Dong
- The Second Clinical Medical School, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Biao Song
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Bei Pei
- The Second Clinical Medical School, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Xuejun Li
- Department of Gastroenterology, The Second Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
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Bao YQ, Zhang Y, Li ZN. Causal associations between gut microbiota and cutaneous melanoma: a Mendelian randomization study. Front Microbiol 2024; 15:1339621. [PMID: 38650882 PMCID: PMC11033470 DOI: 10.3389/fmicb.2024.1339621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
Background Cutaneous melanoma (CM) of the skin stands as the leading cause of mortality among skin cancer-related deaths. Despite the successes achieved with novel therapies such as immunotherapy and targeted therapy, their efficacy remains limited, necessitating further exploration of new treatment modalities. The gut microbiota and CM may be linked, as indicated by a growing body of preclinical and observational research. Nevertheless, the exact correlation between the intestinal microbiota and CM remains to be determined. Therefore, this study aims to assess the potential causal relationship between the gut microbiota and CM. Methods The study utilized exposure data obtained from the MiBioGen consortium's microbiome GWAS, which included a total of 18,340 samples gathered from 24 population-based cohorts. Data at the summary level for CM were acquired from the UK Biobank investigation. The main analytical strategy utilized in this research was the inverse variance weighted (IVW) technique, supported by quality assurance measures like the weighted median model, MR-Egger, simple model, and weighted model approaches. The Cochran's Q test was used to evaluate heterogeneity. To ascertain potential pleiotropy, we employed both the MR-Egger regression and the MR-PRESSO test. Sensitivity analysis was conducted using the leave-one-out method. Results The study found that the class Bacteroidia (OR = 0.997, 95% CI: 0.995-0.999, p = 0.027), genus Parabacteroides (OR = 0.997, 95% CI: 0.994-0.999, p = 0.037), order Bacteroidales (OR = 0.997, 95% CI: 0.995-0.999, p = 0.027), and genus Veillonella (OR = 0.998, 95% CI: 0.996-0.999, p = 0.046) have protective effects on CM. On the order hand, the genus Blautia (OR = 1.003, 95% CI: 1-1.006, p = 0.001) and phylum Cyanobacteria (OR = 1.002, 95% CI: 1-1.004, p = 0.04) are identified as risk factors for CM. Conclusion We comprehensively assessed the potential causal relationship between the gut microbiota and CM and identified associations between six gut microbiota and CM. Among these, four gut microbiota were identified as protective factors for CM, while two gut microbiota were identified as risk factors for CM. This study effectively established a causal relationship between the gut microbiota and CM, thereby providing valuable insights into the mechanistic pathways through which the microbiota impacts the progression of CM.
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Affiliation(s)
- Yan-Qiu Bao
- Department of Medical Research Center, Shaoxing People’s Hospital, Zhejiang University School of Medicine, Shaoxing, Zhejiang, China
- Department of Dermatology, Shaoxing People’s Hospital, Shaoxing, Zhejiang, China
| | - Ying Zhang
- Department of Dermatology, Shaoxing People’s Hospital, Shaoxing, Zhejiang, China
| | - Zhou-Na Li
- Department of Dermatology, Affiliated Hospital of Yanbian University, Yanji, Jilin, China
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Huang G, Zhong X, Zhang M, Xu M, Pei B, Qian D. The association between lipid biomarkers and osteoarthritis based on the National Health and Nutrition Examination Survey and Mendelian randomization study. Sci Rep 2024; 14:1357. [PMID: 38228737 DOI: 10.1038/s41598-024-51523-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/06/2024] [Indexed: 01/18/2024] Open
Abstract
To explore the association between lipid markers and osteoarthritis (OA). First, the National Health and Nutrition Examination Survey (NHANES) database was used to screen participants with lipid markers, OA and relevant covariates, and logistic regression was used to analyze the association between lipid markers and OA; Then, under the theoretical framework of Mendelian randomization (MR), two-sample MR was performed using GWAS data of lipid markers and OA to explore the causal association between the two, which was analyzed by inverse variance weighting (IVW) method. Heterogeneity test, sensitivity analysis and pleiotropy analysis were also performed. The NHANES database screened a total of 3706 participants, of whom 836 had OA and 2870 did not have OA. When lipid markers were used as continuous variables, multivariate logistic results showed an association between HDL, LDL and OA (HDL, OR (95%):1.01 (1.00, 1.01); LDL, OR (95%):1.00 (0.99, 1.00)). When lipid markers were used as categorical variables, multivariate logistic results showed the fourth quartile result of 0.713 (0.513, 0.992) for LDL relative to the first quartile. In MR study, the results of the IVW method for TG, TL, HDL and LDL showed OR (95% CI) of 1.06 (0.97-1.16), 0.95 (0.85-1.06), 0.94 (0.86-1.02) and 0.89 (0.80-0.998) with P-values of 0.21, 0.37. 013, 0.046. The heterogeneity tests and multiplicity analyses showed P-values greater than 0.05, and sensitivity analyses showed no abnormal single nucleotide polymorphisms. Through NHANES database and MR analyses, LDL was found to be a protective factor for OA, while HDL still needs further study. Our results provide new biomarkers for preventive and therapeutic strategies for OA.
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Affiliation(s)
- Guoxin Huang
- Department of Evidence-Based Medicine Center, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Xian Zhong
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu No.1 People's Hospital, Changshu, 215500, China
| | - Meiling Zhang
- Department of the second ward of Orthopedic, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China
| | - Ming Xu
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu No.1 People's Hospital, Changshu, 215500, China.
| | - Bin Pei
- Department of Evidence-Based Medicine Center, Xiangyang No.1 People's Hospital, Hubei University of Medicine, Xiangyang, 441000, China.
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, Changshu Hospital Affiliated to Soochow University, Changshu No.1 People's Hospital, Changshu, 215500, China.
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