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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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Ma X, Wen G, Zhao Z, Lu L, Li T, Gao N, Han G. Alternations in the human skin, gut and vaginal microbiomes in perimenopausal or postmenopausal Vulvar lichen sclerosus. Sci Rep 2024; 14:8429. [PMID: 38600101 PMCID: PMC11006835 DOI: 10.1038/s41598-024-58983-y] [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: 01/17/2024] [Accepted: 04/05/2024] [Indexed: 04/12/2024] Open
Abstract
Vulvar lichen sclerosus (VLS) is a chronic and progressive dermatologic condition that can cause physical dysfunction, disfigurement, and impaired quality of life. However, the etiology of VLS remains unknown. The vulvar skin, intestinal and vaginal microbiomes have been postulated to play important roles in the pathogenesis of this disease. The aim of this study was to compare the compositional characteristics of the vulvar skin, vagina, and gut microbiota between perimenopausal or postmenopausal VLS patients and healthy controls. The study involved six perimenopausal or postmenopausal VLS patients which were based on characteristic clinical manifestations and histologic confirmation and five healthy controls. The pruritus severity of each patient was evaluated using the NRS scale, and the dermatology-specific health-related quality of life was assessed using the Skindex-16. Metagenomic sequencing was performed, and the results were analyzed for alpha and beta diversity. LEfSe analysis were used to investigate the microbial alterations in vulvar skin, gut and vagina. KEGG databases were used to analyze differences in functional abundance. The study found significant differences in alpha diversity between the two groups in stool and vaginal samples (P < 0.05). Patients with VLS had a higher abundance of Enterobacter cloacae, Flavobacterium_branchiophilum, Mediterranea_sp._An20, Parabacteroides_johnsoniiand Streptococcus_bovimastitidis on the vulvar skin, while Corynebacterium_sp._zg-913 was less abundant compared to the control group. The relative abundance of Sphingomonas_sp._SCN_67_18, Sphingobium_sp._Ant17, and Pontibacter_sp_BT213 was significantly higher in the gut samples of patients with VLS.Paenibacillus_popilliae,Gemella_asaccharolytica, and Coriobacteriales_bacterium_DNF00809 compared to the control group. Additionally, the vaginal samples of patients with VLS exhibited a significantly lower relative abundance of Bacteroidales_bacterium_43_8, Bacteroides_sp._CAG:20, Blautia_sp._AM28-10, Fibrobacter_sp._UWB16, Lachnospiraceae_bacterium_AM25-39, Holdemania_filiformis, Lachnospiraceae_bacterium_GAM79, and Tolumonas_sp. Additionally, the butyrate-producing bacterium SS3/4 showed a significant difference compared to the controls. The study found a negative relationship between Sphingobium_sp._Ant17 in stool and Skindex-16 (P < 0.05), while Mediterranea_sp._An20 had a positive correlation with Skindex-16 (P < 0.05) in the skin. Additionally, our functional analysis revealed alterations in Aminoacyl_tRNA_biosynthesis, Glutathione_metabolism, the pentose phosphate pathway, and Alanine__aspartate_and_glutamate_metabolism in the VLS patient group. The study suggests that perimenopausal or postmenopausal patients with VLS have a modified microbiome in the vulvar skin, gut, and vagina. This modification is linked to abnormal energy metabolism, increased oxidative stress, and abnormal amino acid metabolism.
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Affiliation(s)
- Xiaolei Ma
- Department of Dermatology, Peking University International Hospital, Life Park Road No.1 Life Science Park of Zhong Guancun, Chang Ping District, Beijing, People's Republic of China.
| | - Guangdong Wen
- Department of Dermatology, Peking University People's Hospital, Beijing, People's Republic of China
| | - Zheng Zhao
- Department of Dermatology, Peking University International Hospital, Life Park Road No.1 Life Science Park of Zhong Guancun, Chang Ping District, Beijing, People's Republic of China
| | - Lulu Lu
- Department of Dermatology, Peking University International Hospital, Life Park Road No.1 Life Science Park of Zhong Guancun, Chang Ping District, Beijing, People's Republic of China
| | - Tianying Li
- Department of Pathology, Peking University International Hospital, Beijing, People's Republic of China
| | - Na Gao
- Department of Dermatology, Peking University International Hospital, Life Park Road No.1 Life Science Park of Zhong Guancun, Chang Ping District, Beijing, People's Republic of China
| | - Gangwen Han
- Department of Dermatology, Peking University International Hospital, Life Park Road No.1 Life Science Park of Zhong Guancun, Chang Ping District, Beijing, People's Republic of 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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Hu XZ, Fu LL, Ye B, Ao M, Yan M, Feng HC. Gut microbiota and risk of coronary heart disease: a two-sample Mendelian randomization study. Front Cardiovasc Med 2024; 11:1273666. [PMID: 38590695 PMCID: PMC10999620 DOI: 10.3389/fcvm.2024.1273666] [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: 08/07/2023] [Accepted: 03/12/2024] [Indexed: 04/10/2024] Open
Abstract
Background The relationship between gut microbiota composition and coronary heart disease (CHD) has been recently reported in several observational studies. However, the causal effect of gut microbiota on coronary heart disease is uncharted. Objective This study attempted to investigate the effect of gut microbiota on coronary heart disease by Mendelian randomization (MR) analysis. Methods Through the two-sample MR method, single-nucleotide polymorphisms relevant to gut microbiota were selected as instrument variables to evaluate the causal association between gut microbiota and the risk of CHD. Results According to the selection criteria of the inverse variance-weighted average method, Class Actinobacteria, Class Lentisphaeria, Family Clostridiales vadinBB60group, Genus Clostridium innocuum group, Genus Bifidobacterium, Genus Butyricicoccus, Genus Oxalobacter, Genus Turicibacter, and Order Victivallales, presented a suggestive association with coronary heart disease. Conclusion This two-sample Mendelian randomization study found that gut microbiota was causally associated with coronary heart disease. Further randomized controlled trials are needed to clarify the protective effect of probiotics on coronary heart disease and their specific protective mechanisms.
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Affiliation(s)
- Xiang-zhi Hu
- Medical College, Guizhou University, Guiyang, China
| | - Ling-ling Fu
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
| | - Bin Ye
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
| | - Man Ao
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
| | - Ming Yan
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
- Department of Oral and Maxillofacial Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hong-chao Feng
- Department of Oral and Maxillofacial Surgery, Guiyang Hospital of Stomatology, Guiyang, China
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Ma M, Zheng Z, Li J, He Y, Kang W, Ye X. Association between the gut microbiota, inflammatory factors, and colorectal cancer: evidence from Mendelian randomization analysis. Front Microbiol 2024; 15:1309111. [PMID: 38562480 PMCID: PMC10982360 DOI: 10.3389/fmicb.2024.1309111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 03/06/2024] [Indexed: 04/04/2024] Open
Abstract
Background Colorectal cancer (CRC) is one of the most common malignant tumors primarily affecting individuals over the age of 50 years. Recent studies have suggested that the dysbiosis of the gut microbiota, a community of microorganisms in the human gut, is closely associated with the occurrence and development of CRC. Additionally, inflammatory factors (IFs) have also been reported to play a significant role in the development of CRC. However, the causal relationships between the gut microbiota, IFs, and CRC remain unclear. Methods In this study, we performed Mendelian randomization (MR) analysis using publicly available genome-wide association study (GWAS) data to explore the causal relationship between the gut microbiota, IFs, and CRC. The gut microbiota GWAS data were obtained from the MiBioGen study, while the IFs GWAS data were derived from the comprehensive analysis of three independent cohorts. Causal relationship analysis was conducted using appropriate instrumental variables (IVs) and statistical models. Results MR analysis of the gut microbiota and CRC revealed a negative correlation between the Lachnospiraceae species in the gut and CRC risk, while a positive correlation was observed between Porphyromonadaceae species, Lachnospiraceae UCG010 genus, Lachnospira genus, and Sellimonas genus in the gut, and CRC risk. Additionally, we observed a causal relationship between IL-10 and CRC risk. These findings suggest that the dysbiosis of the gut microbiota might be associated with an increased risk of CRC and that specific bacterial groups may play a crucial role in the occurrence and development of CRC. Conclusion Using MR analysis, this study revealed the causal relationships between the gut microbiota, IFs, and CRC. The negative correlation between the Lachnospiraceae species in the gut and CRC risk, as well as the causal relationship between IL-10 and CRC, provide important clues for the potential roles of gut microbiota regulation and inflammatory factor control in the prevention and treatment of CRC.
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Affiliation(s)
| | | | | | | | - Weiming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Xin Ye
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Yang Z, Zhao T, Cheng H, Yang J. Microbiome-enabled genomic selection improves prediction accuracy for nitrogen-related traits in maize. G3 (BETHESDA, MD.) 2024; 14:jkad286. [PMID: 38113533 PMCID: PMC11090461 DOI: 10.1093/g3journal/jkad286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 05/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
Root-associated microbiomes in the rhizosphere (rhizobiomes) are increasingly known to play an important role in nutrient acquisition, stress tolerance, and disease resistance of plants. However, it remains largely unclear to what extent these rhizobiomes contribute to trait variation for different genotypes and if their inclusion in the genomic selection protocol can enhance prediction accuracy. To address these questions, we developed a microbiome-enabled genomic selection method that incorporated host SNPs and amplicon sequence variants from plant rhizobiomes in a maize diversity panel under high and low nitrogen (N) field conditions. Our cross-validation results showed that the microbiome-enabled genomic selection model significantly outperformed the conventional genomic selection model for nearly all time-series traits related to plant growth and N responses, with an average relative improvement of 3.7%. The improvement was more pronounced under low N conditions (8.4-40.2% of relative improvement), consistent with the view that some beneficial microbes can enhance N nutrient uptake, particularly in low N fields. However, our study could not definitively rule out the possibility that the observed improvement is partially due to the amplicon sequence variants being influenced by microenvironments. Using a high-dimensional mediation analysis method, our study has also identified microbial mediators that establish a link between plant genotype and phenotype. Some of the detected mediator microbes were previously reported to promote plant growth. The enhanced prediction accuracy of the microbiome-enabled genomic selection models, demonstrated in a single environment, serves as a proof-of-concept for the potential application of microbiome-enabled plant breeding for sustainable agriculture.
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Affiliation(s)
- Zhikai Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Tianjing Zhao
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Hao Cheng
- Department of Animal Science, University of California Davis, Davis, CA 95616, USA
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
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Chowdhury MR, Hone KGMS, Prévost K, Balthazar P, Avino M, Arguin M, Beaudoin J, Malick M, Desgagné M, Robert G, Scott M, Dubé J, Laforest-Lapointe I, Massé E. Optimizing Fecal Occult Blood Test (FOBT) Colorectal Cancer Screening Using Gut Bacteriome as a Biomarker. Clin Colorectal Cancer 2024; 23:22-34.e2. [PMID: 37980216 DOI: 10.1016/j.clcc.2023.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 11/20/2023]
Abstract
BACKGROUND Colorectal cancer (CRC) is a major cause of cancer mortality in the world. One of the most widely used screening tests for CRC is the immunochemical fecal occult blood test (iFOBT), which detects human hemoglobin from patient's stool sample. Although it is highly efficient in detecting blood from patients with gastro-intestinal lesions, such as polyps and cancers, the iFOBT has a high rate of false positive discovery. Recent studies suggested gut bacteria as a promising noninvasive biomarker for improving the diagnosis of CRC. In this study, we examined the composition of gut bacteria using iFOBT leftover from patients undergoing screening test along with a colonoscopy. METHODS After collecting data from more than 800 patients, we considered 4 groups for this study. The first and second groups were respectively "healthy" in which the patients had either no blood in their stool or had blood but no lesions. The third and fourth groups of patients had both blood in their stools with precancerous and cancerous lesions and considered either as low-grade and high-grade lesion groups, respectively. An amplification of 16S rRNA (V4 region) gene was performed, followed by sequencing along with various statistical and bioinformatic analysis. RESULTS We analyzed the composition of the gut bacteriome at phylum, class, genus, and species levels. Although members of the Firmicute phylum increased in the 3 groups compared to healthy patients, the phylum Actinobacteriota was found to decrease. Moreover, Blautia obeum and Anaerostipes hadrus from the phylum Firmicutes were increased and Collinsella aerofaciens from phylum Actinobacteriota was found decreased when healthy group is compared to the patients with high-grade lesions. Finally, among the 5 machine learning algorithms used to perform our analysis, both elastic net (AUC > 0.7) and random forest (AUC > 0.8) performs well in differentiating healthy patients from 3 other patient groups having blood in their stool. CONCLUSION Our study integrates the iFOBT screening tool with gut bacterial composition to improve the prediction of CRC lesions.
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Affiliation(s)
- Moumita Roy Chowdhury
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Karina Gisèle Mac Si Hone
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada; Department of Biology, University of Sherbrooke, Sherbrooke, Canada
| | - Karine Prévost
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Philippe Balthazar
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Mariano Avino
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Mélina Arguin
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Jude Beaudoin
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Mandy Malick
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Michael Desgagné
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Gabriel Robert
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Michelle Scott
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | - Jean Dubé
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada
| | | | - Eric Massé
- Department of Biochemistry and Functional Genomics, University of Sherbrooke, Sherbrooke, Canada.
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Hou J, Yang M, Wu X, Chen Q, Lu Y, Zhang J, Lin D. Epidermal microorganisms contributed to the toxic mechanism of nZVI and TCEP in earthworms by robbing metal elements and nutrients. ECO-ENVIRONMENT & HEALTH (ONLINE) 2024; 3:80-88. [PMID: 38323088 PMCID: PMC10844675 DOI: 10.1016/j.eehl.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Indexed: 02/08/2024]
Abstract
Disrupting effects of pollutants on symbiotic microbiota have been regarded as an important mechanism of host toxicity, with most current research focusing on the intestinal microbiota. In fact, the epidermal microbiota, which participates in the nutrient exchange between hosts and environments, could play a crucial role in host toxicity via community changes. To compare the contributions of intestinal and epidermal symbiotic microorganisms to host toxicity, this study designed single and combined scenarios of soil contamination [nano zero-valent iron (nZVI) and tris (2-chloroethyl) phosphate (TCEP)], and revealed the coupling mechanisms between intestinal/epidermal symbiotic bacterial communities and earthworm toxicological endpoints. Microbiome analysis showed that 15% of intestinal microbes were highly correlated with host endpoints, compared to 45% of epidermal microbes showing a similar correlation. Functional comparisons revealed that key species on the epidermis were mainly heterotrophic microbes with genetic abilities to utilize metal elements and carbohydrate nutrients. Further verifications demonstrated that when facing the co-contamination of nZVI and TCEP, certain symbiotic microorganisms became dominant and consumed zinc, copper, and manganese along with saccharides and amino acids, which may be responsible for the nutritional deficiencies in the host earthworms. The findings can enrich the understanding of the coupling relationship between symbiotic microorganisms and host toxicity, highlighting the importance of epidermal microorganisms in host resistance to environmental pollution.
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Affiliation(s)
- Jie Hou
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Meirui Yang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Xinyue Wu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Qiqi Chen
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Yuqi Lu
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Jianying Zhang
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- National Demonstration Center for Experimental Environment and Resources Education (Zhejiang University), Hangzhou 310058, China
| | - Daohui Lin
- Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
- Zhejiang Ecological Civilization Academy, Anji 313300, China
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Li H, Hu Y, Huang Y, Ding S, Zhu L, Li X, Lan M, Huang W, Lin X. The mutual interactions among Helicobacter pylori, chronic gastritis, and the gut microbiota: a population-based study in Jinjiang, Fujian. Front Microbiol 2024; 15:1365043. [PMID: 38419635 PMCID: PMC10899393 DOI: 10.3389/fmicb.2024.1365043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 03/02/2024] Open
Abstract
Objectives Helicobacter pylori (H. pylori) is a type of bacteria that infects the stomach lining, and it is a major cause of chronic gastritis (CG). H. pylori infection can influence the composition of the gastric microbiota. Additionally, alterations in the gut microbiome have been associated with various health conditions, including gastrointestinal disorders. The dysbiosis in gut microbiota of human is associated with the decreased secretion of gastric acid. Chronic atrophic gastritis (CAG) and H. pylori infection are also causes of reduced gastric acid secretion. However, the specific details of how H. pylori infection and CG, especially for CAG, influence the gut microbiome can vary and are still an area of ongoing investigation. The incidence of CAG and infection rate of H. pylori has obvious regional characteristics, and Fujian Province in China is a high incidence area of CAG as well as H. pylori infection. We aimed to characterize the microbial changes and find potential diagnostic markers associated with infection of H. pylori as well as CG of subjects in Jinjiang City, Fujian Province, China. Participants Enrollment involved sequencing the 16S rRNA gene in fecal samples from 176 cases, adhering to stringent inclusion and exclusion criteria. For our study, we included healthy volunteers (Normal), individuals with chronic non-atrophic gastritis (CNAG), and those with CAG from Fujian, China. The aim was to assess gut microbiome dysbiosis based on various histopathological features. QIIME and LEfSe analyses were performed. There were 176 cases, comprising 126 individuals who tested negative for H. pylori and 50 who tested positive defined by C14 urea breath tests and histopathological findings in biopsies obtained through endoscopy. CAG was also staged by applying OLGIM system. Results When merging the outcomes from 16S rRNA gene sequencing results, there were no notable variations in alpha diversity among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and H. pylori positive [Hp (+)] and H. pylori negative [Hp (-)] groups. Beta diversity among different groups show significant separation through the NMDS diagrams. LEfSe analyses confirmed 2, 3, and 6 bacterial species were in abundance in the Normal, CNAG, and CAG groups; 26 and 2 species in the OLGIM I and OLGIM II group; 22 significant phylotypes were identified in Hp (+) and Hp (-) group, 21 and 1, respectively; 9 bacterial species exhibited significant differences between individuals with CG who were Hp (+) and those who were Hp (-). Conclusion The study uncovered notable distinctions in the characteristics of gut microbiota among the following groups: Normal, CNAG, and CAG; OLGIM I and OLGIM II; and Hp (+) and Hp (-) groups. Through the analysis of H. pylori infection in CNAG and CAG groups, we found the gut microbiota characteristics of different group show significant difference because of H. pylori infection. Several bacterial genera could potentially serve as diagnostic markers for H. pylori infection and the progression of CG.
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Affiliation(s)
- Hanjing Li
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Yingying Hu
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Yanyu Huang
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Shanshan Ding
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Long Zhu
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Xinghui Li
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Meng Lan
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
| | - Weirong Huang
- Jinjiang Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Jinjiang, China
| | - Xuejuan Lin
- College of Traditional Chinese Medicine, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Research Base of Traditional Chinese Medicine Syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- Key Laboratory of Traditional Chinese Medicine Health Status Identification, Fuzhou, China
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10
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Feng K, Ren F, Xing Z, Zhao Y, Yang C, Liu J, Shang Q, Wang X, Wang X. Microbiome and its implications in oncogenesis: a Mendelian randomization perspective. Am J Cancer Res 2023; 13:5785-5804. [PMID: 38187050 PMCID: PMC10767327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 12/02/2023] [Indexed: 01/09/2024] Open
Abstract
The human microbiome, an intricate ecological network, has garnered significant attention due to its potential implications in oncogenesis. This paper delves into the multifaceted relationships between the microbiome, its metabolites, and cancer development, emphasizing the human intestinal tract as the primary microbial habitat. Highlighting the potential causative associations between microbial disturbances and cancer progression, we underscore the role of specific bacterial strains in various cancers, such as stomach and colorectal cancer. Traditional causality assessment methods, like randomized controlled trials (RCTs), have limitations. Therefore, we advocate using Mendelian Randomization (MR) as a powerful alternative to study causal relationships, leveraging genetic variants as instrumental variables. With the proliferation of genome-wide association studies, MR harnesses genetic variations to infer causality, which is especially beneficial when addressing confounders like diet and lifestyle that can skew microbial research. We systematically review MR's application in understanding the microbiome-cancer nexus, emphasizing its strengths and challenges. While MR offers a unique perspective on causality, it faces hurdles like horizontal pleiotropy and weak instrumental variable bias. Integrating MR with multi-omics data, encompassing genomics, transcriptomics, proteomics, and metabolomics, holds promise for future research, potentially heralding groundbreaking discoveries in microbiology and genetics. This comprehensive review underscores the critical role of the human microbiome in oncogenesis and champions MR as an indispensable tool for advancing our understanding in this domain.
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Affiliation(s)
- Kexin Feng
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Fei Ren
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Zeyu Xing
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Yifan Zhao
- School of Engineering, RMIT UniversityBundoora, VIC 3083, Australia
| | - Chenxuan Yang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Jiaxiang Liu
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Qingyao Shang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Xin Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
| | - Xiang Wang
- Department of Breast Surgical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021, China
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11
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Jiang Z, Mou Y, Wang H, Li L, Jin T, Wang H, Liu M, Jin W. Causal effect between gut microbiota and pancreatic cancer: a two-sample Mendelian randomization study. BMC Cancer 2023; 23:1091. [PMID: 37950180 PMCID: PMC10636952 DOI: 10.1186/s12885-023-11493-y] [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: 02/16/2023] [Accepted: 10/08/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Gut microbiota (GM) comprises a vast and diverse community of microorganisms, and recent studies have highlighted the crucial regulatory roles of various GM and their secreted metabolites in pancreatic cancer (PC). However, the causal relationship between GM and PC has yet to be confirmed. METHODS In the present study, we used two-sample Mendelian randomization (MR) analysis to investigate the causal effect between GM and PC, with genome-wide association study (GWAS) from MiBioGen consortium as an exposure factor and PC GWAS data from FinnGen as an outcome factor. Inverse variance weighted (IVW) was used as the primary method for this study. RESULTS At the genus level, we observed that Senegalimassilia (OR: 0.635, 95% CI: 0.403-0.998, P = 0.049) exhibited a protective effect against PC, while Odoribacter (OR:1.899, 95%CI:1.157-3.116, P = 0.011), Ruminiclostridium 9(OR:1.976,95%CI:1.128-3.461, P = 0.017), Ruminococcaceae (UCG011)(OR:1.433, 95%CI:1.072-1.916, P = 0.015), and Streptococcus(OR:1.712, 95%CI:1.071-1.736, P = 0.025) were identified as causative factors for PC. Additionally, sensitivity analysis, Cochran's Q test, the Mendelian randomization pleiotropy residual sum and outlier (MR-PRESSO), and MR-Egger regression indicated no heterogeneity, horizontal pleiotropy, or reverse causality between GM and PC. CONCLUSIONS Our analysis establishes a causal effect between specific GM and PC, which may provide new insights into the potential pathogenic mechanisms of GM in PC and the assignment of effective therapeutic strategies.
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Grants
- WKJ-ZJ-2201 Scientific research fund of national health commision of China, Key health science and technology program of Zhejiang Province
- WKJ-ZJ-2201 Scientific research fund of national health commision of China, Key health science and technology program of Zhejiang Province
- WKJ-ZJ-2201 Scientific research fund of national health commision of China, Key health science and technology program of Zhejiang Province
- WKJ-ZJ-2201 Scientific research fund of national health commision of China, Key health science and technology program of Zhejiang Province
- WKJ-ZJ-2201 Scientific research fund of national health commision of China, Key health science and technology program of Zhejiang Province
- 2022C03099 Key Project of social welfare program of Zhejiang Science and Technology Department,'Lingyan'Program
- 2022C03099 Key Project of social welfare program of Zhejiang Science and Technology Department,'Lingyan'Program
- 2022C03099 Key Project of social welfare program of Zhejiang Science and Technology Department,'Lingyan'Program
- 2022C03099 Key Project of social welfare program of Zhejiang Science and Technology Department,'Lingyan'Program
- 2022C03099 Key Project of social welfare program of Zhejiang Science and Technology Department,'Lingyan'Program
- Key Project of social welfare program of Zhejiang Science and Technology Department,’Lingyan’Program
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Affiliation(s)
- Zhichen Jiang
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Yiping Mou
- Department of General Surgery, Devision of Dastroenterology and Pancreas, Affiliated People's Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- Key Laboratory of Gastroenterology of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Huiju Wang
- Department of General Surgery, Devision of Dastroenterology and Pancreas, Affiliated People's Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- Key Laboratory of Gastroenterology of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Li Li
- Department of General Surgery, Devision of Dastroenterology and Pancreas, Affiliated People's Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China
- Key Laboratory of Gastroenterology of Zhejiang Province, Hangzhou, 310014, Zhejiang, China
| | - Tianyu Jin
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - He Wang
- The Second School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053, Zhejiang, China
| | - Mingyang Liu
- State Key Laboratory of Molecular Oncology, National Cancer Center, National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
| | - Weiwei Jin
- Department of General Surgery, Devision of Dastroenterology and Pancreas, Affiliated People's Hospital, Zhejiang Provincial People's Hospital, Hangzhou Medical College, Hangzhou, 310014, Zhejiang, China.
- Key Laboratory of Gastroenterology of Zhejiang Province, Hangzhou, 310014, Zhejiang, China.
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12
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Chen B, Diallo MT, Ma Y, Wang D. The association of vitamin D and digestive system cancers: a comprehensive Mendelian randomization study. J Cancer Res Clin Oncol 2023; 149:13155-13162. [PMID: 37479757 DOI: 10.1007/s00432-023-05140-z] [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: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND Hitherto, the association of vitamin D intake and digestive system cancers occurrence still causes disputation among the researchers. This study aimed to investigate the genetic relation between vitamin D ingestion and digestive system cancers (which are esophageal, gastric, hepatic, pancreatic, and colorectal cancers) by a two-sample Mendelian randomization (MR) analysis, using datasets derived from IEU OpenGWAS database. METHODS This study is based on a genome-wide association study (GWAS) for vitamin D and digestive system cancers, with a sample amount ranging from 218,792 to 496,946 European ancestry individuals. The study first investigated the causal relationship between vitamin D and each digestive system cancers using inverse-variance weighting (IVW), weighted medians, and MR-Egger regression and then used meta-analysis to summarize the IVW results for the different cancers. We also performed additional sensitivity tests to assess the validity of the results. RESULTS In this study, we screened out 117 SNPs as potential instrumental variables for 25(OH)D and identified 101 fixed SNPs as instrumental variables for digestive system cancers. The results of the IVW failed to reveal any causal relationship between the genetically predisposed vitamin D level and the risk of digestive system cancers (esophageal cancer p = 0.400, OR = 1.397, 95% CI 0.642-3.040; gastric cancer p = 0.796, OR = 0.939, 95% CI 0.585-1.510; hepatic cancer p = 0.347, OR = 1.445, 95% CI 0.671-3.109; pancreatic cancer p = 0.905, OR = 0.969, 95% CI 0.581-1.618; colorectal cancer p = 0.127, OR = 0.0.841, 95% CI 0.673-1.051). The pooled ORs (odds ratio) are 0.918 (95% CI 0.770-1.097, p = 0.348). CONCLUSION There is no causal relationship between vitamin D and the occurrence of digestive system cancers. The risk of digestive system cancers cannot be alleviated by merely increasing vitamin D intake.
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Affiliation(s)
- Bangquan Chen
- Clinical Medical College, Yangzhou University, Yangzhou, 225001, China
- Medical College of Yangzhou University, Yangzhou, 225001, China
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, 225001, China
- Yangzhou, Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, 225001, China
| | - Maladho Tanta Diallo
- Clinical Medical College, Yangzhou University, Yangzhou, 225001, China
- Medical College of Yangzhou University, Yangzhou, 225001, China
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, 225001, China
- Yangzhou, Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, 225001, China
| | - Yue Ma
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, 225001, China
- Yangzhou, Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, 225001, China
- Nanjing University, Nanjing, 210093, China
| | - Daorong Wang
- Department of Gastrointestinal Surgery, Northern Jiangsu Peoples's Hospital, No. 98 Nantong West Road, Yangzhou, 225001, Jiangsu Province, China.
- General Surgery Institute of Yangzhou, Yangzhou University, Yangzhou, 225001, China.
- Yangzhou, Key Laboratory of Basic and Clinical Transformation of Digestive and Metabolic Diseases, Yangzhou, 225001, China.
- North Jiangsu People's HospitalNanjing University School of Medicine, Yangzhou, 225001, China.
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13
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Wei Y, Huang L, Liu C, Qi M. Causal relationship between Gut Microbiota and Obstructive sleep apnea. Arch Gerontol Geriatr 2023; 113:105052. [PMID: 37148705 DOI: 10.1016/j.archger.2023.105052] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/12/2023] [Accepted: 04/29/2023] [Indexed: 05/08/2023]
Abstract
OBJECTIVE Although observational studies have identified relations between gut microbiota and obstructive sleep apnea (OSA), their causal links remain elusive. Hence, we aimed to investigate this causal relation using the Mendelian randomization (MR) approach. METHODS Summary-level gut microbiota data were acquired using the maximum available genome-wide association study (GWAS) from the MiBioGen consortium while obtaining summary-level OSA data using publicly available GWAS from the FinnGen Consortium. A two-sample MR analysis was used for assessing gut microbiota and OSA causal effect, using the inverse variance-weighted (IVW) approach as the primary analysis method. The results were further examined for pleiotropy and heterogeneity. Moreover, the reverse MR analysis did not find a causal relationship. RESULTS Four gut microbiota were found to have nominally significant association to OSA according to the IVW method. Among them, the family Peptostreptococcaceae (OR = 1.171, 95% CI: 1.027-1.334) and genus Coprococcus3 (OR = 1.163, 95% CI: 1.007-1.343), these two florae that may increase the risk of OSA. Family Acidaminococcaceae (OR = 0.843, 95% CI: 0.729-0.975) and genus Blautia (OR = 0.830, 95% CI: 0.708-0.972) may have an ameliorative effect on OSA. No evidence of pleiotropy or heterogeneity was found. CONCLUSIONS MR analysis indicated that a causal relation is existed between specific gut microbiota and OSA at the genetic prediction level, offering innovative perspectives into the mechanisms underlying gut microbiota-mediated OSA development.
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Affiliation(s)
- Yi Wei
- Department of Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan 250355, China
| | - Liyu Huang
- Department of Medical Imaging, Qingdao Hospital of Traditional Chinese Medicine, Qingdao 266014, China
| | - Chao Liu
- Department of Medical Imaging, Qingdao Hospital of Traditional Chinese Medicine, Qingdao 266014, China.
| | - Ming Qi
- Department of Primary Care, Hospital of Traditional Chinese Medicine, Qingdao 266014, China
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14
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Widjaja F, Rietjens IMCM. From-Toilet-to-Freezer: A Review on Requirements for an Automatic Protocol to Collect and Store Human Fecal Samples for Research Purposes. Biomedicines 2023; 11:2658. [PMID: 37893032 PMCID: PMC10603957 DOI: 10.3390/biomedicines11102658] [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: 09/04/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 10/29/2023] Open
Abstract
The composition, viability and metabolic functionality of intestinal microbiota play an important role in human health and disease. Studies on intestinal microbiota are often based on fecal samples, because these can be sampled in a non-invasive way, although procedures for sampling, processing and storage vary. This review presents factors to consider when developing an automated protocol for sampling, processing and storing fecal samples: donor inclusion criteria, urine-feces separation in smart toilets, homogenization, aliquoting, usage or type of buffer to dissolve and store fecal material, temperature and time for processing and storage and quality control. The lack of standardization and low-throughput of state-of-the-art fecal collection procedures promote a more automated protocol. Based on this review, an automated protocol is proposed. Fecal samples should be collected and immediately processed under anaerobic conditions at either room temperature (RT) for a maximum of 4 h or at 4 °C for no more than 24 h. Upon homogenization, preferably in the absence of added solvent to allow addition of a buffer of choice at a later stage, aliquots obtained should be stored at either -20 °C for up to a few months or -80 °C for a longer period-up to 2 years. Protocols for quality control should characterize microbial composition and viability as well as metabolic functionality.
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Affiliation(s)
- Frances Widjaja
- Division of Toxicology, Wageningen University & Research, 6708 WE Wageningen, The Netherlands;
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15
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Mingdong W, Xiang G, Yongjun Q, Mingshuai W, Hao P. Causal associations between gut microbiota and urological tumors: a two-sample mendelian randomization study. BMC Cancer 2023; 23:854. [PMID: 37697271 PMCID: PMC10496293 DOI: 10.1186/s12885-023-11383-3] [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: 02/16/2023] [Accepted: 09/06/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Dysbiosis of gut microbiota has been linked to numerous diseases, including cancer. The unique role of gut microbiota in urological tumors is gaining prominence. However, it is still controversial whether the dysbiosis of gut microbiota should be one of the etiological factors of bladder cancer (BCa), prostate cancer (PCa) or kidney cancer (KCa). MATERIALS AND METHODS The microbiome genome-wide association study (GWAS) from the MiBioGen consortium (18,340 samples of 24 population-based cohorts) was utilized as the exposure data. Additionally, outcomes data (951 BCa cases and 307,092 controls; 1,631 KCa cases and 238,678 controls; 79,148 PCa cases and 61,106 controls) were extracted from the GWAS of the FinnGen and PRACTICAL consortia. To detect the potential causative bacterial traits for BCa, PCa, and KCa, a two-sample Mendelian randomization (MR) analysis was performed, employing the inverse-variance weighted or Wald ratio method. Sensitivity analyses were subsequently conducted to explore the robustness of the primary results. Finally, the reverse MR analysis was undertaken to mitigate the reverse causation. RESULTS This study suggested that Bifidobacterium (p = 0.030), Actinobacteria (p = 0.037 for phylum, 0.041 for class), and Ruminococcustorques group (p = 0.018), exhibited an association with an increased risk of BCa using either the inverse-variance weighted or Wald ratio method. By utilizing the Wald ratio method, Allisonella (p = 0.004, p = 0.038) was associated with a decreased risk of BCa and PCa, respectively. Furthermore, Ruminococcustorques group (p = 0.028) and Erysipelatoclostridium (p = 0.048) were causally linked to an elevated risk of KCa. CONCLUSIONS This MR study supports that genetically predicted gut microbiota is causally related to BCa, PCa and KCa. Additionally, distinct bacterial traits are identified in relation to each tumor type.
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Affiliation(s)
- Wang Mingdong
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Gao Xiang
- Department of Otolaryngology Head and Neck Surgery, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Quan Yongjun
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Wang Mingshuai
- Department of Urology, Cancer Hospital, Chinese Academy of Medical Sciences, Beijing, China
| | - Ping Hao
- Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing, China.
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16
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Li H, Sheng D, Jin C, Zhao G, Zhang L. Identifying and ranking causal microbial biomarkers for colorectal cancer at different cancer subsites and stages: a Mendelian randomization study. Front Oncol 2023; 13:1224705. [PMID: 37538123 PMCID: PMC10395834 DOI: 10.3389/fonc.2023.1224705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/26/2023] [Indexed: 08/05/2023] Open
Abstract
Introduction The gut microbiome is directly involved in colorectal carcinogenesis, but much of the epidemiological evidence for the effect of the gut microbiome on colorectal cancer (CRC) risk comes from observational studies, and it is unclear whether identified microbial alterations are the cause or consequence of CRC development. Methods Univariate Mendelian randomization (MR) analysis and multivariate MR analysis based on Bayesian model averaging were performed to comprehensively explore the microbial risk factors associated with CRC. The Network Module Structure Shift method was used to identify microbial biomarkers associated with CRC. Mediation analysis was used to explore the dietary habits-microbiota-CRC pathway. Results The results of the four methods showed that 9 bacteria had a robust causal relationship with the development of CRC. Among them, Streptococcus thermophilus reduced the risk of CRC; Eubacterium ventriosum and Streptococcus were beneficial bacteria of malignant tumors of colon (CC); Erysipelotrichaceae was a protective factor for malignant tumors of rectal (CR); Bacteroides ovatus was a risk factor for benign tumors. Finally, the mediation analysis revealed 10 pathways by which dietary regulation bacteria affected the risk of CRC, including alcohol consumption increased the risk of CC by reducing the abundance of Eubacterium ventriosum (mediated proportion: 43.044%), and the mediated proportion of other pathways was 7.026%-34.22%. Discussion These findings will contribute to the understanding of the different carcinogenic mechanisms of intestinal flora in the colon and rectum and the risk of tumor transformation, thereby aiding CRC prevention, early screening, and the development of future strategies to reduce CRC risk.
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Affiliation(s)
- Hongfeng Li
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Dashuang Sheng
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chuandi Jin
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Guoping Zhao
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Zhang
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
- Microbiome-X, National Institute of Health Data Science of China, Cheeloo College of Medicine, Shandong University, Jinan, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- Shandong Children’s Microbiome Center, Children’s Hospital Affiliated to Shandong University, Jinan, China
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Su Q, Jin C, Bo Z, Yang Y, Wang J, Wang J, Zhou J, Chen Y, Zeng H, Chen G, Wang Y. Association between gut microbiota and gastrointestinal cancer: a two-sample bi-directional Mendelian randomization study. Front Microbiol 2023; 14:1181328. [PMID: 37533836 PMCID: PMC10390774 DOI: 10.3389/fmicb.2023.1181328] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 07/04/2023] [Indexed: 08/04/2023] Open
Abstract
Background The gut microbiome is closely related to gastrointestinal (GI) cancer, but the causality of gut microbiome with GI cancer has yet to be fully established. We conducted this two-sample Mendelian randomization (MR) study to reveal the potential causal effect of gut microbiota on GI cancer. Materials and methods Summary-level genetic data of gut microbiome were derived from the MiBioGen consortium and the Dutch Microbiome Project. Summary statistics of six GI cancers were drawn from United Kingdom Biobank. Inverse-variance-weighted (IVW), MR-robust adjusted profile score (MR-RAPS), and weighted-median (WM) methods were used to evaluate the potential causal link between gut microbiota and GI cancer. In addition, we performed sensitivity analyses and reverse MR analyses. Results We identified potential causal associations between 21 bacterial taxa and GI cancers (values of p < 0.05 in all three MR methods). Among them, phylum Verrucomicrobia (OR: 0.17, 95% CI: 0.05-0.59, p = 0.005) retained a strong negative association with intrahepatic cholangiocarcinoma after the Bonferroni correction, whereas order Bacillales (OR: 1.67, 95% CI: 1.23-2.26, p = 0.001) retained a strong positive association with pancreatic cancer. Reverse MR analyses indicated that GI cancer was associated with 17 microbial taxa in all three MR methods, among them, a strong inverse association between colorectal cancer and family Clostridiaceae1 (OR: 0.91, 95% CI: 0.86-0.96, p = 0.001) was identified by Bonferroni correction. Conclusion Our study implicates the potential causal effects of specific microbial taxa on GI cancer, potentially providing new insights into the prevention and treatment of GI cancer through specific gut bacteria.
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Affiliation(s)
- Qing Su
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Chen Jin
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhiyuan Bo
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Yang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Jingxian Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Juejin Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Junxi Zhou
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Yaqing Chen
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Hao Zeng
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
| | - Gang Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yi Wang
- Department of Epidemiology and Biostatistics, School of Public Health and Management, Wenzhou Medical University, Wenzhou, China
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18
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Hatcher C, Richenberg G, Waterson S, Nguyen LH, Joshi AD, Carreras-Torres R, Moreno V, Chan AT, Gunter M, Lin Y, Qu C, Song M, Casey G, Figueiredo JC, Gruber SB, Hampe J, Hampel H, Jenkins MA, Keku TO, Peters U, Tangen CM, Wu AH, Hughes DA, Rühlemann MC, Raes J, Timpson NJ, Wade KH. Application of Mendelian randomization to explore the causal role of the human gut microbiome in colorectal cancer. Sci Rep 2023; 13:5968. [PMID: 37045850 PMCID: PMC10097673 DOI: 10.1038/s41598-023-31840-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
The role of the human gut microbiome in colorectal cancer (CRC) is unclear as most studies on the topic are unable to discern correlation from causation. We apply two-sample Mendelian randomization (MR) to estimate the causal relationship between the gut microbiome and CRC. We used summary-level data from independent genome-wide association studies to estimate the causal effect of 14 microbial traits (n = 3890 individuals) on overall CRC (55,168 cases, 65,160 controls) and site-specific CRC risk, conducting several sensitivity analyses to understand the nature of results. Initial MR analysis suggested that a higher abundance of Bifidobacterium and presence of an unclassified group of bacteria within the Bacteroidales order in the gut increased overall and site-specific CRC risk. However, sensitivity analyses suggested that instruments used to estimate relationships were likely complex and involved in many potential horizontal pleiotropic pathways, demonstrating that caution is needed when interpreting MR analyses with gut microbiome exposures. In assessing reverse causality, we did not find strong evidence that CRC causally affected these microbial traits. Whilst our study initially identified potential causal roles for two microbial traits in CRC, importantly, further exploration of these relationships highlighted that these were unlikely to reflect causality.
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Affiliation(s)
- Charlie Hatcher
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - George Richenberg
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Samuel Waterson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
- North Bristol NHS Trust, Bristol, BS10 5NB, UK
| | - Long H Nguyen
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Amit D Joshi
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Robert Carreras-Torres
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Digestive Diseases and Microbiota Group, Girona Biomedical Research Institute (IDIBGI), 17190, Salt, Girona, Spain
| | - Victor Moreno
- Colorectal Cancer Group, ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Oncology Data Analytics Program, Catalan Institute of Oncology (ICO), Hospitalet de Llobregat, Barcelona, Spain
- Biomedical Research Centre Network for Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Clinical Sciences, Universitat de Barcelona Institute of Complex Systems (UBICS), Faculty of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain
| | - Andrew T Chan
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Marc Gunter
- International Agency for Research on Cancer, 150 Cours Albert Thomas, 69372, Lyon, CEDEX 08, France
| | - Yi Lin
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, 98109, USA
| | - Conghui Qu
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
- Division of Gastroenterology, Clinical and Translational Epidemiology Unit, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jane C Figueiredo
- Department of Medicine, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Stephen B Gruber
- Department of Preventive Medicine, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jochen Hampe
- Department of Medicine I, University Hospital Dresden, Technische Universität Dresden (TU Dresden), Dresden, Germany
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Mark A Jenkins
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC, Australia
| | - Temitope O Keku
- Center for Gastrointestinal Biology and Disease, University of North Carolina, Chapel Hill, NC, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Catherine M Tangen
- SWOG Statistical Center, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Anna H Wu
- Preventative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David A Hughes
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Malte C Rühlemann
- Institute of Clinical Molecular Biology, Christian Albrechts University of Kiel, Kiel, Germany
| | - Jeroen Raes
- Department of Microbiology and Immunology, Rega Instituut, KU Leuven, University of Leuven, Leuven, Belgium
- Center for Microbiology, VIB, Leuven, Belgium
| | - Nicholas J Timpson
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK
| | - Kaitlin H Wade
- MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, BS8 2BN, UK.
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Li J, Bai H, Qiao H, Du C, Yao P, Zhang Y, Cai Y, Jia Y, Wei X, Li C, Liu X, Wang W, Sun S, Feng C, Hu Y, Zhou Z, Zhang S, Zhang Y. Causal effects of COVID-19 on cancer risk: A Mendelian randomization study. J Med Virol 2023; 95:e28722. [PMID: 37185860 DOI: 10.1002/jmv.28722] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/21/2023] [Accepted: 04/03/2023] [Indexed: 05/17/2023]
Abstract
In contemporary literature, little attention has been paid to the association between coronavirus disease-2019 (COVID-19) and cancer risk. We performed the Mendelian randomization (MR) to investigate the causal associations between the three types of COVID-19 exposures (critically ill COVID-19, hospitalized COVID-19, and respiratory syndrome coronavirus 2 (SARS-CoV-2) infection) and 33 different types of cancers of the European population. The results of the inverse-variance-weighted model indicated that genetic liabilities to critically ill COVID-19 had suggestive causal associations with the increased risk for HER2-positive breast cancer (odds ratio [OR] = 1.0924; p-value = 0.0116), esophageal cancer (OR = 1.0004; p-value = 0.0226), colorectal cancer (OR = 1.0010; p-value = 0.0242), stomach cancer (OR = 1.2394; p-value = 0.0331), and colon cancer (OR = 1.0006; p-value = 0.0453). The genetic liabilities to hospitalized COVID-19 had suggestive causal associations with the increased risk for HER2-positive breast cancer (OR = 1.1096; p-value = 0.0458), esophageal cancer (OR = 1.0005; p-value = 0.0440) as well as stomach cancer (OR = 1.3043; p-value = 0.0476). The genetic liabilities to SARS-CoV-2 infection had suggestive causal associations with the increased risk for stomach cancer (OR = 2.8563; p-value = 0.0019) but with the decreasing risk for head and neck cancer (OR = 0.9986, p-value = 0.0426). The causal associations of the above combinations were robust through the test of heterogeneity and pleiotropy. Together, our study indicated that COVID-19 had causal effects on cancer risk.
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Affiliation(s)
- Jia Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haocheng Bai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Qiao
- Department of Orthopedics, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chong Du
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Peizhuo Yao
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yifan Cai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yiwei Jia
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xinyu Wei
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chaofan Li
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xuanyu Liu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Weiwei Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shiyu Sun
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Cong Feng
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yijian Hu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yinbin Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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