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Genome-wide detection of human variants that disrupt intronic branchpoints.
Zhang, P, Philippot, Q, Ren, W, Lei, WT, Li, J, Stenson, PD, Palacín, PS, Colobran, R, Boisson, B, Zhang, SY, et al
Proceedings of the National Academy of Sciences of the United States of America. 2022;(44):e2211194119
Abstract
Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 human genes have been reported to alter splicing and cause disease by disrupting BP. However, until now, no computational approach was available to efficiently detect such variants in massively parallel sequencing data. We established a comprehensive human genome-wide BP database by integrating existing BP data and generating new BP data from RNA sequencing of lariat debranching enzyme DBR1-mutated patients and from machine-learning predictions. We characterized multiple features of BP in major and minor introns and found that BP and BP-2 (two nucleotides upstream of BP) positions exhibit a lower rate of variation in human populations and higher evolutionary conservation than the intronic background, while being comparable to the exonic background. We developed BPHunter as a genome-wide computational approach to systematically and efficiently detect intronic variants that may disrupt BP recognition. BPHunter retrospectively identified 40 of the 48 known pathogenic BP variants, in which we summarized a strategy for prioritizing BP variant candidates. The remaining eight variants all create AG-dinucleotides between the BP and acceptor site, which is the likely reason for missplicing. We demonstrated the practical utility of BPHunter prospectively by using it to identify a novel germline heterozygous BP variant of STAT2 in a patient with critical COVID-19 pneumonia and a novel somatic intronic 59-nucleotide deletion of ITPKB in a lymphoma patient, both of which were validated experimentally. BPHunter is publicly available from https://hgidsoft.rockefeller.edu/BPHunter and https://github.com/casanova-lab/BPHunter.
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Metagenomic analysis of the gut microbiome composition associated with vitamin D supplementation in Taiwanese infants.
Lei, WT, Huang, KY, Jhong, JH, Chen, CH, Weng, SL
Scientific reports. 2021;(1):2856
Abstract
Early childhood is a critical stage for the foundation and development of the gut microbiome, large amounts of essential nutrients are required such as vitamin D. Vitamin D plays an important role in regulating calcium homeostasis, and deficiency can impair bone mineralization. In addition, most people know that breastfeeding is advocated to be the best thing for a newborn; however, exclusively breastfeeding infants are not easily able to absorb an adequate amount of vitamin D from breast milk. Understanding the effects of vitamin D supplementation on gut microbiome can improve the knowledge of infant health and development. A total of 62 fecal sample from healthy infants were collected in Taiwan. Of the 62 infants, 31 were exclusively breastfed infants and 31 were mixed- or formula-fed infants. For each feeding type, one subgroup of infants received 400 IU of vitamin D per day, and the remaining infants received a placebo. In total, there are 15 breastfed and 20 formula-fed infants with additional vitamin D supplementation, and 16 breastfed and 11 formula-fed infants belong to control group, respectively. We performed a comparative metagenomic analysis to investigate the distribution and diversity of infant gut microbiota among different types of feeding regimes with and without vitamin D supplementation. Our results reveal that the characteristics of infant gut microbiota not only depend on the feeding types but also on nutrients intake, and demonstrated that the vitamin D plays an important role in modulating the infant gut microbiota, especially increase the proportion of probiotics in breast-fed infants.
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Prevention of Postdental Procedure Bacteremia: A Network Meta-analysis.
Zeng, BS, Lin, SY, Tu, YK, Wu, YC, Stubbs, B, Liang, CS, Yeh, TC, Chen, TY, Carvalho, AF, Lin, PY, et al
Journal of dental research. 2019;(11):1204-1210
Abstract
Postdental procedure bacteremia is common and troublesome. The comparative efficacy of multiple prophylactic interventions is unclear. We compared the efficacy of interventions for the prevention of postdental procedure bacteremia. We conducted a review of ClinicalKey, Cochrane CENTRAL, Embase, ProQuest, PubMed, ScienceDirect, Web of Science, and ClinicalTrials.gov from inception to December 4, 2018. Randomized controlled trials that evaluated prophylactic interventions for the prevention of postdental procedure bacteremia were eligible. The primary outcome was the incidence of postdental procedure bacteremia. A total of 24 trials were included with 2,147 participants. Our network meta-analysis demonstrated that intravenous administration of 1,000/200 mg of amoxicillin/clavulanate provided the least incidence of postdental procedure bacteremia among all the prophylactic interventions (odds ratio = 0.03, 95% CI = 0.00 to 0.63) as compared with the placebo/controls. Oral 3 g of amoxicillin had the least incidence of postdental procedure bacteremia among all oral or topical forms of prophylactic interventions (odds ratio = 0.10, 95% CI = 0.02 to 0.44) as compared with the placebo/controls. No serious adverse events, such as anaphylactic shock, mortality, and the development of antibiotic-resistant bacteria, were reported. None of the included subjects were of high risk of infectious endocarditis. Our network meta-analysis demonstrates that intravenous amoxicillin/clavulanate and oral amoxicillin might be the best prophylactic interventions in preventing postdental procedure bacteremia among all the oral/topical forms of interventions for the overall populations.
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The influence of prebiotic or probiotic supplementation on antibody titers after influenza vaccination: a systematic review and meta-analysis of randomized controlled trials.
Yeh, TL, Shih, PC, Liu, SJ, Lin, CH, Liu, JM, Lei, WT, Lin, CY
Drug design, development and therapy. 2018;12:217-230
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Influenza vaccination is widely used although concerns regarding its efficacy exist. Both prebiotics and probiotics have been shown to produce protective effects against influenza infection and may enhance the immune response to the vaccination, especially in the elderly. The aim of this systematic review and meta-analysis was to determine the effect of pre- and probiotics on immune response to the influenza vaccination. According to the existing literature, participants who took prebiotics or probiotics were found to have higher hemagglutination inhibition (HI) antibodies, meaning a reduced likelihood of the virus attaching to the host’s red blood cells. Based on these results, the authors conclude both pre- or probiotic supplementation may enhance immune response in three influenza strains. While these results are promising, larger controlled trials are warranted to confirm the effectiveness and establish best clinical practice for supplementation.
Abstract
BACKGROUND Influenza infection is a common disease with a huge disease burden. Influenza vaccination has been widely used, but concerns regarding vaccine efficacy exist, especially in the elderly. Probiotics are live microorganisms with immunomodulatory effects and may enhance the immune responses to influenza vaccination. METHODS We conducted a systematic review and meta-analysis to determine the influence of prebiotics/probiotics/synbiotics supplementation on vaccine responses to influenza vaccination. Studies were systematically identified from electronic databases up to July 2017. Information regarding study population, influenza vaccination, components of supplements, and immune responses were extracted and analyzed. Twelve studies, investigating a total of 688 participants, were included in this review. RESULTS Patients with prebiotics/probiotics supplements were found to have higher influenza hemagglutination inhibition antibody titers after vaccination (for A/H1N1, 42.89 vs 35.76, mean difference =7.14, 95% CI =2.73, 11.55, P=0.002; for A/H3N2, 105.4 vs 88.25, mean difference =17.19, 95% CI =3.39, 30.99, P=0.01; for B strain, 34.87 vs 30.73, mean difference =4.17, 95% CI =0.37, 7.96, P=0.03). CONCLUSION Supplementation with prebiotics or probiotics may enhance the influenza hemagglutination inhibition antibody titers in all A/H1N1, A/H3N2, and B strains (20%, 19.5%, and 13.6% increases, respectively). Concomitant prebiotics or probiotics supplementation with influenza vaccination may hold great promise for improving vaccine efficacy. However, high heterogeneity was observed and further studies are warranted.
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Does Vitamin D Deficiency Affect the Immunogenic Responses to Influenza Vaccination? A Systematic Review and Meta-Analysis.
Lee, MD, Lin, CH, Lei, WT, Chang, HY, Lee, HC, Yeung, CY, Chiu, NC, Chi, H, Liu, JM, Hsu, RJ, et al
Nutrients. 2018;(4)
Abstract
Influenza virus infection is a major global public health problem, and the efficacy of influenza vaccination is not satisfactory. Vitamin D is involved in many immune-mediated inflammatory processes. The impact of vitamin D levels on the immunogenic response to influenza vaccination is not clear. We performed a comprehensive literature search and systematic review of studies that investigated vitamin D and influenza vaccination. Data pertaining to study population, vaccine components, vitamin D levels, and immunogenic response were analyzed. Nine studies, with a combined study population of 2367 patients, were included in the systematic review. Four studies were included in the meta-analysis to investigate the influence of vitamin D deficiency (VDD) on the seroprotection (SP) rates and seroconversion (SC) rates following influenza vaccination. We found no significant association between vitamin D level and the immunogenic response to influenza vaccination. However, strain-specific differences may exist. We observed lower SP rates of influenza A virus subtype H3N2 (A/H3N2) and B strain in VDD patients than patients with normal vitamin D levels (A/H3N2: 71.8% vs. 80.1%, odds ratio (OR): 0.63, 95% confidence interval (CI): 0.43-0.91, p = 0.01; B strain: 69.6% vs. 76.4%, OR: 0.68, 95% CI: 0.5-0.93, p = 0.01). However, the SP rates of A/H1N1 and SC rates of all three strains were not significantly different in VDD and control groups. In conclusion, no association was observed between VDD and immunogenic response to influenza vaccination.
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Effect of Probiotics and Prebiotics on Immune Response to Influenza Vaccination in Adults: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.
Lei, WT, Shih, PC, Liu, SJ, Lin, CY, Yeh, TL
Nutrients. 2017;9(11)
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The influenza virus causes three to five million severe cases per year and currently the main way to minimise both morbidity and mortality is the influenza vaccine. Both prebiotics and probiotics have been shown to demonstrate protective effects against influenza infection. The aim of this systematic review and meta-analysis is to explore the effectiveness of probiotics and prebiotics on immune function in adults after an influenza vaccine. According to the existing literature, participants who took prebiotics or probiotics showed significant improvements in the immune response for three different strains of influenza vaccine. According to these results, the authors conclude that both pre- and pro- biotics can be used in adults prior to a seasonal influenza vaccine. Further large trials are required to both validate these findings as well as have a better understanding of the optimal dose and duration of supplementation.
Abstract
We conducted a meta-analysis to evaluate the effects of probiotics and prebiotics on the immune response to influenza vaccination in adults. We conducted a literature search of Pubmed, Embase, the Cochrane Library, the Cumulative Index to Nursing and Allied Health (CINAHL), Airiti Library, and PerioPath Index to Taiwan Periodical Literature in Taiwan. Databases were searched from inception to July 2017. We used the Cochrane Review risk of bias assessment tool to assess randomized controlled trial (RCT) quality. A total of 20 RCTs comprising 1979 adults were included in our systematic review. Nine RCTs including 623 participants had sufficient data to be pooled in a meta-analysis. Participants who took probiotics or prebiotics showed significant improvements in the H1N1 strain seroprotection rate (with an odds ratio (OR) of 1.83 and a 95% confidence interval (CI) of 1.19-2.82, p = 0.006, I² = 0%), the H3N2 strain seroprotection rate (OR = 2.85, 95% CI = 1.59-5.10, p < 0.001, I² = 0%), and the B strain seroconversion rate (OR = 2.11, 95% CI = 1.38-3.21, p < 0.001, I² = 0%). This meta-analysis suggested that probiotics and prebiotics are effective in elevating immunogenicity by influencing seroconversion and seroprotection rates in adults inoculated with influenza vaccines.