Firmicutes bacteria produce metabolites that maintain the intestinal barrier and mucosal immunity. Firmicutes are reduced in the intestinal microbiota of patients with ulcerative colitis (UC). In a ...phase 1b trial of patients with UC, we evaluated the safety and efficacy of SER-287, an oral formulation of Firmicutes spores, and the effects of vancomycin preconditioning on expansion (engraftment) of SER-287 species in the colon.
We conducted a double-blind trial of SER-287 in 58 adults with active mild-to-moderate UC (modified Mayo scores 4–10, endoscopic subscores ≥1). Participants received 6 days of preconditioning with oral vancomycin (125 mg, 4 times daily) or placebo followed by 8 weeks of oral SER-287 or placebo. Patients were randomly assigned (2:3:3:3) to groups that received placebo followed by either placebo or SER-287 once weekly, or vancomycin followed by SER-287 once weekly, or SER-287 once daily. Clinical end points included safety and clinical remission (modified Mayo score ≤2; endoscopic subscores 0 or 1). Microbiome end points included SER-287 engraftment (dose species detected in stool after but not before SER-287 administration). Engraftment of SER-287 and changes in microbiome composition and associated metabolites were measured by analyses of stool specimens collected at baseline, after preconditioning, and during and 4 weeks after administration of SER-287 or placebo.
Proportions of patients with adverse events did not differ significantly among groups. A higher proportion of patients in the vancomycin/SER-287 daily group (40%) achieved clinical remission at week 8 than patients in the placebo/placebo group (0%), placebo/SER-287 weekly group (13.3%), or vancomycin/SER-287 weekly group (17.7%) (P = .024 for vancomycin/SER-287 daily vs placebo/placebo). By day 7, higher numbers of SER-287 dose species were detected in stool samples from all SER-287 groups compared with the placebo group (P < .05), but this difference was not maintained beyond day 7 in the placebo/SER-287 weekly group. In the vancomycin groups, a greater number of dose species were detected in stool collected on day 10 and all subsequent time points through 4 weeks post dosing compared with the placebo group (P < .05). A higher number of SER-287 dose species were detected in stool samples on days 7 and 10 from subjects who received daily vs weekly SER-287 doses (P < .05). Changes in fecal microbiome composition and metabolites were associated with both vancomycin/SER-287 groups.
In this small phase 1b trial of limited duration, the safety and tolerability of SER-287 were similar to placebo. SER-287 after vancomycin was significantly more effective than placebo for induction of remission in patients with active mild to moderate UC. Engraftment of dose species was facilitated by vancomycin preconditioning and daily dosing of SER-287. ClinicalTrials.gov ID NCT02618187.
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Non-standard structured, multivariate data are emerging in many research areas, including genetics and genomics, ecology, and social science. Suitably defined pairwise distance measures are commonly ...used in distance-based analysis to study the association between the variables. In this work, we consider a linear quantile regression model for pairwise distances. We investigate the large sample properties of an estimator of the unknown coefficients and propose statistical inference procedures correspondingly. Extensive simulations provide evidence of satisfactory finite sample properties of the proposed method. Finally, we applied the method to a microbiome association study to illustrate its utility.
Yeast sporulation efficiency is a quantitative trait and is known to vary among experimental populations and natural isolates. Some studies have uncovered the genetic basis of this variation and have ...identified the role of sporulation genes (IME1, RME1) and sporulation-associated genes (FKH2, PMS1, RAS2, RSF1, SWS2), as well as non-sporulation pathway genes (MKT1, TAO3) in maintaining this variation. However, these studies have been done mostly in experimental populations. Sporulation is a response to nutrient deprivation. Unlike laboratory strains, natural isolates have likely undergone multiple selections for quick adaptation to varying nutrient conditions. As a result, sporulation efficiency in natural isolates may have different genetic factors contributing to phenotypic variation. Using Saccharomyces cerevisiae strains in the genetically and environmentally diverse SGRP collection, we have identified genetic loci associated with sporulation efficiency variation in a set of sporulation and sporulation-associated genes. Using two independent methods for association mapping and correcting for population structure biases, our analysis identified two linked clusters containing 4 non-synonymous mutations in genes - HOS4, MCK1, SET3, and SPO74. Five regulatory polymorphisms in five genes such as MLS1 and CDC10 were also identified as putative candidates. Our results provide candidate genes contributing to phenotypic variation in the sporulation efficiency of natural isolates of yeast.
BackgroundKLRG1 is an inhibitory receptor expressed on T and NK-cells. On CD8-T-cells, KLRG1 is expressed on highly differentiated antigen-specific effector memory T and CD45RA-effector memory T ...cells. These cells display strong anti-tumor cytotoxicity by releasing IFNg and TNFa, however this process is inhibited when KLRG1 is engaged by various tumor-expressed cadherins. The percentage of KLRG1+CD8-T-cells increases with age, suggesting why age is a risk factor for cancer. We hypothesized that patients with KLRG1+CD8-T-cells may benefit from an antagonistic antibody blocking KLRG1-cadherin interactions, thereby restoring the function of cytotoxic T and NK-cells, resulting in broad tumor-killing activity.MethodsAntibodies were generated by immunization of mice followed by humanization. Binding was measured by Octet and FACS using KLRG1-overexpressing cells. Blocking was studied using labelled KLRG1-tetramers. Assays measuring IFNg or TNFa used artificial antigen-presenting cells (aAPC) mixed with KLRG1+CD8-T-cells isolated from PBMCs from healthy donors or cancer patients or from dissociated tumors. A human IgG4-antibody was used as negative control. Cytotoxic assays employed BiTE molecules binding to CD3-expressing T-cells and CD19- or HER2-expressing target cells.ResultsPYX-102, an IgG4-antibody which targets human KLRG1, was isolated from a wild-type mouse hybridoma after immunization with hKLRG1-Fc. Binding affinity (EC50) to human KLRG1 expressed in ExpiCHO cells was 1.0nM. Binding to cynomolgus monkey or mouse KLRG1 was weak or not detected. PYX-102 blocked a hKLRG1-tetramer from binding to E-cadherin-overexpressing K562 cells (EC50=1.1nM). Furthermore, PYX-102 demonstrated binding to CD8-T-cells (2.3nM) and CD56+NK-cells (1.4nM) isolated from human PBMCs.Functionally, we utilized E-cadherin-expressing aAPC which also expressed TCR-activating ligands (TCR-CHO-K1-cells). When co-culturing these cells with KLRG1+CD8-T-cells from healthy donors, the addition of PYX-102 induced pro-inflammatory cytokines IFNg (1,243pg/mL with an EC50=0.29nM) and TNFa (206pg/mL, EC50=0.32 nM). Importantly, IFNg was also induced by PYX-102 when utilizing CCR7-CD8+T-cells from cancer patient PBMCs (1 prostate, 2 kidney) mixed with TCR-CHO-K1-cells. In the same assay but using CD8+tumor-infiltrating lymphocytes (TIL) isolated from 2 dissociated kidney cancers, IFNg-producing CD8+TIL cells were increased by PYX-102. Lastly, using BiTE molecules (CD3xCD19 or CD3xHER2) to bring KLRG1-enriched CD8-T-cells in proximity to CD19- or HER2-expressing target cells, PYX-102 reduced viability of HEK-CD19-E-cadherin or HCC2935-HER2-E-cadherin target cells. Tumor antigen-specific KLRG1+CD8-T-cells were observed in breast, lung, kidney, ovarian, esophageal and colorectal tumors which are known to express cadherins, strongly supporting the rational for targeting KLRG1+CD8-T-cells.ConclusionsOur data on PYX-102, which blocks the KLRG1-cadherin interaction and leads to activation of CD8-T-cells, supports further development of this promising and innovative anti-cancer experimental therapeutic.
Current therapies for recurrent
infection do not address the disrupted microbiome, which supports
spore germination into toxin-producing bacteria. SER-109 is an investigational microbiome therapeutic ...composed of purified Firmicutes spores for the treatment of recurrent
infection.
We conducted a phase 3, double-blind, randomized, placebo-controlled trial in which patients who had had three or more episodes of
infection (inclusive of the qualifying acute episode) received SER-109 or placebo (four capsules daily for 3 days) after standard-of-care antibiotic treatment. The primary efficacy objective was to show superiority of SER-109 as compared with placebo in reducing the risk of
infection recurrence up to 8 weeks after treatment. Diagnosis by toxin testing was performed at trial entry, and randomization was stratified according to age and antibiotic agent received. Analyses of safety, microbiome engraftment, and metabolites were also performed.
Among the 281 patients screened, 182 were enrolled. The percentage of patients with recurrence of
infection was 12% in the SER-109 group and 40% in the placebo group (relative risk, 0.32; 95% confidence interval CI, 0.18 to 0.58; P<0.001 for a relative risk of <1.0; P<0.001 for a relative risk of <0.833). SER-109 led to less frequent recurrence than placebo in analyses stratified according to age stratum (relative risk, 0.24 95% CI, 0.07 to 0.78 for patients <65 years of age and 0.36 95% CI, 0.18 to 0.72 for those ≥65 years) and antibiotic received (relative risk, 0.41 95% CI, 0.22 to 0.79 with vancomycin and 0.09 95% CI, 0.01 to 0.63 with fidaxomicin). Most adverse events were mild to moderate and were gastrointestinal in nature, with similar numbers in the two groups. SER-109 dose species were detected as early as week 1 and were associated with bile-acid profiles that are known to inhibit
spore germination.
In patients with symptom resolution of
infection after treatment with standard-of-care antibiotics, oral administration of SER-109 was superior to placebo in reducing the risk of recurrent infection. The observed safety profile of SER-109 was similar to that of placebo. (Funded by Seres Therapeutics; ECOSPOR III ClinicalTrials.gov number, NCT03183128.).
Genome-wide association studies (GWAS) have become an important method for mapping the genetic loci underlying complex phenotypic traits in many species. A crucial issue when performing GWAS is to ...control for the underlying population structure because not doing so can lead to spurious associations. Population structure is a particularly important issue in nonhuman species since it is often difficult to control for population structure during the study design phase, requiring population structure to be corrected statistically after the data have been collected. It has not yet been established if GWAS is a feasible approach in Saccharomyces cerevisiae, an important model organism and agricultural species. We thus performed an empirical study of statistical methods for controlling for population structure in GWAS using a set of 201 phenotypic traits measured in multiple resequenced strains of S. cerevisiae. We complemented our analysis of real data with an extensive set of simulations. Our main result is that a mixed linear model using the local ancestry of the strain as a covariate is effective at controlling for population structure, consistent with the mosaic structure of many S. cerevisiae strains. We further studied the evolutionary forces acting on the GWAS SNPs and found that SNPs associated with variation in phenotypic traits are enriched for low minor allele frequencies, consistent with the action of negative selection on these SNPs. Despite the effectiveness of local ancestry correction, GWAS remains challenging in highly structured populations, such as S. cerevisiae. Nonetheless, we found that, even after correcting for population structure, there is still sufficient statistical power to recover biologically meaningful associations.
Abstract
Background
The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the phase 3 ECOSPOR ...III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live; VOWST Oral Spores VOS, formerly SER-109; Seres Therapeutics) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI).
Methods
Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and weeks 1, 2, 8, and 24 posttreatment.
Results
Baseline (n = 151) and serial posttreatment stool samples collected through 24 weeks (total N = 472) from 182 patients (59.9% female; mean age: 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single time point from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated versus the healthy cohort. By week 1, there was a greater decline in ARG abundance in VOS versus placebo (P = .003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non–spore-forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated.
Conclusions
This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.
In a post hoc analysis of ECOSPOR III study patients with recurrent Clostridioides difficile infection, VOWST Oral Spores rapidly and significantly reduced antimicrobial resistance genes compared with placebo, supporting microbiome therapeutics as a potential novel approach to combatting antimicrobial resistance.
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