Primary sclerosing cholangitis (PSC) is a progressive, chronic cholestatic liver disease characterized by inflammatory and fibrotic destruction of the intrahepatic and/or extrahepatic bile ducts. PSC often progresses to biliary cirrhosis, portal hypertension, and liver failure (1,2). In up to 80% of patients (3), ulcerative colitis (UC) or Crohn's disease (CD) will also be present (1). Medications used for the treatment of UC have not been effective in reducing inflammation or bringing about remission in PSC (4,5). Currently, there is no Food and Drug Administration–approved medical therapy for PSC.
It has been postulated that bacteria may stimulate an aberrant immune response resulting in the perpetuation of the biliary inflammation seen in PSC. One hypothesis is that bacteria gain access to the liver and biliary tree through translocation across an abnormal and inflamed intestinal mucosa into the portal venous system (5,6). In addition, the immune reaction in PSC is believed to be mediated by autoantibodies, including perinuclear anti-neutrophil cytoplasmic antibody, that recognize the bacterial antigen cell division protein FtsZ (7). Animal models have demonstrated that an enteric dysbiosis can lead to hepatobiliary inflammation with features similar to PSC (5). A dysbiosis has been identified in patients with PSC, distinct from those with inflammatory bowel disease (IBD) without PSC. In addition, unique microbial signatures have been identified in the bile of patients with PSC, strengthening this hypothesis (8,9). However, the concept of a general dysbiosis is controversial, and in this article, we will use it as a dependent change in the hosts' microbiota, which falls outside of the normal parameter space for that individual (10).
However, there has been limited success using antibiotics in treating PSC. Metronidazole has been shown to result in modest improvement in liver enzymes (11). Oral vancomycin has also been advanced as a potentially promising therapy (12). An initial report of 3 pediatric patients and a subsequent small, uncontrolled series of oral vancomycin in 14 children showed improvement in liver tests and symptoms (13,14); however, this has not been replicated in adults (15).
Recent advances in fecal microbiota transplantation (FMT) are changing the treatment paradigm for recurrent Clostridioides difficile infection but are also leading to a better understanding of the microbial contribution to other chronic diseases (16). Four randomized trials and numerous case reports suggest that FMT may be a promising therapy for UC (17). Therefore, restoration of the microbiome is a reasonable target for therapy in PSC because there is no treatment, given the complexity of PSC-IBD and the known interactions between genes, mucosal immunity, immune cell tracking, and the microbiome (18).
An open-label, investigator-initiated, single-center pilot academic study (Brigham and Women's Hospital Clinical Trials Center) enrolled patients with PSC with concurrent IBD between January 2016 and June 2017 (19). Eligible patients were adults aged 18 years or older and required a confirmed diagnosis of PSC with typical cholangiographic findings >6 months in duration, alkaline phosphatase (ALP) > 1.5× the upper limit of normal, and no evidence of cirrhosis on the last magnetic resonance cholangiopancreatography (within 6 months). In addition, patients were required to have documentation of typical histopathology for UC or CD with colonic involvement. A 4-week washout period for ursodeoxycholic acid (UDCA) was required. Exclusion criteria included cirrhosis, isolated small bowel CD, patients who were pregnant or nursing, patients who were unable or unwilling to undergo a colonoscopy, active malignancy, chronic kidney disease (glomerular filtration rate <60 mL/min/1.72 m2), or history of valvular heart disease. Patients who had taken UDCA within 4 weeks of screening, antibiotics within 2 months of screening, or probiotics within 1 month of screening were excluded. Patients on biologic therapy for their IBD were also excluded. Azathioprine and mesalamine/5-ASA were permitted as concomitant therapies.
Liver enzyme profiles, stool microbiota analysis, and metabolomic profiling were conducted at baseline and weeks 1, 4, 8, 12, and 24 post-FMT. The primary outcome was safety. The secondary efficacy outcome was a decrease in ALP levels ≥50% from baseline at any point during the 24-week post-FMT follow-up period. ALP was selected to be aligned with international consensus guidelines (20), although a more conservative target of ≥50% decrease was chosen, given its imprecision. Additional secondary outcomes include microbial diversity post-FMT compared with baseline and bile acid profiles post-FMT compared with pre-FMT samples and the donor. The study protocol conformed to the ethical guidelines of the 1975 Declaration of Helsinki and was approved by the Institutional Review Board at the Brigham and Women's Hospital, and all patients provided written informed consent before participation (NCT02424175). In addition, Food and Drug Administration approval via investigational new drug application (IND 16324, 2015) was obtained.
Given that there are no data on the effect size of FMT in PSC, this was designed as a proof-of-concept safety study. A sample size of 10 was chosen for feasibility, given the rarity of this disease.
Fecal microbiota transplantation preparation
Screening of the donor
Donor material was produced at a large stool bank based on a previously described protocol (OpenBiome, Somerville) (21). Briefly, donors were subjected to rigorous health and infection screening processes. Potential donors underwent an on-site clinical assessment and a 200-point health questionnaire. Thereafter, the potential donor undergoes a battery of stool and serological tests, aimed at screening for bacterial, viral, and fungal infectious diseases (22).
Fecal microbiota transplantation
All participants underwent a standard-of-care bowel preparation with polyethylene glycol on the day before the colonoscopy. No antibiotics were administered before the FMT. Colonoscopy was performed to the cecum with fecal material administered in the right colon. All patients received material (90 mL) from a single donor.
Microbiota composition analysis
16S rRNA gene sequencing.
Stool samples were collected for sequencing from donors and patients at baseline and weeks 1, 4, 8, 12, and 24 post-FMT. Samples were stored by flash freezing at −80°C. DNA extraction, PCR amplification of the 16S rRNA gene's V4 region, and Illumina paired-end sequencing were performed at the University of Michigan core facility, as described previously (23).
16S rRNA gene processing.
Primers were trimmed, paired ends merged, and de novo operational taxonomic units (OTUs) identified with a custom pipeline. To have maximum resolution for engraftment analysis, OTUs were defined by unique 16S rRNA gene sequences, i.e., 100% sequence identity. OTUs represented in fewer than 2 unique samples were discarded, resulting in a final median depth of 26,988 reads/sample and 64,510 OTUs across the study. Taxonomic assignments for each OTU were called using UTAX trained on the RDP database.
Bacterial community analysis.
Samples were rarefied to the lowest sample read count (2,592 reads) for alpha diversity analysis. Paired t-tests were used to compare diversity or donor similarity before vs after FMT, and independent t-tests were used for all other comparisons. Because previous reports have consistently shown low diversity in PSC microbiomes (24,25) and that healthy donor FMT increases diversity (26), all reported P values are 1-sided. For each patient, engrafting OTUs were identified based on the presence in both the FMT donor and the patient's first post-FMT stool sample, as well as depletion in the patient's pre-FMT stool sample. Engrafting OTUs were classified as “frequent engrafters” if they were observed as engrafting in greater than half the patients. Correlations with ALP improvement were performed by transforming unrarefied OTU read counts to relative abundances, subtracting baseline abundances, averaging across all post-FMT samples for each patient, and calculating the Spearman's rank correlation to the patient's baseline-normalized ALP level at 24 weeks post-FMT.
ULTRA PERFORMANCE LIQUID CHROMATOGRAPHY–MASS SPECTROMETRY PROFILING AND ANALYSIS OF FECAL BILE ACIDS
Stool sample preparation for UPLC-MS was performed as previously described (27). Stool extract bile acid analysis was obtained using ACQUITY UPLC (Waters, Elstree, United Kingdom) coupled to a Xevo G2 Q-ToF mass spectrometer equipped with an electrospray ionization source operating in the negative ion mode, using the method described by Sarafian et al. (28)
Quality control (QC) samples were prepared through the pooling of equal volumes of the fecal filtrates. QC samples were used as an assay performance monitor (29) and as a proxy to remove features with high variation. In addition, QC samples were spiked with mixtures of bile acid standards [55 bile acid standards, including 36 nonconjugated, 12 conjugated with taurine, and 7 conjugated with glycine (Steraloids, Newport, RI)] and were coanalyzed with the stool extracts to determine the chromatographic retention times of bile acids and to facilitate the identification of metabolites.
Waters raw data files were converted to NetCDF format, and data were extracted using XCMS (v1.50) package with R (v3.1.1) software. Probabilistic quotient normalization (30) was applied to correct for dilution effects, and chromatographic features with coefficient of variation >30% in QC samples were excluded from further analysis. The relative intensities of the features were corrected to the dry weight of the stool samples. Secondary bile acids were defined as those produced from primary bile acids via gut microbial 7alpha-dehydroxylation, whereas tertiary bile acids were those produced from primary bile acids via processes involving other forms of microbial modification, e.g., 7alpha-/beta-isomerization of chenodeoxycholic acid to form UDCA.
Multivariate analysis of ultra performance liquid chromatography–mass spectrometry bile acid profiling data was performed on pareto-scaled data. Statistical analysis of bile acid data was performed using GraphPad Prism, v7.03.
Ten patients were enrolled and underwent a single FMT from a single donor. Among the cohort, the mean age was 41.1 years (SD 15.7), 8 patients (80%) were men, and 9 (90%) had large-duct PSC. Nine patients had concurrent UC (6 with total Mayo score 0 and 3 with total Mayo score 1), and 1 had Crohn's colitis (Harvey Bradshaw Index 0 and Crohn's Disease Endoscopic Index of Severity 0). The mean baseline ALP level was 489 U/L (Table 1). Six patients were withdrawn from UDCA before the start of the study.
With regard to the primary outcome, safety, there were no related adverse events. Specifically, there were no serious and non–serious-related adverse events including deaths or infectious complications. Only 1 serious adverse event was noted and believed to be unrelated to the FMT. One patient had an episode of sinusitis that occurred 54 days post-FMT and required an emergency department visit and a course of doxycycline. In addition, 1 patient did not tolerate being off UDCA, and after discussion with his treating hepatologist, this treatment was restarted before the week 4 visit. Given any changes in liver biochemistries would be difficult to interpret in this patient, we have removed this patient from the per protocol analysis.
With regard to the secondary analysis, overall, the intention-to-treat analysis revealed that 3/10 patients (30%) experienced a ≥50% decrease in ALP levels. Although less important in cholestatic disease, 70% (7/10) experienced a 30% decrease (exploratory post hoc analysis) in at least one of their serum liver enzymes [alanine aminotransferase (ALT) and aspartate aminotransferase (AST)] post-FMT.
In terms of the per protocol analysis, 33% (3/9) of patients with PSC experienced a ≥50% decrease in ALP levels (Figure 1), and 77% (7/9) experienced a 30% decrease in at least one of their liver biomarkers (ALT and AST) post-FMT.
Microbiota composition analysis
The composition of the microbiota of patients with PSC differed from that of the donor at baseline pre-FMT and is more similar to the composition of the donor 1 week post-FMT (Figure 2, Figure 3). In addition, there was a trend toward lower pre-FMT PSC community diversity compared with that of healthy donors (Figure 3, P = 0.053). Diversity and similarity to donor increased in all patients post-FMT, with changes seen as early as week 1 (P ≤ 0.01) (Figure 3), and maintained an upward trend throughout week 24 (Figure 3). Most patients showed global microbiome engraftment signals, including increased diversity and similarity to donor, that were stable over the study duration (Figure 3). A total of 2,204 engrafter OTUs, defined as OTUs present in the donor, missing pre-FMT, and present in patients 1 week post-FMT, were delivered (Figure 4). Engrafter OTUs represented a diverse set of taxonomic classes and included Desulfovibrio and Faecalibacterium, which have been previously identified as depleted in PSC (24,25). Importantly, abundance of frequently engrafting OTUs in patients post-FMT tended to be correlated with decreased ALP levels (Figure 5). OTUs associated with ALP improvement were enriched among the OTUs engrafting in greater than half the patients, including the short-chain fatty acid–producing genera Odoribacter, Alistipes, and Erysipelotrichaceae incertae sedis (31).
Ultra performance liquid chromatography–mass spectrometry bile acid profiling data
Multivariate analysis of ultra performance liquid chromatography–mass spectrometry bile acid profiling data by PCA demonstrated clustering of serial samples by study participant (Figure 6a), but there was no clear effect of FMT on stool bile acid profile clustering (Figure 6b). No valid supervised multivariate models could be constructed between stool bile acid profiles pre-FMT and post-FMT at any time point, consistent with FMT having no statistically significant effect on bile acid profiles; however, bile acid profiles pre-FMT were similar in overall composition to that of the donor (Figure 6c).
Multivariate regression analysis between ALP levels and all mean integrated peaks from spectra was performed using PLS, with excellent correlation identified (P < 0.0001). On Spearman's rank analysis across all samples, a negative correlation was found between liver enzymes and relative UDCA levels (r = −0.423 for ALP, r = −0.53 for AST, and r = −0.61 for ALT) and percentage of tertiary bile acids of total bile acids (r = −0.40 for ALP, r = −0.56 for AST, and r = −0.61 for ALT). A positive correlation was found between liver enzymes and percent of amino-conjugated bile acids as a percentage of total bile acids (r = 0.39 for ALP, r = 0.41 for AST, and r = 0.43 for ALT). On linear regression analysis across all samples, a negative correlation was found between ALP and % tertiary bile acids (P = 0.0028) (Figure 7a), but a positive correlation between ALP and % tauroconjugates (P = 0.01) (Figure 7b) and % glycoconjugates (P = 0.0004) (Figure 7c).
To our knowledge, this is the first study to demonstrate that FMT is safe in PSC. In addition, we found that in PSC, FMT increases bacterial diversity and that engraftment may correlate with an improvement in ALP among patients with PSC. It has been demonstrated that the gut microbiome of patients with both PSC and IBD is unique to that of patients with only IBD and healthy controls, although the specific microbial signature is not consistent (25,32). However, the role of the microbiome in the pathogenesis of this disease remains unclear.
This study demonstrated that FMT was able to increase bacterial diversity as early as week 1, with persistence through to week 24, indicating that a single FMT may be sufficient to induce engraftment in this population. However, it has been reported that multiple FMTs are required to obtain remission in UC (33). Accordingly, we speculate that it may be possible to observe a further decrease in ALP levels if multi-FMT dosing in patients with PSC is performed. This emphasizes the need for dose finding and dose regimen studies in this nascent field.
We report a correlation between the abundance of engrafter OTUs and a decrease in ALP levels. ALP levels improved in 33% of patients, albeit with variable dynamics, after FMT. When looking at overall alpha diversity, this correlation was not appreciated, although alpha diversity is an oversimplified metric. However, when you evaluate individual, frequently engrafting OTUs, ALP improvement was appreciated. In particular, these frequently engrafting OTUs included genera capable of producing short-chain fatty acids, which are known to be depleted in IBD (34).
Overall, bile acid profiles did not change after FMT. This raises the question of whether FMT acts through alterations in gut microbiota–metabolomic interactions involving metabolites other than bile acids. Our multivariate regression analysis (PLS) showed excellent correlation between ALP levels and spectral features, which does contain some lipid classes. Because we did not use authentic standards for those, it is difficult to formally identify these by this technique alone; however, such metabolites are likely to be an additional explanation for the regression results. As such, it may be hypothesized that FMT may be improving hepatic function, underscored by improved ALP, in patients with PSC through a downstream effect on key lipid metabolites. Thus, although no changes in bile acids were observed, FMT still may be having a positive functional effect mediated through the immune system (35).
This study has several limitations. First, it was an uncontrolled, small pilot trial, and the secondary clinical outcome assessments were not blinded. However, a strong placebo effect seems unlikely in patients with a chronic, progressive disease with an objective laboratory-based outcome. The merits of ALP as a marker of disease are under debate, although continues to be reported as a surrogate end point for measuring disease progression by international consensus guidelines (20). Second, all patients on UDCA did have a washout period of 4 weeks, and it is possible that this was not long enough. In addition, this was a study with heterogeneous patients, notably that 1 patient had small-duct PSC, which may have a different natural history, then large-duct PSC. We used only a single donor for all 10 patients in this trial. It is unclear whether the results seen could have been obtained with another donor's material. Last, it is unclear what the preferred delivery location of FMT material for PSC will be, given that upper gastrointestinal administration might have a more direct effect on the biliary tree microbiota.
Given our design limitations, we would recommend that future studies should consider including gamma-glutamyltransferase, serum bile acids, FGF19, and C4 to assess bile acid synthesis rates and cholestasis and serum markers of fibrosis such as ELF and elastography. Although fecal calprotectin was not done, and histology was not collected, a colonoscopy was conducted at baseline, and all patients had no endoscopic disease activity.
In conclusion, this is the first human trial of FMT for the treatment of PSC. Here, we demonstrate that FMT is safe in this population. We also noted an improvement in overall microbial diversity that persists after FMT. In addition, we have demonstrated that the abundance of engrafter OTUs present in patients post-FMT correlated with a decrease in ALP levels. Further studies are needed on the utility of isolating those engrafter OTUs and more broadly to understand the role of the microbiome in the pathophysiology of PSC to permit a significant impact through FMT or more targeted therapy.
CONFLICTS OF INTEREST
Guarantor of the article: Jessica R. Allegretti, MD, MPH.
Specific author contributions: J.R.A. initiated study concept and design acquisition of data, analysis and interpretation of data, and drafting of the manuscript. M.S., Y.G., and S.T. analyzed and interpreted microbiome sequencing results. B.H.M., J.R.M., and A.P. analyzed and interpreted the metabolomics results. M.C. participated in data acquisition. Z.K. participated in interpretation of data and critical revision of the manuscript. D.S.P. and J.R.K. provided critical revisions of the manuscript.
Financial support: The trial was funded by PSC Partners Seeking a Cure. BHM is the recipient of a Medical Research Council Clinical Research Training Fellowship (grant reference: MR/R000875/1). The Division of Integrative Systems Medicine and Digestive Disease at Imperial College London receives financial support from the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre (BRC) based at Imperial College Healthcare NHS Trust and Imperial College London.
Potential competing interests: J.R.A. consults for and has received research support from Finch Therapeutics Group. Z.K., M.S., Y.G., and S.T. are employees of Finch Therapeutics Group.
WHAT IS KNOWN
- ✓ Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver condition with no approved therapies.
- ✓ The microbiome has been implemented in the pathogenesis of PSC.
- ✓ FMT has been shown to restore the microbiome in other chronic diseases.
WHAT IS NEW HERE
- ✓ FMT is safe in patients with PSC.
- ✓ Strong engrafter OTUs correlate with a decrease in alkaline phosphatase levels.
The authors acknowledge PSC Partners for funding this work.
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