Faculty Bibliography

Gut-dwelling Prevotella copri (P. copri), the most prevalent Prevotella species in the human gut, have been associated with diet and disease. However, our understanding of their diversity and function remains rudimentary because studies have been limited to 16S and metagenomic surveys and experiments using a single type strain. Here, we describe the genomic diversity of 83 P. copri isolates from 11 human donors. We demonstrate that genomically distinct isolates, which can be categorized into different P. copri complex clades, utilize defined sets of polysaccharides. These differences are exemplified by variations in susC genes involved in polysaccharide transport as well as polysaccharide utilization loci (PULs) that were predicted in part from genomic and metagenomic data. Functional validation of these PULs showed that P. copri isolates utilize distinct sets of polysaccharides from dietary plant, but not animal, sources. These findings reveal both genomic and functional differences in polysaccharide utilization across human intestinal P. copri strains.

Background/Purpose : Patient-reported outcomes (PROs) are an important part of clinical decision making and are frequently used in combination with objective measures of disease activity and physicians' clinical assessment to help guide treatment decisions. Discrepancies between PROs and clinical measures of disease activity can lead to over-treated or under-treated disease and patient dissatisfaction. We sought to examine the correlation between minimal disease activity (MDA) with PROs as measured by the NIH Patient-Reported Outcomes Measurement Information System (PROMIS) Global Health (GH) questionnaire, and assess the effect of demographics, psoriatic arthritis related comorbidities, and number of comorbidities on PROMIS GH and MDA status. Methods : A cross-sectional study was performed within Psoriatic Arthritis Research Consortium (PARC), a cohort of adult psoriatic arthritis patients meeting CASPAR criteria enrolled between 2016-2019. PARC is a longitudinal observational cohort study conducted at four institutions in the United States. The mean differences of PROMIS Physical, Mental and Fatigue T-scores between patients in MDA compared to those not in MDA were compared using the two sample t-tests. Correlations between MDA scores (0-7 criteria met) and PROMIS Physical, Mental and Fatigue T-scores were calculated using Spearman rank correlation. Higher T-scores on PROMIS measures mean 'more' of that concept for PROMIS Physical and Mental domains. Logistic regression model was used to evaluate contribution of additional covariates on MDA, including age, gender, hypertension, dyslipidemia, BMI, diabetes, smoking and number of comorbidities (Table 2). The odds ratios and 95% confidence intervals were presented. Multiple imputation was performed to impute missing data points. Data analysis was performed in SAS software (Version 9.4; Cary, NC). Results : 235 patients (50% female, mean age 51+/-13.9) were included. 129 were in MDA and 106 were not in MDA. Patients in MDA had significantly higher PROMIS Physical, Mental and improved Fatigue T-scores compared to non-MDA patients (Table 1; p< 0.001). There was a positive correlation between MDA scores and PROMIS scores in Physical and Mental domains; correlation was strongest for PROMIS Physical T-score (Figure 1; r=0.65, p< 0.001). There was a moderate correlation between MDA and PROMIS Fatigue T-score (Figure 1; r=-0.51, p< 0.001). In the univariate analysis, there was a statistically significant association between hypertension and number of comorbidities with MDA status (Table 2). However, this effect was not observed in the multivariate analysis. Conclusion : Achieving MDA was associated with a positive effect on patients' physical, mental and fatigue domains, irrespective of their demographics or PsA comorbidities. However, patients with a greater number of comorbidities were less likely to be in MDA. In this study, the PROMIS Physical domain had a higher correlation with MDA scores compared to the Mental domain and PROMIS Fatigue. PROMIS measures may be a useful tool in assessing disease activity from the patient's perspective. (Table Presented)

Background/Purpose : The multi-dimensional health assessment questionnaire (MDHAQ) is a patient-reported outcome that is commonly used in clinical practice in the US and comprises of 10 items. Although the validated Health Assessment Questionnaire Disability Index (HAQDI) measures similar constructs as the MDHAQ, is less commonly used and has 16 items. Therefore, the objective of this study is to assess if the MDHAQ (divided by 3.33 to transform to the same scale as HAQDI) can substitute for the HAQDI in ACR20 assessment and cohort studies. Methods : Between 2016-2019, patients with PsA were enrolled in the Psoriatic Arthritis Research Consortium (PARC), a longitudinal observational cohort at four United States institutions: University of Pennsylvania, Cleveland Clinic, New York University, and University of Utah. Baseline patient characteristics were descriptively reported. A priori we hypothesized that the MDHAQ and HAQDI would have high correlation at baseline ( >0.8) and among the change scores ( >0.8) and that responsiveness would be similar. Correlations were calculated among the total scores using Spearman's correlation coefficients at baseline and follow-up visit. Change scores (e.g., score at visit 1 minus score at visit 2) and standardized mean responses were calculated. Sensitivity analyses excluding patients with low disease activity were calculated. We additionally examined agreement with the 20% improvement cut-offto determine the potential effect of using MDHAQ in the ACR20 criteria in place of HAQDI. Results : HAQDI and MDHAQ data were available in 438 visits in which both questionnaires were completed and 161 patients with HAQDI and MDHAQ at two time points. The mean age was 51.5 +/- 14.6 years old, 53% were male, and most had low disease activity with mean swollen (66) and tender (68) joint counts 2.3 +/- 4.4 and 4.3 +/- 6.4, respectively. At baseline, the mean HAQDI was 0.64 +/- 0.62 (range 0-3) and the mean MDHAQ was 1.9 +/- 1.7 (range 0-10; Table 1). Dividing the MDHAQ by 3.33 to transform it to the same scale as the HAQDI resulted in a transformed MDHAQ mean of 0.56 +/- 0.48 with a mean excursion from the HAQDI score of 0.07 +/- 0.35 (Figure 1). Among all time points, the Spearman's correlation coefficient between the two instruments was 0.84 and among the first visit only, the coefficient was 0.83. The mean change over two visits in the HAQDI was -0.07 +/- 0.4, with a standardized response mean (SRM) of 0.19 and mean change in the MDHAQ was -0.16 +/- 1.1 with an SRM of 0.14. The Spearman's correlation coefficient among the two change variables was 0.55 (Table 2). Using the 20% criteria for the ACR20, the agreement among use of HAQ-DI and MDHAQ is 74%. When excluding patients with a clinical Disease Activity index for Psoriatic Arthritis (c-DAPSA) score < 14 (i.e., low disease activity), the correlation coefficients were similar. Conclusion : Although the HAQDI consists of more questions than the MDHAQ, the total scores correlated well when analyzed cross-sectionally. However, the correlation was moderate between the change over time. Using the 20% improvement cut-off, most were correctly classified with MDHAQ but MDHAQ cannot directly replace HAQDI for the ACR20 criteria. (Figure Presented )

Background/Purpose : Psoriatic arthritis (PsA) is a heterogenous inflammatory disease affecting skin, joints, and other domains. While psychiatric diseases (i.e., depression and anxiety) are known comorbidities, little is known about their impact on disease severity and patient reported outcomes (PROs). The objective of this study was to characterize the prevalence of psychiatric comorbidities in an academic combined psoriasis-psoriatic arthritis center and determine their impact on PsA clinical and patient derived outcomes. Methods : Consecutive adult patients meeting CASPAR criteria for PsA (n=436) were prospectively recruited at the NYU Psoriatic Arthritis Center. All data was collected from clinical visits utilizing a standardized EPIC template. Depression was defined by established diagnosis and/or use of anti-depressant medications. Objective measures of disease severity included swollen and tender joint counts (SJC/TJC) and PROs including RAPID3 scores. Data was analyzed using statistical software R. Results : Our cohort was comprised of 436 patients: 54% male, mean age of 47 years, and mostly Caucasians (74.1%). Within our population, 19.5% had depression, 15.6% had anxiety, and 4.8% had ADHD (Table 1). Of those with depression, 71% were on anti-depressive medication. At the initial visit, patients with PsA and depression were more likely to be on medication(s) for PsA (80% vs 65%, p=.01) and had a trend towards higher rates of biologic use (47.5% vs 40.4%, p=.126). Those with depression had a similar TJC to their non-depressed counterparts, but had a trend towards fewer swollen joints and concomitant higher RAPID3 scores (Table 2). When analyzing repeated outcome measures over subsequent visits, individuals with depression were similarly more likely to have a higher TJC, a lower SJC, and a higher RAPID3 score (although only RAPID3 was found to be statistically significant, p=.004). Importantly, these findings persisted when analyzing participants that were matched with propensity scores to adjust for age, sex, comorbidities, and medication use. In addition to joint activity, psoriasis activity measured by body surface area (BSA) was lower in those who were depressed (1.4% vs 3.03%, p=.001) and these differences were maintained over subsequent visits. Conclusion : Our results expand on prior reports of significantly elevated rates of depression in PsA. Notably, individuals with depression were more likely to be on medication(s) for their PsA, had fewer swollen joints, and a lower BSA but, paradoxically reported higher RAPID3 scores. This discrepancy is likely a manifestation of how depression could affect the way patients experience their PsA despite apparent improvement in skin and joint symptoms. Depression should, therefore, be considered a critical comorbidity when addressing PsA care in routine visits. Further work is needed to understand whether modulation of psychiatric comorbidities can lead to improved PsA outcomes

Background/Purpose : About 30% of patients with skin psoriasis (PsO) develop psoriatic arthritis (PsA). The reasons for why only some progress to synovio-enthesial disease from skin involvement remains unknown. Genetic, environmental and clinical-demographic factors have been implicated, but are yet to be characterized in specialized, combined care centers. We aim to describe clinical phenotypes differentiating patients with PsO from those with PsA at a large, urban tertiary care PsO-PsA clinic. Methods : Consecutive adult patients meeting CASPAR criteria for PsA (n= 448) or with dermatologist diagnosed skin psoriasis only (n=161) were prospectively recruited at the NYU Psoriatic Arthritis Center and the NYU Psoriasis and Psoriatic Arthritis Clinic. All data was collected utilizing clinical visit notes and additional on-site questionnaires. Type of psoriasis and body surface area (BSA) was determined by dermatologists or rheumatologists specializing in psoriatic disease. Data was analyzed using statistical software SPSS using chi squared test with Yates Continuity Correction for dichotomous/categorical variables and t-test for continuous variables. Results : Patients with PsO were more likely to be older (52.7 vs. 48.9, p=.032) and have hypertension, obesity, diabetes, and history of myocardial infarction (Figure 1). Patients with PsO had a statistically higher BSA than those with PsA (5.8% vs 3.1%, p=.003). While the type of psoriasis was similar, the site of psoriasis involvement (specifically the scalp and nail) differentiated the populations (Table 1). In PsA compared to PsO, the odds ratio of scalp involvement was 2.96 (95% Confidence Interval [CI] 2.02, 4.34) and that of nail involvement was 14.66 (95% CI 8.21, 26.16). Inverse psoriasis was not different between groups. Additionally, those with PsA were much more likely to have a first degree relative (FDR) with psoriasis compared to those with cutaneous disease alone (31.9% vs. 12.0%, p=.007) (Figure 1). Conclusion : We report for the first time the comorbidities and psoriasis features of PsA and PsO populations in a large, combined center. We found that scalp involvement and any nail involvement was more prevalent in the PsA as compared to PsO. Only one previous study has identified scalp psoriasis[1] as a possible risk factor for progression, while previous studies looking at nail psoriasis reported much lower odds ratios[1,2]. Patients with PsA also demonstrated a higher number of FDRs with skin psoriasis, reinforcing the notion of strong heritability in PsA. The identification of risk factors for progression is of critical importance to study natural history of psoriatic disease and to inform the adequate design of prevention trials in psoriasis patients who have enriched features associated with future transition to synovio-enthesial disease

Background/Purpose : Although a number of genetic factors, including susceptibility alleles, have been identified in rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is only 15% (Silman AJ et al, Br J Rheumatol 1993). Given this relatively low rate, environmental factors (including smoking, the microbiome and others) likely play a significant role in disease pathogenesis. Several prior studies have highlighted this relationship. Two examples include oral Porphyromonas gingivalis , which has been implicated in the citrullination of peptides (Hitchon CA et al, J Rheumatol 2010), and intestinal Prevotella copri , which is significantly increased in new-onset RA (Scher JU et al, Elife, 2013). In our study, we sought to further understand this relationship by exploring the microbial, metabolomic and cytokine differences in MZ twins with discordant disease. Methods : Fecal and blood samples were collected from nine pairs of MZ twins where one sibling was diagnosed with RA and the other unaffected. Fecal samples underwent bacterial DNA extraction, amplification and 16S rRNA gene sequencing. Additionally, gas chromatography mass spectrometry (GC-MS) was used to quantify fecal metabolites and multiplex assays were used to quantify fecal and plasma ACPA autoantigens as well as other cytokines (Sokolove J et al, PLoS One, 2012.). Analysis was performed using R, Quantitative Insights into Microbial Ecology (QIIME) and Linear discriminant analysis Effect Size (LEfSe). Results : Microbiome analysis revealed no significant differences in overall bacterial alpha or beta diversity between unaffected and RA twins. On average, RA twins had higher relative abundance of Bacteroidales (RA 56.6% vs Unaffected 47.9%) and lower abundance of Clostridiales (RA 34.5% vs Unaffected 42.8%). LEfSe analysis showed differentially higher abundance of Unclassified Veillonellaceae in unaffected twins (p=0.042). Unaffected twins also demonstrated higher levels of fecal octanoate (p=0.008), a medium-chain fatty acid with beneficial immune effects, as well as significantly increased levels of plasma IL-3 (p=0.039). Conversely, several fecal and plasma citrullinated/ non-citrullinated peptides were significantly higher in RA twins compared to their unaffected siblings (p< 0.05). Conclusion : We characterized differences in the bacterial microbiome, metabolites, cytokines and citrullinated/noncitrullinated peptides in MZ twins discordant for RA. We found changes in the abundance of particular taxa, as well as higher levels of octanoate and IL-3 in unaffected twins, further suggesting the possibility that the initial citrullination and autoimmune events in this disease may occur in the intestinal mucosa. Understanding the immune mechanisms Figure 2 Unaffected twins demonstrate higher levels of octanoate and IL-3, whereas RA twins have significantly higher levels of fecal and plasma citrullinated/non-citrullinated peptides. (A-B) Boxplots of fatty acid metabolites and IL-3 abundance comparing unaffected and RA twins. (C) Tables of plasma and fecal citrullinated/non-citrullinated peptides comparing unaffected and RA twins. Only the top ten peptides by p-value are listed. For all panels, statistical significance calculated using the Wilcoxon signed-rank test. orchestrated by the gut microbiota and their downstream effects may ultimately shed light on the pathogenesis of RA beyond genetic susceptibility and allow us to potentially alter the course of disease development and progression

Background/Purpose : Prevalence of sacroiliitis (SI) in Crohn's disease (CD) varies widely (range 4% -39%), depending on criteria utilized to define the disease (e.g. inflammatory back pain, plain radiographs or MRI). Sacroiliitis may remain underdiagnosed in CD patients given lack of association with clinical symptoms of back pain and CD activity. However, patients with CD often undergo magnetic resonance enterography (MRE) to assess extent, severity of small bowel CD and radiographic healing, affording clinicians the opportunity to evaluate for the presence of active and/or chronic SI. We sought to identify the prevalence of sacroiliitis in CD patients utilizing MRE and determine its relationship with CD activity, especially with concurrent biologic therapy. Methods : All CD subjects undergoing MRE between years 2014-2018 at a large IBD referral center were identified. A musculoskeletal radiologist, blinded to clinical data, reviewed all MRE exams for the presence of acute bone marrow edema (BME) lesions and chronic lesions suggestive of acute and chronic SI, respectively. A second radiologist, also blinded, assessed MRE for mucosal CD activity using validated measures. Charts were reviewed for demographics, IBD characteristics, presence of back pain, clinical and endoscopic activity of CD, and Crohn's therapies within 3 months of MRE. Comparisons were made between CD subjects with and without SI using chi-square test. Univariate and multivariate logistic regression were used to determine risk factors of SI. Results : 258 subjects with CD underwent MRE during the study period with a mean age of 35 years old, 53% (n=138) were male, and mean duration of CD at the time of MRE was 9 years. Few reported back pain (8%) and 14% had previously seen a rheumatologist. Overall, 17% (n=45) of patients had MR evidence of sacroiliitis (Table 1). Female gender, presence of back pain, and later age of CD diagnosis were associated with signs of sacroiliitis (p=0.05, p< 0.001, p=0.04 respectively; Table 2). Stricturing phenotype was associated with a lower rate of SI (7% vs. 24%; p=0.018), but inflammatory or penetrating phenotypes were not. CD location, activity as noted by clinical scores, endoscopic disease activity, or radiographic disease activity on MRE, were not associated with sacroiliitis (Table 2). On multivariable analysis, back pain was associated with the presence of sacroiliitis on MRE (OR 3.0, 95% CI 1.1-5.6; p=0.04). Concurrent CD therapy with biologics did not lower the risk of sacroiliitis. Conclusion : Although often underdiagnosed, SI is a common comorbid condition in CD. While recent history of back pain was associated with the presence of sacroiliitis visualized on MRE, no correlations were found with other clinical and endoscopic markers of CD activity. Moreover, concurrent CD therapy, especially biologics, was not associated with a lower risk of sacroiliitis on MRE. With limited clinical clues and CD characteristics to suggest sacroiliitis, gastroenterologists can utilize MRE as a screening tool to detect SI and refer CD patients to rheumatologists. Presence of SI on MRE in CD patients with back pain may help identify a subset of individuals likely to benefit from switching to therapies with proven efficacy in axial SpA

Background/Purpose : The trillions of microorganisms (microbiota) found within the human gut play a critical role in shaping the immune system, yet these complex microbial communities are also highly sensitive to numerous environmental factors. While much of the focus to date has been on dietary intake, emerging data has begun to suggest that the use of pharmaceutical drugs, even those that are not considered to be antibiotics, can alter the human gut microbiota with unknown consequences for treatment outcomes. Here, we examine the effect of methotrexate (MTX), which is first-line therapy for rheumatoid arthritis (RA), on microbiota composition and physiology as well as downstream consequences on the host ' s immune system. Methods : To examine the effect of MTX on human gut microbiota composition in vivo , gnotobiotic mice were colonized with microbiota from either healthy or RA patient donors and treated with oral MTX at varying doses. We performed high-throughput sequencing of the 16S rRNA gene to examine changes in taxonomic composition. We looked at the effects of varying the route of administration or co-administration with folic acid. To determine the direct effects of MTX on bacterial growth, we treated monocultures of 42 different human gut isolates with MTX and monitored growth using optical density. To identify MTX-induced transcriptional changes, we performed RNA-Seq on 4 isolates treated with MTX. To determine the effects of MTX on bacterial taxonomy in vivo , fecal samples from RA patients (100% fulfilling ACR criteria) starting MTX were profiled longitudinally using 16S sequencing. To determine if MTX-induced shifts reduce the inflammatory potential of the RA microbiome, microbiota from RA patient donors either before or after MTX initiation were transplanted into germ-free mice. These mice were challenged with an inflammatory trigger with dextran-sodium sulfate (DSS), and immune profiling was done to assess inflammation. Results : MTX altered community composition in vivo in humanized mice, leading to reduced Bacteroidetes and increased Firmicutes. Varying the route of drug administration or co-administration with folic acid produced similar, reproducible shifts. MTX directly altered growth of many human gut isolates. At the phylum level, Bacteroidetes tended to be more sensitive than Firmicutes, recapitulating the trends observed in gnotobiotic mice in vivo . RNA-Seq revealed that MTX alters transcriptional pathways involved in purine and pyrimidine metabolism. Furthermore, longitudinal analyses of the in vivo gut microbiotas of RA patients showed that MTX-induced shifts in bacterial relative abundance are associated with improved drug response. Transplant experiments revealed that mice harboring MTXaltered microbiota exhibited a reduced Th17 and Th1 response to DSS compared to mice harboring pre-treatment microbiota, suggesting that MTX alters the inflammatory potential of the RA patient microbiome. Conclusion : Together, these results suggest that the mechanism-of-action of non-antibiotic drugs may be due in part to off-target effects on the gut microbiota, while providing a critical first step towards explaining long-standing differences in drug response between patients

Background/Purpose : Early treatment initiation in rheumatoid arthritis (RA) is fundamental to avoid chronic joint destruction and disability. Despite remarkable advances in RA therapeutics, oral methotrexate (MTX) remains the anchor drug and mainstay of treatment worldwide. However, MTX bioavailability has a wide inter-individual variability and >50% of patients with moderate or severe RA show no or suboptimal improvement in their symptoms in response to MTX. The reasons for these disparities in treatment response remain unclear. Prior studies have shown that the biotransformation of MTX is altered in germ-free and microbiome-depleted mice, prompting us to hypothesize that inter-individual differences in the human gut microbiome could impact drug bioavailability and thus clinical efficacy. We sought to determine differences in the microbiome of drug-naive, new onset RA (NORA) patients that could predict response to MTX therapy. Methods : We enrolled 27 drug-naive, NORA patients priori to MTX initiation (test cohort), and classified them as either MTX-responders (MTX-R; 39% of the cohort) or non-responders (MTX-NR; 61%) based on a stringent definition of clinical response (delta improvement of DAS28 >1.8 by month 4). We performed 16S rRNA gene and Shotgun Metagenomic sequencing on the baseline gut microbiomes of these NORA patients and confirmed the results in an independent validation cohort (n=31). NMR and LC-MS were performed in ex vivo incubations to measure the capacity of each NORA microbiome to metabolize MTX. Results : Our analysis revealed significant associations between the abundance of gut bacterial taxa and future MTX response. Patients that responded to therapy had significantly lower microbial diversity (p< 0.05). A significant difference in overall gut microbial community structure was also observed between groups (Bray-Curtis distance; PERMANOVA < 0.05). At the class level, we observed statistically higher abundance of Clostridia and lower abundance of Bacteroidia in MTX-NR (p< 0.05; q< 0.2). Furthermore, the baseline metagenome separated most MTX-R from MTX-NR (PCoA; PERMANOVA p< 0.05). We identified 8 microbial modules and 23 pathways, whose abundance significantly differed between groups (p< 0.05, q< 0.2), including genes related with purine and MTX metabolism, indicating a major difference in metabolic and biosynthetic potential between the microbiome of MTX-R and MTX-NR patients. Machine learning techniques were applied to this metagenomic data, resulting in a robust model based on bacterial gene abundance that accurately predicted response to MTX in an independent cohort. Finally, MTX available levels remaining after ex vivo incubation with distal gut samples from pre-treatment RA patients significantly correlated with the magnitude of future clinical response, suggesting a direct effect of the gut microbiome on MTX bioavailability and response to therapy. Conclusion : Together, these results provide the first step towards predicting response to oral MTX in NORA patients and support the utility of the gut microbiome as a prognostic tool and perhaps even as a target for manipulation in the treatment of rheumatic and autoimmune disease