Sabina Mir

Serial Fecal Microbiota Transplantation Alters Mucosal Gene Expression in Pediatric Ulcerative Colitis

Serial Fecal Microbiota Transplantation Alters Mucosal Gene Expression in Pediatric Ulcerative Colitis

DNA methylation-associated colonic mucosal immune and defense responses in treatment-naïve pediatric ulcerative colitis

Inflammatory bowel diseases (IBD) are emerging globally, indicating that environmental factors may be important in their pathogenesis. Colonic mucosal epigenetic changes, such as DNA methylation, can occur in response to the environment and have been implicated in IBD pathology. However, mucosal DNA methylation has not been examined in treatment-naïve patients. We studied DNA methylation in untreated, left sided colonic biopsy specimens using the Infinium HumanMethylation450 BeadChip array. We analyzed 22 control (C) patients, 15 untreated Crohn’s disease (CD) patients, and 9 untreated ulcerative colitis (UC) patients from two cohorts. Samples obtained at the time of clinical remission from two of the treatment-naïve UC patients were also included into the analysis. UC-specific gene expression was interrogated in a subset of adjacent samples (5 C and 5 UC) using the Affymetrix GeneChip PrimeView Human Gene Expression Arrays. Only treatment-naïve UC separated from control. One-hundred-and-twenty genes with significant expression change in UC (> 2-fold, P < 0.05) were associated with differentially methylated regions (DMRs). Epigenetically associated gene expression changes (including gene expression changes in the IFITM1, ITGB2, S100A9, SLPI, SAA1, and STAT3 genes) were linked to colonic mucosal immune and defense responses. These findings underscore the relationship between epigenetic changes and inflammation in pediatric treatment-naïve UC and may have potential etiologic, diagnostic, and therapeutic relevance for IBD.

Microbiota separation and C-reactive protein elevation in treatment-naive pediatric granulomatous Crohn disease.

Objectives: In patients with inflammatory bowel diseases (IBDs), the presence of noncaseating mucosal granuloma is sufficient for diagnosing Crohn disease (CD) and may represent a specific immune response or microbial-host interaction. The cause of granulomas in CD is unknown and their association with the intestinal microbiota has not been addressed with high-throughput methodologies. Methods: The mucosal microbiota from 3 different pediatric centers was studied with 454 pyrosequencing of the bacterial 16S rRNA gene and the fungal small subunit (SSU) ribosomal region in transverse colonic biopsy specimens from 26 controls and 15 treatment-naïve pediatric CD cases. Mycobacterium avium subspecies paratuberculosis (MAP) was tested with real-time polymerase chain reaction. The correlation of granulomatous inflammation with C-reactive protein was expanded to 86 treatment-naïve CD cases. Results: The CD microbiota separated from controls by distance-based redundancy analysis (P = 0.035). Mucosal granulomata found in any portion of the intestinal tract associated with an augmented colonic bacterial microbiota divergence (P = 0.013). The granuloma-based microbiota separation persisted even when research center bias was eliminated (P = 0.04). Decreased Roseburia and Ruminococcus in granulomatous CD were important in this separation; however, principal coordinates analysis did not reveal partitioning of the groups. CRP levels >1 mg/dL predicted the presence of mucosal granulomata (odds ratio 28 [6–134.32]; 73% sensitivity, 91% specificity). Conclusions: Granulomatous CD associates with microbiota separation and C-reactive protein elevation in treatment-naïve children; however, overall dysbiosis in pediatric CD appears rather limited. Geographical/center bias should be accounted for in future multicenter microbiota studies.

Whole-Exome Sequencing Reveals GPIHBP1 Mutations in Infantile Colitis With Severe Hypertriglyceridemia

ABSTRACT Severe congenital hypertriglyceridemia (HTG) is a rare disorder caused by mutations in genes affecting lipoprotein lipase (LPL) activity. Here we report a 5-week-old Hispanic girl with severe HTG (12,031 mg/dL, normal limit 150 mg/dL) who presented with the unusual combination of lower gastrointestinal bleeding and milky plasma. Initial colonoscopy was consistent with colitis, which resolved with reduction of triglycerides. After negative sequencing of the LPL gene, whole-exome sequencing revealed novel compound heterozygous mutations in GPIHBP1. Our study broadens the phenotype of GPIHBP1-associated HTG, reinforces the effectiveness of whole-exome sequencing in Mendelian diagnoses, and implicates triglycerides in gastrointestinal mucosal injury.

Maternal micronutrients can modify colonic mucosal microbiota maturation in murine offspring

Epidemiologic data suggest that early nutritional exposures may inflict persistent changes in the developing mammalian “super-organism” (i.e., the host and its residing microbiota). Such persistent modifications could predispose young adults to inflammatory bowel diseases (IBD). We recently observed that the dietary supplementation of four micronutrients to dams augmented colitis susceptibility in murine offspring in association with mucosal microbiota composition changes. In this study the effects of the four micronutrients on the microbiota of dams and female mice was examined. Additionally, age dependent microbiota composition shifts during pediatric development were delineated from the previous offspring data sets. Maternal and adult female microbiota did not separate secondary to the nutritional intervention. Significant microbiota composition changes occurred from postnatal day 30 (P30) to P90 at the level of 1 phylum and 15 genera. Most of these changes were absent or opposite in the maternally supplemented offspring. Nutritionally induced alterations in mucosal microbiota maturation may be contributors to colitis susceptibility in mammals.

Monotonous diets protect against acute colitis in mice: Epidemiologic and therapeutic implications

Objectives: Multiple characteristics of industrialization have been proposed to contribute to the global emergence of inflammatory bowel diseases (IBDs: Crohn disease and ulcerative colitis). Major changes in eating habits during the last decades and the effectiveness of exclusive enteral nutrition in the treatment of Crohn disease indicate the etiologic importance of dietary intake in IBDs. A uniform characteristic of nutrition in developing countries (where the incidence of IBD is low) and exclusive enteral nutrition is their consistent nature for prolonged periods; however, the potentially beneficial effect of dietary monotony in respect to mammalian intestinal inflammation has not been examined. Methods: The association between alternating (2 different complete chows) and persistent regular diets, and dextran sulfate sodium colitis susceptibility in C57BL/6J mice was studied. Colonic mucosal microbiota changes were investigated by high-throughput pyrosequencing of the 16S rRNA gene. Results: The severity of colitis increased upon dietary alternation compared with consistent control feeding. The microbiota of the alternating nutritional group clustered discretely from both control groups. Conclusions: Our findings highlight that monotonous dietary intake may decrease mammalian vulnerability against colitis in association with microbiota separation. The epidemiologic and therapeutic implications of our results are also discussed.

Duration of disease may predict response to infliximab in pediatric ulcerative colitis.

Background: Infliximab (IFX) is an established treatment modality for moderate to severe pediatric ulcerative colitis (UC). The purpose of this study was to identify clinical and laboratory parameters, which predict response to IFX in pediatric UC defined by colectomy as the primary outcome measure. Postsurgical complications were examined as well. Methods: A retrospective chart review was performed on children younger than 19 years who received IFX therapy at Texas Children’s Hospital, Houston, Texas for the treatment of UC from January 2005 to April 2012. Demographics, laboratory data, clinical subtype, duration of disease, transfusion requirement, number of IFX infusions, concurrent medications, and postoperative complication with regard to IFX exposure were examined. Results: Forty-seven patients (22 male and 25 female; average age at diagnosis: 11.4 y) received IFX. Twenty-six (55.3%) required colectomy, 20 (42.6%) of which occurred within a year of therapy initiation. Disease duration <20 months before IFX initiation, increased the likelihood of a colectomy within a year [OR: 3.8 (95% CI, 1.6-13.3), P=0.044]. Blood transfusion requirement before IFX was associated with higher rates of colectomy within a year [OR: 9.78 (95% CI, 2.2-43.3), P=0.0028]. Preoperative exposure to IFX within 8 weeks did not significantly increase postoperative complications (P=0.26). Serum albumin levels at diagnosis did not predict colectomy. Conclusions: Shorter disease duration and need for blood transfusion may be useful indicators of limited response to IFX in pediatric UC.

Prenatal Methyl-Donor Supplementation Augments Colitis in Young Adult Mice

Inflammatory bowel diseases (IBD) have become highly prevalent in developed countries. Environmentally triggered exaggerated immune responses against the intestinal microbiome are thought to mediate the disorders. The potential dietary origins of the disease group have been implicated. However, the effects of environmental influences on prenatal developmental programming in respect to orchestrating postnatal microbiome composition and predilection towards mammalian colitis have not been examined. We tested how transient prenatal exposure to methyl donor micronutrient (MD) supplemented diets may impact predilection towards IBD in a murine dextran sulfate sodium (DSS) colitis model. Prenatal MD supplementation was sufficient to modulate colonic mucosal Ppara expression (3.2 fold increase; p=0.022) and worsen DSS colitis in young adulthood. The prenatal dietary exposure shifted the postnatal colonic mucosal and cecal content microbiomes. Transfer of the gut microbiome from prenatally MD supplemented young adult animals into germ free mice resulted in increased colitis susceptibility in the recipients compared to controls. Therefore, the prenatal dietary intervention induced the postnatal nurturing of a colitogenic microbiome. Our results show that prenatal nutritional programming can modulate the mammalian host to harbor a colitogenic microbiome. These findings may be relevant for the nutritional developmental origins of IBD.

Loss of n-6 fatty acid induced pediatric obesity protects against acute murine colitis

Dietary influences may affect microbiome composition and host immune responses, thereby modulating propensity toward inflammatory bowel diseases (IBDs): Crohn disease (CD) and ulcerative colitis (UC). Dietary n‐6 fatty acids have been associated with UC in prospective studies. However, the critical developmental period when (n‐6) consumption may induce UC is not known. We examined the effects of transiently increased n‐6 consumption during pediatric development on subsequent dextran‐sulfate‐sodium (DSS)‐induced acute murine colitis. The animals transiently became obese then rapidly lost this phenotype. Interestingly, mice were protected against DSS colitis 40 days after n‐6 consumption. The transient high n‐6‐induced protection against colitis was fat type‐ and dietary reversal‐dependent and could be transferred to germ‐free mice by fecal microbiota transplantation. We also detected decreased numbers of chemokine receptor (Cxcr)5+ CD4+ T cells in the mesenteric lymph nodes (MLNs) of transiently n‐6‐fed mice. Further experiments revealed that anti‐chemokine ligand (Cxc1)13 (the ligand of Cxcr5) antibody treatment decreased DSS colitis severity, implicating the importance of the Cxcr5‐Cxcl13 pathway in mammalian colitis. Consecutively, we found elevated CXCL13 concentrations (CD: 1.8‐fold, P= 0.0077; UC: 1.9‐fold, P= 0.056) in the serum of untreated pediatric IBD patients. The human serologic observations supported the translational relevance of our findings.—Nagy‐Szakal, D., Mir, S. A. V., Harris, R. A., Dowd, S. E., Yamada, T., Lacorazza, H. D., Tatevian, N., Smith, C. W., de Zoeten, E. F., Klein, J., Kellermayer, R. Loss of n‐6 fatty acid induced pediatric obesity protects against acute murine colitis. FASEB J. 29, 3151‐3159 (2015). www.fasebj.org

Tu1192 Clinical, Epigenetic, and Metagenomic Responses to Serial Fecal Microbiome Transplants in Pediatric Ulcerative Colitis

G A A b st ra ct s and 4 mood-related questions. Emma provided correct answers. Emma v1 tested general knowledge and nutrition. Emma v2 featured more questions, 2 levels of difficulty, and was categorized by General, Anatomy & Testing, Medications, and Nutrition. We obtained information on sex, age group (10-14yr vs. 15-18yr), IBD-type, medications, and history of surgery. Feedback from patients and clinicians was obtained in both versions. Results: Sites 1 and 2 tested Emma v1 between February-August, and May-August 2013, respectively. Emma v2 was tested from November 1-November 23, 2013, and May-August 2013, respectively. A total of 58 patients (59% male, 67% Crohns) played Emma v1, while 33 patients (64% male, 58% Crohns) played Emma v2. Seven patients played both versions; only 7 patients played EMMA v2 at site 2. In Emma v1, 82% of disease-related questions were answered correctly. The mean mood scores for sadness (1.3, SD=0.69, range 1-4), anxiety (1.4, SD=0.9, range 1-5), energy (2.6, SD=1.5, range 1-5), and IBD-related QOL (2.0, SD= 1.5, range 1-5) indicated generally good functioning. In Emma v2, 61.1% of total knowledge questions were answered correctly, while percentages in General, Anatomy/Testing, Medications, and Nutrition were 66.8%, 65.8%, 74.5%, and 79.6%, respectively. Neither age nor IBD-type was correlated with disease knowledge. Of patients with difficult questions, 58.4% were answered correctly. The mean mood scores for sadness (1.6, SD=1.03, range 1-4), anxiety (2.2, SD=1.2, range 1-5), energy (2.2, SD=1.3, range 1-5), and IBD-related QOL (1.9, SD=1.3, range 1-5) indicated generally good functioning. Four patients were referred for mental health support. Conclusions: Pediatric patients with IBD need more diseaserelated education. The Emma ipad game has the potential to evaluate and teach gaps in knowledge, assess emotional functioning, and increase patient engagement.