Decoding the glycoproteome: a new frontier for biomarker discovery in cancer.

Cancer early detection and treatment response prediction continue to pose significant challenges. Cancer liquid biopsies focusing on detecting circulating tumor cells (CTCs) and DNA (ctDNA) have shown enormous potential due to their non-invasive nature and the implications in precision cancer management. Recently, liquid biopsy has been further expanded to profile glycoproteins, which are the products of post-translational modifications of proteins and play key roles in both normal and pathological processes, including cancers. The advancements in chemical and mass spectrometry-based technologies and artificial intelligence-based platforms have enabled extensive studies of cancer and organ-specific changes in glycans and glycoproteins through glycomics and glycoproteomics. Glycoproteomic analysis has emerged as a promising tool for biomarker discovery and development in early detection of cancers and prediction of treatment efficacy including response to immunotherapies. These biomarkers could play a crucial role in aiding in early intervention and personalized therapy decisions. In this review, we summarize the significant advance in cancer glycoproteomic biomarker studies and the promise and challenges in integration into clinical practice to improve cancer patient care.

Warning Signs From the Crypt: Aberrant Protein Glycosylation Marks Opportunities for Early Colorectal Cancer Detection.

Colorectal cancer (CRC) remains a leading cause of cancer-related deaths despite being the most preventable and treatable forms of cancer when caught early through screening. There is an unmet need for novel screening approaches with improved accuracy, less invasiveness, and reduced costs. In recent years, evidence has accumulated around particular biological events that happen during the adenoma-to-carcinoma transition, especially focusing on precancerous immune responses in the colonic crypt. Protein glycosylation plays a central role in driving those responses, and recently, numerous reports have been published on how aberrant protein glycosylation both in colonic tissue and on circulating glycoproteins reflects these precancerous developments. The complex field of glycosylation, which exceeds complexity of proteins by several orders of magnitude, can now be studied primarily because of the availability of new high-throughput technologies such as mass spectrometry and artificial intelligence-powered data processing. This has now opened new avenues for studying novel biomarkers for CRC screening. This review summarizes the early events taking place from the normal colon mucosa toward adenoma and adenocarcinoma formation and associated critical protein glycosylation phenomena, both on the tissue level and in the circulation. These insights will help establish an understanding in the interpretation of novel CRC detection modalities that involve high-throughput glycomics.

Autotaxin loss accelerates intestinal inflammation by suppressing TLR4-mediated immune responses.

Autotaxin (ATX) converts lysophosphatidylcholine and sphingosyl-phosphorylcholine into lysophosphatidic acid and sphingosine 1-phosphate, respectively. Despite the pivotal function of ATX in lipid metabolism, mechanisms by which ATX regulates immune and inflammatory disorders remain elusive. Here, using myeloid cell lineage-restricted Atx knockout mice, we show that Atx deficiency disrupts membrane microdomains and lipid rafts, resulting in the inhibition of Toll-like receptor 4 (TLR4) complex formation and the suppression of adaptor recruitment, thereby inhibiting TLR4-mediated responses in macrophages. Accordingly, TLR4-induced innate immune functions, including phagocytosis and iNOS expression, are attenuated in Atx-deficient macrophages. Consequently, Atx-/- mice exhibit a higher bacterial prevalence in the intestinal mucosa compared to controls. When combined with global Il10-/- mice, which show spontaneous colitis due to the translocation of luminal commensal microbes into the mucosa, myeloid cell lineage-restricted Atx knockout accelerates colitis development compared to control littermates. Collectively, our data reveal that Atx deficiency compromises innate immune responses, thereby promoting microbe-associated gut inflammation.

The effects of inflammatory bowel disease on caregivers: significant burden and loss of productivity.

BACKGROUND: Caregiver burden is the emotional, physical, practical, and/or financial burden associated with taking care of a patient with a chronic condition. Limited literature on caregiver burden in Inflammatory Bowel Diseases (IBD) has accounted for some predictors, but its effect on work productivity (absenteeism and presenteeism) is unknown. METHODS: In a prospective study, patients and their respective caregivers were surveyed from November 2015 until July 2017. Data on demographics, work productivity, quality of life, disease activity, caregiver burden and productivity were collected. The burden on caregivers was assessed and associations between caregiver productivity and caregiver burden were analyzed. Additionally, predictors for caregiver burden were identified. RESULTS: One hundred two IBD patients and their respective caregiver were included. In total, 39% of IBD caregivers experienced burden. Caregivers with burden experienced significantly more absenteeism and presenteeism (65 and 85% respectively). Furthermore, 51% of caregivers felt that they should be doing more for their care recipient and felt they could do a better job at caregiving. Predictors of burden included race/ethnicity, history of fistulas, diagnosis of ulcerative colitis, higher caregiver education, and hours spent caregiving. CONCLUSION: Caregivers with burden had significantly more productivity decrease compared to those without burden. Additionally, the majority of caregivers feel they should be providing more and better care for their recipients. The development of strategies to address caregiver's distress and perceived burden when caring for IBD patients is warranted.

Long-term Evaluation of Allogeneic Bone Marrow-derived Mesenchymal Stromal Cell Therapy for Crohn's Disease Perianal Fistulas.

BACKGROUND AND AIMS: The long-term safety and efficacy of allogeneic bone marrow-derived mesenchymal stromal cell [bmMSC] therapy in perianal Crohn's disease [CD] fistulas is unknown. We aimed to provide a 4-year clinical evaluation of allogeneic bmMSC treatment of perianal CD fistulas. METHODS: A double-blind dose-finding study for local bmMSC therapy in 21 patients with refractory perianal fistulising Crohn's disease was performed at the Leiden University Medical Center in 2012-2014. All patients treated with bmMSCs [1 x 107 bmMSCs cohort 1, n = 5; 3 × 107 bmMSCs cohort 2, n = 5; 9 × 107 bmMSCs cohort 3, n = 5] were invited for a 4-year evaluation. Clinical events were registered, fistula closure was evaluated, and anti-human leukocyte antigen [HLA] antibodies were assessed. Patients were also asked to undergo a pelvic magnetic resonance imaging [MRI] and rectoscopy. RESULTS: Thirteen out of 15 patients [87%] treated with bmMSCs were available for long-term follow-up. Two non-MSC related malignancies were observed. No serious adverse events thought to be related to bmMSC therapy were found. In cohort 2 [n = 4], all fistulas were closed 4 years after bmMSC therapy. In cohort 1 [n = 4] 63%, and in cohort 3 [n = 5] 43%, of the fistulas were closed, respectively. In none of the patients anti-HLA antibodies could be detected 24 weeks and 4 years after therapy. Pelvic MRI showed significantly smaller fistula tracts after 4 years. CONCLUSIONS: Allogeneic bmMSC therapy for CD-associated perianal fistulas is also in the long-term a safe therapy. In bmMSC-treated patients, fistulas with closure at Week 24 were still closed after 4 years.

A Multi-Level Fit-Based Quality Improvement Initiative to Improve Colorectal Cancer Screening in a Managed Care Population.

INTRODUCTION: Colorectal cancer (CRC) is a common but largely preventable disease with suboptimal screening rates despite national guidelines to screen individuals age 50-75. Single-component interventions aimed to improve screening uptake only modestly improve rates; data suggest that multi-modal approaches may be more effective. METHODS: We designed, implemented, and evaluated the impact of a multi-modal intervention on CRC screening uptake among unscreened patients in a large managed care population. Patient-level components included a mailed letter with education about screening options and pre-colonoscopy telephone counseling. For providers, we facilitated communication of screening test results and work-flow for abnormal results. System-level modifications included establishment of a patient navigator, expedited work-up for abnormal results, and stream-lined colonoscopy scheduling. We measured the rate of screening uptake overall, screening uptake by modality, change in the proportion of the population screened, and positive fecal immunochemical test (FIT) follow-up rates in the 1-year study period. RESULTS: There were 5093 patients in the intervention cohort. Of these, 33.2% participated in FIT or colonoscopy screening within 1 year of the mailing. A total of 1078 (21.2%) participants completed a FIT and 611 (12.0%) completed a screening colonoscopy. The screening rate in the managed care population increased from 65.1 to 76.6%. Fifty-nine patients (5.5%) had a positive FIT, of which 30 (50.8%) completed a diagnostic colonoscopy. CONCLUSION: Multi-modal interventions can result in substantial improvement in CRC screening uptake in large and diverse managed care populations. TRANSLATIONAL IMPACT: Health systems should shift their focus from single-level to multi-level interventions when addressing barriers to CRC screening.

Standardization of mesenchymal stromal cell therapy for perianal fistulizing Crohn's disease.

BACKGROUND: Local administration of mesenchymal stromal cells (MSCs) into the fistula tract seems to improve patient outcome in perianal fistulas due to Crohn's disease (CD). In this paper we propose a standardized and validated protocol for the local administration of MSCs for CD perianal fistulas to be able to reliably assess efficacy. MATERIALS AND METHODS: A working group consisting of gastroenterologists and surgeons with expertise in the treatment of perianal CD developed a consensus perianal fistula treatment protocol for local MSC treatment of perianal fistulizing CD. The treatment protocol was validated during a trial of allogeneic bone marrow-derived MSCs for the treatment of refractory perianal Crohn's fistulas. RESULTS: Localization and classification of perianal fistulas with MRI and rectoscopy is of crucial importance prior to surgical intervention with local therapy administration. Examination under anesthesia is necessary to incise and drain abscesses when present. Optimization of medical treatment when active luminal CD is present, is the first step before embarking on surgery and local therapy administration. In addition, strictures preventing the surgeon from adequately performing the surgical procedure have to be endoscopically dilated. Curettage of the fistula tract has an important role as long-standing CD perianal fistulas close poorly without removal of their epithelial lining. To diminish bacterial contamination of the fistula, the internal opening has to be closed. The origin of the fistula is the internal opening, therefore, efficacy of MSCs is presumably the highest when they are injected into the tissue around the internal opening. CONCLUSION: In this article, we propose a standardized method of local MSC administration for perianal fistulizing CD. The use of this standardized and validated protocol for the administration of local treatment of CD perianal fistulas will allow reliable comparison of the efficacy of local therapies in future.

Using insurance claims to predict and improve hospitalizations and biologics use in members with inflammatory bowel diseases.

OBJECTIVE: Inflammatory Bowel Disease (IBD) is an inflammatory disorder of the gastrointestinal tract that can necessitate hospitalization and the use of expensive biologics. Models predicting these interventions may improve patient quality of life and reduce expenditures. MATERIALS AND METHODS: We used insurance claims from 2011 to 2013 to predict IBD-related hospitalizations and the initiation of biologics. We derived and optimized our model from a 2011 training set of 7771 members, predicting their outcomes the following year. The best-performing model was then applied to a 2012 validation set of 7450 members to predict their outcomes in 2013. RESULTS: Our models predicted both IBD-related hospitalizations and the initiation of biologics, with average positive predictive values of 17% and 11%, respectively - each a 200% improvement over chance. Further, when we used topic modeling to identify four member subpopulations, the positive predictive value of predicting hospitalization increased to 20%. DISCUSSION: We show that our hospitalization model, in concert with a mildly-effective interventional treatment plan for members identified as high-risk, may both improve patient outcomes and reduce insurance expenditures. CONCLUSION: The success of our approach provides a roadmap for how claims data can complement traditional medical decision making with personalized, data-driven predictive medicine.

Clinical Pharmacokinetic and Pharmacodynamic Considerations in the Treatment of Inflammatory Bowel Disease.

According to recent clinical consensus, pharmacotherapy of inflammatory bowel disease (IBD) is, or should be, personalized medicine. IBD treatment is complex, with highly different treatment classes and relatively few data on treatment strategy. Although thorough evidence-based international IBD guidelines currently exist, appropriate drug and dose choice remains challenging as many disease (disease type, location of disease, disease activity and course, extraintestinal manifestations, complications) and patient characteristics [(pharmaco-)genetic predisposition, response to previous medications, side-effect profile, necessary onset of response, convenience, concurrent therapy, adherence to (maintenance) therapy] are involved. Detailed pharmacological knowledge of the IBD drug arsenal is essential for choosing the right drug, in the right dose, in the right administration form, at the right time, for each individual patient. In this in-depth review, clinical pharmacodynamic and pharmacokinetic considerations are provided for tailoring treatment with the most common IBD drugs. Development (with consequent prospective validation) of easy-to-use treatment algorithms based on these considerations and new pharmacological data may facilitate optimal and effective IBD treatment, preferably corroborated by effectiveness and safety registries.

Long-term Outcome of Early Combined Immunosuppression Versus Conventional Management in Newly Diagnosed Crohn's Disease.

BACKGROUND AND AIMS: Long-term outcomes of early combined immunosuppression [top-down] compared to conventional management [step-up] in recently diagnosed Crohn's disease [CD] are unknown. We aimed to investigate long-term outcomes of participants of the Step-up/Top-down-trial. METHODS: Trial participants' medical records were reviewed retrospectively. For 16 semesters following the 2-year trial, we recorded: clinical activity, medication use, flares, hospitalization, surgery and fistulas. Colonoscopy reports were scored as: endoscopic remission, aphthous/small ulcers or large ulcers. The primary endpoint was the proportion of semesters in remission. RESULTS: Data were available from 119/133 patients [step-up n = 60]. During a median follow-up of 8 years, clinical remission rates were similar (70% vs 73% [p = 0.85] in step-up and top-down patients, respectively). A shorter time to flare was observed in step-up patients [median five vs nine semesters, p = 0.01]. Cumulatively, 62% of step-up patients used corticosteroids compared to 41% of top-down patients [p = 0.02]. Anti-tumour necrosis factor [anti-TNF] use was higher in the step-up group [73% vs 54%, p = 0.04]. No differences were found in to time to CD hospitalization [respectively 13 vs 14 semesters, p = 0.30], new fistula [14 vs 15 semesters, p = 0.20] or CD surgery [14 vs 15 semesters, p = 0.25]. Mucosal healing 2 years after treatment was associated with a reduced anti-TNF use, but not with differences in other long-term outcomes. Endoscopic remission occurred at similar rates between groups. CONCLUSIONS: Top-down treatment did not result in increased clinical remission during long-term follow-up, compared to step-up treatment. However, lower relapse rates and a reduced use of anti-TNF agents and corticosteroids were observed. No difference was found in rates of endoscopic remission, hospitalization, surgery or new fistulas.

The effect of arthropathies on illness perceptions, coping strategies, outcomes, and their changes over time in patients with inflammatory bowel disease: a 12-month follow-up study.

OBJECTIVES: Arthropathies are a common extraintestinal manifestation (EIM) in inflammatory bowel disease (IBD). This study evaluated the differences in illness perceptions, coping strategies, and illness outcomes between patients with IBD with and without arthropathies at baseline and examined changes at 12 months in these variables in patients with arthropathies. METHODS: In total, 204 patients with (n=123) and without (n=81) arthropathies completed questionnaires at baseline and after 1 year, assessing illness perceptions, coping strategies, quality of life, and work and activity impairment. A linear regression analysis assessed the effect of arthropathies on these factors compared with patients without arthropathies. A mixed model analysis evaluated changes in illness perceptions, coping strategies, and outcomes in patients with arthropathies over time. RESULTS: Patients with arthropathies had more persistent thoughts on symptomatology and the variability of symptoms, held more negative views on the effects of illness, had heightened emotions that affected daily functioning, and had a poorer understanding of IBD than patients without arthropathies. Patients with arthropathies could more efficiently divert attention, felt more useful to others, and perceived a reduced physical and mental health and an increased activity impairment compared with patients without arthropathies. At follow-up, patients with arthropathies were more sceptical about the effectiveness of medical treatment but were better able to adapt their activities to their complaints compared with baseline. CONCLUSION: Patients with arthropathies in IBD adopt different illness perceptions and coping strategies and have different outcomes compared with patients without arthropathies, which is important to know when designing behavioral and physical interventions to improve functioning.

The Xenobiotic Transporter Mdr1 Enforces T Cell Homeostasis in the Presence of Intestinal Bile Acids.

CD4+ T cells are tightly regulated by microbiota in the intestine, but whether intestinal T cells interface with host-derived metabolites is less clear. Here, we show that CD4+ T effector (Teff) cells upregulated the xenobiotic transporter, Mdr1, in the ileum to maintain homeostasis in the presence of bile acids. Whereas wild-type Teff cells upregulated Mdr1 in the ileum, those lacking Mdr1 displayed mucosal dysfunction and induced Crohn's disease-like ileitis following transfer into Rag1-/- hosts. Mdr1 mitigated oxidative stress and enforced homeostasis in Teff cells exposed to conjugated bile acids (CBAs), a class of liver-derived emulsifying agents that actively circulate through the ileal mucosa. Blocking ileal CBA reabsorption in transferred Rag1-/- mice restored Mdr1-deficient Teff cell homeostasis and attenuated ileitis. Further, a subset of ileal Crohn's disease patients displayed MDR1 loss of function. Together, these results suggest that coordinated interaction between mucosal Teff cells and CBAs in the ileum regulate intestinal immune homeostasis.

Short article: Absence of serological rheumatoid arthritis biomarkers in inflammatory bowel disease patients with arthropathies.

OBJECTIVE: Biomarkers that are associated with future progression to rheumatoid arthritis (RA) and joint destruction have been discovered previously in patients with arthralgia. The present study examined these RA biomarkers in inflammatory bowel disease (IBD) patients with arthropathies. PATIENTS AND METHODS: Sera from 155 IBD patients with and 99 IBD patients without arthropathies were analyzed for immunoglobulin (Ig) M rheumatoid factor (RF), IgA-RF, anti-cyclic citrullinated peptide 2, anti-cyclic citrullinated peptide 3.1, and anti-carbamylated protein antibody positivity using enzyme-linked immunosorbent assays. The prevalence of the autoantibodies in the IBD patients was compared with the prevalence in RA patients. RESULTS: No differences were found in biomarker positivity between IBD patients with and without arthropathies. Significantly more biomarker positivity (P<0.001) was observed in RA patients compared with IBD patients with arthropathies. Also, smoking turned out to be significantly associated with positivity for IgM-RF or IgA-RF. CONCLUSION: Our findings suggest that there is no apparent clinical value in the detection of RA biomarkers in serum of IBD patients to help identify arthropathies.

The impact of value-based healthcare for inflammatory bowel diseases on healthcare utilization: a pilot study.

BACKGROUND AND OBJECTIVES: Value-based healthcare (VBHC) is considered to be the solution that will improve quality and decrease costs in healthcare. Many hospitals are implementing programs on the basis of this strategy, but rigorous scientific reports are still lacking. In this pilot study, we present the first-year outcomes of a VBHC program for inflammatory bowel disease (IBD) management that focuses on highly coordinated care, task differentiation of providers, and continuous home monitoring. METHODS: IBD patients treated within the VBHC program were identified in an administrative claims database from a commercial insurer allowing comparisons to matched controls. Only patients for whom data were available the year before and after starting the program were included. Healthcare utilization including visits, hospitalizations, laboratory and imaging tests, and medications were compared between groups. RESULTS: In total, 60 IBD patients treated at the VBHC Center were identified and were matched to 177 controls. Significantly fewer upper endoscopies were performed (-10%, P=0.012), and numerically fewer surgeries (-25%, P=0.49), hospitalizations (-28%, 0=0.71), emergency department visits (-37%, P=0.44), and imaging studies (-25 to -86%) were observed. In addition, 65% fewer patients (P=0.16) used steroids long term. IBD-related costs were 16% ($771) lower than expected (P=0.24). CONCLUSION: These are the first results of a successfully implemented VBHC program for IBD. Encouraging trends toward fewer emergency department visits, hospitalizations, and long-term corticosteroid use were observed. These results will need to be confirmed in a larger sample with more follow-up.

Is Stem Cell Therapy Ready for Prime Time in Treatment of Inflammatory Bowel Diseases?

Autologous hematopoietic stem cell transplantation (HSCT) and mesenchymal stromal cell therapy have been proposed for patients with refractory Crohn's disease (CD) and fistulizing CD, respectively. Will these highly advanced techniques be available only for select patients, at specialized centers, or is further clinical development justified, with the aim of offering widespread, more definitive therapeutic options for often very difficult to treat disease? Patients with CD who are eligible for HSCT have typically been failed by most approved therapies, have undergone multiple surgeries, and have coped with years of disease activity and poor quality of life. The objective of HSCT is to immediately shut down the immune response and allow the transplanted stem cells to develop into self-tolerant lymphocytes. For patients with fistulizing CD, mesenchymal stromal cell therapy deposits MSCs locally, into fistulizing tracts, to down-regulate the local immune response and induce wound healing. Recent trials have produced promising results for HSCT and mesenchymal stromal cell therapy as alternatives to systemic therapies and antibiotics for patients with inflammatory bowel diseases, but are these immunotherapies ready for prime time?

Five-year Safety Data From ENCORE, a European Observational Safety Registry for Adults With Crohn's Disease Treated With Infliximab [Remicade®] or Conventional Therapy.

BACKGROUND AND AIMS: The ENCORE registry aimed at comparing the long-term safety of Crohn's disease [CD] treatment with infliximab [Remicade®] and with conventional therapies in real-world clinical practice. METHODS: The 5-year, prospective, observational ENCORE registry followed patients with CD in nine European countries, who received treatment with infliximab, conventional therapies, or switched to infliximab from conventional therapy. Adverse events [AEs] in pre-specified categories and serious AEs were recorded at least every 6 months of the 5-year observation period. Frequency of events was evaluated, and multivariable analyses using follow-up time [Cox proportion hazards model] and exposure time [Poisson regression] were used to identify risk factors for time to AEs in pre-specified categories. RESULTS: Patients who received infliximab [N = 1541], conventional therapies [N = 1121], or switched to infliximab [N = 298] were followed for medians of 60.4, 55.6, and 42.5 months, respectively. Infliximab median exposure was 18.7 and 19.3 months in the infliximab and switched-to-infliximab groups, respectively. In time-to-event Cox proportion hazards [PH] analyses adjusting for confounders, infliximab [vs conventional therapy] was associated with serious infections (hazard ratio [HR] = 1.64, 95% confidence interval [CI]: 1.17, 2.31] and haematological conditions [HR = 2.91, CI: 1.51, 5.59], and not associated with lymphoproliferative disorders/malignancy [HR = 1.44, CI: 0.86, 2.42] or death [HR = 1.22, CI: 0.63, 2.36]. Prednisone use was associated with higher mortality [HR = 3.58, CI: 1.49, 8.61]. In exposure-adjusted Poisson regression analyses, infliximab was associated with lower mortality (risk ratio [[RR] 0.39, CI: 0.17, 0.88]). CONCLUSIONS: Data from 5-year safety follow-up of patients with CD in the ENCORE registry demonstrate that infliximab [Remicade®] exposure is associated with increased risk of serious infections and haematological conditions, whereas mortality may be decreased.

Value redefined for inflammatory bowel disease patients: a choice-based conjoint analysis of patients' preferences.

PURPOSE: Value-based healthcare is an upcoming field. The core idea is to evaluate care based on achieved outcomes divided by the costs. Unfortunately, the optimal way to evaluate outcomes is ill-defined. In this study, we aim to develop a single, preference based, outcome metric, which can be used to quantify overall health value in inflammatory bowel disease (IBD). METHODS: IBD patients filled out a choice-based conjoint (CBC) questionnaire in which patients chose preferable outcome scenarios with different levels of disease control (DC), quality of life (QoL), and productivity (Pr). A CBC analysis was performed to estimate the relative value of DC, QoL, and Pr. A patient-centered composite score was developed which was weighted based on the stated preferences. RESULTS: We included 210 IBD patients. Large differences in stated preferences were observed. Increases from low to intermediate outcome levels were valued more than increases from intermediate to high outcome levels. Overall, QoL was more important to patients than DC or Pr. Individual outcome scores were calculated based on the stated preferences. This score was significantly different from a score not weighted based on patient preferences in patients with active disease. CONCLUSIONS: We showed the feasibility of creating a single outcome metric in IBD which incorporates patients' values using a CBC. Because this metric changes significantly when weighted according to patients' values, we propose that success in healthcare should be measured accordingly.

Informatics-Based Discovery of Disease-Associated Immune Profiles.

Advances in flow and mass cytometry are enabling ultra-high resolution immune profiling in mice and humans on an unprecedented scale. However, the resulting high-content datasets challenge traditional views of cytometry data, which are both limited in scope and biased by pre-existing hypotheses. Computational solutions are now emerging (e.g., Citrus, AutoGate, SPADE) that automate cell gating or enable visualization of relative subset abundance within healthy versus diseased mice or humans. Yet these tools require significant computational fluency and fail to show quantitative relationships between discrete immune phenotypes and continuous disease variables. Here we describe a simple informatics platform that uses hierarchical clustering and nearest neighbor algorithms to associate manually gated immune phenotypes with clinical or pre-clinical disease endpoints of interest in a rapid and unbiased manner. Using this approach, we identify discrete immune profiles that correspond with either weight loss or histologic colitis in a T cell transfer model of inflammatory bowel disease (IBD), and show distinct nodes of immune dysregulation in the IBDs, Crohn's disease and ulcerative colitis. This streamlined informatics approach for cytometry data analysis leverages publicly available software, can be applied to manually or computationally gated cytometry data, is suitable for any clinical or pre-clinical setting, and embraces ultra-high content flow and mass cytometry as a discovery engine.