Introduction

Inflammatory bowel diseases (IBD), comprising Crohn´s disease (CD) and ulcerative colitis (UC), are characterised by chronic, relapsing and remitting inflammation of the gastrointestinal tract. Despite significant efforts to understand the pathogenetic mechanisms of IBD, the elucidation of its etiopathology and progression remains incomplete. This study aimed to clarify IBD pathogenesis using a multiomic approach in serum, urine, intestinal tissue and stool samples.

Aims & Methods

We performed a multiomic analysis (transcriptomic, proteomic, metabolomic and metagenomic) in a discovery cohort of 53 patients with active CD, 50 patients with active UC, and 33 healthy controls (HC). Transcriptomic and proteomic analysis of intestinal tissue was performed by RNA-seq and liquid chromatography-mass spectrometry, respectively. Serum and urine samples were used for metabolome study using nuclear magnetic resonance, and metagenomic analysis of stool samples was performed by 16rRNA gene sequencing.

Results

Gene expression profiles showed a detailed transcriptome landscape of intestinal tissue in patients with CD and UC. A total of 4,105 proteins were identified in mucosal biopsies, of which 2,128 were differentially expressed (DE) between CD and HC, 2,715 proteins DE in UC compared with HC, and 1,653 proteins DE between CD and UC. Metabolomic analyses revealed metabolites and pathways related to ketone, amino sugar and methyl histidine metabolism, Warburg effect, and ammonia recycling deregulated in IBD patients. Moreover, metagenomic results indicated that CD and UC differ in their microbial populations according to beta diversity. In comparison to HC, the microbial population in CD was different, and its alpha diversity was significantly lower.

Conclusion

The results showed that some of the identified analytes could play essential roles in the pathogenesis of CD and UC. New potential key mechanisms that could help to understand the information of omics layers that underlies the pathogenesis of IBD have been outlined.

Disclosure

None

Introduction

Inflammatory bowel diseases (IBD), which includes Crohn´s disease (CD) and ulcerative colitis (UC), are complex and heterogeneous diseases characterized by a multifactorial etiology. IBD prevalence is increasing worldwide. The availability of diverse treatments with different mechanisms of action have revolutionized the ability to achieve clinical remission and endoscopic healing. The aim of this study was to achieve a deeper understanding of the mechanism of action and response to different IBD treatments using a multiomic approach.

Aims & Methods

We analysed the metabolome of serum and urine, metagenome of stool samples and transcriptome and proteome of mucosal biopsies from 53 patients with moderate-to-severe CD and 50 UC patients initiating biologic therapy (anti-TNF, ustekinumab or vedolizumab) or tofacitinib. Patients were assessed at 14 weeks for endoscopic remission and were categorized into responders or non-responders. The methodologies employed in this study were RNA-seq analysis, liquid chromatography-mass spectrometry, nuclear magnetic resonance, and 16S rRNA gene sequencing.

Results

The multiomic analyses revealed substantial alterations in the transcriptome, proteome, metabolome and metagenome of both responders and non-responders IBD patients before and after treatment (14 weeks) to different biologics and tofacitinib. Gene enrichment analysis showed noteworthy differences in all study comparisons, except for patients with CD and UC who did respond to anti-TNF and tofacitinib. Functional enrichment analysis of differentially expressed proteins indicated several processes that could be potentially involved in the mechanisms of action of different treatments. More differences were observed in lipoproteins than in serum and urine metabolites in the different study comparisons. Finally, metagenomic findings indicated changes in the composition of gut bacteria communities among CD patients treated with ustekinumab and UC patients treated with tofacitinib (responders vs non-responders at 14 weeks).

Conclusion

The present study provides novel insights into the mechanisms of action of different IBD treatments from a multiomic approach. Nonetheless, multiomic data integration and validation studies are needed to confirm these findings within a more extensive and independent cohort of patients.

Introduction

Inflammatory bowel diseases (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), are complex conditions characterized by significant clinical, immunological, molecular, genetic, and microbiological heterogeneity. Current therapeutic strategies, particularly biologics and Janus kinase (JAK) inhibitors, are effective for inducing clinical remission and controlling inflammation. However, one-third of patients fail to respond to these treatments, highlighting the need for predictive biomarkers to better tailor therapy and improve outcomes.

Aims & Methods

In this study, we conducted a multi-omic approach, integrating transcriptomics, proteomics, metabolomics, and metagenomics to identify biomarkers of treatment response in IBD. A cohort of 57 active CD and 70 active UC patients was analyzed before and after 14 weeks of treatment with anti-TNF, ustekinumab, vedolizumab, or tofacitinib. Response was evaluated using endoscopic criteria, categorizing patients as responders or non-responders. Biological samples [serum, urine, serum extracellular vesicles (EVs), intestinal biopsies, and stool] were analysed using RNA sequencing, liquid chromatography-mass spectrometry, nuclear magnetic resonance, and 16S rRNA gene sequencing to assess molecular and microbial profiles.

Results

Our results identified multiple mRNAs, proteins and metabolites associated with treatment response. Gene expression analysis in intestinal tissue showed significant differences between UC patients responders and non-responders to vedolizumab. Proteomic analysis of serum EVs and intestinal tissue samples revealed differentially expressed proteins between different study groups. Metabolomic analysis identified deregulation of 24 serum lipoproteins from CD responders to ustekinumab compared to non-responders. Pathway analysis highlighted significant enrichment in ketone and butyrate metabolism, mitochondrial electron transport chain activity, carnitine synthesis, and fatty acid oxidation pathways. Metagenomic analysis revealed microbial differences in UC patients responders to anti-TNF therapy compared to non-responders.

Conclusion

This multi-omics analysis uncovers promising biomarkers that could serve as predictive indicators of therapeutic response to biologics and JAK inhibitors. Nevertheless, further studies are crucial to confirm these findings and evaluate their clinical relevance in identifying patients most likely to respond to tailored therapeutic interventions. One of the challenges is integrating results from different omics approaches to create a more holistic understanding of the disease, potentially opening doors for more precise/early detection through multipanel biomarkers.

Introduction

The therapeutic goal in inflammatory bowel disease (IBD), which includes Crohn´s disease (CD) and ulcerative colitis (UC), is the control of the inflammatory process through drugs (biologic and JAK-inhibitor therapies) that generally have a high cost and may have side effects. Unfortunately, only one-third of patients respond to these treatments and there are no markers that accurately predict this response.

Aims & Methods

The aim of this study was to identify potential serum metabolic biomarkers predictive of response to different drugs for IBD at baseline (before treatment), which could facilitate the selection of the most appropriate therapy for each patient. For this purpose, a prospective and multicenter study was conducted including CD and UC patients who initiate biologic (anti-TNF, ustekinumab or vedolizumab) or JAK-inhibitor (tofacitinib) therapies. Patients were assessed at 14 weeks to determine if they had achieved endoscopic response, based on the SES-CD and on the endoscopic sub score of the Partial Mayo Score. The analysis of the serum metabolome and deconvolution of the serum lipoprotein profile into 110 fractions were conducted using nuclear magnetic resonance for quantitative differential analysis comparing baseline serum samples of responders compared with non-responders.

Results

A total of 150 patients were included (30 CD anti-TNF, 30 UC anti-TNF, 30 CD ustekinumab, 30 UC vedolizumab, and 30 UC tofacitinib). Table 1 shows a summary of the most relevant results obtained during the metabolomic analysis, which revealed metabolites and lipoproteins (common or drug-specific) with significantly altered levels (p<0.05) in the baseline serum samples of subsequent responders compared to non-responders. Moreover, based on ROC curves, potential biomarkers with good sensitivity and specificity for distinguishing between responders and non-responders before treatment were identified. Finally, our analysis identified alanine, aspartate, glutamate, arginine and butanoate metabolism, and the citrate cycle, as the main baseline altered metabolic pathways that could be associated with the response to IBD treatment.

Table 1. Summary of identified potential metabolic biomarkers predictive of endoscopic response to IBD treatment.

Study group	Number of Biomarkers*		Best AUC values**
	Metabolites	Lipoproteins
CD anti-TNF	2	3	0.83; 0.81; 0.78; 0.75; 0.74
UC anti-TNF	1	7	0.88; 0.84; 0.83; 0.77; 0.76; 0.73
CD ustekinumab	4	24	0.96; 0.95; 0.94; 0.91; 0.90; 0.89; 0.87; 0.80
UC vedolizumab	5	8	0.90; 0.79; 0.78
UC tofacitinib	3	8	0.98; 0.96; 0.91; 0.88; 0.87; 0.85

​*Biomarkers with significantly altered levels (p<0.05) in the baseline serum of responders vs non-responders patients. **AUC corresponding to the biomarkers with the best sensitivity and specificity for distinguishing between responders and non-responders patients before treatment. AUC: Area Under the Curve calculated using the Metabolanalyst software in univariate analysis; CD: Crohn's disease; IBD: Inflammatory bowel disease; UC: Ulcerative colitis.

Conclusion

The present study represents an effort towards personalized medicine in targeted therapy selection in IBD patients, which is an important unmet need. Although it needs further validation, we were able to identify a number of serum metabolites and lipoproteins with the potential of predicting response to biologic and JAK-inhibitor therapies.

Introduction

The therapeutic goal in inflammatory bowel disease (IBD), which includes Crohn´s disease (CD) and ulcerative colitis (UC), is the control of the inflammatory process frequently through biologic and JAK-inhibitor therapies, which are generally expensive and can cause adverse effects. Unfortunately, only about one-third of patients respond to these treatments, and there are no markers that accurately predict this response.

Aims & Methods

The aim of this study was to identify potential serum and urinary metabolic biomarkers predictive of IBD response to different drugs at baseline (before treatment), which could facilitate the selection of the most appropriate therapy for each patient. For this purpose, a prospective multicenter study was conducted including CD and UC patients who initiated biologic (anti-TNF, ustekinumab or vedolizumab) or JAK-inhibitor (tofacitinib) therapies. Patients were assessed at 14 weeks to determine if they had achieved an endoscopic response, based on the SES-CD and on the endoscopic subscore of the Partial Mayo Score. The analyses of the serum and urine metabolome, along with the deconvolution of the serum lipoprotein profile, were performed using nuclear magnetic resonance for a quantitative differential analysis comparing the baseline serum samples of responders and non-responders.

Results

A total of 150 patients were included (30 CD anti-TNF, 30 UC anti-TNF, 30 CD ustekinumab, 30 UC vedolizumab and 30 UC tofacitinib). Metabolomic analysis identified 55 potential predictive biomarkers of IBD treatment response with significantly altered levels (p<0.05) in the baseline urine and serum samples of subsequent responders compared to non-responders. Among them, 44 were drug-specific and none were shared between serum and urine. Moreover, based on ROC curve analysis, some of these biomarkers showed good sensitivity and specificity for distinguishing between responders and non-responders before treatment (Table 1). Finally, the integrated metabolite set enrichment analysis of urine and serum samples identified distinct biological pathways associated with the response to each treatment for IBD, with common pathways highlighted, including the metabolism of short-chain fatty acids, the citrate cycle and the metabolism of amino acids such as alanine, aspartate, glutamate, and arginine.

Conclusion

The present study represents a step towards personalized medicine in the selection of targeted therapies for IBD patients, addressing an important unmet need. Although further validation is needed, we have identified serum and urinary metabolic biomarkers with the potential to predict response to biologic and JAK-inhibitor therapies.

Table 1. Summary of potential metabolic biomarkers identified as predictive of endoscopic response before each IBD treatment.

*Biomarkers with significantly altered levels (p<0.05) in baseline serum or urine samples of responders vs non-responders. **AUC corresponding to the biomarkers with the best sensitivity and specificity for distinguishing between responder and non-responder patients before treatment. AUC: Area Under the Curve calculated using the Metabolanalyst software in univariate analysis; CD: Crohn's disease; IBD: Inflammatory bowel disease; UC: Ulcerative colitis.

Clinical Case Summary

A 77-year-old man underwent liver transplantation in 2008 due to alcoholic cirrhosis associated with hemochromatosis, and was taking tacrolimus and mycophenolate mofetil since that.
He was admitted in the Emergency Department in February 2023 with right upper quadrant abdominal pain and diarrhea for one week. Abdominal computed tomography(CT) showed ileal thickening. Laboratory tests revealed leukocytosis(19,000 leukocytes/mm3) and elevated C-reactive protein(16 mg/dL). Acute gastroenteritis was assumed and he was discharged on metronidazole with clinical improvement. One month later, he returned to the Emergency Department with abdominal pain for two days. CT revealed concentric wall thickening of the last ileal loop and a probable enteromesenteric fistula. He was admitted for further evaluation. Colonoscopy revealed deep mucosal ulceration of the terminal ileum. After colonoscopy, his abdominal pain worsened, so he repeated the abdominal CT, which showed a new organized collection in the right flank measuring 63 mm and small gas bubbles of pneumoperitoneum in the right upper quadrant. He underwent ileocecal resection with terminal ileostomy, and the histopathological evaluation revealed a neoplasm composed of atypical lymphoid proliferation, with positive immunohistochemistry for CD45, CD20, CD79a, BCL2, and BCL6, compatible with diffuse large B-cell lymphoma. After staging and exclusion of distant disease, the patient was proposed for chemotherapy following reduction of immunosuppression.
The clinical presentation of Inflammatory Bowel Disease can be quite heterogeneous and several pathologies can mimic its clinical, endoscopic, and/or histological findings. This case illustrates the importance of considering the diagnosis of small bowel lymphoma as a differential diagnosis of Crohn's disease, especially in elderly patients with risk factors, such as chronic immunosuppression.