Introduction

Targeted therapies have revolutionized the management of immune-mediated inflammatory diseases (IMIDs), however, there is a substantial number of patients who respond poorly to a given drug. There is a big need to understand the factors that are associated with this heterogeneity.

Aims & Methods

The DoCTIS project (1) aims to characterize molecular variation both at the disease and drug response levels across six different IMIDs. We applied single cell RNA sequencing to 360 peripheral blood mononuclear cell (PBMC) samples from 176 patients from six prevalent IMIDs –psoriasis (PS), psoriatic arthritis (PsA), Crohn’s Disease (CD), ulcerative colitis (UC), rheumatoid arthritis (RA), and systemic lupus erythematosus (SLE)- treated with five different drugs targeting TNF, IL12p40, IL6R, BLySS, IL17 and JAK pathways. All patients were analyzed at two time points including baseline and at the week of clinical response creating an immune landscape of more than two million peripheral immune cells.

Results

We found large inter-disease differences both at the compositional and genetic regulatory programs. ScRNA-Seq analysis revealed large differences at the systemic level between the six IMIDs. Compositional analyses demonstrated that the circulating immune cell profiles of UC and CD were more similar to each other than to the rest of IMIDs, and also identified differences in pDC, MAIT, NK CD16- and T CD4+ Memory subsets between both diseases. At the transcriptional level, we found the expected upregulated interferon response signature affecting multiple cell types in SLE, but also novel findings like strong regulatory differences in B and CD14+ monocyte compartments between UC and CD, two diseases with a highly shared genetic risk. The impact of each drug was found to be largely disease-specific. Furthermore, we found multiple regulatory features associated with the effect of each drug as well the association to response.

Conclusion

The scRNA-Seq atlas developed in DoCTIS provides a unique resource for the understanding of drug response and disease heterogeneity across immune-mediated inflammatory diseases.

References

1. Decision on Optimal Combinatorial Therapies in IMIDS using Systems Approaches (DoCTIS). https://doctis.eu/

Disclosure

Antonio Julià: None declared, Yolanda Guillén: None declared, Paloma Vela Casasempere: None declared, Antonio Fernández Nebro: None declared, Carlos Marras: None declared, Santos Castañeda Bristol-Myers Squibb, Eli Lilly, Bristol-Myers Squibb, Jaime Calvo Alén: None declared, Jesús Tornero Molina: None declared, Juan de Dios Cañete Crespillo: None declared, Eugeni Domènech: None declared, Javier Gisbert: None declared, Jose M Carrascosa: None declared, Eduardo Fonseca: None declared, Luis Bujanda Fernández de Pierola: None declared, Valle García Sánchez: None declared, Britta Siegmund: AbbVie, AlfaSigma, BMS, CED Service GmbH, Dr. Falk Pharma, Eli Lilly, MSD, Ferring, Galapagos, Janssen, Pfizer, and Takeda, Abivax, Boehringer Ingelheim, Endpoint Health, Gilead, Janssen, Landos, Materia Prima, PredictImmune, Giampiero Girolomoni: AbbVie, Almirall, Amgen, Boehringer-Ingelheim, Bristol-Myers Squibb, Eli-Lilly, Leo Pharma, Merck Serono, Novartis, Pfizer, Pierre Fabre, Samsung bioepis and Sanofi, Almirall, Amgen, Bristol-Myers Squibb, Eli-Lilly, Leo Pharma, Merck Serono, Novartis, Pfizer, Samsung bioepis and Sanofi, Pfizer, Holger Heyn: Mirxes, Moderna, Nanostring, Omniscope, Singularity, Laura Jimenez: None declared, Pere Santamaría: None declared, Edgar Angelats: None declared, Rick Myers: None declared, Sergio H. Martínez-Mateu: None declared, Juan Angel Patiño Galindo: None declared, Ernest Choy: AbbVie, Amgen, Biocon, Biogen, Chugai, Eli Lilly, Fresenus Kabi, Gilead, Janssen, Novartis, Pfizer, Regeneron, Roche, RPharm, and Sanofi, Bio-Cancer, Biogen, Novartis, PFizer, and Sanofi, AbbVie, Amgen, Bristol-Myers Squibb, Chugai, Eli Lilly, Fresenus Kabi, Galapagos, Gilead, Novartis, Pfizer, Regeneron, Roche, RPharm, Sanofi, and UCB Pharma, Sara Marsal: None declared

Introduction

MORF-057 is an oral α₄β₇ integrin inhibitor that prevents immune cell entry into the gut to alleviate inflammation.

Aims & Methods

EMERALD-2 is a phase 2b, randomized, double-blind, placebo-controlled study evaluating MORF-057 efficacy and safety in adults with moderately to severely active ulcerative colitis (UC). Participants with Modified Mayo Score (MMS) 5–9, inadequate/loss of response or intolerance to conventional or advanced therapy (AT), and who were integrin inhibitor-naïve received 1 of 3 MORF-057 doses or placebo (1:1:1:1). The primary efficacy endpoint was clinical remission at Week 12; secondary and exploratory efficacy endpoints were rates of clinical response and endoscopic improvement, respectively. Pharmacokinetic and pharmacodynamic endpoints and safety were evaluated. The study is registered with ClinicalTrials.gov (NCT05611671).

Results

The study enrolled 280 participants (mean [SD] age, 40.2 [14.6] years; 55.4% male; mean [SD] time since UC diagnosis, 6.7 [7.2] years). At baseline, mean (SD) MMS was 6.7 (1.0); 39.3% of participants were on a stable corticosteroid dose, 20.4% were on an immunomodulator, and 31.1% were AT-experienced.
Clinical remission rate with MORF-057 at Week 12 was dose dependent, ranging from 17.1% (100 mg QD) to 31.9% (200 mg BID) vs. 24.3% with placebo (Table 1), with the same trend in the AT-experienced subgroup (N=87; 100 mg QD, 4.3%; 100 mg BID, 13.6%; 200 mg BID, 21.1%; placebo, 13.0%). Compared with placebo, 200 mg BID MORF-057 had numerically higher clinical response and endoscopic and histo-endoscopic mucosal improvement (HEMI) rates, with the latter 2 endpoints showing an increasing trend with higher doses.

Table 1. Efficacy endpoints in EMERALD-2 at Week 12

Rate (proportion of patients, %)	MORF-057			Placebo (n=70)
	100 mg QD (n=70)	100 mg BID (n=71)	200 mg BID (n=69)
Clinical Remissiona	17.1	23.9	31.9	24.3
Clinical Responseb	57.1	53.5	62.3	54.3
Endoscopic Improvementc	31.4	32.4	43.5	31.4
Histo-Endoscopic Mucosal Improvementd	27.1	31.0	42.0	25.7

^aBased on MMS (stool frequency=0/1, RB=0, MES=0/1 [excluding friability]). Non-significant vs. placebo.
^b≥2-point reduction in MMS and ≥30% change from baseline, and ≥1-point reduction in RB score from baseline or RB=0/1.
^cMES≤1.
^dMES=0/1 (excluding friability) and neutrophil infiltration in <5% of crypts; no crypt destruction; and no erosions, ulcerations, or granulation tissue (Geboes scoring).
MES, Mayo Endoscopic Subscore; MMS, Modified Mayo Score; RB, rectal bleeding.

There was a dose-dependent increasing trend in α4β7 receptor occupancy. Treatment-emergent adverse events (TEAEs) in the MORF-057 groups were mostly of mild (42/76, 55.3%) or moderate (25/76, 32.9%) severity; TEAE frequency was similar to the placebo group (36.0% [pooled rate for 3 dose regimens] vs. 34.8%). Among all participants, there were 5 serious AEs not considered treatment-related (UC exacerbation [n=2], AST increase, pneumothorax, vertebral disc herniation). There were no cases of progressive multifocal leukoencephalopathy or meaningfully increased absolute lymphocyte count and no deaths.

Conclusion

Dose-dependent responses to MORF-057 were observed for clinical remission and hard-to-achieve endpoints such as HEMI at Week 12. The clinical remission rate with MORF-057 was numerically higher but did not achieve statistical significance vs. placebo, which showed higher-than-expected responses. MORF-057 had a favorable safety profile with no meaningful safety findings. The study is ongoing to evaluate maintenance safety and efficacy, with further clinical development of MORF-057 planned.

Disclosure

BES: Honoraria for consulting--AbbVie, Adiso Therapeutics, Agomab, Alimentiv, Amgen, AnaptysBio, Arena Pharmaceuticals, Artugen Therapeutics, Astra Zeneca, Biolojic Design, Biora Therapeutics, Boehringer Ingelheim, Boston Pharmaceuticals, Calibr, Celgene, Celltrion, ClostraBio, Equillium, Enthera, Enveda Biosciences, Evommune, Ferring, Fresenius Kabi, Fzata, Galapagos, Genentech (Roche), Gilead Sciences, GlaxoSmithKline, Gossamer Bio, Imhotex, Index Pharmaceuticals, Innovation Pharmaceuticals, Inotrem, Kaleido, Kallyope, Merck & Co., Microbiotica, Mitsubishi Tanabe, Mobius Care, Morphic Therapeutics, MRM Health, Nexus Therapeutics, Nimbus Discovery, Odyssey Therapeutics, OSE Immunotherapeutics, Palisade Bio, Progenity, Prometheus Biosciences, Prometheus Laboratories, Protagonist Therapeutics, Q32 Bio, Rasayana Therapeutics, Recludix Therapeutics, Reistone Biopharma, Sanofi, Sorriso Therapeutics, Spyre Therapeutics, Surrozen, Target RWE, Teva, TLL Pharmaceutical, Tr1X, Union Therapeutics, Ventyx Biosciences. Consulting and speaking fees--Abivax. Consulting and speaking fees and other support--Eli Lilly and Company. Research grants, consulting and speaking fees, and other support--Bristol Myers Squibb, Eli Lilly and Company, Janssen, Pfizer, Takeda. Research grants and consulting fees--Janssen. Stock/stock options--Ventyx Biopharma.
BGF: Senior Scientific Director at Alimentiv Inc. Consulting--AbbVie, Abivax, Adiso, AgomAB Therapeutics, Akros, Alira Health, Ally Bridge Group, AnaptysBio, Apini Therapeutics, Argenx, Attovia Tx, Avoro Capital Advisors, Belmore Law, BioFactura, BioJamp, Biora Therapeutics, Blackbird Laboratories, Boehringer-Ingelheim, Boxer Capital, Celsius Therapeutics, Celgene/Bristol Myers Squibb, Celltrion, Clarivate, Connect BioPharma, Disc Medicine, Duality, EcoR1, Eli Lilly and Company, Ensho Therapeutics, Equillium, Evida, Enveda, Faes Farma, First Wave, Forbion, Galapagos, Galen Atlantica, Genentech/Roche, General Atlantic, Genesis Therapeutics, Gilead, Gossamer Pharma, GSK, Imhotex, ImmiDomics, Immunic Therapeutics, Intercept, Janssen, Japan Tobacco Inc., Klick Health, LifeMine Therapeutics, Mage Biologics, Merck, Mestag, Mirador Therapeutics, Mobius Care, Monte Rosa Tx, Morphic Therapeutics, Nexys Therapeutics, Nighthawk Therapeutics, Nimbus Therapeutics, Novartis, OncoC4, OrbiMed, Orphagen, Palisade Bio, Pendopharm, Pfizer, Protagonist,32 Bio, REDX, Roche, Roivant/Televant, Sanofi, Sobi, Sorriso, Spyre Therapeutics, SRT Therapeutics, Sun Pharma, Surrozen Inc., Synedgen, Takeda, Teva, Triastek, Trex Bio, TR1X Inc. TVM Lifesciences, Ventyx Biosciences, Versant Ventures, Vida Ventures, Zagbio. Speaker's Bureau--AbbVie, Janssen, Takeda. Scientific Advisory Board (DSMB)--AbbVie, AnaptysBio, Boehringer-Ingelheim, Celgene/Bristol Myers Squibb, Eli Lilly and Company, Genentech/Roche, Janssen, Merck, MiroBio, Origo BioPharma, Pfizer, REDX Pharma, Sanofi, Takeda, Teva, Ecor1Capital, Morphic, GSK. Stock shareholder--Connect BioPharma, EnGene. Provided expert testimony--Belmore Law.
SS: Received fees--AbbVie, Amgen, Arena, Biogen, Bristol Meyers Squibb, Celgene, Celltrion, Falk, Ferring, Fresenius Kabi, Galapagos, Gilead, IMAB, Janssen, Eli Lilly and Company, MSD, Mylan, Novartis, Pfizer, Protagonist, Provention Bio, Roche, Sandoz/Hexal, Shire, Takeda, Ventyx.
LP-B: Consulting--AbbVie, Abivax, Adacyte, Alimentiv, Amgen, Applied Molecular Transport, Arena, Banook, Biogen, Bristol Myers Squibb, Celltrion, Connect Biopharm, Cytoki Pharma, Enthera, Ferring, Fresenius Kabi, Galapagos, Genentech, Gilead, Gossamer Bio, GSK, IAC Image Analysis, Index Pharmaceuticals, Inotrem, Janssen, Lilly, Medac, Mopac, Morphic, MSD, Nordic Pharma, Novartis, Oncodesign Precision Medicine, ONO Pharma, OSE Immunotherapeuthics, Pandion Therapeuthics, Par' Immune, Pfizer, Prometheus, Protagonist, Roche, Samsung, Sandoz, Sanofi, Satisfay, Takeda, Telavant, Theravance, Thermo Fischer, Tigenix, Tillots, Viatris, Vectivbio, Ventyx, Ysopia. Grants--Celltrion, Fresenius Kabi, Medac, MSD, Takeda. Lectures--AbbVie, Alfasigma, Amgen, Arena, Biogen, Celltrion, Ferring, Galapagos, Genentech, Gilead, Janssen, Kern Pharma, Eli Lilly and Company, Medac, MSD, Nordic Pharma, Pfizer, Sandoz, Takeda, Tillots, Viatris. Travel support--AbbVie, Alfasigma, Amgen, Celltrion, Connect Biopharm, Ferring, Galapagos, Genentech, Gilead, Gossamer Bio, Janssen, Eli Lilly and Company, Medac, Morphic, MSD, Pfizer, Sandoz, Takeda, Thermo Fischer, Tillots.
SD: Consultancy fees--AbbVie, Alimentiv, Allergan, Amgen, Applied Molecular Transport, AstraZeneca, Athos Therapeutics, Biogen, Boehringer Ingelheim, Bristol Myers Squibb, Celgene, Celltrion, Dr Falk Pharma, Eli Lilly and Company, Enthera, Ferring Pharmaceuticals Inc., Gilead, Hospira, Inotrem, Janssen, Johnson & Johnson, Morphic, MSD, Mundipharma, Mylan, Pfizer, Roche, Sandoz, Sublimity Therapeutics, Takeda, Teladoc Health, TiGenix, UCB Inc., Vial, Vifor. Lecture fees--AbbVie, Amgen, Ferring Pharmaceuticals Inc., Gilead, Janssen, Mylan, Pfizer, Takeda.
BA, MC, YW, SKL, MM, AW, XZ, NME: Employees and stockholders of Eli Lilly and Company.

Introduction

Small intestinal bacterial overgrowth (SIBO) is a clinical syndrome with abdominal complaints and malabsorption. Despite concerns over cure rates, recurrence, and antibiotic resistance, rifaximin (RIF) remains the primary treatment. Berberine (BBR), an affordable traditional medicine, has demonstrated gut microbiota modulation, making it a promising alternative.

Aims & Methods

We conducted an open-label, non-inferiority randomized controlled trial (BRIEFSIBO) comparing BBR and RIF in SIBO patients. Patients were randomly assigned to receive either RIF or BBR. The primary outcome was breath test (BT) conversion to negative, with symptom scores and the Bristol stool scale as secondary outcomes.

Results

A total of 186 patients completed the study. No significant baseline differences were found between groups in age, gender, BMI, smoking, or alcohol use. BBR demonstrated non-inferior efficacy to RIF for primary outcome (BT eradication) at Week 2 (ITT: BBR 45%, RIF 51%, Z=2.407, P=0.008; PP: BBR 44%, RIF 47%, Z=2.4787, P=0.007) and Week 6 (ITT: BBR 53%, RIF 44%, Z=4.3244, P<0.001; PP: BBR 54%, RIF 45%, Z=4.077, P<0.001). What's more, BBR demonstrated non-inferior efficacy to RIF for secondary outcome (clinical improvement) at Week 2 (ITT: BBR 68%, RIF 75%, Z=2.9209, P=0.0017; PP: BBR 73%, RIF 72%, Z=3.3531, P=0.0004) and Week 6 (ITT: BBR 75%, RIF 80%, Z=2.8514, P=0.0022; PP: BBR 81%, RIF 86%, Z=3.0747, P=0.0011). Following a four-week period of discontinuation, the rate of combined expiratory and symptomatic relapse in patients treated with RIF was 8.57%. In contrast, no such relapses were observed in patients treated with BBR. BT values at 60–90 minutes and AUC decreased in both groups, though RIF showed recurrent peak values during follow-up. A novel breath peak acceleration parameter, reflecting local gut gas load, decreased in both groups. BBR significantly improved bloating at Week 6, whereas RIF improved bowel movement frequency. At Week 6, patients were classified into response, relapse, and nonresponse groups to identify optimal candidates for each drug. RIF responders showed significant improvement in bloating and bowel-related symptoms (P<0.05). Baseline gut microbiota analysis revealed significant β diversity differences between three groups in BBR but not in RIF. Genus-level microbiota composition differed between responders, with BBR responders exhibiting higher baseline proportions of Phascolarctobacterium, Klebsiella, and Haemophilus, and lower Coprobacter. At Week 6, both groups showed enriched Bacteroides, while BBR responders had elevated Phascolarctobacterium, Streptococcus, and Haemophilus, with lower Bifidobacterium.

Conclusion

BBR is non-inferior to RIF for SIBO treatment and offer a promising and cost-effectiveness new option.

References

1. Pimentel M, Saad RJ, Long MD, et al. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol 2020;115(2):165-78. doi: 10.14309/ajg.0000000000000501
2. Bushyhead D, Quigley EMM. Small Intestinal Bacterial Overgrowth-Pathophysiology and Its Implications for Definition and Management. Gastroenterology 2022;163(3):593-607. doi: 10.1053/j.gastro.2022.04.002
3. Quigley EMM, Murray JA, Pimentel M. AGA Clinical Practice Update on Small Intestinal Bacterial Overgrowth: Expert Review. Gastroenterology 2020;159(4):1526-32. doi: 10.1053/j.gastro.2020.06.090
4. Leite G, Rezaie A, Mathur R, et al. Defining Small Intestinal Bacterial Overgrowth by Culture and High Throughput Sequencing. Clin Gastroenterol Hepatol 2024;22(2):259-70. doi: 10.1016/j.cgh.2023.06.001
5. Svedlund J, Sjödin I, Dotevall G. GSRS--a clinical rating scale for gastrointestinal symptoms in patients with irritable bowel syndrome and peptic ulcer disease. Dig Dis Sci 1988;33(2):129-34.
6. Liu ZJ, Wei H, Duan LP, et al. [Clinical features of irritable bowel syndrome with small intestinal bacterial overgrowth and a preliminary study of effectiveness of Rifaximin]. Zhonghua Yi Xue Za Zhi 2016;96(24):1896-902. doi: 10.3760/cma.j.issn.0376-2491.2016.24.005
7. Guo H, Lu S, Zhang J, et al. Berberine and rifaximin effects on small intestinal bacterial overgrowth: Study protocol for an investigator-initiated, double-arm, open-label, randomized clinical trial (BRIEF-SIBO study). Front Pharmacol. 2023;14:1121435. doi:10.3389/fphar.2023.1121435