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Harun R, Lu J, Kassir N, Zhang W. Machine Learning-Based Quantification of Patient Factors Impacting Remission in Patients With Ulcerative Colitis: Insights from Etrolizumab Phase III Clinical Trials. Clin Pharmacol Ther 2024; 115:815-824. [PMID: 37828747 DOI: 10.1002/cpt.3076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/04/2023] [Indexed: 10/14/2023]
Abstract
Etrolizumab, an investigational anti-β7 integrin monoclonal antibody, has undergone evaluation for safety and efficacy in phase III clinical trials on patients with moderate to severe ulcerative colitis (UC). Etrolizumab was terminated because mixed efficacy results were shown in the induction and maintenance phase in patients with UC. In this post hoc analysis, we characterized the impact of explanatory variables on the probability of remission using XGBoost machine learning (ML) models alongside with the SHapley Additive exPlanations framework for explainability. We used patient-level data encompassing demographics, physiology, disease history, clinical questionnaires, histology, serum biomarkers, and etrolizumab drug exposure to develop ML models aimed at predicting remission. Baseline covariates and early etrolizumab exposure at week 4 in the induction phase were utilized to develop an induction ML model, whereas covariates from the end of the induction phase and early etrolizumab exposure at week 4 in the maintenance phase were used to develop a maintenance ML model. Both the induction and maintenance ML models exhibited good predictive performance, achieving an area under the receiver operating characteristic curve (AUROC) of 0.74 ± 0.03 and 0.75 ± 0.06 (mean ± SD), respectively. Compared with placebo, the highest tertile of etrolizumab exposure contributed to 15.0% (95% confidence interval (CI): 9.7-19.9) and 17.0% (95% CI: 8.1-26.4) increases in remission probability in the induction and maintenance phases, respectively. Additionally, the key covariates that predicted remission were CRP, MAdCAM-1, and stool frequency for the induction phase and white blood cells, fecal calprotectin and age for the maintenance phase. These findings hold significant implications for establishing stratification factors in the design of future clinical trials.
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Affiliation(s)
- Rashed Harun
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
- PTC Genomics, Bioinformatics & Biospecimens, Genentech, Inc., South San Francisco, California, USA
| | - James Lu
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| | - Nastya Kassir
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
| | - Wenhui Zhang
- Clinical Pharmacology, Genentech, Inc., South San Francisco, California, USA
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Wiendl M, Dedden M, Liu LJ, Schweda A, Paap EM, Ullrich KAM, Hartmann L, Wieser L, Vitali F, Atreya I, Müller TM, Günther C, Atreya R, Neurath MF, Zundler S. Etrolizumab-s fails to control E-Cadherin-dependent co-stimulation of highly activated cytotoxic T cells. Nat Commun 2024; 15:1043. [PMID: 38310086 PMCID: PMC10838339 DOI: 10.1038/s41467-024-45352-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Despite promising preclinical and earlier clinical data, a recent phase III trial on the anti-β7 integrin antibody etrolizumab in Crohn's disease (CD) did not reach its primary endpoint. The mechanisms leading to this outcome are not well understood. Here we characterize the β7+ T cell compartment from patients with CD in comparison to cells from individuals without inflammatory bowel disease. By flow cytometric, transcriptomic and functional profiling of circulating T cells, we find that triple-integrin-expressing (α4+β7+β1hi) T cells have the potential to home to the gut despite α4β7 blockade and have a specific cytotoxic signature. A subset of triple-integrin-expressing cells readily acquires αE expression and could be co-stimulated via E-Cadherin-αEβ7 interactions in vitro. Etrolizumab-s fails to block such αEβ7 signalling at high levels of T cell stimulation. Consistently, in CD patients treated with etrolizumab, T cell activation correlates with cytotoxic signatures. Collectively, our findings might add one important piece to the puzzle to explain phase III trial results with etrolizumab, while they also highlight that αEβ7 remains an interesting target for future therapeutic approaches in inflammatory bowel disease.
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Affiliation(s)
- Maximilian Wiendl
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Mark Dedden
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Li-Juan Liu
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Anna Schweda
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Eva-Maria Paap
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Karen A-M Ullrich
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Leonie Hartmann
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Luisa Wieser
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Francesco Vitali
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Imke Atreya
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Tanja M Müller
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Claudia Günther
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Raja Atreya
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany
| | - Sebastian Zundler
- Department of Medicine 1, University Hospital Erlangen and Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany.
- Deutsches Zentrum Immuntherapie, University Hospital Erlangen, Erlangen, Germany.
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Moein A, Langenhorst J, Plan EL, Jin JY, Kågedal M, Kassir N. A disease model predicting placebo response and remission status of patients with ulcerative colitis using modified Mayo score. Clin Transl Sci 2023; 16:2310-2322. [PMID: 37718498 PMCID: PMC10651636 DOI: 10.1111/cts.13632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/16/2023] [Accepted: 08/21/2023] [Indexed: 09/19/2023] Open
Abstract
The Mayo Clinical Score is used in clinical trials to describe the clinical status of patients with ulcerative colitis (UC). It comprises four subscores: rectal bleeding (RB), stool frequency (SF), physician's global assessment, and endoscopy (ENDO). According to recent US Food and Drug Administration guidelines (Ulcerative colitis: developing drugs for treatment, Guidance Document, https://www.fda.gov/regulatory-information/s. 2022), clinical response and remission should be based on modified Mayo Score (mMS) relying on RB, SF, and ENDO. Typically, ENDO is performed at the beginning and end of each phase, whereas RB and SF are more frequently available. Item response theory (IRT) models allow the shared information to be used for prediction of all subscores at each observation time; therefore, it leverages information from RB and SF to predict ENDO. A UC disease IRT model was developed based on four etrolizumab phase III studies to describe the longitudinal mMS subscores, placebo response, and remission at the end of induction and maintenance. For each subscore, a bounded integer model was developed. The placebo response was characterized by a mono-exponential function acting on all mMS subscores similarly. The final model reliably predicted longitudinal mMS data. In addition, remission was well-predicted by the model, with only 5% overprediction at the end of induction and 3% underprediction at the end of maintenance. External evaluation of the final model using placebo arms from five different studies indicated adequate performance for both longitudinal mMS subscores and remission status. These results suggest utility of the current disease model for informed decision making in UC clinical development, such as assisting future clinical trial designs and evaluations.
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Affiliation(s)
- Anita Moein
- Genentech, Inc., South San Francisco, California, USA
| | | | | | - Jin Y Jin
- Genentech, Inc., South San Francisco, California, USA
| | - Matts Kågedal
- Genentech, Inc., South San Francisco, California, USA
| | - Nastya Kassir
- Genentech, Inc., South San Francisco, California, USA
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