A random forest model predicts responses to infliximab in Crohn’s disease based on clinical and serological parameters

References

• Ye BD, Pesegova M, Alexeeva O, et al. Efficacy and safety of biosimilar CT-P13 compared with originator infliximab in patients with active Crohn's disease: an international, randomised, double-blind, phase 3 non-inferiority study. Lancet. 2019;393(10182):1699–1707.
   PubMed Web of Science ®Google Scholar
• Kobayashi T, Hishida A, Tanaka H, et al. Real-world experience of anti-tumor necrosis factor therapy for internal fistulas in Crohn's disease: a retrospective multicenter cohort study. Inflamm Bowel Dis. 2017;23(12):2245–2251.
   PubMed Web of Science ®Google Scholar
• Singh S, Fumery M, Sandborn WJ, et al. Systematic review and network meta-analysis: first- and second-line biologic therapies for moderate-severe Crohn's disease. Aliment Pharmacol Ther. 2018;48(4):394–409.
   PubMed Web of Science ®Google Scholar
• Panaccione R, Sandborn WJ, D’Haens G, et al. Clinical benefit of long-term adalimumab treatment in patients with Crohn's disease following loss of response or intolerance to infliximab: 96-week efficacy data from gain/adhere trials. J Crohns Colitis. 2018;12(8):930–938.
   PubMed Web of Science ®Google Scholar
• Dignass A, Van Assche G, Lindsay JO, et al. The second European evidence-based consensus on the diagnosis and management of Crohn's disease: current management. J Crohns Colitis. 2010;4(1):28–62.
   PubMed Web of Science ®Google Scholar
• Kindler V, Sappino A-P, Grau GE, et al. The inducing role of tumor necrosis factor in the development of bactericidal granulomas during BCG infection. Cell. 1989;56(5):731–740.
   PubMed Web of Science ®Google Scholar
• Pedersen N, Elkjaer M, Duricova D, et al. eHealth: Individualisation of infliximab treatment and disease course via a self-managed web-based solution in Crohn's disease. Aliment Pharmacol Ther. 2012;36(9):840–849.
   PubMed Web of Science ®Google Scholar
• Arnott ID, McNeill G, Satsangi J. An analysis of factors influencing short-term and sustained response to infliximab treatment for Crohn's disease. Aliment Pharmacol Ther. 2003;17(12):1451–1457.
   PubMed Web of Science ®Google Scholar
• Bramuzzo M, Arrigo S, Romano C, et al. Efficacy and safety of infliximab in very early onset inflammatory bowel disease: a national comparative retrospective study. United European Gastroenterol J. 2019;7(6):759–766.
   PubMed Web of Science ®Google Scholar
• Prieto-Perez R, Almoguera B, Cabaleiro T, et al. Association between genetic polymorphisms and response to anti-TNFs in patients with inflammatory bowel disease. IJMS. 2016;17(2):225.
   Web of Science ®Google Scholar
• Bar-Yoseph H, Levhar N, Selinger L, et al. Early drug and anti-infliximab antibody levels for prediction of primary non-response to infliximab therapy. Aliment Pharmacol Ther. 2018;47(2):212–218.
   PubMed Web of Science ®Google Scholar
• Steenholdt C, Brynskov J, Thomsen OO, et al. Implications of infliximab treatment failure and influence of personalized treatment on patient-reported health-related quality of life and productivity outcomes in Crohn's disease. ECCOJC. 2015;9(11):1032–1042.
   Web of Science ®Google Scholar
• Le Berre C, Ananthakrishnan AN, Danese S, et al. Ulcerative Colitis and Crohn’s disease have similar burden and goals for treatment. Clin Gastroenterol Hepatol. 2020;18(1):14–23.
   PubMed Web of Science ®Google Scholar
• Guan Y, Zhang H, Quang D, et al. Machine learning to predict anti-tumor necrosis factor drug responses of rheumatoid arthritis patients by integrating clinical and genetic markers. Arthritis Rheumatol. 2019;71(12):1987–1996.
   PubMed Web of Science ®Google Scholar
• Vande Casteele N, Khanna R, Levesque BG, et al. The relationship between infliximab concentrations, antibodies to infliximab and disease activity in Crohn's disease. Gut. 2015;64(10):1539–1545.
   PubMed Web of Science ®Google Scholar
• Hradsky O, Potuznikova K, Siroka J, et al. Prediction of thiopurine metabolite levels based on haematological and biochemical parameters. J Pediatr Gastroenterol Nutr. 2019;69(4):e105–e110.
   PubMed Web of Science ®Google Scholar
• Grossberg LB, Papamichael K, Feuerstein JD, et al. A survey study of gastroenterologists' attitudes and barriers toward therapeutic drug monitoring of anti-TNF therapy in inflammatory bowel disease. Inflamm Bowel Dis. 2018;24(1):191–197.
   Web of Science ®Google Scholar
• Feng T, Chen B, Li L, et al. Serum interleukin 9 levels predict disease severity and the clinical efficacy of infliximab in patients with Crohn's disease. Inflamm Bowel Dis. 2017;23(10):1817–1824.
   PubMed Web of Science ®Google Scholar
• Cutler A, Stevens JR. Random forests for microarrays. Methods Enzymol. 2006;411:422–432.
   PubMed Web of Science ®Google Scholar
• Chen X, Ishwaran H. Random forests for genomic data analysis. Genomics. 2012;99(6):323–329.
   PubMed Web of Science ®Google Scholar
• Gomollon F, Dignass A, Annese V, et al. 3rd European evidence-based consensus on the diagnosis and management of Crohn's disease 2016: part 1: diagnosis and medical management. ECCOJC. 2017;11(1):3–25.
   Web of Science ®Google Scholar
• Kuroda D, Sawayama H, Kurashige J, et al. Controlling nutritional status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection. Gastric Cancer. 2018;21(2):204–212.
   PubMed Web of Science ®Google Scholar
• Wang Z, Meng Y, Weng F, et al. An effective CNN method for fully automated segmenting subcutaneous and visceral adipose tissue on CT scans. Ann Biomed Eng. 2020;48(1):312–328.
   PubMed Web of Science ®Google Scholar
• O'Connor M, Ryan J, Foley S. Best single-slice location to measure visceral adipose tissue on paediatric CT scans and the relationship between anthropometric measurements, gender and VAT volume in children. BJR. 2015;88(1054):20140711.
   Google Scholar
• Rebours V, Gaujoux S, d'Assignies G, et al. Obesity and fatty pancreatic infiltration are risk factors for pancreatic precancerous lesions (PanIN). Clin Cancer Res. 2015;21(15):3522–3528.
   PubMed Web of Science ®Google Scholar
• Guiu B, Petit JM, Bonnetain F, et al. Visceral fat area is an independent predictive biomarker of outcome after first-line bevacizumab-based treatment in metastatic colorectal cancer. Gut. 2010;59(3):341–347.
   PubMed Web of Science ®Google Scholar
• Silverberg MS, Satsangi J, Ahmad T, et al. Toward an integrated clinical, molecular and serological classification of inflammatory bowel disease: report of a working party of the 2005 Montreal World Congress of Gastroenterology. Can J Gastroenterol. 2005;19 (Suppl A):5A–36A.
   PubMed Web of Science ®Google Scholar
• Satsangi J, Silverberg MS, Vermeire S, et al. The Montreal classification of inflammatory bowel disease: controversies, consensus and implications. Gut. 2006;55(6):749–753.
   PubMed Web of Science ®Google Scholar
• Shkurin A, Vellido A. Using random forests for assistance in the curation of G-protein coupled receptor databases. Biomed Eng Online. 2017;16(Suppl 1):75.
   PubMed Web of Science ®Google Scholar
• Targan SR, Hanauer SB, van Deventer SJ, et al. A short-term study of chimeric monoclonal antibody cA2 to tumor necrosis factor-alpha for Crohn's disease. Crohn's disease cA2 study group. N Engl J Med. 1997;337(15):1029–1035.
   PubMed Web of Science ®Google Scholar
• Laharie D, Bourreille A, Branche J, et al. Ciclosporin versus infliximab in patients with severe ulcerative colitis refractory to intravenous steroids: a parallel, open-label randomised controlled trial. Lancet. 2012;380(9857):1909–1915.
   PubMed Web of Science ®Google Scholar
• Stevens TW, Matheeuwsen M, Lonnkvist MH, et al. Systematic review: predictive biomarkers of therapeutic response in inflammatory bowel disease-personalised medicine in its infancy. Aliment Pharmacol Ther. 2018;48(11-12):1213–1231.
   PubMed Web of Science ®Google Scholar
• Naviglio S, Giuffrida P, Stocco G, et al. How to predict response to anti-tumor necrosis factor agents in inflammatory bowel disease. Expert Rev Gastroenterol Hepatol. 2018;12(8):797–810.
   PubMed Web of Science ®Google Scholar
• Lichtenstein GR. Comprehensive review: anti-tumor necrosis factor agents in inflammatory bowel disease and factors implicated in treatment response. Therap Adv Gastroenterol. 2013;6(4):269–293.
   PubMed Web of Science ®Google Scholar
• Flamant M, Roblin X. Inflammatory bowel disease: towards a personalized medicine. Therap Adv Gastroenterol. 2018;11:1756283X1774502. 1756283X17745029.
   PubMed Web of Science ®Google Scholar
• Billiet T, Papamichael K, de Bruyn M, et al. A matrix-based model predicts primary response to infliximab in Crohn's disease. ECCOJC. 2015;9(12):1120–1126.
   Web of Science ®Google Scholar
• Peyrin-Biroulet L, Loftus EV, Jr., Colombel JF, et al. Long-term complications, extraintestinal manifestations, and mortality in adult Crohn's disease in population-based cohorts. Inflamm Bowel Dis. 2011;17(1):471–478.
   PubMed Web of Science ®Google Scholar
• Calvert CR, Lal S. Approaches to intestinal failure in Crohn's disease. Proc Nutr Soc. 2011;70(3):336–341.
   PubMed Web of Science ®Google Scholar
• Santarpia L, Alfonsi L, Castiglione F, et al. Nutritional rehabilitation in patients with malnutrition due to Crohn's disease. Nutrients. 2019;11(12):2947.
   PubMed Web of Science ®Google Scholar
• Yamamoto T, Nakahigashi M, Umegae S, et al. Prospective clinical trial: enteral nutrition during maintenance infliximab in Crohn's disease. J Gastroenterol. 2010;45(1):24–29.
   PubMed Web of Science ®Google Scholar
• Hirai F, Takeda T, Takada Y, et al. Efficacy of enteral nutrition in patients with Crohn's disease on maintenance anti-TNF-alpha antibody therapy: a meta-analysis. J Gastroenterol. 2020;55(2):133–141.
   PubMed Web of Science ®Google Scholar
• Hirai F, Ishida T, Takeshima F, et al. Effect of a concomitant elemental diet with maintenance anti-tumor necrosis factor-alpha antibody therapy in patients with Crohn's disease: a multicenter, prospective cohort study. J Gastroenterol Hepatol. 2019;34(1):132–139.
   PubMed Web of Science ®Google Scholar
• Kamata N, Oshitani N, Watanabe K, et al. Efficacy of concomitant elemental diet therapy in scheduled infliximab therapy in patients with Crohn's disease to prevent loss of response. Dig Dis Sci. 2015;60(5):1382–1388.
   PubMed Web of Science ®Google Scholar
• Nguyen DL, Palmer LB, Nguyen ET, et al. Specialized enteral nutrition therapy in Crohn's disease patients on maintenance infliximab therapy: a meta-analysis. Therap Adv Gastroenterol. 2015;8(4):168–175.
   PubMed Web of Science ®Google Scholar
• Cabrerizo S, Cuadras D, Gomez-Busto F, et al. Serum albumin and health in older people: review and meta-analysis. Maturitas. 2015;81(1):17–27.
   PubMed Web of Science ®Google Scholar
• Dotan I, Ron Y, Yanai H, et al. Patient factors that increase infliximab clearance and shorten half-life in inflammatory bowel disease: a population pharmacokinetic study. Inflamm Bowel Dis. 2014;20(12):2247–2259.
   PubMed Web of Science ®Google Scholar
• Brandse JF, Mould D, Smeekes O, et al. A real-life population pharmacokinetic study reveals factors associated with clearance and immunogenicity of infliximab in inflammatory bowel disease. Inflammatory Bowel Diseases. 2017;23(4):650–660.
   PubMed Web of Science ®Google Scholar
• Ordas I, Mould DR, Feagan BG, et al. Anti-TNF monoclonal antibodies in inflammatory bowel disease: pharmacokinetics-based dosing paradigms. Clin Pharmacol Ther. 2012;91(4):635–646.
   PubMed Web of Science ®Google Scholar
• Brandse JF, van den Brink GR, Wildenberg ME, et al. Loss of infliximab into feces is associated with lack of response to therapy in patients with severe ulcerative colitis. Gastroenterology. 2015;149(2):350–355.
   PubMed Web of Science ®Google Scholar
• Wedrychowicz A, Zajac A, Tomasik P. Advances in nutritional therapy in inflammatory bowel diseases: review. World J Gastroenterol. 2016;22(3):1045–1066.
   PubMed Web of Science ®Google Scholar
• Shen W, Cao L, Li Y, et al. Visceral fat is associated with mucosal healing of infliximab treatment in Crohn's disease. Dis Colon Rectum. 2018;61(6):706–712.
   PubMed Web of Science ®Google Scholar
• Gonçalves P, Magro F, Martel F. Metabolic inflammation in inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(2):453–467.
   PubMed Web of Science ®Google Scholar
• Ha CWY, Martin A, Sepich-Poore GD, et al. Translocation of viable gut microbiota to mesenteric adipose drives formation of creeping fat in humans. Cell. 2020;183(3):666–683.e17.
   PubMed Web of Science ®Google Scholar
• Sina C, Kemper C, Derer S. The intestinal complement system in inflammatory bowel disease: shaping intestinal barrier function. Semin Immunol. 2018;37:66–73.
   PubMed Web of Science ®Google Scholar
• Hodgson HJ, Potter BJ, Jewell DP. Humoral immune system in inflammatory bowel disease: i. complement levels. Gut. 1977;18(9):749–753.
   PubMed Web of Science ®Google Scholar
• Sunderhauf A, Skibbe K, Preisker S, et al. Regulation of epithelial cell expressed C3 in the intestine: relevance for the pathophysiology of inflammatory bowel disease? Mol Immunol. 2017;90:227–238.
   PubMed Web of Science ®Google Scholar
• Borba EF, Carvalho JF, Bonfa E. Mechanisms of dyslipoproteinemias in systemic lupus erythematosus. Clin Dev Immunol. 2006;13(2-4):203–208.
   PubMed Web of Science ®Google Scholar
• van Leuven SI, Hezemans R, Levels JH, et al. Enhanced atherogenesis and altered high density lipoprotein in patients with Crohn's disease. J Lipid Res. 2007;48(12):2640–2646.
   PubMed Web of Science ®Google Scholar
• Boyer JF, Gourraud PA, Cantagrel A, et al. Traditional cardiovascular risk factors in rheumatoid arthritis: a meta-analysis. Joint Bone Spine. 2011;78(2):179–183.
   PubMed Web of Science ®Google Scholar
• Heinecke JW. The HDL proteome: a marker and perhaps mediator of coronary artery disease. J Lipid Res. 2009;50(Suppl):S167–S171.
   PubMed Web of Science ®Google Scholar
• Norata GD, Pirillo A, Ammirati E, et al. Emerging role of high density lipoproteins as a player in the immune system. Atherosclerosis. 2012;220(1):11–21.
   PubMed Web of Science ®Google Scholar