51
|
Raine T, Verstockt B, Kopylov U, Karmiris K, Goldberg R, Atreya R, Burisch J, Burke J, Ellul P, Hedin C, Holubar SD, Katsanos K, Lobaton T, Schmidt C, Cullen G. ECCO Topical Review: Refractory Inflammatory Bowel Disease. J Crohns Colitis 2021; 15:1605-1620. [PMID: 34160593 DOI: 10.1093/ecco-jcc/jjab112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inflammatory bowel disease is a chronic disease with variable degrees of extent, severity, and activity. A proportion of patients will have disease that is refractory to licensed therapies, resulting in significant impairment in quality of life. The treatment of these patients involves a systematic approach by the entire multidisciplinary team, with particular consideration given to medical options including unlicensed therapies, surgical interventions, and dietetic and psychological support. The purpose of this review is to guide clinicians through this process and provide an accurate summary of the available evidence for different strategies.
Collapse
Affiliation(s)
- Tim Raine
- Department of Gastroenterology, Addenbrooke's Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Bram Verstockt
- Department of Gastroenterology and Hepatology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
- Department of Chronic Diseases and Metabolism, TARGID - IBD, KU Leuven, Leuven, Belgium
| | - Uri Kopylov
- Department of Gastroenterology, Sheba Medical Center, Ramat Gan, Israel
- Sackler School of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Rimma Goldberg
- Department of Gastroenterology, Monash Health and School of Clinical Sciences, Monash University, Melbourne, VIC, Australia
| | - Raja Atreya
- Department of Medicine 1, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Johan Burisch
- Gastrounit, Medical Division, Hvidovre Hospital, University of Copenhagen, Copenhagen, Denmark
| | - John Burke
- Colorectal and General Surgery, Beaumont Hospital, Dublin, Ireland
| | - Pierre Ellul
- Department of Medicine, Division of Gastroenterology, Mater Dei Hospital, Msida, Malta
| | - Charlotte Hedin
- Karolinska Institutet, Department of Medicine Solna, Stockholm, Sweden
- Karolinska University Hospital, Gastroenterology Unit, Department of Gastroenterology, Dermatovenereology and Rheumatology, Stockholm, Sweden
| | - Stefan D Holubar
- Department of Colon & Rectal Surgery, Cleveland Clinic, Cleveland, OH, USA
| | - Konstantinos Katsanos
- Department of Gastroenterology and Hepatology, University and Medical School of Ioannina, Ioannina, Greece
| | - Triana Lobaton
- Department of Gastroenterology, Ghent University Hospital, Ghent, Belgium
| | - Carsten Schmidt
- Medical Faculty of the Friedrich Schiller University, Jena, Germany
| | - Garret Cullen
- Centre for Colorectal Disease, St Vincent's University Hospital and School of Medicine, University College Dublin, Gastroenterology, Dublin, Ireland
| |
Collapse
|
52
|
Chen Z, Zheng X, Wu X, Wu J, Li X, Wei Q, Zhang X, Fang L, Jin O, Gu J. Adalimumab Therapy Restores the Gut Microbiota in Patients With Ankylosing Spondylitis. Front Immunol 2021; 12:700570. [PMID: 34539629 PMCID: PMC8441001 DOI: 10.3389/fimmu.2021.700570] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 08/17/2021] [Indexed: 01/31/2023] Open
Abstract
Growing evidence suggests that the gut microbiota is involved in the initiation and progression of ankylosing spondylitis (AS). In this study, we aimed to explore the gut microbiome alterations during adalimumab therapy and verify microbiome biomarkers predicting treatment response. By evaluating the gut microbial features of 30 AS patients before and after adalimumab therapy for 6 months and 24 healthy controls, we confirmed that the microbiome was restored remarkably after 6 months of adalimumab therapy in AS patients. We then compared the baseline gut microbiome of 22 adalimumab responders with 8 non-responders, a higher abundance of Comamonas was revealed in the latter, although no statistical difference was found after adjusting for the false discovery rate. These results suggested that adalimumab therapy restored the gut microbiome in AS patients and indicated the utility of gut microbiome to be potential biomarkers for therapeutic evaluation. These findings provided an insight into the development of predictive tools and the establishment of precise medical interventions for clinical practice.
Collapse
Affiliation(s)
- Zena Chen
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xuqi Zheng
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xinyu Wu
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jialing Wu
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xiaomin Li
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Qiujing Wei
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Xi Zhang
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Linkai Fang
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ou Jin
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jieruo Gu
- Rheumatology and Immunology Department, Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
53
|
Truong A, Zaghiyan KN, Mirocha J, Melmed GY, McGovern DPB, Syal G, Ha CY, Targan SR, Fleshner PR. Antitumour necrosis factor therapy is associated with de novo Crohn's disease after ileal pouch-anal anastomosis. Colorectal Dis 2021; 23:2416-2424. [PMID: 34157179 PMCID: PMC8440372 DOI: 10.1111/codi.15772] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 05/02/2021] [Accepted: 05/09/2021] [Indexed: 12/12/2022]
Abstract
AIM Tumour necrosis factor inhibitors (TNFi) have revolutionized the management of moderate to severe ulcerative colitis (UC) since their approval for UC in 2005. However, many patients ultimately require surgery with ileal pouch-anal anastomosis (IPAA). Development of de novo Crohn's disease (CD) following IPAA is an increasingly common and devastating complication, sometimes progressing to pouch failure. The aim of this study was to evaluate the association of preoperative TNFi exposure and the development of de novo CD after IPAA. METHOD A prospective single-centre inflammatory bowel disease (IBD) registry was searched for consecutive patients with UC undergoing IPAA during a 25-year period ending July 2018. Patients with preoperative CD or IBD-unclassified were excluded. De novo CD was diagnosed upon endoscopic evidence of five or more mucosal ulcers proximal to the ileal pouch any time after surgery and/or pouch fistula occurring more than three months after ileostomy closure. RESULTS The study cohort consisted of 400 patients with a median follow-up of 44.0 (IQR 11-113) months. Sixty-two (16%) patients developed de novo CD 28.0 (IQR 6-67) months following ileostomy closure. Survival analysis of TNFi era patients revealed a significant increase in de novo CD risk in those with preoperative TNFi exposure. Multivariable proportional hazards modelling revealed two independent predictors for de novo CD development: older age was protective (HR 0.89 per 5-year increase; P = 0.009) and preoperative TNFi exposure was hazardous (HR 2.10; P = 0.011). CONCLUSION This prospective study is the first to suggest an association between preoperative TNFi exposure and the development of de novo CD.
Collapse
Affiliation(s)
- Adam Truong
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Karen N Zaghiyan
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - James Mirocha
- Department of Biostatistics, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Gil Y Melmed
- Department of Gastroenterology - Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Dermot PB McGovern
- Department of Gastroenterology - Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Gaurav Syal
- Department of Gastroenterology - Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Christina Y Ha
- Department of Gastroenterology - Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Stephan R Targan
- Department of Gastroenterology - Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Phillip R Fleshner
- Division of Colorectal Surgery, Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, CA
| |
Collapse
|
54
|
Schräpel C, Kovar L, Selzer D, Hofmann U, Tran F, Reinisch W, Schwab M, Lehr T. External Model Performance Evaluation of Twelve Infliximab Population Pharmacokinetic Models in Patients with Inflammatory Bowel Disease. Pharmaceutics 2021; 13:pharmaceutics13091368. [PMID: 34575443 PMCID: PMC8468301 DOI: 10.3390/pharmaceutics13091368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 01/12/2023] Open
Abstract
Infliximab is approved for treatment of various chronic inflammatory diseases including inflammatory bowel disease (IBD). However, high variability in infliximab trough levels has been associated with diverse response rates. Model-informed precision dosing (MIPD) with population pharmacokinetic models could help to individualize infliximab dosing regimens and improve therapy. The aim of this study was to evaluate the predictive performance of published infliximab population pharmacokinetic models for IBD patients with an external data set. The data set consisted of 105 IBD patients with 336 infliximab concentrations. Literature review identified 12 published models eligible for external evaluation. Model performance was evaluated with goodness-of-fit plots, prediction- and variability-corrected visual predictive checks (pvcVPCs) and quantitative measures. For anti-drug antibody (ADA)-negative patients, model accuracy decreased for predictions > 6 months, while bias did not increase. In general, predictions for patients developing ADA were less accurate for all models investigated. Two models with the highest classification accuracy identified necessary dose escalations (for trough concentrations < 5 µg/mL) in 88% of cases. In summary, population pharmacokinetic modeling can be used to individualize infliximab dosing and thereby help to prevent infliximab trough concentrations dropping below the target trough concentration. However, predictions of infliximab concentrations for patients developing ADA remain challenging.
Collapse
Affiliation(s)
- Christina Schräpel
- Clinical Pharmacy, Saarland University, 66123 Saarbrücken, Germany; (C.S.); (L.K.); (D.S.)
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany; (U.H.); (M.S.)
| | - Lukas Kovar
- Clinical Pharmacy, Saarland University, 66123 Saarbrücken, Germany; (C.S.); (L.K.); (D.S.)
| | - Dominik Selzer
- Clinical Pharmacy, Saarland University, 66123 Saarbrücken, Germany; (C.S.); (L.K.); (D.S.)
| | - Ute Hofmann
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany; (U.H.); (M.S.)
| | - Florian Tran
- Institute of Clinical Molecular Biology, Kiel University and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany;
- Department of Internal Medicine I, University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Walter Reinisch
- Department of Internal Medicine III, Medical University of Vienna, 1090 Vienna, Austria;
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch-Institute of Clinical Pharmacology, University of Tübingen, 70376 Stuttgart, Germany; (U.H.); (M.S.)
- Departments of Clinical Pharmacology, Pharmacy and Biochemistry, University of Tübingen, 72076 Tübingen, Germany
| | - Thorsten Lehr
- Clinical Pharmacy, Saarland University, 66123 Saarbrücken, Germany; (C.S.); (L.K.); (D.S.)
- Correspondence: ; Tel.: +49-681-302-70255
| |
Collapse
|
55
|
Derosa L, Routy B, Desilets A, Daillère R, Terrisse S, Kroemer G, Zitvogel L. Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology? Cancer Discov 2021; 11:2396-2412. [PMID: 34400407 DOI: 10.1158/2159-8290.cd-21-0236] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 05/18/2021] [Accepted: 06/17/2021] [Indexed: 11/16/2022]
Abstract
The cancer-immune dialogue subject to immuno-oncological intervention is profoundly influenced by microenvironmental factors. Indeed, the mucosal microbiota-and more specifically, the intestinal ecosystem-influences the tone of anticancer immune responses and the clinical benefit of immunotherapy. Antibiotics blunt the efficacy of immune checkpoint inhibitors (ICI), and fecal microbial transplantation may restore responsiveness of ICI-resistant melanoma. Here, we review the yin and yang of intestinal bacteria at the crossroads between the intestinal barrier, metabolism, and local or systemic immune responses during anticancer therapies. We discuss diagnostic tools to identify gut dysbiosis and the future prospects of microbiota-based therapeutic interventions. SIGNIFICANCE: Given the recent proof of concept of the potential efficacy of fecal microbial transplantation in patients with melanoma primarily resistant to PD-1 blockade, it is timely to discuss how and why antibiotics compromise the efficacy of cancer immunotherapy, describe the balance between beneficial and harmful microbial species in play during therapies, and introduce the potential for microbiota-centered interventions for the future of immuno-oncology.
Collapse
Affiliation(s)
- Lisa Derosa
- Gustave Roussy Cancer Campus, Villejuif, France. .,Université Paris-Saclay, Ile-de-France, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France
| | - Bertrand Routy
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Quebec, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Quebec, Canada
| | - Antoine Desilets
- Hematology-Oncology Division, Department of Medicine, Centre Hospitalier de l'Université de Montréal (CHUM), Montréal, Quebec, Canada.,Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Quebec, Canada
| | | | - Safae Terrisse
- Gustave Roussy Cancer Campus, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
| | - Guido Kroemer
- Gustave Roussy Cancer Campus, Villejuif, France.,Université Paris-Saclay, Ile-de-France, France.,EverImmune, Gustave Roussy Cancer Campus, Villejuif, France.,Centre de Recherche des Cordeliers, INSERM U1138, Equipe Labellisée-Ligue contre le Cancer, Université de Paris, Institut Universitaire de France, Paris, France.,Metabolomics and Cell Biology Platforms, Gustave Roussy, Villejuif, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Laurence Zitvogel
- Gustave Roussy Cancer Campus, Villejuif, France. .,Université Paris-Saclay, Ile-de-France, France.,Institut National de la Santé Et de la Recherche Médicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France.,Cancer Medicine Department, Gustave Roussy, Villejuif, France.,EverImmune, Gustave Roussy Cancer Campus, Villejuif, France.,Suzhou Institute for Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, China.,Karolinska Institute, Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden.,Center of Clinical Investigations in Biotherapies of Cancer (BIOTHERIS) 1428, Villejuif, France
| |
Collapse
|
56
|
The Role of Biomarkers in Surgery for Ulcerative Colitis: A Review. J Clin Med 2021; 10:jcm10153362. [PMID: 34362144 PMCID: PMC8348722 DOI: 10.3390/jcm10153362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/25/2021] [Accepted: 07/28/2021] [Indexed: 12/19/2022] Open
Abstract
Ulcerative colitis (UC) is an inflammatory condition that generally affects the rectum and extends proximally into the colon in a continuous, distal-to-proximal pattern. Surgical resection (total proctocolectomy) is the only cure for UC and is often necessary in managing complicated or refractory disease. However, recent advances in biologically targeted therapies have resulted in improved disease control, and surgery is required in only a fraction of cases. This ever-increasing array of options for medical management has added complexity to surgical decision-making. In some circumstances, the added time required to ensure failure of medical therapy can delay colectomy in patients who will ultimately need it. Indeed, many patients with severe disease undergo trials of multiple medical therapies prior to considering surgery. In severe cases of UC, continued medical management has been associated with a delay to surgical intervention and higher rates of morbidity and mortality. Biomarkers represent a burgeoning field of research, particularly in inflammatory bowel disease and cancer. This review seeks to highlight the different possible settings for surgery in UC and the role various biomarkers might play in each.
Collapse
|
57
|
Ruszkowski J, Daca A, Szewczyk A, Dębska-Ślizień A, Witkowski JM. The influence of biologics on the microbiome in immune-mediated inflammatory diseases: A systematic review. Biomed Pharmacother 2021; 141:111904. [PMID: 34328113 DOI: 10.1016/j.biopha.2021.111904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/27/2021] [Accepted: 07/06/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Immune-mediated inflammatory diseases (IMIDs) are a group of several chronic disorders with elusive pathogenesis that results in dysregulation of the normal immune response and leads to organ-specific or systemic inflammation. There are many reports on gastrointestinal or skin dysbiosis in patients with IMIDs; however, it is not clear whether dysbiosis is a cause or a result of the observed inflammation. We aimed to determine whether treatment of IMIDs patients with biologics affects their microbiota in comparison with baseline or placebo. METHODS We searched for studies in MEDLINE, Embase, Scopus, and Web of Science. Due to both high heterogeneity and lacking data, vote-counting and structured tables were used to summarize the data. RESULTS AND LIMITATIONS A total of 25 longitudinal human studies with 816 IMIDs patients receiving biologics were included. Data on α-diversity change are inconclusive. Most evidence supports the increase in all α-diversity metrics in responding inflammatory bowel disease (IBD) patients; however, vote counting did not confirm the significance of the directional change. In case of β-diversity, treatment with biologics made patients' microbiome more similar to the microbiome of healthy controls in 5 out of 7 studies. The changes in taxa abundance and predicted functionality of microbiome were systematically summarized. Limited number and quality of the included studies highly restricted the conclusions of the study. CONCLUSIONS Local inflammation may play pivotal role in the gut microbiome disruption in IMIDs patients. The effect of the biologics on human microbiota should be evaluated in randomized controlled trials and transparently reported.
Collapse
Affiliation(s)
- Jakub Ruszkowski
- Department of Pathophysiology, Faculty of Medicine, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland; Department of Nephrology, Transplantology and Internal Medicine, Faculty of Medicine, Medical University of Gdańsk, Poland.
| | - Agnieszka Daca
- Department of Pathology and Experimental Rheumatology, Faculty of Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Adrian Szewczyk
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Gdańsk, Gdańsk, Poland
| | - Alicja Dębska-Ślizień
- Department of Nephrology, Transplantology and Internal Medicine, Faculty of Medicine, Medical University of Gdańsk, Poland
| | - Jacek M Witkowski
- Department of Pathophysiology, Faculty of Medicine, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| |
Collapse
|
58
|
Wu N, Mah C, Koentgen S, Zhang L, Grimm MC, El-Omar E, Hold GL. Inflammatory bowel disease and the gut microbiota. Proc Nutr Soc 2021; 80:1-11. [PMID: 34165053 DOI: 10.1017/s002966512100197x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Inflammatory bowel disease (IBD) is a group of immune-mediated disorders characterised by a chronic, relapsing-remitting inflammation predominantly affecting the gastrointestinal tract. IBD is incurable, affecting people in their most productive years. IBD is historically seen as a disease of Westernised nations although in recent times other countries have seen an exponential rise in cases. Although the exact pathogenesis remains unclear, evidence suggests that microbiota changes play a critical role in IBD pathogenesis. Over the past two decades, IBD has become one of the most studied human conditions linked to the gut microbiota. However, deciphering the intricate link between the gut microbiota and therapeutic efficacy remains elusive. This review will summarise the current evidence relating to the gut microbiota and its involvement in IBD pathogenesis as well as the impact of IBD treatments including pharmaceutical-, nutraceutical- and microbial-focused regimens on the gut microbiota.
Collapse
Affiliation(s)
- Nan Wu
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Cassandra Mah
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Sabrina Koentgen
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Leo Zhang
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael C Grimm
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Emad El-Omar
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Georgina L Hold
- Microbiome Research Centre, St George and Sutherland Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| |
Collapse
|
59
|
Alshehri D, Saadah O, Mosli M, Edris S, Alhindi R, Bahieldin A. Dysbiosis of gut microbiota in inflammatory bowel disease: Current therapies and potential for microbiota-modulating therapeutic approaches. Bosn J Basic Med Sci 2021; 21:270-283. [PMID: 33052081 PMCID: PMC8112554 DOI: 10.17305/bjbms.2020.5016] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 09/17/2020] [Indexed: 12/16/2022] Open
Abstract
There is a growing body of evidence reinforcing the unique connections between the host microbiome, health, and diseases. Due to the extreme importance of the symbiotic relationship between the intestinal microbiome and the host, it is not surprising that any alteration in the gut microbiota would result in various diseases, including inflammatory bowel disease (IBD), Crohn's disease, (CD) and ulcerative colitis (UC). IBD is a chronic, relapsing-remitting condition that is associated with significant morbidity, mortality, compromised quality of life, and costly medical care. Dysbiosis is believed to exacerbate the progression of IBD. One of the currently used treatments for IBD are anti-tumor necrosis factor (TNF) drugs, representing a biologic therapy that is reported to have an impact on the gut microbiota composition. The efficacy of anti-TNF agents is hindered by the possibility of non-response, which occurs in 10-20% of treated patients, and secondary loss of response, which occurs in up to 30% of treated patients. This underscores the need for novel therapies and studies that evaluate the role of the gut microbiota in these conditions. The success of any therapeutic strategy for IBD depends on our understanding of the interactions that occur between the gut microbiota and the host. In this review, the health and disease IBD-associated microbiota patterns will be discussed, in addition to the effect of currently used therapies for IBD on the gut microbiota composition, as well as new therapeutic approaches that can be used to overcome the current treatment constraints.
Collapse
Affiliation(s)
- Dikhnah Alshehri
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Biology, Faculty of Science, Tabuk University, Tabuk, Saudi Arabia
| | - Omar Saadah
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; Inflammatory Bowel Disease Research Group, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Mahmoud Mosli
- Inflammatory Bowel Disease Research Group, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sherif Edris
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt; Princess Al Jawhara Albrahim Center of Excellence in Research of Hereditary Disorders (PACER-HD), Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rashad Alhindi
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmed Bahieldin
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Ain Shams University, Cairo, Egypt
| |
Collapse
|
60
|
Evaluation of changes in intestinal microbiota in Crohn's disease patients after anti-TNF alpha treatment. Sci Rep 2021; 11:10016. [PMID: 33976272 PMCID: PMC8113350 DOI: 10.1038/s41598-021-88823-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 04/14/2021] [Indexed: 02/08/2023] Open
Abstract
Intestinal dysbiosis is key in the onset and development of Crohn’s disease (CD). We evaluated the microbiota changes in CD patients before and after a six-month anti-TNF treatment, comparing these changes with the microbiota of healthy subjects. This prospective multicenter observational study involved 27 CD patients initiating anti-TNF treatment and 16 healthy individuals. Inflammatory activity was determined at baseline, 3 and 6 months, classifying patients into responders and non-responders. Fecal microbiota was analyzed by massive genomic sequencing thought 16S rRNA amplicon sequencing before and after six months of anti-TNF treatment. The CD cohort showed a decrease in genera of the class Clostridia, short-chain fatty acid producers, and an increase in the phylum Proteobacteria (p < 0.01) versus the healthy cohort. After anti-TNF treatment, the phylum Proteobacteria also increased in non-responders versus responders (13/27) (p < 0.005), with the class Clostridia increasing. In addition, alpha diversity increased in responders versus non-responders (p < 0.01), tending towards eubiosis. An association was found (p < 0.001) in the F.prausnitzii/E.coli ratio between responders and non-responders. The F/E ratio was the most accurate biomarker of anti-TNF response (area under the curve 0.87). Thus, anti-TNF treatment allows partial restoration of intestinal microbiota in responders and the F.prausnitzii/E.coli ratio can provide a reliable indicator of response to anti-TNF in CD.
Collapse
|
61
|
Determining Gut Microbial Dysbiosis: a Review of Applied Indexes for Assessment of Intestinal Microbiota Imbalances. Appl Environ Microbiol 2021; 87:AEM.00395-21. [PMID: 33741632 PMCID: PMC8208139 DOI: 10.1128/aem.00395-21] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Assessing “dysbiosis” in intestinal microbial communities is increasingly considered a routine analysis in microbiota studies, and it has added relevant information to the prediction and characterization of diseases and other adverse conditions. However, dysbiosis is not a well-defined condition. Assessing “dysbiosis” in intestinal microbial communities is increasingly considered a routine analysis in microbiota studies, and it has added relevant information to the prediction and characterization of diseases and other adverse conditions. However, dysbiosis is not a well-defined condition. A variety of different dysbiosis indexes have been suggested and applied, but their underlying methodologies, as well as the cohorts and conditions for which they have been developed, differ considerably. To date, no comprehensive overview and comparison of all the different methodologies and applications of such indexes is available. Here, we list all types of dysbiosis indexes identified in the literature, introduce their methodology, group them into categories, and discuss their potential descriptive and clinical applications as well as their limitations. Thus, our focus is not on the implications of dysbiosis for disease but on the methodological approaches available to determine and quantify this condition.
Collapse
|
62
|
Evaluation of anti-TNF therapeutic response in patients with inflammatory bowel disease: Current and novel biomarkers. EBioMedicine 2021; 66:103329. [PMID: 33862588 PMCID: PMC8054158 DOI: 10.1016/j.ebiom.2021.103329] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/14/2022] Open
Abstract
Neutralizing tumour necrosis factor (TNF) antibodies have been widely used to treat inflammatory bowel disease (IBD) in the clinical practice. In this review, the principal biomarker analysis revealed that faecal calprotectin, C-reactive protein, serum or mucosal concentrations of anti-TNF monoclonal antibodies (mAbs) and antibodies to anti-TNF mAbs are commonly used as current biomarkers in the evaluation of anti-TNF therapeutic efficacy. However, mucosal cytokine transcripts. microRNAs, proteomics and faecal and mucosal gut microbiota profile and mucosal histological features are reported to be novel candidates of biomarkers with high clinical utility in the evaluation of anti-TNF therapeutic efficacy in patients with IBD. Therefore, a robust validation of novel promising biomarkers and comparison studies between current used and novel biomarkers are urgently required to improve their value in the evaluation of therapeutic efficacy and optimization of personalized medicine and identification of IBD candidates for anti-TNF therapy in future clinical practice.
Collapse
|
63
|
Bolte LA, Klaassen MAY, Collij V, Vich Vila A, Fu J, van der Meulen TA, de Haan JJ, Versteegen GJ, Dotinga A, Zhernakova A, Wijmenga C, Weersma RK, Imhann F. Patient attitudes towards faecal sampling for gut microbiome studies and clinical care reveal positive engagement and room for improvement. PLoS One 2021; 16:e0249405. [PMID: 33831035 PMCID: PMC8031379 DOI: 10.1371/journal.pone.0249405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 03/17/2021] [Indexed: 12/30/2022] Open
Abstract
Faecal sample collection is crucial for gut microbiome research and its clinical applications. However, while patients and healthy volunteers are routinely asked to provide stool samples, their attitudes towards sampling remain largely unknown. Here, we investigate the attitudes of 780 Dutch patients, including participants in a large Inflammatory Bowel Disease (IBD) gut microbiome cohort and population controls, in order to identify barriers to sample collection and provide recommendations for gut microbiome researchers and clinicians. We sent questionnaires to 660 IBD patients and 112 patients with other disorders who had previously been approached to participate in gut microbiome studies. We also conducted 478 brief interviews with participants in our general population cohort who had collected stool samples. Statistical analysis of the data was performed using R. 97.4% of respondents reported that they had willingly participated in stool sample collection for gut microbiome research, and most respondents (82.9%) and interviewees (95.6%) indicated willingness to participate again, with their motivations for participating being mainly altruistic (57.0%). Responses indicated that storing stool samples in the home freezer for a prolonged time was the main barrier to participation (52.6%), but clear explanations of the sampling procedures and their purpose increased participant willingness to collect and freeze samples (P = 0.046, P = 0.003). To account for participant concerns, gut microbiome researchers establishing cohorts and clinicians trying new faecal tests should provide clear instructions, explain the rationale behind their protocol, consider providing a small freezer and inform patients about study outcomes. By assessing the attitudes, motives and barriers surrounding participation in faecal sample collection, we provide important information that will contribute to the success of gut microbiome research and its near-future clinical applications.
Collapse
Affiliation(s)
- Laura A. Bolte
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Marjolein A. Y. Klaassen
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Valerie Collij
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arnau Vich Vila
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jingyuan Fu
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pediatrics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Taco A. van der Meulen
- Department of Oral and Maxillofacial Surgery, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jacco J. de Haan
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Gerbrig J. Versteegen
- Department of Medical Psychology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Alexandra Zhernakova
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rinse K. Weersma
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Floris Imhann
- Department of Gastroenterology and Hepatology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| |
Collapse
|
64
|
Shang L, Yu H, Liu H, Chen M, Zeng X, Qiao S. Recombinant antimicrobial peptide microcin J25 alleviates DSS-induced colitis via regulating intestinal barrier function and modifying gut microbiota. Biomed Pharmacother 2021; 139:111127. [PMID: 33819810 DOI: 10.1016/j.biopha.2020.111127] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/03/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022] Open
Abstract
Inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), is rising constantly all over the world. However, current medical treatments are not universally practical. Microcin J25 (MccJ25), a member of the lasso peptides class, has excellent antimicrobial activity both in vitro and in vivo. Here, we assessed the anti-inflammatory effects of MccJ25 through DSS-induced UC mouse model. MccJ25 significantly ameliorated the UC-associated parameters such as decreased body weight, increased disease activity index (DAI) and shortened colon length. MccJ25 also provides barrier protection by preserving structural integrity and reducing inflammatory infiltrates of colon epithelium. The underlying mechanism may be associated with gut microbiota. To test this uncertainty, co-housing experiment was performed, and results indicate homogenized microbiota could relief the inflammatory. Meanwhile, we also proved the prominent role of the possible targets of MccJ25, namely genus Lactobacillus, Bacteroides and Akkermansia (as well as the possible strains related to the important OTUs) in inflammation status through comprehensive analysis. In conclusion, MccJ25 effectively attenuates inflammation and improves disrupted barrier function, and the MccJ25-modified gut microbiota plays a central role in this process.
Collapse
Affiliation(s)
- Lijun Shang
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
| | - Haitao Yu
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Hongbin Liu
- Shenzhen Institutes of Advanced Technology, Chinese Academy of Science, Shenzhen 518000, PR China
| | - Meixia Chen
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Xiangfang Zeng
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China
| | - Shiyan Qiao
- State Key Laboratory of Animal Nutrition, Ministry of Agriculture Feed Industry Centre, China Agricultural University, Beijing 100193, PR China; Beijing Bio-Feed Additives Key Laboratory, Beijing 100193, PR China.
| |
Collapse
|
65
|
Treatments of inflammatory bowel disease toward personalized medicine. Arch Pharm Res 2021; 44:293-309. [PMID: 33763844 DOI: 10.1007/s12272-021-01318-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 03/06/2021] [Indexed: 12/12/2022]
Abstract
Inflammatory bowel disease (IBD), including ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory disease characterized by intestinal inflammation and epithelial injury. For the treatment of IBD, 5-aminosalicylic acids, corticosteroids, immunomodulators, and biologic agents targeting tumor necrosis factor (TNF)-α, α4β7-integrin, and interleukin (IL)-12/23 have been widely used. Especially, anti-TNF-α antibodies are the first biologic agents that presently remain at the forefront. However, 10-30% of patients resist biologic agents, including anti-TNF-α agents (primary non-responder; PNR), and 20-50% of primary responders develop treatment resistance within one year (secondary loss of response; SLR). Nonetheless, the etiologies of PNR and SLR are not clearly understood, and predictors of response to biologic agents are also not defined yet. Numerous studies are being performed to discover prediction markers of the response to biologic agents, and this review will introduce currently available therapeutic options for IBD, biologics under investigation, and recent studies exploring various predictive factors related to PNR and SLR.
Collapse
|
66
|
Jonaitis P, Kiudelis V, Streleckiene G, Gedgaudas R, Skieceviciene J, Kupcinskas J. Novel Biomarkers in the Diagnosis of Benign and Malignant Gastrointestinal Diseases. Dig Dis 2021; 40:1-13. [PMID: 33647906 DOI: 10.1159/000515522] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 02/26/2021] [Indexed: 02/02/2023]
Abstract
BACKGROUND Various noninvasive biomarkers have been used in the diagnosis, prognosis, and treatment of different gastrointestinal (GI) diseases for years. Novel technological developments and profound perception of molecular processes related to GI diseases over the last decade have allowed researchers to evaluate genetic, epigenetic, and many other potential molecular biomarkers in different diseases and clinical settings. Here, we present a review of recent and most relevant articles in order to summarize major findings on novel biomarkers in the diagnosis of benign and malignant GI diseases. SUMMARY Genetic variations, noncoding RNAs (ncRNAs), cell-free DNA (cfDNA), and microbiome-based biomarkers have been extensively analyzed as potential biomarkers in benign and malignant GI diseases. Multiple single-nucleotide polymorphisms have been linked with a number of GI diseases, and these observations are further being used to build up disease-specific genetic risk scores. Micro-RNAs and long ncRNAs have a large potential as noninvasive biomarkers in the management of inflammatory bowel diseases and GI tumors. Altered microbiome profiles were observed in multiple GI diseases, but most of the findings still lack translational clinical application. As of today, cfDNA appears to be the most potent biomarker for early detection and screening of GI cancers. Key Messages: Novel noninvasive molecular biomarkers show huge potential as useful tools in the diagnostics and management of different GI diseases. However, the use of these biomarkers in real-life clinical practice still remains limited, and further large studies are needed to elucidate the ultimate role of these potential noninvasive clinical tools.
Collapse
Affiliation(s)
- Paulius Jonaitis
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vytautas Kiudelis
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Greta Streleckiene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rolandas Gedgaudas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Department of Gastroenterology and Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| |
Collapse
|
67
|
Dalal RS, Ananthakrishnan AN, Hamilton MJ, Winter RW. Two Strikes but Not Out: Deep Remission of Ulcerative Colitis with Ustekinumab After Primary Non-response to Infliximab and Vedolizumab. Dig Dis Sci 2021; 66:733-737. [PMID: 33569666 DOI: 10.1007/s10620-021-06852-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/12/2021] [Indexed: 12/20/2022]
Affiliation(s)
- Rahul S Dalal
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Crohn's and Colitis Center, Brigham and Women's Hospital, Boston, MA, 02467, USA
| | - Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Matthew J Hamilton
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA.,Crohn's and Colitis Center, Brigham and Women's Hospital, Boston, MA, 02467, USA
| | - Rachel W Winter
- Division of Gastroenterology, Hepatology and Endoscopy, Brigham and Women's Hospital, Boston, MA, USA. .,Harvard Medical School, Boston, MA, USA. .,Crohn's and Colitis Center, Brigham and Women's Hospital, Boston, MA, 02467, USA.
| |
Collapse
|
68
|
Predictors and Early Markers of Response to Biological Therapies in Inflammatory Bowel Diseases. J Clin Med 2021; 10:jcm10040853. [PMID: 33669579 PMCID: PMC7922976 DOI: 10.3390/jcm10040853] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/22/2022] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic conditions that primarily affect the gastrointestinal tract, with a complex pathogenesis; they are characterized by a significant heterogeneity of clinical presentations and of inflammatory pathways that sustain intestinal damage. After the introduction of the first biological therapies, the pipeline of therapies for IBD has been constantly expanding, and a significant number of new molecules is expected in the next few years. Evidence from clinical trials and real-life experiences has taught us that up to 40% of patients do not respond to a specific drug. Unfortunately, to date, clinicians lack a valid tool that can predict each patient’s response to therapies and that could help them in choosing what drug to administer. Several candidate biomarkers have been investigated so far, with conflicting results: clinical, genetic, immunological, pharmacokinetic and microbial markers have been tested, but no ideal marker has been identified so far. Based on recent evidence, multiparametric models seemingly hold the greatest potential for predicting response to therapy. In this narrative review, we aim to summarize the current knowledge on predictors and early markers of response to biological therapies in IBD.
Collapse
|
69
|
Franzin M, Stefančič K, Lucafò M, Decorti G, Stocco G. Microbiota and Drug Response in Inflammatory Bowel Disease. Pathogens 2021; 10:211. [PMID: 33669168 PMCID: PMC7919657 DOI: 10.3390/pathogens10020211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 02/06/2023] Open
Abstract
A mutualistic relationship between the composition, function and activity of the gut microbiota (GM) and the host exists, and the alteration of GM, sometimes referred as dysbiosis, is involved in various immune-mediated diseases, including inflammatory bowel disease (IBD). Accumulating evidence suggests that the GM is able to influence the efficacy of the pharmacological therapy of IBD and to predict whether individuals will respond to treatment. Additionally, the drugs used to treat IBD can modualate the microbial composition. The review aims to investigate the impact of the GM on the pharmacological therapy of IBD and vice versa. The GM resulted in an increase or decrease in therapeutic responses to treatment, but also to biotransform drugs to toxic metabolites. In particular, the baseline GM composition can help to predict if patients will respond to the IBD treatment with biologic drugs. On the other hand, drugs can affect the GM by incrementing or reducing its diversity and richness. Therefore, the relationship between the GM and drugs used in the treatment of IBD can be either beneficial or disadvantageous.
Collapse
Affiliation(s)
- Martina Franzin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
| | - Katja Stefančič
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| | - Marianna Lucafò
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Giuliana Decorti
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34127 Trieste, Italy;
- Institute for Maternal and Child Health—IRCCS “Burlo Garofolo”, 34137 Trieste, Italy;
| | - Gabriele Stocco
- Department of Life Sciences, University of Trieste, 34127 Trieste, Italy; (K.S.); (G.S.)
| |
Collapse
|
70
|
Anka Idrissi D, Senhaji N, Aouiss A, Khalki L, Tijani Y, Zaid N, Marhoume FZ, Naya A, Oudghiri M, Kabine M, Zaid Y. IL-1 and CD40/CD40L platelet complex: elements of induction of Crohn's disease and new therapeutic targets. Arch Pharm Res 2021; 44:117-132. [PMID: 33394309 DOI: 10.1007/s12272-020-01296-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 11/21/2020] [Indexed: 12/15/2022]
Abstract
Ulcerative colitis (UC) and Crohn's disease (CD) are chronic and multifactorial diseases that affect the intestinal tract, both characterized by recurrent inflammation of the intestinal mucosa, resulting in abdominal pain, diarrhea, vomiting and, rectal bleeding. Inflammatory bowel diseases (IBD) regroup these two disorders. The exact pathological mechanism of IBD remains ambiguous and poorly known. In genetically predisposed patients, defects in intestinal mucosal barrier are due to an uncontrolled inflammatory response to normal flora. In addition to the genetic predisposition, these defects could be triggered by environmental factors or by a specific lifestyle which is widely accepted as etiological hypothesis. The involvement of the CD40/CD40L platelet complex in the development of IBD has been overwhelmingly demonstrated. CD40L is climacteric in cell signalling in innate and adaptive immunity, the CD40L expression on the platelet cell surface gives them an immunological competence. The IL-1, a major inflammation mediator could be involved in different ways in the development of IBD. Here, we provide a comprehensive review regarding the role of platelet CD40/CD40L in the pathophysiological effect of IL-1 in the development of Crohn's disease (CD). This review could potentially help future approaches aiming to target these two pathways for therapeutic purposes and elucidate the immunological mechanisms driving gut inflammation.
Collapse
Affiliation(s)
- Doha Anka Idrissi
- Department of Biology, Faculty of Sciences, Hassan II University, Casablanca, Morocco
| | - Nezha Senhaji
- Laboratory of Genetic and Molecular Pathology, Faculty of Medicine, Hassan II University, Casablanca, Morocco
| | - Asmae Aouiss
- Department of Biology, Faculty of Sciences, Hassan II University, Casablanca, Morocco
| | - Loubna Khalki
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Youssef Tijani
- Faculty of Medicine, Mohammed VI University of Health Sciences (UM6SS), Casablanca, Morocco
| | - Nabil Zaid
- Faculty of Sciences, Department of Biology, Mohammed V University, Rabat, Morocco
| | - Fatima Zahra Marhoume
- Faculty of Sciences and Technology, Laboratory of Biochemistry and Neuroscience, Integrative and Computational Neuroscience Team, Hassan First University, Settat, Morocco
| | - Abdallah Naya
- Department of Biology, Faculty of Sciences, Hassan II University, Casablanca, Morocco
| | - Mounia Oudghiri
- Department of Biology, Faculty of Sciences, Hassan II University, Casablanca, Morocco
| | - Mostafa Kabine
- Department of Biology, Faculty of Sciences, Hassan II University, Casablanca, Morocco
| | - Younes Zaid
- Faculty of Sciences, Department of Biology, Mohammed V University, Rabat, Morocco. .,Research Center of Abulcasis, University of Health Sciences, Rabat, Morocco.
| |
Collapse
|
71
|
Dudzińska E, Strachecka A, Gil-Kulik P, Kocki J, Bogucki J, Shemedyuk N, Gryzinska M. Influence of the Treatment Used in Inflammatory Bowel Disease on the Protease Activities. Int J Gen Med 2020; 13:1633-1642. [PMID: 33380821 PMCID: PMC7767739 DOI: 10.2147/ijgm.s267036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/10/2020] [Indexed: 11/24/2022] Open
Abstract
Introduction There is growing evidence that intestinal proteases have a role in the pathogenesis of gastrointestinal inflammatory diseases. Inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC), has an additional source of proteases represented by infiltrated and activated inflammatory cells. The aim of our study was to determine proteolytic system activity in patients with CD and UC. We limited the number of proteases tested by determining proteases active in acidic, neutral and alkaline pH. Materials and Methods The study included 40 patients with IBD – 20 CD patients and 20 UC patients. The control group consisted of 20 healthy subjects. Among the 20 CD patients, 17 were treated with aminosalicylates, 14 with azathioprine, and 4 with corticosteroids, while 8 patients were undergoing biological treatment. Among the 20 UC patients, 19 were treated with aminosalicylates, 8 with azathioprine, and 3 with corticosteroids. The total protein concentration was assayed by the Lowry method. The optimal pH was assayed in pH from 2.2 to 12.8, separated by 0.2 intervals. Proteolytic activities were determined against different substrates (gelatine, haemoglobin, ovalbumin, albumin, cytochrome C, and casein), and haemoglobin was the optimal substrate. Protease activities were determined according to Anson method. Determination of the activities of natural inhibitors of acidic, neutral and alkaline proteases is based on the Lee and Lin method. Results Decreases were observed in the activities of acid proteases (pH 5), alkaline proteases (pH 7), and neutral proteases (pH 7.6 and 8.6) in the groups of CD patients in remission in comparison with the active phase. In the group of patients with biologically treated CD patients, acid protease activity (pH 5.0) was lower than in CD patients not receiving biological treatment. Activities of neutral (pH 7.0) and alkaline (pH 7.6 and 8.6) proteases in the plasma of patients with UC in remission were lower in comparison to the active phase. Activities of acid (pH 5.0) and alkaline (8.6) protease inhibitors were higher in CD patients in the active phase in comparison to remission. In UC patients with exacerbation of the disease, the activity of alkaline (pH 8.6) protease inhibitors was increased compared to remission. Conclusion 1. Our research may suggest that the immunomodulatory treatment used in IBD, aimed at reducing the level of leukocytes and reduction of inflammation, may contribute to a reduction in protease activity. 2. The decrease of protease activities in patients with CD and UC in remission may be a marker suggesting the patients’ response to the treatment.
Collapse
Affiliation(s)
- Ewa Dudzińska
- Chair of Public Health, Medical University of Lublin, Lublin 20-093, Poland
| | - Aneta Strachecka
- Subdepartment of General and Molecular Genetics, Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| | - Paulina Gil-Kulik
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, Lublin 20-080, Poland
| | - Janusz Kocki
- Chair of Medical Genetics, Department of Clinical Genetics, Medical University of Lublin, Lublin 20-080, Poland
| | - Jacek Bogucki
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University, Lublin 20-093, Poland
| | - Natalya Shemedyuk
- Department Biotechnology and Radiology, Stepan Gzhytskyi National University of Veterinary Medicine and Biotechnologies, Lviv 79010, Ukraine
| | - Magdalena Gryzinska
- Subdepartment of General and Molecular Genetics, Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, Lublin 20-950, Poland
| |
Collapse
|
72
|
Mahajna H, Ben-Horin S. Novel bio-genetic predictors of response to biologic treatment in inflammatory bowel diseases. Curr Opin Pharmacol 2020; 55:132-140. [PMID: 33249396 DOI: 10.1016/j.coph.2020.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/29/2020] [Accepted: 10/11/2020] [Indexed: 02/07/2023]
Abstract
Despite the evolving therapeutic armamentarium, the treatment of IBD patients remains challenging and many patients fail to respond to biologic agents. With the limited yield of clinical factors to predict the outcome of biologic treatments, studies have focused on identifying genetic alterations and circulating or tissue biomarkers to identify patients who are likely to respond to therapy. In this review, we examine the current knowledge and status of genetic, expression biomarkers, and microbiome predictors. The search for genetic predictors has yielded many genetic loci variants, but few were reproducible. Expression studies of putative biomarkers show promising results, especially with TREM1, oncostatin M and TNF biomarkers, but confirmatory studies are warranted. Finally, the microbiome is emerging as an important player with specific taxa and functional pathways differentially abundant and enriched in responders versus non-responders to certain biologics. Integrating different factors into a robust predictive model, which is both reproducible, accurate and affordable, remains the main challenge before these individualized strategies can reach clinical use.
Collapse
Affiliation(s)
- Hussein Mahajna
- Gastroenterology Department, Sheba Medical Center, Affiliated to Tel-Aviv University, Tel-Aviv, Israel.
| | - Shomron Ben-Horin
- Gastroenterology Department, Sheba Medical Center, Affiliated to Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
73
|
Mucosal microbiota and gene expression are associated with long-term remission after discontinuation of adalimumab in ulcerative colitis. Sci Rep 2020; 10:19186. [PMID: 33154436 PMCID: PMC7644643 DOI: 10.1038/s41598-020-76175-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Given that sustained remission is the ultimate treatment goal in the management of patients with ulcerative colitis (UC), the decision to stop anti-tumor necrosis factor (anti-TNF) treatment in UC patients is difficult. The aim of this study was to evaluate mucosal microbiota and gene expression profiles associated with long-term remission after discontinuation of anti-TNF therapy. In nine UC patients who received anti-TNF therapy for 6 months, microbiota isolated from uninflamed mucosae and gene expression in inflamed and uninflamed mucosae were investigated at week 0 and at week 24. At treatment initiation, Fusobacterium sp. and Veillonella dispar were over-represented in the relapse group compared with the non-relapse group. After treatment, Dorea sp. and Lachnospira sp. were over-represented in the non-relapse group. In the relapse group only, a significant shift in gut bacterial community composition was found between week 0 and week 24. Gene expression of ALIX (PDCD6IP) and SLC9A3 was significantly higher in the non-relapse group than in the relapse group. Lastly, we used machine learning methods to identify relevant gene signatures associated with sustained remission. Statistical analyses of microbiota and expression profiles revealed differences between UC patients who did or did not keep remission after the discontinuation of TNF inhibitors. Trial registration: UMIN000020785: Evaluation of adalimumab therapy in mesalazine-resistant or -intolerant ulcerative colitis; an observational study (EARLY study).
Collapse
|
74
|
Caenepeel C, Sadat Seyed Tabib N, Vieira-Silva S, Vermeire S. Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease. Aliment Pharmacol Ther 2020; 52:1453-1468. [PMID: 32969507 DOI: 10.1111/apt.16096] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Intestinal bacteria produce metabolites and by-products necessary for homeostasis. Imbalance in this equilibrium is linked to multiple pathologies including inflammatory bowel disease (IBD). The role of the gut microbiota in determining treatment response is becoming apparent, and may act as biomarker for efficacy. AIM To describe knowledge about the intestinal microbiota on disease severity and treatment outcomes in IBD METHODS: Descriptive review using PubMed to identify literature on the intestinal microbiota in IBD RESULTS: Severe IBD has a less diverse microbiota with fewer commensal microbiota communities and more opportunistic pathogenic bacteria originating from the oral cavity or respiratory tract. IBD treatments can alter gut microbiota composition, but in vitro/in vivo studies are needed to prove causation. A diversification of the microbiota is observed during remission. Patients with a more diverse baseline microbiome and higher microbial diversity show better response to anti-tumour necrosis factor-α, vedolizumab and ustekinumab therapy. Higher abundance of short chain fatty acid-producing bacteria, fewer mucus-colonising bacteria and lower abundance of pro-inflammatory bacteria have also been associated with a favourable outcome. Predictive models, based on a combination of microbiota, clinical data and serological markers, have good accuracy for treatment outcome and disease severity. CONCLUSION The intestinal microbiota in IBD carries a set of promising biomarkers of disease activity and prediction of therapeutic outcome. Current insights may also help in designing microbiota modulation strategies to improve outcomes in IBD.
Collapse
Affiliation(s)
| | | | - Sara Vieira-Silva
- Department of Microbiology and Immunology, Laboratory of Molecular Bacteriology, Rega Institute for Medical Research, VIB, KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Chronic Diseases & Metabolism, Translational Research Center for Gastrointestinal Disorders, KU Leuven, Leuven, Belgium.,Department of Gastroenterology and Hepatology, University Hospitals Leuven, Leuven, Belgium
| |
Collapse
|
75
|
Ota S, Sakuraba H, Hiraga H, Yoshida S, Satake M, Akemoto Y, Tanaka N, Watanabe R, Takato M, Murai Y, Ueno K, Niioka T, Hayakari M, Ishiguro Y, Fukuda S. Cyclosporine protects from intestinal epithelial injury by modulating butyrate uptake via upregulation of membrane monocarboxylate transporter 1 levels. Biochem Biophys Rep 2020; 24:100811. [PMID: 33102812 PMCID: PMC7578528 DOI: 10.1016/j.bbrep.2020.100811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/25/2020] [Accepted: 08/27/2020] [Indexed: 01/22/2023] Open
Abstract
Background and aims A relationship between treatment outcomes and intestinal microbiota in patients with inflammatory bowel diseases has been demonstrated. Cyclosporine treatment leads to rapid improvement in severe ulcerative colitis. We hypothesized that the potent effects of cyclosporine would be exerted through relationships between intestinal epithelial cells (IECs) and the host microbiota. The present study was designed to elucidate the effects of cyclosporine on monocarboxylate transporter 1 (MCT1) regulation and butyrate uptake by IECs. Methods Colitis was induced in C57BL6 mice via the administration of 4% dextran sulfate sodium in drinking water, following which body weights, colon lengths, and histological scores were evaluated. To examine the role of butyrate in the protective effects of cyclosporine, MCT1 inhibitor and an antibiotic cocktail was administered and tributyrin (TB; a prodrug of butyrate) was supplemented; MCT1 protein expression and acetylated histone 3 (AcH3) signals in IECs, as well as the MCT1-membrane fraction of Caco-2 cells, were evaluated. To explore butyrate uptake, as s butyrate derivatives, 3-bromopyruvic acid (3-BrPA) and 1-pyrenebutyric acid were used. Results Treatment with cyclosporine inhibited body weight loss and colon length shortening. However, treatment with MCT1 inhibitor and the antibiotic cocktail negated the efficacy of cyclosporine, whereas TB supplementation restored its protective effect. Furthermore, cyclosporine upregulated MCT1 expression in the membrane and the AcH3 signal in IECs, while also inducing higher anti-inflammatory cytokine production compared to that in the vehicle-treated mice. The transcription level of MCT1 mRNA in IECs and Caco-2 cells did not increase with cyclosporine treatment; however, cyclosporine treatment increased membrane MCT1 expression in these cells and uptake of butyrate derivative. Conclusion Cyclosporine treatment modulates butyrate uptake via the post-transcriptional upregulation of membrane MCT1 levels in IECs. The protective effect of cyclosporine needs microbiota-derived butyrate. Cyclosporine increased the fraction of MCT1 at the cell membrane. Cyclosporine enhanced butyrate uptake and regulatory cytokine expression.
Collapse
Affiliation(s)
- Shinji Ota
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hirotake Sakuraba
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Hiroto Hiraga
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Shukuko Yoshida
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan.,Shibata Irika Co.Ltd.Hirosaki, Japan
| | - Miwa Satake
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Yui Akemoto
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Nahoko Tanaka
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Rina Watanabe
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Maeda Takato
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Yasuhisa Murai
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Kayo Ueno
- Division of Pharmaceutical Science, Hirosaki University Hospital, Hirosaki, Japan
| | - Takenori Niioka
- Division of Pharmaceutical Science, Hirosaki University Hospital, Hirosaki, Japan
| | - Makoto Hayakari
- Division of Pharmaceutical Science, Hirosaki University Hospital, Hirosaki, Japan
| | - Yoh Ishiguro
- Division of Clinical Research, Hirosaki National Hospital, National Hospital Organization, Hirosaki, Japan
| | - Shinsaku Fukuda
- Department of Gastroenterology and Hematology, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| |
Collapse
|
76
|
Zhuang X, Tian Z, Feng R, Li M, Li T, Zhou G, Qiu Y, Chen B, He Y, Chen M, Zeng Z, Zhang S. Fecal Microbiota Alterations Associated With Clinical and Endoscopic Response to Infliximab Therapy in Crohn's Disease. Inflamm Bowel Dis 2020; 26:1636-1647. [PMID: 33026078 DOI: 10.1093/ibd/izaa253] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Gut microbiota dysbiosis is associated with the occurrence and development of Crohn disease (CD). Currently, infliximab (IFX) is used more and more to treat CD; however, gut microbiota alterations during IFX therapy are variable and sometimes even contradictory. We longitudinally identified microbial changes during IFX therapy associated with the clinical and endoscopic response to IFX treatment in CD. METHODS Fecal-associated microbiota was analyzed using 16S sequencing in 49 patients with active CD who were prospectively recruited at baseline, week 6, and week 30, respectively. Moreover, a model trained on the gut microbiota alterations at week 6 was developed to investigate their potential to predict clinical and endoscopic responses to IFX therapy at weeks 14 and 30. RESULTS Characteristics of fecal microbiota composition in patients with CD after IFX treatment displayed an increased diversity and richness, a significant gain in short-chain fatty acid -producing bacteria, and a loss of pathogenic bacteria. Furthermore, certain functional profiles of Kyoto Encyclopedia of Genes and Genomes pathways were predictably altered during the treatment period. Increased proportions of Lachnospiraceae and Blautia were associated with IFX efficacy; the combined increase of these taxa at week 6 showed 83.4% and 84.2% accuracy in predicting clinical response at weeks 14 and 30, respectively, with a predictive value of 89.1% in predicting endoscopic response at week 30. CONCLUSIONS We found that IFX diminished CD-related gut microbial dysbiosis by modifying microbiota composition and function. Specifically, increased Lachnospiraceae and Blautia at week 6 are associated with the clinical and endoscopic response to IFX, providing potentially predictive biomarkers for IFX treatment decision-making.
Collapse
Affiliation(s)
- Xiaojun Zhuang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhenyi Tian
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Rui Feng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Manying Li
- Department of Medical Ultrasonics, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Tong Li
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Gaoshi Zhou
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yun Qiu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Baili Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Yao He
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Zhirong Zeng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Shenghong Zhang
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong, China
| |
Collapse
|
77
|
Kuballa A, Geraci M, Johnston M, Sorrentino D. The Gut Microbial Profile of Preclinical Crohn's Disease Is Similar to That of Healthy Controls. Inflamm Bowel Dis 2020; 26:1682-1690. [PMID: 32339246 DOI: 10.1093/ibd/izaa072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND AND AIMS It is unclear whether microbial dysbiosis plays an etiologic role in Crohn's disease (CD) or is the result of protracted inflammation. Here, we test the hypothesis that dysbiosis predates clinical CD in asymptomatic first-degree relatives (FDRs) of CD patients: normal (FDR1), with borderline inflammation (FDR2), and with frank, very early inflammation (FDR3). METHODS The gut microbial diversity was tested in ileocecal biopsies through next generation sequencing of the 16S rRNA gene in 10 healthy controls (HCs), 22 patients with active, untreated CD, and 25 FDRs (9 FDR1; 12 FDR2; 4 FDR3). The metagenomic functions of 41 microbiome-related processes were inferred by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) analysis. RESULTS Compared with HCs, alpha diversity in CD patients was decreased, with an observed decrease in Faecalibacterium prausnitzii and increase in Bacteroides fragilis. In FDRs, microbial diversity was unchanged compared with HCs. In Operational Taxonomic Units and PICRUSt Principal coordinates and component analyses, the ellipse centroid of FDRs was diagonally opposed to that of CD patients, but close to the HC centroid. In both analyses, statistically significant differences in terms of beta diversity were found between CD and HC but not between FDR and HC. CONCLUSIONS In FDRs (including FDR3-who bear preclinical/biologic onset disease), we found that the microbial profile is remarkably similar to HC. If confirmed in larger studies, this finding suggests that clinical CD-associated dysbiosis could result from the changed microenvironment due to disease evolution over time.
Collapse
Affiliation(s)
- Anna Kuballa
- Inflammation Research Cluster, School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Marco Geraci
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Meredith Johnston
- Inflammation Research Cluster, School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs, QLD, Australia
| | - Dario Sorrentino
- IBD Center, Division of Gastroenterology, Virginia Tech Carilion School of Medicine, Roanoke, VA, USA.,Department of Clinical and Experimental Medical Sciences, University of Udine School of Medicine, Udine, Italy
| |
Collapse
|
78
|
Vatn S, Carstens A, Kristoffersen AB, Bergemalm D, Casén C, Moen AEF, Tannaes TM, Lindstrøm J, Detlie TE, Olbjørn C, Lindquist CM, Söderholm JD, Gomollón F, Kalla R, Satsangi J, Vatn MH, Jahnsen J, Halfvarson J, Ricanek P. Faecal microbiota signatures of IBD and their relation to diagnosis, disease phenotype, inflammation, treatment escalation and anti-TNF response in a European Multicentre Study (IBD-Character). Scand J Gastroenterol 2020; 55:1146-1156. [PMID: 32780604 DOI: 10.1080/00365521.2020.1803396] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
METHOD We examined faecal samples, using the GA-map™ Dysbiosis Test, to associate gut microbiota composition with Crohn's disease (CD) and ulcerative colitis (UC) and to identify markers for future biomarker identification. We conducted a prospective case-control study (EU-ref. no. 305676) in an inception cohort of 324 individuals (64 CD, 84 UC, 116 symptomatic non-IBD controls and 44 healthy controls) across five European centres and examined 54 predetermined bacterial markers. We categorized patients according to the Montreal Classification and calculated the dysbiosis index (DI). Non-parametric tests were used to compare groups and the Bonferroni correction to adjust for multiple comparisons. RESULTS The fluorescent signals (FSSs) for Firmicutes and Eubacterium hallii were lower in inflammatory bowel disease (IBD) vs. symptomatic controls (p<.05). FSS for Firmicutes, Lachnospiraceae, Eubacterium hallii and Ruminococcus albus/bromii were lower, whereas the signal for Bacteroides Fragilis was higher in UC vs. symptomatic controls (p<.05). FSS was higher for Bifidobacterium spp., Eubacterium hallii, Actinobacteria and Firmicutes among patients with ulcerative proctitis, compared to extensive colitis (p<.05). In CD, we observed no association with disease location. The DI correlated with faecal-calprotectin in both CD and in UC (p<.001). In terms of treatment escalation and anti-TNF response, differences were observed for some bacterial markers, but none of these associations were statistically significant. CONCLUSION Our data reveal that the GA-map™ Dysbiosis Test holds the potential to characterize the faecal microbiota composition and to assess the degree of dysbiosis in new-onset IBD. On the other hand, our results cannot demonstrate any proven diagnostic or predictive value of this method to support clinical decision making.
Collapse
Affiliation(s)
- S Vatn
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - A Carstens
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Internal Medicine, Ersta Hospital, Stockholm, Sweden
| | | | - D Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - C Casén
- Genetic Analysis AS, Oslo, Norway
| | - A E F Moen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - T M Tannaes
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Clinical Molecular Biology (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | - J Lindstrøm
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway.,Department of Pediatric and Adolescent Medicine, Akershus University Hospital, Lørenskog, Norway
| | - T E Detlie
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - C Olbjørn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - C M Lindquist
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - J D Söderholm
- Digestive Diseases Unit, IIS Aragón, Zaragoza, Spain
| | - F Gomollón
- Gastrointestinal Unit, Centre for Genomics and Molecular Medicine, Division of Medical and Radiological Sciences, University of Edinburgh, Edinburgh, UK
| | - R Kalla
- Translational Gastroenterology Unit, Medical Sciences/Experimental Medicine Division, University of Oxford, Oxford, UK
| | - J Satsangi
- Translational Gastroenterology Unit, Medical Sciences/Experimental Medicine Division, University of Oxford, Oxford, UK
| | - M H Vatn
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - J Jahnsen
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - J Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - P Ricanek
- Department of Gastroenterology, Division of Medicine, Akershus University Hospital, Lørenskog, Norway
| | | |
Collapse
|
79
|
Abstract
Crohn disease and ulcerative colitis are complex immune-mediated diseases that are characterized by a heterogeneity in presentation and clinical course. Although various clinical covariates predict adverse outcomes in these patients, they are insufficiently informative. The gut microbiome likely plays a central role in the pathogenesis of these diseases. Consequently, microbiome-based biomarkers may play an important role in risk stratification and disease prediction. Initial cross-sectional studies showed a reduced gut microbial diversity in patients with Crohn disease or ulcerative colitis, a depletion of phyla with anti-inflammatory effects such as those belonging to Firmicutes, and an increased abundance of potentially pathogenic bacteria in specific disease phenotypes. Subsequent studies longitudinally tracking microbial changes and clinical outcomes have shown dynamic changes correlating with or predictive of disease activity and resistance to therapy. The development of multicenter cohorts using harmonized protocols is essential to robustly validate these biomarkers and facilitate the integration of their evaluation into clinical practice. .
Collapse
Affiliation(s)
- Ashwin N Ananthakrishnan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| |
Collapse
|
80
|
Chen H, Li H, Liu Z. Interplay of intestinal microbiota and mucosal immunity in inflammatory bowel disease: a relationship of frenemies. Therap Adv Gastroenterol 2020; 13:1756284820935188. [PMID: 32952611 PMCID: PMC7485159 DOI: 10.1177/1756284820935188] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 05/26/2020] [Indexed: 02/04/2023] Open
Abstract
Inflammatory bowel diseases (IBDs), including ulcerative colitis and Crohn's disease, are chronic inflammatory disorders of the gastrointestinal tract. With in-depth studies on the mechanisms of the initiation and development of IBD, increasing lines of evidence have focused on the intestinal microbiota in the pathogenesis of IBD. The imbalance between the host and intestinal microbiota induces dysregulated immune response in intestinal mucosa and plays a pivotal role in the initiation of disease and ongoing bowel destruction. This review focuses on recent advances in intestinal microbiota regulation of mucosal immune response as well as novel approaches based on intestinal microbiota alterations in the diagnosis and evaluation of therapeutic response in IBD.
Collapse
|
81
|
Atreya R, Neurath MF, Siegmund B. Personalizing Treatment in IBD: Hype or Reality in 2020? Can We Predict Response to Anti-TNF? Front Med (Lausanne) 2020; 7:517. [PMID: 32984386 PMCID: PMC7492550 DOI: 10.3389/fmed.2020.00517] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
The advent of anti-TNF agents as the first approved targeted therapy in the treatment of inflammatory bowel disease (IBD) patients has made a major impact on our existing therapeutic algorithms. They have not only been approved for induction and maintenance treatment in IBD patients, but have also enabled us to define and achieve novel therapeutic outcomes, such as combination of clinical symptom control and endoscopic remission, as well as mucosal healing. Nevertheless, approximately one third of treated patients do not respond to initiated anti-TNF therapy and these treatments are associated with sometimes severe systemic side-effects. There is therefore the currently unmet clinical need do establish predictive markers of response to identify the subgroup of IBD patients, that have a heightened probability of response. There have so far been approaches from different fields of IBD research, to descry markers that would empower us to apply TNF-inhibitors in a more rational manner. These markers encompass findings from disease-related and clinical factors, pharmacokinetics, biochemical markers, blood and stool derived parameters, pharmacogenomics, microbial species, metabolic compounds, and mucosal factors. Furthermore, changes in the intestinal immune cell composition in response to therapeutic pressure of anti-TNF treatment have recently been implicated in the process of molecular resistance to these drugs. Insights into factors that determine resistance to anti-TNF therapy give reasonable hope, that a more targeted approach can then be utilized in these non-responders. Here, IL-23 could be identified as one of the key factors determining resistance to TNF-inhibitors. Growing insights into the molecular mechanism of action of TNF-inhibitors might also enable us to derive critical molecular markers that not only mediate the clinical effects of anti-TNF therapy, but which level of expression might also correlate with its therapeutic efficacy. In this narrative review, we present an overview of currently identified possible predictive markers for successful anti-TNF therapy and discuss identified molecular pathways that drive resistance to these substances. We will also point out the necessity and difficulty of developing and validating a diagnostic marker concerning clinically relevant outcome parameters, before they can finally enter daily clinical practice and enable a more personalized therapeutic approach.
Collapse
Affiliation(s)
- Raja Atreya
- Department of Medicine, Medical Clinic 1, University Hospital Erlangen, University of Erlangen-Nürnberg Erlangen, Erlangen, Germany.,Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany.,The Transregio 241 IBDome Consortium, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine, Medical Clinic 1, University Hospital Erlangen, University of Erlangen-Nürnberg Erlangen, Erlangen, Germany.,Deutsches Zentrum Immuntherapie (DZI), Erlangen, Germany
| | - Britta Siegmund
- The Transregio 241 IBDome Consortium, Berlin, Germany.,Medizinische Klinik m. S. Gastroenterologie, Infektiologie und Rheumatologie, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany
| |
Collapse
|
82
|
Yang Q, Wang Y, Jia A, Wang Y, Bi Y, Liu G. The crosstalk between gut bacteria and host immunity in intestinal inflammation. J Cell Physiol 2020; 236:2239-2254. [PMID: 32853458 DOI: 10.1002/jcp.30024] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 07/20/2020] [Accepted: 08/12/2020] [Indexed: 12/20/2022]
Abstract
The gut of mammals is considered as a harmonious ecosystem mediated by intestinal microbiota and the host. Both bacteria and mammalian immune cells show region-related distribution characteristics, and the interaction between the two could be demonstrated by synergetic roles in maintaining intestinal homeostasis and dysregulation in intestinal inflammation. The harmonious interplay between bacteria and host requires fine-tuned regulations by environmental and genetic factors. Thus, the disturbed immune response to microbial components or metabolites and dysbiosis related to immunodeficiency are absolute risk factors to intestinal inflammation and cancer. In this review, we discuss the crosstalk between bacteria and host immunity in the gut and highlight the critical roles of bidirectional regulation between bacteria and the mammalian immune system involved in intestinal inflammation.
Collapse
Affiliation(s)
- Qiuli Yang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yuexin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Anna Jia
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yufei Wang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, Institute of Cell Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
83
|
Sanchis-Artero L, Martínez-Blanch JF, Manresa-Vera S, Cortés-Castell E, Rodriguez-Morales J, Cortés-Rizo X. Evaluation of Changes in Gut Microbiota in Patients with Crohn's Disease after Anti-Tnfα Treatment: Prospective Multicenter Observational Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:E5120. [PMID: 32679874 PMCID: PMC7399935 DOI: 10.3390/ijerph17145120] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/10/2020] [Accepted: 07/10/2020] [Indexed: 12/21/2022]
Abstract
Background: Crohn's disease is believed to result from the interaction between genetic susceptibility, environmental factors and gut microbiota, leading to an aberrant immune response. The objectives of this study are to evaluate the qualitative and quantitative changes in the microbiota of patients with Crohn's disease after six months of anti-tumor-necrosis factor (anti-TNFα) (infliximab or adalimumab) treatment and to determine whether these changes lead to the recovery of normal microbiota when compared to a control group of healthy subjects. In addition, we will evaluate the potential role of the Faecalibacterium prausnitzii/Escherichia coli and Faecalibacterium prausnitzii/Clostridium coccoides ratios as indicators of therapeutic response to anti-TNFα drugs. Methods/Design: This prospective multicenter observational study will comprise a total of 88 subjects: 44 patients with Crohn's disease scheduled to start anti-TNFα treatment as described in the drug specifications to control the disease and 44 healthy individuals who share the same lifestyle and eating habits. The presence of inflammatory activity will be determined by the Harvey-Bradshaw index, analytical parameters in blood, including C-reactive protein, and fecal calprotectin levels at commencement of the study, at three months and at six months, allowing the classification of patients into responders and non-responders. Microbiota composition and the quantitative relationship between Faecalibacterium prausnitzii and Escherichia coli and between Faecalibacterium prausnitzii and Clostridium coccoidesgroup as indicators of dysbiosis will be studied at inclusion and six months after initiation of treatment using ultra sequencing with Illumina technology and comparative bioinformatics analysis for the former relationship, and digital droplet PCR using stool samples for the latter. Upon inclusion, patients will complete a survey of dietary intake for the three days prior to stool collection, which will be repeated six months later in a second collection to minimize dietary bias. Discussion: In this study, massive sequencing, a reliable new tool, will be applied to identify early biomarkers of response to anti-TNF treatment in patients with Crohn's disease to improve clinical management of these patients, reduce morbidity rates and improve efficiency.
Collapse
Affiliation(s)
- Laura Sanchis-Artero
- Inflammatory Bowel Disease Unit. Department of Digestive Diseases, Hospital of Sagunto, Av. Ramón y Cajal s/n, 46520 Sagunto, Valencia, Spain; (L.S.-A.); (J.R.-M.); (X.C.-R.)
| | - Juan Francisco Martínez-Blanch
- Genomics Laboratory. ADM-Lifesequencing. Parque Científico Universidad de Valencia. Catedrático Agustín Escardino Benlloch, 9. Edificio 2, 46980 Paterna, Valencia, Spain;
| | - Sergio Manresa-Vera
- Genomics Laboratory. ADM-Lifesequencing. Parque Científico Universidad de Valencia. Catedrático Agustín Escardino Benlloch, 9. Edificio 2, 46980 Paterna, Valencia, Spain;
| | - Ernesto Cortés-Castell
- Department of Pharmacology, Pediatrics and Organic Chemistry Miguel Hernández University, Carretera de Valencia—Alicante S/N, 03550 San Juan de Alicante, Alicante, Spain;
| | - Josefa Rodriguez-Morales
- Inflammatory Bowel Disease Unit. Department of Digestive Diseases, Hospital of Sagunto, Av. Ramón y Cajal s/n, 46520 Sagunto, Valencia, Spain; (L.S.-A.); (J.R.-M.); (X.C.-R.)
| | - Xavier Cortés-Rizo
- Inflammatory Bowel Disease Unit. Department of Digestive Diseases, Hospital of Sagunto, Av. Ramón y Cajal s/n, 46520 Sagunto, Valencia, Spain; (L.S.-A.); (J.R.-M.); (X.C.-R.)
| |
Collapse
|
84
|
Gisbert JP, Chaparro M. Predictors of Primary Response to Biologic Treatment [Anti-TNF, Vedolizumab, and Ustekinumab] in Patients With Inflammatory Bowel Disease: From Basic Science to Clinical Practice. J Crohns Colitis 2020; 14:694-709. [PMID: 31777929 DOI: 10.1093/ecco-jcc/jjz195] [Citation(s) in RCA: 152] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND Inflammatory bowel diseases [IBD]-ulcerative colitis and Crohn's disease-are commonly treated with biologic drugs. However, only approximately two-thirds of patients have an initial response to these therapies. Personalised medicine has the potential to optimise efficacy, decrease the risk of adverse drug events, and reduce costs by establishing the most suitable therapy for a selected patient. AIM The present study reviews the potential predictors of short-term primary response to biologic treatment, including not only anti-tumour necrosis factor [TNF] agents [such as infliximab, adalimumab, certolizumab, and golimumab] but also vedolizumab and ustekinumab. METHODS We performed a systematic bibliographical search to identify studies investigating predictive factors of response to biologic therapy. RESULTS For anti-TNF agents, most of the evaluated factors have not demonstrated usefulness, and many others are still controversial. Thus, only a few factors may have a potential role in the prediction of the response, including disease behaviour/phenotype, disease severity, C-reactive protein, albumin, cytokine expression in serum, previous anti-TNF therapy, some proteomic markers, and some colorectal mucosa markers. For vedolizumab, the availability of useful predictive markers seems to be even lower, with only some factors showing a limited value, such as the expression of α4β7 integrin in blood, the faecal microbiota, some proteomic markers, and some colorectal mucosa markers. Finally, in the case of ustekinumab, no predictive factor has been reported yet to be helpful in clinical practice. CONCLUSION In summary, currently no single marker fulfils all criteria for being an appropriate prognostic indicator of response to any biologic treatment in IBD.
Collapse
Affiliation(s)
- Javier P Gisbert
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa [IIS-IP], Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD], Madrid, Spain
| | - María Chaparro
- Gastroenterology Unit, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa [IIS-IP], Universidad Autónoma de Madrid, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas [CIBEREHD], Madrid, Spain
| |
Collapse
|
85
|
Seong G, Kim N, Joung JG, Kim ER, Chang DK, Chun J, Hong SN, Kim YH. Changes in the Intestinal Microbiota of Patients with Inflammatory Bowel Disease with Clinical Remission during an 8-Week Infliximab Infusion Cycle. Microorganisms 2020; 8:microorganisms8060874. [PMID: 32527024 PMCID: PMC7356282 DOI: 10.3390/microorganisms8060874] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/30/2020] [Accepted: 06/04/2020] [Indexed: 12/13/2022] Open
Abstract
This study investigated changes in the intestinal microbiota during 8-week infliximab maintenance therapy in inflammatory bowel disease (IBD) patients in clinical remission. Microbial compositional differences were analyzed according to the trough level of infliximab (TLI) and mucosal healing (MH) status. 16S rRNA gene-based microbiome profiling was performed on 10 and 74 fecal samples from 10 healthy volunteers and 40 adult IBD patients, respectively. Fecal sampling occurred at 1–2 weeks (1W) and 7–8 weeks (7W) after infliximab infusion. TLI was measured by ELISA at 8 weeks, immediately before the subsequent infusion; MH was evaluated by endoscopy within 3 months. There were no significant changes in microbial composition, species richness, or diversity indices between 1W and 7W. However, 7W samples from the patients with TLI ≥ 5 μg/mL showed an increased species richness compared with patients with TLI < 5 μg/mL, and patients with MH showed increased diversity compared with non-MH patients. Beta-diversity analysis showed clustering between samples in the MH and non-MH groups. LEfSe analysis identified differential composition of Faecalibacterium prausnitzii group according to TLI and MH. In conclusion, these results suggest the potential of fecal microbiota as a response indicator.
Collapse
Affiliation(s)
- Gyeol Seong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea; (G.S.); (E.R.K.); (D.K.C.)
| | - Namil Kim
- ChunLab, Inc., Nambusunhwan-ro, Seocho-gu, Seoul 06725, Korea; (N.K.); (J.C.)
| | - Je-Gun Joung
- Samsung Genome Institute, Samsung Medical Center, 81 Irwon-ro, Gangnam-gu, Seoul 06351, Korea;
| | - Eun Ran Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea; (G.S.); (E.R.K.); (D.K.C.)
| | - Dong Kyung Chang
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea; (G.S.); (E.R.K.); (D.K.C.)
| | - Jongsik Chun
- ChunLab, Inc., Nambusunhwan-ro, Seocho-gu, Seoul 06725, Korea; (N.K.); (J.C.)
| | - Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea; (G.S.); (E.R.K.); (D.K.C.)
- Correspondence: (S.N.H.); (Y.-H.K.); Tel.: +82-2-3410-3409 (S.N.H. & Y.-H.K.); Fax: +82-2-3410-6983 (S.N.H. & Y.-H.K.)
| | - Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81 Irwon-ro, Gangnam-gu, Seoul 135-710, Korea; (G.S.); (E.R.K.); (D.K.C.)
- Correspondence: (S.N.H.); (Y.-H.K.); Tel.: +82-2-3410-3409 (S.N.H. & Y.-H.K.); Fax: +82-2-3410-6983 (S.N.H. & Y.-H.K.)
| |
Collapse
|
86
|
Strömbeck A, Lasson A, Strid H, Sundin J, Stotzer PO, Simrén M, Magnusson MK, Öhman L. Fecal microbiota composition is linked to the postoperative disease course in patients with Crohn's disease. BMC Gastroenterol 2020; 20:130. [PMID: 32366222 PMCID: PMC7197162 DOI: 10.1186/s12876-020-01281-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/22/2020] [Indexed: 12/17/2022] Open
Abstract
Background The role of the fecal microbiota composition for the postoperative disease course of patients with Crohn’s disease (CD) who have undergone ileocecal resection remains to be established. In this study, we investigated if the fecal microbiota composition, determined by a high throughput test quantifying a pre-selected set of bacteria, is associated with the postoperative disease course of CD patients. Methods Fecal samples were obtained from healthy subjects as well as from CD patients, 3–10 weeks and 1 year after ileocaecal resection. The fecal microbial composition was analyzed by Genetic Analysis GA-map Dysbiosis test, targeting ≥300 bacteria on different taxonomic levels. Postoperative disease status was assessed endoscopically according to Rutgeerts scoring system 1 year after surgery. Differences in fecal microbiota composition between groups were analyzed by multivariate factor analyses and cluster analysis. Microbial stability over time was determined using Bray-Curtis dissimilarity. Results One year after surgery, the fecal microbiota composition differed between CD patients (n = 21) and healthy subjects (n = 7). At this time point, the microbiota composition of CD patients was associated with disease course, clearly separating patients with disease relapse (n = 8) and patients in remission (n = 13). Further, the microbial within-patient stability was high during the first year after surgery, irrespective of disease course. Conclusion The fecal microbiota composition of CD patients, analyzed by GA-map Dysbiosis test, is subject to little variation over time, and may potentially be used as a non-invasive diagnostic tool for the postoperative disease course.
Collapse
Affiliation(s)
- Anna Strömbeck
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden.
| | - Anders Lasson
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborg Hospital, Borås, Sweden
| | - Johanna Sundin
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Per-Ove Stotzer
- Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Internal Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Box 435, 405 30, Gothenburg, Sweden
| |
Collapse
|
87
|
Estevinho MM, Rocha C, Correia L, Lago P, Ministro P, Portela F, Trindade E, Afonso J, Peyrin-Biroulet L, Magro F. Features of Fecal and Colon Microbiomes Associate With Responses to Biologic Therapies for Inflammatory Bowel Diseases: A Systematic Review. Clin Gastroenterol Hepatol 2020; 18:1054-1069. [PMID: 31526845 DOI: 10.1016/j.cgh.2019.08.063] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/20/2019] [Accepted: 08/23/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS We performed a systematic review of changes in fecal and colon microbiomes of patients with inflammatory bowel diseases (IBDs) receiving treatment with monoclonal antibodies against tumor necrosis factor, integrins, or cytokines. We explored associations among microbiome composition and functions (at baseline and throughout the treatment) and therapy-related outcomes to determine whether colon or fecal microbiomes might be used as biomarkers of response to therapy. METHODS We searched the PubMed, Web of Science, and Science Direct databases through February 2019 for studies of associations among the microbiomes of fecal or colon samples, biologic therapies, and IBDs. We used the critical appraisal skills program checklist to assess the quality of the study methods. RESULTS From the 787 citations identified, 10 studies met the inclusion criteria. Changes in microbiomes of fecal or colon samples after treatment did not differ significantly among biologic agents; all produced decreases in relative abundances of Escherichia and Enterococcus and increases in genera that produce short-chain fatty acids. Fecal or colon microbiomes of patients who responded to therapy with antagonists of tumor necrosis factor or interleukins had higher α-diversity and increased relative abundances of different genera (Faecalibacterium, Roseburia, or Clostridium) from the Clostridiales order, either at baseline or during follow-up evaluation. Patients in remission after treatment with antibodies against integrins had decreased abundances of Roseburia. CONCLUSIONS In a systematic review of 10 studies, we found evidence for consistent changes in microbiomes of fecal and colon samples from patients with IBD who responded to treatment with biologic agents. Prospective studies are needed to determine what changes are associated significantly with treatment, whether these changes are causes or effects of response, or whether the composition of the intestinal microbiome can be used to select treatments for patients with IBD.
Collapse
Affiliation(s)
- Maria Manuela Estevinho
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal; Department of Gastroenterology, Centro Hospitalar Vila Nova de Gaia/Espinho, Vila Nova de Gaia, Portugal
| | - Cátia Rocha
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal; Faculty of Medicine, University of Porto, Porto, Portugal; Instituto de Saúde Ambiental, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Luís Correia
- Department of Gastroenterology and Hepatology, Hospital de Santa Maria, University of Lisbon, Lisbon, Portugal
| | - Paula Lago
- Department of Gastroenterology, Centro Hospitalar do Porto, Porto, Portugal
| | - Paula Ministro
- Department of Gastroenterology, Centro Hospitalar Tondela-Viseu, Viseu, Portugal
| | | | - Eunice Trindade
- Department of Paediatrics, Centro Hospitalar São João, Porto, Portugal
| | - Joana Afonso
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Laurent Peyrin-Biroulet
- Institut National de la Sante et de la Recherche Médicale U954, Department of Gastroenterology, Nancy University Hospital, Lorraine University, Nancy, France
| | - Fernando Magro
- Department of Biomedicine, Unit of Pharmacology and Therapeutics, Faculty of Medicine, University of Porto, Porto, Portugal; Department of Gastroenterology, Centro Hospitalar São João, Porto, Portugal; Center for Drug Discovery and Innovative Medicines (MedInUP), Porto, Portugal.
| | | |
Collapse
|
88
|
Scher JU, Nayak RR, Ubeda C, Turnbaugh PJ, Abramson SB. Pharmacomicrobiomics in inflammatory arthritis: gut microbiome as modulator of therapeutic response. Nat Rev Rheumatol 2020; 16:282-292. [PMID: 32157196 PMCID: PMC11221369 DOI: 10.1038/s41584-020-0395-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
In the past three decades, extraordinary advances have been made in the understanding of the pathogenesis of, and treatment options for, inflammatory arthritides, including rheumatoid arthritis and spondyloarthritis. The use of methotrexate and subsequently biologic therapies (such as TNF inhibitors, among others) and oral small molecules have substantially improved clinical outcomes for many patients with inflammatory arthritis; for others, however, these agents do not substantially improve their symptoms. The emerging field of pharmacomicrobiomics, which investigates the effect of variations within the human gut microbiome on drugs, has already provided important insights into these therapeutics. Pharmacomicrobiomic studies have demonstrated that human gut microorganisms and their enzymatic products can affect the bioavailability, clinical efficacy and toxicity of a wide array of drugs through direct and indirect mechanisms. This discipline promises to facilitate the advent of microbiome-based precision medicine approaches in inflammatory arthritis, including strategies for predicting response to treatment and for modulating the microbiome to improve response to therapy or reduce drug toxicity.
Collapse
Affiliation(s)
- Jose U Scher
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA.
| | - Renuka R Nayak
- Rheumatology Division, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Carles Ubeda
- Centro Superior de Investigacion en Salud Publica - FISABIO, Valencia, Spain
- CIBER en Epidemiologia y Salud Publica, Madrid, Spain
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Steven B Abramson
- Department of Medicine, Division of Rheumatology, New York University Langone Health, New York, NY, USA
| |
Collapse
|
89
|
Dovrolis N, Michalopoulos G, Theodoropoulos GE, Arvanitidis K, Kolios G, Sechi LA, Eliopoulos AG, Gazouli M. The Interplay between Mucosal Microbiota Composition and Host Gene-Expression is Linked with Infliximab Response in Inflammatory Bowel Diseases. Microorganisms 2020; 8:microorganisms8030438. [PMID: 32244928 PMCID: PMC7143962 DOI: 10.3390/microorganisms8030438] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/18/2020] [Accepted: 03/19/2020] [Indexed: 12/16/2022] Open
Abstract
Even though anti-TNF therapy significantly improves the rates of remission in inflammatory bowel disease (IBD) patients, there is a noticeable subgroup of patients who do not respond to treatment. Dysbiosis emerges as a key factor in IBD pathogenesis. The aim of the present study is to profile changes in the gut microbiome and transcriptome before and after administration of the anti-TNF agent Infliximab (IFX) and investigate their potential to predict patient response to IFX at baseline. Mucosal biopsy samples from 20 IBD patients and nine healthy controls (HC) were examined for differences in microbiota composition (16S rRNA gene sequencing) and mucosal gene expression (RT-qPCR) at baseline and upon completion of IFX treatment, accordingly, via an in silico pipeline. Significant differences in microbiota composition were found between the IBD and HC groups. Several bacterial genera, which were found only in IBD patients and not HC, had their populations dramatically reduced after anti-TNF treatment regardless of response. Alpha and beta diversity metrics showed significant differences between our study groups. Correlation analysis revealed six microbial genera associated with differential expression of inflammation-associated genes in IFX treatment responders at baseline. This study shows that IFX treatment has a notable impact on both the gut microbial composition and the inflamed tissue transcriptome in IBD patients. Importantly, our results identify enterotypes that correlate with transcriptome changes and help differentiate IFX responders versus non-responders at baseline, suggesting that, in combination, these signatures can be an effective tool to predict anti-TNF response.
Collapse
Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis 68100, Greece; (N.D.); (K.A.); (G.K.)
| | | | - George E. Theodoropoulos
- 1st Propaedeutic University Surgery Clinic, Hippocratio General Hospital, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece;
| | - Kostantinos Arvanitidis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis 68100, Greece; (N.D.); (K.A.); (G.K.)
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis 68100, Greece; (N.D.); (K.A.); (G.K.)
| | - Leonardo A. Sechi
- Department of Biomedical Sciences, University of Sassari, Sassari 07100, Italy;
| | - Aristidis G. Eliopoulos
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece;
- Centre of Basic Research, Biomedical Research Foundation of the Academy of Athens (BRFAA) 11527, Greece
| | - Maria Gazouli
- Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Athens 11527, Greece;
- Correspondence: ; Tel./Fax: +30-21-07462231
| |
Collapse
|
90
|
Changes in the Intestinal Microbiota Are Seen Following Treatment with Infliximab in Children with Crohn's Disease. J Clin Med 2020; 9:jcm9030687. [PMID: 32143438 PMCID: PMC7141282 DOI: 10.3390/jcm9030687] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 02/08/2023] Open
Abstract
The aim of the study was to determine the impact of biological treatment with tumor necrosis factor α antibodies (anti-TNF-α) on the intestinal microbiome of children with severe Crohn's disease (CD) and to evaluate the differences in the intestinal microbiome between patients treated with biological therapy and healthy children. Microbiota composition was analyzed by 16S next-generation sequencing (NGS) and microbial profiles were compared between studied groups. Fifty-four samples (from 18 patients before and after anti-TNF-α induction therapy and 18 healthy children) were used in the sequencing analysis. Shannon's diversity index (p = 0.003, adj. p = 0.010) and observed operational taxonomic units (OTUs) (p = 0.007, adj. p = 0.015) were different between controls and patients with prior therapy for CD. Statistically significant dissimilarities between beta diversity metrics, indicating distinct community composition across groups, were observed in patients with CD before and after therapy. We did not observe any differences between controls and patients with CD after therapy. Core microbiome analysis at species level showed that 32 species were present only in patients with CD but not in controls. The results show that biological treatment is associated with changes in the intestinal microbiome of patients with CD: these changes result in an intestinal microbiome pattern similar to that seen in healthy children. Long-term observation is necessary to determine whether treatment can lead to full restoration of a healthy-like microbiome.
Collapse
|
91
|
Lucafò M, Franzin M, Lagatolla C, Franca R, Bramuzzo M, Stocco G, Decorti G. Emerging Insights on the Interaction Between Anticancer and Immunosuppressant Drugs and Intestinal Microbiota in Pediatric Patients. Clin Transl Sci 2020; 13:238-259. [PMID: 31675176 PMCID: PMC7070880 DOI: 10.1111/cts.12722] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 02/06/2023] Open
Abstract
Diseases affecting the immune system, such as inflammatory bowel disease (IBD), juvenile idiopathic arthritis (JIA), and acute lymphoblastic leukemia (ALL), are pathological conditions affecting the pediatric population and are often associated with alterations in the intestinal microbiota, such as a decrease in bacterial diversity. Growing evidence suggests that gut microbiota can interfere with chemotherapeutic and immunosuppressant drugs, used in the treatment of these diseases, reducing or facilitating drug efficacy. In particular, the effect of intestinal microflora through translocation, immunomodulation, metabolism, enzymatic degradation, and reduction of bacterial diversity seems to be one of the reasons of interindividual variability in the therapeutic response. Although the extent of the role of intestinal microflora in chemotherapy and immunosuppression remains still unresolved, current evidence on bacterial compositional shifts will be taken in consideration together with clinical response to drugs for a better and personalized therapy. This review is focused on the effect of the intestinal microbiota on the efficacy of pharmacological therapy of agents used to treat IBD, JIA, and ALL.
Collapse
Affiliation(s)
- Marianna Lucafò
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
| | - Martina Franzin
- PhD Course in Reproductive and Developmental SciencesUniversity of TriesteTriesteItaly
| | | | - Raffaella Franca
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| | - Matteo Bramuzzo
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
| | - Gabriele Stocco
- Department of Life SciencesUniversity of TriesteTriesteItaly
| | - Giuliana Decorti
- Institute for Maternal and Child Health – IRCCS “Burlo Garofolo”TriesteItaly
- Department of Medical, Surgical and Health SciencesUniversity of TriesteTriesteItaly
| |
Collapse
|
92
|
Klingberg E, Magnusson MK, Strid H, Deminger A, Ståhl A, Sundin J, Simrén M, Carlsten H, Öhman L, Forsblad-d'Elia H. A distinct gut microbiota composition in patients with ankylosing spondylitis is associated with increased levels of fecal calprotectin. Arthritis Res Ther 2019; 21:248. [PMID: 31771630 PMCID: PMC6880506 DOI: 10.1186/s13075-019-2018-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 10/01/2019] [Indexed: 02/06/2023] Open
Abstract
Background Ankylosing spondylitis (AS) shares many characteristics with inflammatory bowel disease (IBD). Intestinal microbiota most likely plays an important role in the development of IBDs and may also be involved in the pathogenesis of AS. We aimed to define and compare the fecal microbiota composition in patients with AS, ulcerative colitis (UC), and healthy controls (HC) and to determine relationships between fecal microbiota, fecal calprotectin, and disease-related variables in AS. Methods Fecal microbiota composition was assessed with GA-map™ Dysbiosis Test (Genetic Analysis, Oslo, Norway), which also reports the degree of deviation of the microbiota composition compared with a healthy control population, a Dysbiosis Index (DI) score 1–5. The AS patients were assessed with questionnaires, back mobility tests, fecal calprotectin, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP). Results Totally, 150 patients with AS (55% men, median age 55.5 years, median BASDAI 3.2), 18 patients with UC (56% men, median age 30.5 years), and 17 HC (65% men, median age 22 years) were included. Principal component analysis showed highly separate clustering of fecal microbiota from the patients with AS, UC, and HC. Compared with HC, fecal microbiota in AS was characterized by a higher abundance of Proteobacteria, Enterobacteriaceae, Bacilli, Streptococcus species, and Actinobacteria, but lower abundance of Bacteroides and Lachnospiraceae. Further, fecal microbiota composition differed between patients with normal (≤ 50 mg/kg, n = 57) and increased (≥ 200 mg/kg, n = 36) fecal calprotectin. Patients with increased fecal calprotectin had lower abundance of bacteria with anti-inflammatory properties such as Faecalibacterium prausnitzii and Clostridium and higher abundance of the genus Streptococcus. No association was found between the fecal microbiota composition and HLAB27 status, disease activity, function, or medication. Dysbiosis (defined as DI ≥ 3) was found in 87% of AS patients. Conclusions Patients with AS have a distinct fecal microbiota signature, which is linked to fecal calprotectin levels, a marker of intestinal inflammation, but not to other clinical parameters. These findings suggest a local interplay between intestinal microbiota and gut inflammation in AS. Trial registration ClinicalTrials.gov, NCT00858819. Registered March 9, 2009.
Collapse
Affiliation(s)
- Eva Klingberg
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden. .,Department of Rheumatology, Sahlgrenska University Hospital, Gröna stråket 14, SE-41345, Gothenburg, Sweden.
| | - Maria K Magnusson
- Department of Microbiology and Immunology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Hans Strid
- Department of Internal Medicine, Södra Älvsborgs sjukhus, Borås, Sweden.,Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anna Deminger
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Arne Ståhl
- Department of Microbiology and Immunology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Johanna Sundin
- Department of Microbiology and Immunology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Department of Internal Medicine and Clinical Nutrition, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Department of Microbiology and Immunology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Center for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hans Carlsten
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Lena Öhman
- Department of Microbiology and Immunology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Helena Forsblad-d'Elia
- Department of Rheumatology and Inflammation Research, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Department of Public Health and Clinical Medicine, Rheumatology, Umeå University, Umeå, Sweden
| |
Collapse
|
93
|
Aden K, Rehman A, Waschina S, Pan WH, Walker A, Lucio M, Nunez AM, Bharti R, Zimmerman J, Bethge J, Schulte B, Schulte D, Franke A, Nikolaus S, Schroeder JO, Vandeputte D, Raes J, Szymczak S, Waetzig GH, Zeuner R, Schmitt-Kopplin P, Kaleta C, Schreiber S, Rosenstiel P. Metabolic Functions of Gut Microbes Associate With Efficacy of Tumor Necrosis Factor Antagonists in Patients With Inflammatory Bowel Diseases. Gastroenterology 2019; 157:1279-1292.e11. [PMID: 31326413 DOI: 10.1053/j.gastro.2019.07.025] [Citation(s) in RCA: 154] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 06/18/2019] [Accepted: 07/04/2019] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Altered interactions between the mucosal immune system and intestinal microbiota contribute to pathogenesis of inflammatory bowel diseases (IBD). It is not clear how inhibitors of cytokines, such as antagonists of tumor necrosis factor (anti-TNF), affect the intestinal microbiome. We investigated the effects of anti-TNF agents on gut microbe community structure and function in a longitudinal 2-step study of patients with IBD. We correlated our findings with outcomes of treatment and investigated patterns of metabolites in fecal samples before and after anti-TNF therapy. METHODS We performed a prospective study of 2 cohorts of patients in Germany; the discovery cohort comprised 12 patients with IBD, 17 patients with rheumatic disease, and 19 healthy individuals (controls); fecal samples were collected at baseline and 2, 6, and 30 weeks after induction of anti-TNF therapy. The validation cohort comprised 23 patients with IBD treated with anti-TNF or vedolizumab (anti-α4β7 integrin) and 99 healthy controls; fecal samples were collected at baseline and at weeks 2, 6, and 14. Fecal microbiota were analyzed by V3-V4 16S ribosomal RNA gene amplicon sequencing. Clinical response and remission were determined by clinical disease activity scores. Metabolic network reconstruction and associated fecal metabolite level inference was performed in silico using the AGORA (Assembly of Gut Organisms through Reconstruction and Analysis) resource. Metabolomic analyses of fecal samples from a subset of patients were performed to validate metabolites associated with treatment outcomes. RESULTS Anti-TNF therapy shifted the diversity of fecal microbiota in patients with IBD, but not with rheumatic disease, toward that of controls. Across timepoints, diversity indices did not vary significantly between patients with IBD who did or did not achieve clinical remission after therapy. In contrast, in silico modeling of metabolic interactions between gut microbes found metabolite exchange to be significantly reduced at baseline in fecal samples from patients with IBD and to be associated with later clinical remission. Predicted levels of butyrate and substrates involved in butyrate synthesis (ethanol or acetaldehyde) were significantly associated with clinical remission following anti-TNF therapy, verified by fecal metabolomic analyses. CONCLUSIONS Metabolic network reconstruction and assessment of metabolic profiles of fecal samples might be used to identify patients with IBD likely to achieve clinical remission following anti-TNF therapy and increase our understanding of the heterogeneity of IBD.
Collapse
Affiliation(s)
- Konrad Aden
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Ateequr Rehman
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Silvio Waschina
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Wei-Hung Pan
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Alesia Walker
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Marianna Lucio
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Alejandro Mena Nunez
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Richa Bharti
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Zimmerman
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johannes Bethge
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Berenice Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Dominik Schulte
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanna Nikolaus
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Johann Oltmann Schroeder
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Doris Vandeputte
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Jeroen Raes
- VIB-KU Leuven Center for Microbiology, Campus Gasthuisberg, Leuven, Belgium
| | - Silke Szymczak
- Institute of Medical Informatics and Statistics, University of Kiel, Kiel, Germany
| | | | - Rainald Zeuner
- Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philippe Schmitt-Kopplin
- Research Unit Analytical BioGeoChemistry, Helmholtz ZentrumMünchen, German Research Centre for Environmental Health (GmbH), Neuherberg, Germany
| | - Christoph Kaleta
- Institute for Experimental Medicine, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany; Department of Internal Medicine I., Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University and University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany.
| |
Collapse
|
94
|
Yin J, Sternes PR, Wang M, Song J, Morrison M, Li T, Zhou L, Wu X, He F, Zhu J, Brown MA, Xu H. Shotgun metagenomics reveals an enrichment of potentially cross-reactive bacterial epitopes in ankylosing spondylitis patients, as well as the effects of TNFi therapy upon microbiome composition. Ann Rheum Dis 2019; 79:132-140. [DOI: 10.1136/annrheumdis-2019-215763] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 02/07/2023]
Abstract
ObjectivesDiverse evidence including clinical, genetic and microbiome studies support a major role of the gut microbiome in the common immune-mediated arthropathy, ankylosing spondylitis (AS). We set out to (1) further define the key microbial characteristics driving disease, and (2) examine the effects of tumour necrosis factor-inhibitor (TNFi) therapy upon the microbiome.MethodsThe stools from a case–control cohort of 250 Han-Chinese subjects underwent shotgun metagenomic sequencing. All subjects were genotyped using the Illumina CoreExome SNP microarray.ResultsPrevious reports of gut dysbiosis in AS were reconfirmed and several notable bacterial species and functional categories were differentially abundant. TNFi therapy was correlated with a restoration the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. Enrichment of bacterial peptides homologous to HLA-B27-presented epitopes was observed in the stools of patients with AS, suggesting that either HLA-B27 fails to clear these or that they are involved in driving HLA-B27-associated immune reactions. TNFi therapy largely restored the perturbed microbiome observed in untreated AS cases to that of healthy controls, including several important bacterial species that have been previously associated with AS and other related diseases. TNFi therapy of patients with AS was also associated with a reduction of potentially arthritogenic bacterial peptides, relative to untreated patients.ConclusionThese findings emphasise the key role that the gut microbiome plays in driving the pathogenesis of AS and highlight potential therapeutic and/or preventative targets.
Collapse
|
95
|
Ribaldone DG, Caviglia GP, Abdulle A, Pellicano R, Ditto MC, Morino M, Fusaro E, Saracco GM, Bugianesi E, Astegiano M. Adalimumab Therapy Improves Intestinal Dysbiosis in Crohn's Disease. J Clin Med 2019; 8:jcm8101646. [PMID: 31601034 PMCID: PMC6832711 DOI: 10.3390/jcm8101646] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
The response to treatment with biologic drugs, in patients with Crohn’s disease, could be associated with changes in gut microbiota composition. The aim of our study was to analyse the modification of microbiota during adalimumab therapy in patients with Crohn’s disease. We performed a prospective study in patients with Crohn’s disease analysing gut microbiota before start of adalimumab therapy (T0) and after six months of therapy (T1). Among the 20 included patients, the phylum Proteobacteria fell from 15.7 ± 3.5% at T0 to 10.3 ± 3.4% at T1 (p = 0.038). Furthermore, the trend in relation to therapeutic success was analysed. Regarding bacterial phyla, Proteobacteria decreased in patients in whom therapeutic success was obtained, passing from a value of 15.8% (± 4.6%) to 6.8 ± 3.1% (p = 0.049), while in non-responder patients, percentages did not change (T0 = 15.6 ± 5.7%, T1 = 16.8 ± 7.6%, p = 0.890). Regarding the Lachnospiraceae family, in patients with normalization of C reactive protein six 6 months of adalimumab therapy, it increased from 16.6 ± 3.1% at T0 to 23.9 ± 2.6% at T1 (p = 0.049). In conclusion, in patients who respond to Adalimumab therapy by decreasing inflammation, there is a trend of intestinal eubiosis being restored.
Collapse
Affiliation(s)
| | | | - Amina Abdulle
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy.
| | | | - Maria Chiara Ditto
- S.C. Reumatologia, Città della Salute e della Scienza di Torino, 10126 Turin, Italy.
| | - Mario Morino
- Department of Surgical Sciences, University of Turin, 10124 Turin, Italy.
| | - Enrico Fusaro
- S.C. Reumatologia, Città della Salute e della Scienza di Torino, 10126 Turin, Italy.
| | | | | | - Marco Astegiano
- Unit of Gastroenterology, Molinette Hospital, 10126 Turin, Italy.
| |
Collapse
|
96
|
Wang C, Baer HM, Gaya DR, Nibbs RJB, Milling S. Can molecular stratification improve the treatment of inflammatory bowel disease? Pharmacol Res 2019; 148:104442. [PMID: 31491469 PMCID: PMC6902263 DOI: 10.1016/j.phrs.2019.104442] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 09/02/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023]
Abstract
Inflammatory bowel disease (IBD) is a debilitating chronic inflammatory disease of the gastrointestinal (GI) tract. It affects more than 3.5 million people in the western world and places a huge financial burden on healthcare systems. IBD is highly heterogeneous; disease severity and outcomes in IBD are highly variable, and patients may experience episodes of relapse and remission. However, treatment often follows a step-up model whereby the patients start with anti-inflammatory agents (corticosteroids or immunosuppressants) and step-up to monoclonal anti-tumour necrosis factor-α (TNFα) antibodies and then other biologics if the initial drugs cannot control disease. Unfortunately, many patients do not respond to the costly biologics, and thus often still require gut-resective surgery, which decreases quality of life. In order to decrease rates of surgery and ineffective treatments, it is important to identify markers that accurately predict disease progression and treatment responses, to inform decisions about the best choice of therapeutics. Here we examine molecular approaches to patient stratification that aim to increase the effectiveness of treatments and potentially reduce healthcare costs. In the future, it may become possible to stratify patients based on their suitability for specific molecular-targeted therapeutic agents, and eventually use molecular stratification for personalised medicine in IBD.
Collapse
Affiliation(s)
- Claire Wang
- Institute of Infection, Inflammation & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Hannah M Baer
- Institute of Infection, Inflammation & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Daniel R Gaya
- Gastroenterology Unit, Glasgow Royal Infirmary, Glasgow, UK
| | - Robert J B Nibbs
- Institute of Infection, Inflammation & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Simon Milling
- Institute of Infection, Inflammation & Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK.
| |
Collapse
|
97
|
Liu B, Yang L, Cui Z, Zheng J, Huang J, Zhao Q, Su Z, Wang M, Zhang W, Liu J, Wang T, Li Q, Lu H. Anti-TNF-α therapy alters the gut microbiota in proteoglycan-induced ankylosing spondylitis in mice. Microbiologyopen 2019; 8:e927. [PMID: 31556231 PMCID: PMC6925169 DOI: 10.1002/mbo3.927] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/01/2019] [Accepted: 08/06/2019] [Indexed: 12/21/2022] Open
Abstract
Ankylosing spondylitis is a chronic, progressive disease, and its treatment is relevant to the gut microbiota. Anti-tumor necrosis factor-alpha (anti-TNF-α) therapy alters the gut microbiota in many diseases, including inflammatory bowel disease. However, little is known about the effect of TNF-α blocker treatment on the gut microbiota in ankylosing spondylitis. Herein, the effect of a TNF-α blocker on the gut microbiota in proteoglycan-induced arthritis was investigated. Proteoglycan-induced mice were treated with an rhTNFR:Fc solution of etanercept (5 µg/g) for 4 weeks. rhTNFR:Fc treatment attenuated the arthritis incidence and severity of arthritis in the proteoglycan-induced mice and decreased inflammation in the ankle joints and ameliorated ileal tissue destruction. Moreover, high gut permeability occurred, and zonula occludens-1 and occludin protein levels were reduced in proteoglycan-induced mice. These levels were significantly restored by the administration of rhTNFR:Fc. The serum TNF-α and IL-17 levels were also decreased. In addition, flora analysis via 16S rDNA high-throughput sequencing revealed that rhTNFR:Fc treatment restored the gut microbiota composition to a composition similar to that in control mice. In conclusion, anti-TNF-α therapy attenuated proteoglycan-induced arthritis progression and modulated the gut microbiota and intestinal barrier function. These results provide new insights for anti-TNF-α therapy strategies via regulating the gut microbiota in ankylosing spondylitis.
Collapse
Affiliation(s)
- Bin Liu
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lianjun Yang
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zhifei Cui
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Junchi Zheng
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jincheng Huang
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, Henan, China
| | - Qinghao Zhao
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Zhihai Su
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Min Wang
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Weicong Zhang
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Jinshi Liu
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Tingxuan Wang
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Qingchu Li
- Department of Orthopedic Surgery, Academy of Orthopedics of Guangdong Province, Orthopaedic Hospital of Guangdong Province, The Third Affiliated Hospital, Southern Medical University, Guangzhou, China
| | - Hai Lu
- Department of Spine surgery, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| |
Collapse
|
98
|
Gazouli M, Dovrolis N, Franke A, Spyrou GM, Sechi LA, Kolios G. Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach. Gut Pathog 2019; 11:31. [PMID: 31249629 PMCID: PMC6570833 DOI: 10.1186/s13099-019-0312-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
Background Crohn’s disease (CD) and Ulcerative colitis (UC) are the two main entities of inflammatory bowel disease (IBD). Previous works have identified more than 200 risk factors (including loci and signaling pathways) in populations of predominantly European ancestry. Our study was conducted on an extended population-specific cohort of 573 Greek IBD patients (364 CD and 209 UC) and 445 controls. Aims To highlight the different genetic and functional background of IBD and its phenotypes, utilizing contemporary systems bioinformatics methodologies. Methods Disease-associated SNPs, obtained via our own 89 loci IBD risk GWAS panel, were detected with the whole genome association analysis toolset PLINK. These SNPs were used as input for 2 novel and different pathway analysis methods to detect functional interactions. Specifically, PathwayConnector was used to create complementary networks of interacting pathways whereas; the online database of protein interactions STRING provided protein–protein association networks and their derived pathways. Network analyses metrics were employed to identify proteins with high significance and subsequently to rank the signaling pathways those participate in. Results The reported complementary pathway and enriched protein–protein association networks reveal several novel and well-known key players, in the functional background of IBD like Toll-like receptor, TNF, Jak-STAT, PI3K-Akt, T cell receptor, Apoptosis, MAPK and B cell receptor signaling pathways. IBD subphenotypes are found to have distinct genetic and functional profiles which can contribute to their accurate identification and classification. As a secondary result we identify an extended network of diseases with common molecular background to IBD. Conclusions IBD’s burden on the quality of life of patients and intricate functional background presents us constantly with new challenges. Our data and methodology provide researchers with new insights to a specific population, but also, to possible differentiation markers of disease classification and progression. This work, not only provides new insights into the interplay among IBD risk variants and their related signaling pathways, elucidates the mechanisms underlying IBD and its clinical sequelae, but also, introduces a generalized bioinformatics-based methodology which can be applied to studies of different disorders. Electronic supplementary material The online version of this article (10.1186/s13099-019-0312-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maria Gazouli
- 1Laboratory of Biology, Medical School, National and Kapodistrian University of Athens, Michalakopoulou 176, 11527 Athens, Greece
| | - Nikolas Dovrolis
- 2Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Xanthi, Greece
| | - Andre Franke
- 3Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - George M Spyrou
- 4Bioinformatics ERA Chair, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Leonardo A Sechi
- 5Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - George Kolios
- 2Laboratory of Pharmacology, Department of Medicine, Democritus University of Thrace, Xanthi, Greece
| |
Collapse
|
99
|
Longitudinal multi-omics of host-microbe dynamics in prediabetes. Nature 2019; 569:663-671. [PMID: 31142858 PMCID: PMC6666404 DOI: 10.1038/s41586-019-1236-x] [Citation(s) in RCA: 328] [Impact Index Per Article: 65.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/16/2019] [Indexed: 12/16/2022]
Abstract
Type 2 diabetes mellitus (T2D) is a growing health problem, but little is known about its early disease stages, its effects on biological processes or the transition to clinical T2D. To understand the earliest stages of T2D better, we obtained samples from 106 healthy individuals and individuals with prediabetes over approximately four years and performed deep profiling of transcriptomes, metabolomes, cytokines, and proteomes, as well as changes in the microbiome. This rich longitudinal data set revealed many insights: first, healthy profiles are distinct among individuals while displaying diverse patterns of intra- and/or inter-personal variability. Second, extensive host and microbial changes occur during respiratory viral infections and immunization, and immunization triggers potentially protective responses that are distinct from responses to respiratory viral infections. Moreover, during respiratory viral infections, insulin-resistant participants respond differently than insulin-sensitive participants. Third, global co-association analyses among the thousands of profiled molecules reveal specific host-microbe interactions that differ between insulin-resistant and insulin-sensitive individuals. Last, we identified early personal molecular signatures in one individual that preceded the onset of T2D, including the inflammation markers interleukin-1 receptor agonist (IL-1RA) and high-sensitivity C-reactive protein (CRP) paired with xenobiotic-induced immune signalling. Our study reveals insights into pathways and responses that differ between glucose-dysregulated and healthy individuals during health and disease and provides an open-access data resource to enable further research into healthy, prediabetic and T2D states.
Collapse
|
100
|
Atreya R, Neurath MF. Mechanisms of molecular resistance and predictors of response to biological therapy in inflammatory bowel disease. Lancet Gastroenterol Hepatol 2019; 3:790-802. [PMID: 30353856 DOI: 10.1016/s2468-1253(18)30265-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 07/25/2018] [Accepted: 07/27/2018] [Indexed: 02/07/2023]
Abstract
Biological therapy has led to marked improvements in treatment of patients with inflammatory bowel disease, and an increasing number of drugs has been approved for treatment. However, only a subgroup of patients responds to therapy, highlighting the need to identify biomarkers for therapeutic response to allow personalised medicine in inflammatory bowel disease. Potential markers of response to biological therapy have been identified; however, studies also suggest that changes in the composition of immune cell infiltrates in response to therapeutic pressure lead to molecular resistance to these drugs. For instance, the cytokine interleukin 23 has been identified as a driver of evasion of apoptosis in response to anti-tumour necrosis factor drugs in patients with Crohn's disease, leading to expansion of apoptosis-resistant T cells and drug resistance. In this Review, we examine the concept of molecular resistance to biological therapy and discuss implications for future therapy.
Collapse
Affiliation(s)
- Raja Atreya
- Department of Medicine 1, University Hospital Erlangen, and Ludwig Demling Endoscopy Center of Excellence, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Markus F Neurath
- Department of Medicine 1, University Hospital Erlangen, and Ludwig Demling Endoscopy Center of Excellence, University of Erlangen-Nuremberg, Erlangen, Germany.
| |
Collapse
|